WorldWideScience

Sample records for biogeochemical modeling system

  1. Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

    Science.gov (United States)

    Chang, C.; Li, M.; Yeh, G.

    2010-12-01

    The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

  2. The UK Earth System Models Marine Biogeochemical Evaluation Toolkit, BGC-val

    Science.gov (United States)

    de Mora, Lee

    2017-04-01

    The Biogeochemical Validation toolkit, BGC-val, is a model and grid independent python-based marine model evaluation framework that automates much of the validation of the marine component of an Earth System Model. BGC-val was initially developed to be a flexible and extensible system to evaluate the spin up of the marine UK Earth System Model (UKESM). However, the grid-independence and flexibility means that it is straightforward to adapt the BGC-val framework to evaluate other marine models. In addition to the marine component of the UKESM, this toolkit has been adapted to compare multiple models, including models from the CMIP5 and iMarNet inter-comparison projects. The BGC-val toolkit produces multiple levels of analysis which are presented in a simple to use interactive html5 document. Level 1 contains time series analyses, showing the development over time of many important biogeochemical and physical ocean metrics, such as the Global primary production or the Drake passage current. The second level of BGC-val is an in-depth spatial analyses of a single point in time. This is a series of point to point comparison of model and data in various regions, such as a comparison of Surface Nitrate in the model vs data from the world ocean atlas. The third level analyses are specialised ad-hoc packages to go in-depth on a specific question, such as the development of Oxygen minimum zones in the Equatorial Pacific. In additional to the three levels, the html5 document opens with a Level 0 table showing a summary of the status of the model run. The beta version of this toolkit is available via the Plymouth Marine Laboratory Gitlab server and uses the BSD 3 clause license.

  3. Modeling the physical and biogeochemical response of a marine shelf system to a tropical cyclone

    Science.gov (United States)

    Condie, S. A.; Herzfeld, M.; Margvelashvili, N.; Andrewartha, J. R.

    2009-11-01

    We describe the first use of a fully integrated biogeochemical model to explore the response of a marine shelf system to a tropical cyclone. Ocean currents, nutrients, sediments and plankton dynamics were simulated under conditions representative of Tropical Cyclone Bobby, which traversed the Australian North West Shelf in February 1995. Results show strong upwelling of nutrients and a phytoplankton bloom. While chlorophyll changes were similar to those estimated from satellite data in other coastal systems exposed to cyclonic conditions, the overall phytoplankton response was limited by cyclone induced sediment resuspension and the net contribution to annual primary production on the shelf was relatively small. In contrast, sediment loads exported off the shelf during Bobby were found to be more than 50 times modeled annual loads in years with little cyclone exposure and equivalent to at least 20 years of annual river-loads to the North West Shelf.

  4. Marine geochemical data assimilation in an efficient Earth System Model of global biogeochemical cycling

    Directory of Open Access Journals (Sweden)

    A. Ridgwell

    2007-01-01

    Full Text Available We have extended the 3-D ocean based "Grid ENabled Integrated Earth system model" (GENIE-1 to help understand the role of ocean biogeochemistry and marine sediments in the long-term (~100 to 100 000 year regulation of atmospheric CO2, and the importance of feedbacks between CO2 and climate. Here we describe the ocean carbon cycle, which in its first incarnation is based around a simple single nutrient (phosphate control on biological productivity. The addition of calcium carbonate preservation in deep-sea sediments and its role in regulating atmospheric CO2 is presented elsewhere (Ridgwell and Hargreaves, 2007. We have calibrated the model parameters controlling ocean carbon cycling in GENIE-1 by assimilating 3-D observational datasets of phosphate and alkalinity using an ensemble Kalman filter method. The calibrated (mean model predicts a global export production of particulate organic carbon (POC of 8.9 PgC yr−1, and reproduces the main features of dissolved oxygen distributions in the ocean. For estimating biogenic calcium carbonate (CaCO3 production, we have devised a parameterization in which the CaCO3:POC export ratio is related directly to ambient saturation state. Calibrated global CaCO3 export production (1.2 PgC yr-1 is close to recent marine carbonate budget estimates. The GENIE-1 Earth system model is capable of simulating a wide variety of dissolved and isotopic species of relevance to the study of modern global biogeochemical cycles as well as past global environmental changes recorded in paleoceanographic proxies. Importantly, even with 12 active biogeochemical tracers in the ocean and including the calculation of feedbacks between atmospheric CO2 and climate, we achieve better than 1000 years per (2.4 GHz CPU hour on a desktop PC. The GENIE-1 model thus provides a viable alternative to box and zonally-averaged models for studying global biogeochemical cycling over all but the very longest (>1 000 000 year time-scales.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  7. An integrated multi-level watershed-reservoir modeling system for examining hydrological and biogeochemical processes in small prairie watersheds.

    Science.gov (United States)

    Zhang, Hua; Huang, Guo H; Wang, Dunling; Zhang, Xiaodong; Li, Gongchen; An, Chunjiang; Cui, Zheng; Liao, Renfei; Nie, Xianghui

    2012-03-15

    Eutrophication of small prairie reservoirs presents a major challenge in water quality management and has led to a need for predictive water quality modeling. Studies are lacking in effectively integrating watershed models and reservoir models to explore nutrient dynamics and eutrophication pattern. A water quality model specific to small prairie water bodies is also desired in order to highlight key biogeochemical processes with an acceptable degree of parameterization. This study presents a Multi-level Watershed-Reservoir Modeling System (MWRMS) to simulate hydrological and biogeochemical processes in small prairie watersheds. It integrated a watershed model, a hydrodynamic model and an eutrophication model into a flexible modeling framework. It can comprehensively describe hydrological and biogeochemical processes across different spatial scales and effectively deal with the special drainage structure of small prairie watersheds. As a key component of MWRMS, a three-dimensional Willows Reservoir Eutrophication Model (WREM) is developed to addresses essential biogeochemical processes in prairie reservoirs and to generate 3D distributions of various water quality constituents; with a modest degree of parameterization, WREM is able to meet the limit of data availability that often confronts the modeling practices in small watersheds. MWRMS was applied to the Assiniboia Watershed in southern Saskatchewan, Canada. Extensive efforts of field work and lab analysis were undertaken to support model calibration and validation. MWRMS demonstrated its ability to reproduce the observed watershed water yield, reservoir water levels and temperatures, and concentrations of several water constituents. Results showed that the aquatic systems in the Assiniboia Watershed were nitrogen-limited and sediment flux played a crucial role in reservoir nutrient budget and dynamics. MWRMS can provide a broad context of decision support for water resources management and water quality

  8. Coupled physical/biogeochemical modeling including O2-dependent processes in the Eastern Boundary Upwelling Systems: application in the Benguela

    Directory of Open Access Journals (Sweden)

    E. Gutknecht

    2013-06-01

    Full Text Available The Eastern Boundary Upwelling Systems (EBUS contribute to one fifth of the global catches in the ocean. Often associated with Oxygen Minimum Zones (OMZs, EBUS represent key regions for the oceanic nitrogen (N cycle. Important bioavailable N loss due to denitrification and anammox processes as well as greenhouse gas emissions (e.g, N2O occur also in these EBUS. However, their dynamics are currently crudely represented in global models. In the climate change context, improving our capability to properly represent these areas is crucial due to anticipated changes in the winds, productivity, and oxygen content. We developed a biogeochemical model (BioEBUS taking into account the main processes linked with EBUS and associated OMZs. We implemented this model in a 3-D realistic coupled physical/biogeochemical configuration in the Namibian upwelling system (northern Benguela using the high-resolution hydrodynamic ROMS model. We present here a validation using in situ and satellite data as well as diagnostic metrics and sensitivity analyses of key parameters and N2O parameterizations. The impact of parameter values on the OMZ off Namibia, on N loss, and on N2O concentrations and emissions is detailed. The model realistically reproduces the vertical distribution and seasonal cycle of observed oxygen, nitrate, and chlorophyll a concentrations, and the rates of microbial processes (e.g, NH4+ and NO2− oxidation, NO3− reduction, and anammox as well. Based on our sensitivity analyses, biogeochemical parameter values associated with organic matter decomposition, vertical sinking, and nitrification play a key role for the low-oxygen water content, N loss, and N2O concentrations in the OMZ. Moreover, the explicit parameterization of both steps of nitrification, ammonium oxidation to nitrate with nitrite as an explicit intermediate, is necessary to improve the representation of microbial activity linked with the OMZ. The simulated minimum oxygen

  9. Modelling shelf-ocean exchange and its biogeochemical consequences in coastal upwelling systems

    DEFF Research Database (Denmark)

    Muchamad, Al Azhar

    margin bathymetry, and 3) what processes determine the observed variability of total organic carbon (TOC) content in shelf sediments underlying the upwelling system, with implications for the formation of petroleum source rocks. Here, a numerical ocean modeling approach is used in this thesis to explore...

  10. Modelling shelf-ocean exchange and its biogeochemical consequences in coastal upwelling systems

    DEFF Research Database (Denmark)

    Muchamad, Al Azhar

    margin bathymetry, and 3) what processes determine the observed variability of total organic carbon (TOC) content in shelf sediments underlying the upwelling system, with implications for the formation of petroleum source rocks. Here, a numerical ocean modeling approach is used in this thesis to explore...... processes and the development of anoxia/euxinia under the present day or past geological conditions. Thirdly and last, processes controlling distribution of total organic carbon (TOC) content in sediments across the continental margin is evaluated by application of the model to the Benguela upwelling system....... In the model, biological primary production and shelf bottom-water anoxia result in enhanced sedimentary TOC concentrations on the mid shelf and upper slope. The simulated TOCs implicate that bottom lateral transport only has a significant effect on increasing the deposition of the organic carbon on the mid...

  11. Investigating the Role of Biogeochemical Processes in the Northern High Latitudes on Global Climate Feedbacks Using an Efficient Scalable Earth System Model

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Atul K. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2016-09-14

    The overall objectives of this DOE funded project is to combine scientific and computational challenges in climate modeling by expanding our understanding of the biogeophysical-biogeochemical processes and their interactions in the northern high latitudes (NHLs) using an earth system modeling (ESM) approach, and by adopting an adaptive parallel runtime system in an ESM to achieve efficient and scalable climate simulations through improved load balancing algorithms.

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

    Science.gov (United States)

    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.

  13. Effects of Model Resolution and Ocean Mixing on Forced Ice-Ocean Physical and Biogeochemical Simulations Using Global and Regional System Models

    Science.gov (United States)

    Jin, Meibing; Deal, Clara; Maslowski, Wieslaw; Matrai, Patricia; Roberts, Andrew; Osinski, Robert; Lee, Younjoo J.; Frants, Marina; Elliott, Scott; Jeffery, Nicole; Hunke, Elizabeth; Wang, Shanlin

    2018-01-01

    The current coarse-resolution global Community Earth System Model (CESM) can reproduce major and large-scale patterns but is still missing some key biogeochemical features in the Arctic Ocean, e.g., low surface nutrients in the Canada Basin. We incorporated the CESM Version 1 ocean biogeochemical code into the Regional Arctic System Model (RASM) and coupled it with a sea-ice algal module to investigate model limitations. Four ice-ocean hindcast cases are compared with various observations: two in a global 1° (40˜60 km in the Arctic) grid: G1deg and G1deg-OLD with/without new sea-ice processes incorporated; two on RASM's 1/12° (˜9 km) grid R9km and R9km-NB with/without a subgrid scale brine rejection parameterization which improves ocean vertical mixing under sea ice. Higher-resolution and new sea-ice processes contributed to lower model errors in sea-ice extent, ice thickness, and ice algae. In the Bering Sea shelf, only higher resolution contributed to lower model errors in salinity, nitrate (NO3), and chlorophyll-a (Chl-a). In the Arctic Basin, model errors in mixed layer depth (MLD) were reduced 36% by brine rejection parameterization, 20% by new sea-ice processes, and 6% by higher resolution. The NO3 concentration biases were caused by both MLD bias and coarse resolution, because of excessive horizontal mixing of high NO3 from the Chukchi Sea into the Canada Basin in coarse resolution models. R9km showed improvements over G1deg on NO3, but not on Chl-a, likely due to light limitation under snow and ice cover in the Arctic Basin.

  14. Assessing biogeochemical effects and best management practice for a wheat-maize cropping system using the DNDC model

    Science.gov (United States)

    Cui, F.; Zheng, X.; Liu, C.; Wang, K.; Zhou, Z.; Deng, J.

    2014-01-01

    Contemporary agriculture is shifting from a single-goal to a multi-goal strategy, which in turn requires choosing best management practice (BMP) based on an assessment of the biogeochemical effects of management alternatives. The bottleneck is the capacity of predicting the simultaneous effects of different management practice scenarios on multiple goals and choosing BMP among scenarios. The denitrification-decomposition (DNDC) model may provide an opportunity to solve this problem. We validated the DNDC model (version 95) using the observations of soil moisture and temperature, crop yields, aboveground biomass and fluxes of net ecosystem exchange of carbon dioxide, methane, nitrous oxide (N2O), nitric oxide (NO) and ammonia (NH3) from a wheat-maize cropping site in northern China. The model performed well for these variables. Then we used this model to simulate the effects of management practices on the goal variables of crop yields, NO emission, nitrate leaching, NH3 volatilization and net emission of greenhouse gases in the ecosystem (NEGE). Results showed that no-till and straw-incorporated practices had beneficial effects on crop yields and NEGE. Use of nitrification inhibitors decreased nitrate leaching and N2O and NO emissions, but they significantly increased NH3 volatilization. Irrigation based on crop demand significantly increased crop yield and decreased nitrate leaching and NH3 volatilization. Crop yields were hardly decreased if nitrogen dose was reduced by 15% or irrigation water amount was reduced by 25%. Two methods were used to identify BMP and resulted in the same BMP, which adopted the current crop cultivar, field operation schedules and full straw incorporation and applied nitrogen and irrigation water at 15 and 25% lower rates, respectively, than the current use. Our study indicates that the DNDC model can be used as a tool to assess biogeochemical effects of management alternatives and identify BMP.

  15. Effects of parameter indeterminacy in pelagic biogeochemical modules of Earth System Models on projections into a warming future: The scale of the problem

    Science.gov (United States)

    Löptien, U.; Dietze, H.

    2017-07-01

    Numerical Earth System Models are generic tools used to extrapolate present climate conditions into a warming future and to explore geoengineering options. Most of the current-generation models feature a simple pelagic biogeochemical model component that is embedded into a three-dimensional ocean general circulation model. The dynamics of these biogeochemical model components is essentially controlled by so-called model parameters most of which are poorly known. Here we explore the feasibility to estimate these parameters in a full-fledged three-dimensional Earth System Model by minimizing the misfit to noisy observations. The focus is on parameter identifiability. Based on earlier studies, we illustrate problems in determining a unique estimate of those parameters that prescribe the limiting effect of nutrient- and light-depleted conditions on carbon assimilation by autotrophic phytoplankton. Our results showcase that for typical models and evaluation metrics no meaningful "best" unique parameter set exists. We find very different parameter sets which are, on the one hand, equally consistent with our (synthetic) historical observations while, on the other hand, they propose strikingly differing projections into a warming climate.

  16. A regional scale modeling framework combining biogeochemical model with life cycle and economic analysis for integrated assessment of cropping systems.

    Science.gov (United States)

    Tabatabaie, Seyed Mohammad Hossein; Bolte, John P; Murthy, Ganti S

    2018-06-01

    The goal of this study was to integrate a crop model, DNDC (DeNitrification-DeComposition), with life cycle assessment (LCA) and economic analysis models using a GIS-based integrated platform, ENVISION. The integrated model enables LCA practitioners to conduct integrated economic analysis and LCA on a regional scale while capturing the variability of soil emissions due to variation in regional factors during production of crops and biofuel feedstocks. In order to evaluate the integrated model, the corn-soybean cropping system in Eagle Creek Watershed, Indiana was studied and the integrated model was used to first model the soil emissions and then conduct the LCA as well as economic analysis. The results showed that the variation in soil emissions due to variation in weather is high causing some locations to be carbon sink in some years and source of CO 2 in other years. In order to test the model under different scenarios, two tillage scenarios were defined: 1) conventional tillage (CT) and 2) no tillage (NT) and analyzed with the model. The overall GHG emissions for the corn-soybean cropping system was simulated and results showed that the NT scenario resulted in lower soil GHG emissions compared to CT scenario. Moreover, global warming potential (GWP) of corn ethanol from well to pump varied between 57 and 92gCO 2 -eq./MJ while GWP under the NT system was lower than that of the CT system. The cost break-even point was calculated as $3612.5/ha in a two year corn-soybean cropping system and the results showed that under low and medium prices for corn and soybean most of the farms did not meet the break-even point. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Insights from Modeling the Integrated Climate, Biogeochemical Cycles, Human Activities and Their Interactions in the ACME Earth System Model

    Science.gov (United States)

    Leung, L. R.; Thornton, P. E.; Riley, W. J.; Calvin, K. V.

    2017-12-01

    Towards the goal of understanding the contributions from natural and managed systems to current and future greenhouse gas fluxes and carbon-climate and carbon-CO2 feedbacks, efforts have been underway to improve representations of the terrestrial, river, and human components of the ACME earth system model. Broadly, our efforts include implementation and comparison of approaches to represent the nutrient cycles and nutrient limitations on ecosystem production, extending the river transport model to represent sediment and riverine biogeochemistry, and coupling of human systems such as irrigation, reservoir operations, and energy and land use with the ACME land and river components. Numerical experiments have been designed to understand how terrestrial carbon, nitrogen, and phosphorus cycles regulate climate system feedbacks and the sensitivity of the feedbacks to different model treatments, examine key processes governing sediment and biogeochemistry in the rivers and their role in the carbon cycle, and exploring the impacts of human systems in perturbing the hydrological and carbon cycles and their interactions. This presentation will briefly introduce the ACME modeling approaches and discuss preliminary results and insights from numerical experiments that lay the foundation for improving understanding of the integrated climate-biogeochemistry-human system.

  18. On the coupling of benthic and pelagic biogeochemical models

    NARCIS (Netherlands)

    Soetaert, K.E.R.; Middelburg, J.J.; Herman, P.M.J.; Buis, K.

    2000-01-01

    Mutual interaction of water column and sediment processes is either neglected or only crudely approximated in many biogeochemical models. We have reviewed the approaches to couple benthic and pelagic biogeochemical models. It is concluded that they can be classified into a hierarchical set

  19. NASA Ocean Biogeochemical Model assimilating ESRID data global monthly 2/3x1.25 degrees VR2014

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA Ocean Biogeochemical Model -- Assimilated Monthly Data The NASA Ocean Biogeochemical Model (NOBM) is a comprehensive, interactive ocean biogeochemical model...

  20. The acclimative biogeochemical model of the southern North Sea

    Science.gov (United States)

    Kerimoglu, Onur; Hofmeister, Richard; Maerz, Joeran; Riethmüller, Rolf; Wirtz, Kai W.

    2017-10-01

    Ecosystem models often rely on heuristic descriptions of autotrophic growth that fail to reproduce various stationary and dynamic states of phytoplankton cellular composition observed in laboratory experiments. Here, we present the integration of an advanced phytoplankton growth model within a coupled three-dimensional physical-biogeochemical model and the application of the model system to the southern North Sea (SNS) defined on a relatively high resolution (˜ 1.5-4.5 km) curvilinear grid. The autotrophic growth model, recently introduced by Wirtz and Kerimoglu (2016), is based on a set of novel concepts for the allocation of internal resources and operation of cellular metabolism. The coupled model system consists of the General Estuarine Transport Model (GETM) as the hydrodynamical driver, a lower-trophic-level model and a simple sediment diagenesis model. We force the model system with realistic atmospheric and riverine fluxes, background turbidity caused by suspended particulate matter (SPM) and open ocean boundary conditions. For a simulation for the period 2000-2010, we show that the model system satisfactorily reproduces the physical and biogeochemical states of the system within the German Bight characterized by steep salinity; nutrient and chlorophyll (Chl) gradients, as inferred from comparisons against observation data from long-term monitoring stations; sparse in situ measurements; continuous transects; and satellites. The model also displays skill in capturing the formation of thin chlorophyll layers at the pycnocline, which is frequently observed within the stratified regions during summer. A sensitivity analysis reveals that the vertical distributions of phytoplankton concentrations estimated by the model can be qualitatively sensitive to the description of the light climate and dependence of sinking rates on the internal nutrient reserves. A non-acclimative (fixed-physiology) version of the model predicted entirely different vertical profiles

  1. Integrated water system simulation by considering hydrological and biogeochemical processes: model development, with parameter sensitivity and autocalibration

    Science.gov (United States)

    Zhang, Y. Y.; Shao, Q. X.; Ye, A. Z.; Xing, H. T.; Xia, J.

    2016-02-01

    Integrated water system modeling is a feasible approach to understanding severe water crises in the world and promoting the implementation of integrated river basin management. In this study, a classic hydrological model (the time variant gain model: TVGM) was extended to an integrated water system model by coupling multiple water-related processes in hydrology, biogeochemistry, water quality, and ecology, and considering the interference of human activities. A parameter analysis tool, which included sensitivity analysis, autocalibration and model performance evaluation, was developed to improve modeling efficiency. To demonstrate the model performances, the Shaying River catchment, which is the largest highly regulated and heavily polluted tributary of the Huai River basin in China, was selected as the case study area. The model performances were evaluated on the key water-related components including runoff, water quality, diffuse pollution load (or nonpoint sources) and crop yield. Results showed that our proposed model simulated most components reasonably well. The simulated daily runoff at most regulated and less-regulated stations matched well with the observations. The average correlation coefficient and Nash-Sutcliffe efficiency were 0.85 and 0.70, respectively. Both the simulated low and high flows at most stations were improved when the dam regulation was considered. The daily ammonium-nitrogen (NH4-N) concentration was also well captured with the average correlation coefficient of 0.67. Furthermore, the diffuse source load of NH4-N and the corn yield were reasonably simulated at the administrative region scale. This integrated water system model is expected to improve the simulation performances with extension to more model functionalities, and to provide a scientific basis for the implementation in integrated river basin managements.

  2. Combined biogeophysical and biogeochemical effects of large-scale forest cover changes in the MPI earth system model

    Directory of Open Access Journals (Sweden)

    S. Bathiany

    2010-05-01

    Full Text Available Afforestation and reforestation have become popular instruments of climate mitigation policy, as forests are known to store large quantities of carbon. However, they also modify the fluxes of energy, water and momentum at the land surface. Previous studies have shown that these biogeophysical effects can counteract the carbon drawdown and, in boreal latitudes, even overcompensate it due to large albedo differences between forest canopy and snow. This study investigates the role forest cover plays for global climate by conducting deforestation and afforestation experiments with the earth system model of the Max Planck Institute for Meteorology (MPI-ESM. Complete deforestation of the tropics (18.75° S–15° N exerts a global warming of 0.4 °C due to an increase in CO2 concentration by initially 60 ppm and a decrease in evapotranspiration in the deforested areas. In the northern latitudes (45° N–90° N, complete deforestation exerts a global cooling of 0.25 °C after 100 years, while afforestation leads to an equally large warming, despite the counteracting changes in CO2 concentration. Earlier model studies are qualitatively confirmed by these findings. As the response of temperature as well as terrestrial carbon pools is not of equal sign at every land cell, considering forests as cooling in the tropics and warming in high latitudes seems to be true only for the spatial mean, but not on a local scale.

  3. Wetland biogeochemical processes and simulation modeling

    Science.gov (United States)

    Bai, Junhong; Huang, Laibin; Gao, Haifeng; Jia, Jia; Wang, Xin

    2018-02-01

    As the important landscape with rich biodiversity and high productivity, wetlands can provide numerous ecological services including playing an important role in regulating global biogeochemical cycles, filteringpollutants from terrestrial runoff and atmospheric deposition, protecting and improving water quality, providing living habitats for plants and animals, controlling floodwaters, and retaining surface water flow during dry periods (Reddy and DeLaune, 2008; Qin and Mitsch, 2009; Zhao et al., 2016). However, more than 50% of the world's wetlands had been altered, degraded or lost through a wide range of human activities in the past 150 years, and only a small percentage of the original wetlands remained around the world after over two centuries of intensive development and urbanization (O'connell, 2003; Zhao et al., 2016).

  4. Hyporheic flow and transport processes: mechanisms, models, and biogeochemical implications

    Science.gov (United States)

    Boano, Fulvio; Harvey, Judson W.; Marion, Andrea; Packman, Aaron I.; Revelli, Roberto; Ridolfi, Luca; Anders, Wörman

    2014-01-01

    Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed."

  5. Towards coupled physical-biogeochemical models of the ocean carbon cycle

    Science.gov (United States)

    Rintoul, Stephen R.

    1992-01-01

    The purpose of this review is to discuss the critical gaps in our knowledge of ocean dynamics and biogeochemical cycles. It is assumed that the ultimate goal is the design of a model of the earth system that can predict the response to changes in the external forces driving climate.

  6. Converting copepod vital rates into units appropriate for biogeochemical models

    Science.gov (United States)

    Frangoulis, C.; Carlotti, F.; Eisenhauer, L.; Zervoudaki, S.

    2010-01-01

    The conversion of units is one of the difficulties of model parameterisation. Conversion errors may result not only from incorrect choices of conversion factors, but also from incorrect choices of the value itself. In biogeochemical models, mesozooplankton, is the highest trophic level of the food web, and it is very often reduced to a single variable generally considered as a representation of the copepod community, the dominant taxa in mesozooplankton. If this simplifies the information to be obtained for the stock, a correct parameterisation of the processes related to the copepod community is already a tricky task due to the wide range of copepod species, sizes, stages and behaviour. The goal of this paper is to improve the communication between experimentalists and modellers by giving indications for the conversion of copepod vital rates from experimental to biogeochemical model units. This includes the choice of values, conversion factors, terminology distinction and the scale transfer. To begin with, we briefly address the common problem of the conversion of a rate per individual to a rate per mass. Then, we focus on unit conversion problems for each specific rate and give recommendations. Finally, we discuss the problem of scale transfer between the level of organisation at which the rate value is measured at characteristic time and space-scales versus the level of representation of the corresponding process in the model, with its different characteristic time and space-scales .

  7. Modelling benthic biophysical drivers of ecosystem structure and biogeochemical response

    Science.gov (United States)

    Stephens, Nicholas; Bruggeman, Jorn; Lessin, Gennadi; Allen, Icarus

    2016-04-01

    The fate of carbon deposited at the sea floor is ultimately decided by biophysical drivers that control the efficiency of remineralisation and timescale of carbon burial in sediments. Specifically, these drivers include bioturbation through ingestion and movement, burrow-flushing and sediment reworking, which enhance vertical particulate transport and solute diffusion. Unfortunately, these processes are rarely satisfactorily resolved in models. To address this, a benthic model that explicitly describes the vertical position of biology (e.g., habitats) and biogeochemical processes is presented that includes biological functionality and biogeochemical response capturing changes in ecosystem structure, benthic-pelagic fluxes and biodiversity on inter-annual timescales. This is demonstrated by the model's ability to reproduce temporal variability in benthic infauna, vertical pore water nutrients and pelagic-benthic solute fluxes compared to in-situ data. A key advance is the replacement of bulk parameterisation of bioturbation by explicit description of the bio-physical processes responsible. This permits direct comparison with observations and determination of key parameters in experiments. Crucially, the model resolves the two-way interaction between sediment biogeochemistry and ecology, allowing exploration of the benthic response to changing environmental conditions, the importance of infaunal functional traits in shaping benthic ecological structure and the feedback the resulting bio-physical processes exert on pore water nutrient profiles. The model is actively being used to understand shelf sea carbon cycling, the response of the benthos to climatic change, food provision and other societal benefits.

  8. Error assessment of biogeochemical models by lower bound methods (NOMMA-1.0)

    Science.gov (United States)

    Sauerland, Volkmar; Löptien, Ulrike; Leonhard, Claudine; Oschlies, Andreas; Srivastav, Anand

    2018-03-01

    Biogeochemical models, capturing the major feedbacks of the pelagic ecosystem of the world ocean, are today often embedded into Earth system models which are increasingly used for decision making regarding climate policies. These models contain poorly constrained parameters (e.g., maximum phytoplankton growth rate), which are typically adjusted until the model shows reasonable behavior. Systematic approaches determine these parameters by minimizing the misfit between the model and observational data. In most common model approaches, however, the underlying functions mimicking the biogeochemical processes are nonlinear and non-convex. Thus, systematic optimization algorithms are likely to get trapped in local minima and might lead to non-optimal results. To judge the quality of an obtained parameter estimate, we propose determining a preferably large lower bound for the global optimum that is relatively easy to obtain and that will help to assess the quality of an optimum, generated by an optimization algorithm. Due to the unavoidable noise component in all observations, such a lower bound is typically larger than zero. We suggest deriving such lower bounds based on typical properties of biogeochemical models (e.g., a limited number of extremes and a bounded time derivative). We illustrate the applicability of the method with two real-world examples. The first example uses real-world observations of the Baltic Sea in a box model setup. The second example considers a three-dimensional coupled ocean circulation model in combination with satellite chlorophyll a.

  9. A Coupled Model of Multiphase Flow, Reactive Biogeochemical Transport, Thermal Transport and Geo-Mechanics.

    Science.gov (United States)

    Tsai, C. H.; Yeh, G. T.

    2015-12-01

    In this investigation, a coupled model of multiphase flow, reactive biogeochemical transport, thermal transport and geo-mechanics in subsurface media is presented. It iteratively solves the mass conservation equation for fluid flow, thermal transport equation for temperature, reactive biogeochemical transport equations for concentration distributions, and solid momentum equation for displacement with successive linearization algorithm. With species-based equations of state, density of a phase in the system is obtained by summing up concentrations of all species. This circumvents the problem of having to use empirical functions. Moreover, reaction rates of all species are incorporated in mass conservation equation for fluid flow. Formation enthalpy of all species is included in the law of energy conservation as a source-sink term. Finite element methods are used to discretize the governing equations. Numerical experiments are presented to examine the accuracy and robustness of the proposed model. The results demonstrate the feasibility and capability of present model in subsurface media.

  10. Assimilation of ocean colour data into a Biogeochemical Flux Model of the Eastern Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    G. Triantafyllou

    2007-08-01

    Full Text Available An advanced multivariate sequential data assimilation system has been implemented within the framework of the European MFSTEP project to fit a three-dimensional biogeochemical model of the Eastern Mediterranean to satellite chlorophyll data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS. The physics are described by the Princeton Ocean Model (POM while the biochemistry of the ecosystem is tackled with the Biogeochemical Flux Model (BFM. The assimilation scheme is based on the Singular Evolutive Extended Kalman (SEEK filter, in which the error statistics were parameterized by means of a suitable set of Empirical Orthogonal Functions (EOFs. To avoid spurious long-range correlations associated with the limited number of EOFs, the filter covariance matrix was given compact support through a radius of influence around every data point location. Hindcast experiments were performed for one year over 1999 and forced with ECMWF 6 h atmospheric fields. The solution of the assimilation system was evaluated against the assimilated data and the MedAtlas climatology, and by assessing the impact of the assimilation on non-observed biogeochemical processes. It is found that the assimilation of SeaWiFS data improves the overall behavior of the BFM model and efficiently removes long term biases from the model despite some difficulties during the spring bloom period. Results, however, suggest the need of subsurface data to enhance the estimation of the ecosystem variables in the deep layers.

  11. Past and present of sediment and carbon biogeochemical cycling models

    Directory of Open Access Journals (Sweden)

    F. T. Mackenzie

    2004-01-01

    Full Text Available The global carbon cycle is part of the much more extensive sedimentary cycle that involves large masses of carbon in the Earth's inner and outer spheres. Studies of the carbon cycle generally followed a progression in knowledge of the natural biological, then chemical, and finally geological processes involved, culminating in a more or less integrated picture of the biogeochemical carbon cycle by the 1920s. However, knowledge of the ocean's carbon cycle behavior has only within the last few decades progressed to a stage where meaningful discussion of carbon processes on an annual to millennial time scale can take place. In geologically older and pre-industrial time, the ocean was generally a net source of CO2 emissions to the atmosphere owing to the mineralization of land-derived organic matter in addition to that produced in situ and to the process of CaCO3 precipitation. Due to rising atmospheric CO2 concentrations because of fossil fuel combustion and land use changes, the direction of the air-sea CO2 flux has reversed, leading to the ocean as a whole being a net sink of anthropogenic CO2. The present thickness of the surface ocean layer, where part of the anthropogenic CO2 emissions are stored, is estimated as of the order of a few hundred meters. The oceanic coastal zone net air-sea CO2 exchange flux has also probably changed during industrial time. Model projections indicate that in pre-industrial times, the coastal zone may have been net heterotrophic, releasing CO2 to the atmosphere from the imbalance between gross photosynthesis and total respiration. This, coupled with extensive CaCO3 precipitation in coastal zone environments, led to a net flux of CO2 out of the system. During industrial time the coastal zone ocean has tended to reverse its trophic status toward a non-steady state situation of net autotrophy, resulting in net uptake of anthropogenic CO2 and storage of carbon in the coastal ocean, despite the significant calcification

  12. Monitoring strategies and scale appropriate hydrologic and biogeochemical modelling for natural resource management

    DEFF Research Database (Denmark)

    Bende-Michl, Ulrike; Volk, Martin; Harmel, Daren

    2011-01-01

    -appropriate hydrologic and biogeochemical modelling for natural resource management’ session at the 2008 International Environmental Modelling and Simulation Society conference, Barcelona, Spain. The outcomes of the session and recent international studies exemplify the need for a stronger collaboration...... techniques, and 3) representation of hydrologic and biogeochemical phenomena in model development and practical application for natural resource management....

  13. Modelling biogeochemical-stratigraphic dynamics of clinoform successions over geological timescales

    DEFF Research Database (Denmark)

    Legarth, Jens Jakob Fosselius; Bjerrum, Christian J.

    are investigated with our novel dynamic biogeochemical-stratigraphic model which explicitly calculates sediment and biogeochemical tracer erosion and deposition over multi-kilo-years. In the model organic and uranium enrichment in the distal clinoform develops as a transgressive nature. As a result part...

  14. NASA Ocean Biogeochemical Model assimilating satellite chlorophyll data global daily VR2017 (NOBM_DAY) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — This is the assimilated daily data from NASA Ocean Biogeochemical Model (NOBM). The NOBM is a comprehensive, interactive ocean biogeochemical model coupled with a...

  15. NASA Ocean Biogeochemical Model assimilating satellite chlorophyll data global monthly VR2017 (NOBM_MON) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — This is the assimilated monthly data from NASA Ocean Biogeochemical Model (NOBM). The NOBM is a comprehensive, interactive ocean biogeochemical model coupled with a...

  16. Modelling of transport and biogeochemical processes in pollution plumes: Literature review of model development

    DEFF Research Database (Denmark)

    Brun, A.; Engesgaard, Peter Knudegaard

    2002-01-01

    A literature survey shows how biogeochemical (coupled organic and inorganic reaction processes) transport models are based on considering the complete biodegradation process as either a single- or as a two-step process. It is demonstrated that some two-step process models rely on the Partial Equi....... A second paper [J. Hydrol. 256 (2002) 230-249], reports the application of the model to a field study of biogeochemical transport processes in a landfill plume in Denmark (Vejen). (C) 2002 Elsevier Science B.V. All rights reserved....

  17. Nitrous Oxide Emissions from Biofuel Crops and Parameterization in the EPIC Biogeochemical Model

    Science.gov (United States)

    This presentation describes year 1 field measurements of N2O fluxes and crop yields which are used to parameterize the EPIC biogeochemical model for the corresponding field site. Initial model simulations are also presented.

  18. Benthic-Pelagic Coupling in Biogeochemical and Climate Models: Existing Approaches, Recent developments and Roadblocks

    Science.gov (United States)

    Arndt, Sandra

    2016-04-01

    Marine sediments are key components in the Earth System. They host the largest carbon reservoir on Earth, provide the only long term sink for atmospheric CO2, recycle nutrients and represent the most important climate archive. Biogeochemical processes in marine sediments are thus essential for our understanding of the global biogeochemical cycles and climate. They are first and foremost, donor controlled and, thus, driven by the rain of particulate material from the euphotic zone and influenced by the overlying bottom water. Geochemical species may undergo several recycling loops (e.g. authigenic mineral precipitation/dissolution) before they are either buried or diffuse back to the water column. The tightly coupled and complex pelagic and benthic process interplay thus delays recycling flux, significantly modifies the depositional signal and controls the long-term removal of carbon from the ocean-atmosphere system. Despite the importance of this mutual interaction, coupled regional/global biogeochemical models and (paleo)climate models, which are designed to assess and quantify the transformations and fluxes of carbon and nutrients and evaluate their response to past and future perturbations of the climate system either completely neglect marine sediments or incorporate a highly simplified representation of benthic processes. On the other end of the spectrum, coupled, multi-component state-of-the-art early diagenetic models have been successfully developed and applied over the past decades to reproduce observations and quantify sediment-water exchange fluxes, but cannot easily be coupled to pelagic models. The primary constraint here is the high computation cost of simulating all of the essential redox and equilibrium reactions within marine sediments that control carbon burial and benthic recycling fluxes: a barrier that is easily exacerbated if a variety of benthic environments are to be spatially resolved. This presentation provides an integrative overview of

  19. Biogeochemical Modeling of the Second Rise of Oxygen

    Science.gov (United States)

    Smith, M. L.; Catling, D.; Claire, M.; Zahnle, K.

    2014-03-01

    The rise of atmospheric oxygen set the tempo for the evolution of complex life on Earth. Oxygen levels are thought to have increased in two broad steps: one step occurred in the Archean ~ 2.45 Ga (the Great Oxidation Event or GOE), and another step occured in the Neoproterozoic ~750-580 Ma (the Neoprotoerozoic Oxygenation Event or NOE). During the NOE, oxygen levels increased from ~1-10% of the present atmospheric level (PAL) (Holland, 2006), to ~15% PAL in the late Neoproterozoic, to ~100% PAL later in the Phanerozoic. Complex life requires O2, so this transition allowed complex life to evolve. We seek to understand what caused the NOE. To explore causes for the NOE, we build upon the biogeochemical model of Claire et al. (2006), which calculates the redox evolution of the atmosphere, ocean, biosphere, and crust in the Archean through to the early Proterozoic. In this model, the balance between oxygenconsuming and oyxgen-producing fluxes evolves over time such that at ~2.4 Ga, the rapidly acting sources of oxygen outweigh the rapidly-acting sinks. Or, in other words, at ~2.4 Ga, the flux of oxygen from organic carbon burial exceeds the sinks of oxygen from reaction with reduced volcanic and metamoprphic gases. The model is able to drive oxygen levels to 1-10% PAL in the Proterozoic; however, the evolving redox fluxes in the model cannot explain how oxygen levels pushed above 1-10% in the late Proterozoic. The authors suggest that perhaps another buffer, such as sulfur, is needed to describe Proterozoic and Phanerozoic redox evolution. Geologic proxies show that in the Proterozoic, up to 10% of the deep ocean may have been sulfidic. With this ocean chemistry, the global sulfur cycle would have worked differently than it does today. Because the sulfur and oxygen cycles interact, the oxygen concentration could have permanently changed due to an evolving sulfur cycle (in combination with evolving redox fluxes associated with other parts of the oxygen cycle and carbon

  20. Skill assessment of the coupled physical-biogeochemical operational Mediterranean Forecasting System

    Science.gov (United States)

    Cossarini, Gianpiero; Clementi, Emanuela; Salon, Stefano; Grandi, Alessandro; Bolzon, Giorgio; Solidoro, Cosimo

    2016-04-01

    The Mediterranean Monitoring and Forecasting Centre (Med-MFC) is one of the regional production centres of the European Marine Environment Monitoring Service (CMEMS-Copernicus). Med-MFC operatively manages a suite of numerical model systems (3DVAR-NEMO-WW3 and 3DVAR-OGSTM-BFM) that provides gridded datasets of physical and biogeochemical variables for the Mediterranean marine environment with a horizontal resolution of about 6.5 km. At the present stage, the operational Med-MFC produces ten-day forecast: daily for physical parameters and bi-weekly for biogeochemical variables. The validation of the coupled model system and the estimate of the accuracy of model products are key issues to ensure reliable information to the users and the downstream services. Product quality activities at Med-MFC consist of two levels of validation and skill analysis procedures. Pre-operational qualification activities focus on testing the improvement of the quality of a new release of the model system and relays on past simulation and historical data. Then, near real time (NRT) validation activities aim at the routinely and on-line skill assessment of the model forecast and relays on the NRT available observations. Med-MFC validation framework uses both independent (i.e. Bio-Argo float data, in-situ mooring and vessel data of oxygen, nutrients and chlorophyll, moored buoys, tide-gauges and ADCP of temperature, salinity, sea level and velocity) and semi-independent data (i.e. data already used for assimilation, such as satellite chlorophyll, Satellite SLA and SST and in situ vertical profiles of temperature and salinity from XBT, Argo and Gliders) We give evidence that different variables (e.g. CMEMS-products) can be validated at different levels (i.e. at the forecast level or at the level of model consistency) and at different spatial and temporal scales. The fundamental physical parameters temperature, salinity and sea level are routinely validated on daily, weekly and quarterly base

  1. Investigating the initial stages of soil formation in glacier forefields using the new biogeochemical model: SHIMMER

    Science.gov (United States)

    Bradley, James; Anesio, Alexandre; Arndt, Sandra; Sabacka, Marie; Barker, Gary; Benning, Liane; Blacker, Joshua; Singarayer, Joy; Tranter, Martyn; Yallop, Marian

    2016-04-01

    observations from chronosequences from the forefield of Midtre Lovénbreen, Svalbard (78°N), to investigate the first 120 years of soil development. We carried out an in depth analysis of the model dynamics and determined the most sensitive parameters. We then used laboratory measurements to derive values for those parameters: bacterial growth rate, growth efficiency and temperature dependency. By applying the model to the High-Arctic forefield and integrating the measured parameter values, we could refine the model and easily predict the rapid accumulation of microbial biomass that was observed in our field data. Furthermore, we show that the bacterial production is dominated by autotrophy (rather than heterotrophy). Heterotrophic production in young soils (0-20 years) is supported by labile substrate, whereas carbon stocks in older soils (60-120 years) are more refractory. Nitrogen fixing organisms are responsible for the initial accumulation of available nitrates in the soil. However, microbial processes alone do not explain the build-up of organic matter observed in the field data record. Consequently, the model infers that allochthonous deposition of organic material may play a significant contributory role that could accelerate or facilitate further microbial growth. SHIMMER provides a quantitative evaluation on the dynamics of glacier forefield systems that have previously largely been explored through qualitative interpretation of datasets. References Bradley J.A., Singarayer J.S., Anesio A.M. (2014) Microbial community dynamics in the forefield of glaciers. Proceedings Biological sciences / The Royal Society 281(1795), 2793-2802. (doi:10.1098/rspb.2014.0882). Bradley J.A., Anesio A.M., Singarayer J.S., Heath M.R., Arndt S. (2015) SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems. Geosci Model Dev 8(10), 3441-3470. (doi:10.5194/gmd-8-3441-2015).

  2. A model simulation of biogeochemical conditions along the British Columbia Continental Shelf

    Science.gov (United States)

    Peña, Angelica; Fine, Isaac; Masson, Diane

    2017-04-01

    The British Columbia shelf is at the northern end of the California Current System and is influenced by summer coastal upwelling, mesoscale eddies, and freshwater inputs. A regional coupled circulation-biogeochemical (ROMS) model of this region has been developed to gain a better understanding of the potential impact of climate variability and change on lower trophic levels and the biogeochemistry of the region. A first step to address the impacts of climate variability on marine ecosystem is to develop biophysical models that simulate the present ecosystem state in relation to the climate record and can be used to examine the influence of different forcing acting, at different scales, on ecological processes. This talk will will evaluate the capability of the model to reproduce observations and to respond to main episodic events (seasonal cycle and El Niño events).

  3. Terrestrial biogeochemical feedbacks in the climate system: from past to future

    Energy Technology Data Exchange (ETDEWEB)

    Arneth, A.; Harrison, S. P.; Zaehle, S.; Tsigaridis, K; Menon, S; Bartlein, P.J.; Feichter, J; Korhola, A; Kulmala, M; O' Donnell, D; Schurgers, G; Sorvari, S; Vesala, T

    2010-01-05

    The terrestrial biosphere plays a major role in the regulation of atmospheric composition, and hence climate, through multiple interlinked biogeochemical cycles (BGC). Ice-core and other palaeoenvironmental records show a fast response of vegetation cover and exchanges with the atmosphere to past climate change, although the phasing of these responses reflects spatial patterning and complex interactions between individual biospheric feedbacks. Modern observations show a similar responsiveness of terrestrial biogeochemical cycles to anthropogenically-forced climate changes and air pollution, with equally complex feedbacks. For future conditions, although carbon cycle-climate interactions have been a major focus, other BGC feedbacks could be as important in modulating climate changes. The additional radiative forcing from terrestrial BGC feedbacks other than those conventionally attributed to the carbon cycle is in the range of 0.6 to 1.6 Wm{sup -2}; all taken together we estimate a possible maximum of around 3 Wm{sup -2} towards the end of the 21st century. There are large uncertainties associated with these estimates but, given that the majority of BGC feedbacks result in a positive forcing because of the fundamental link between metabolic stimulation and increasing temperature, improved quantification of these feedbacks and their incorporation in earth system models is necessary in order to develop coherent plans to manage ecosystems for climate mitigation.

  4. Biogeochemical mass balances in a turbid tropical reservoir. Field data and modelling approach

    Science.gov (United States)

    Phuong Doan, Thuy Kim; Némery, Julien; Gratiot, Nicolas; Schmid, Martin

    2014-05-01

    The turbid tropical Cointzio reservoir, located in the Trans Mexican Volcanic Belt (TMVB), behaves as a warm monomictic water body (area = 6 km2, capacity 66 Mm3, residence time ~ 1 year). It is strategic for the drinking water supply of the city of Morelia, capital of the state of Michoacán, and for downstream irrigation during the dry season. This reservoir is a perfect example of a human-impacted system since its watershed is mainly composed of degraded volcanic soils and is subjected to high erosion processes and agricultural loss. The reservoir is threatened by sediment accumulation and nutrients originating from untreated waters in the upstream watershed. The high content of very fine clay particles and the lack of water treatment plants lead to serious episodes of eutrophication (up to 70 μg chl. a L-1), high levels of turbidity (Secchi depth water vertical profiles, reservoir inflow and outflow) we determined suspended sediment (SS), carbon (C), nitrogen (N) and phosphorus (P) mass balances. Watershed SS yields were estimated at 35 t km2 y-1 of which 89-92 % were trapped in the Cointzio reservoir. As a consequence the reservoir has already lost 25 % of its initial storage capacity since its construction in 1940. Nutrient mass balances showed that 50 % and 46 % of incoming P and N were retained by sedimentation, and mainly eliminated through denitrification respectively. Removal of C by 30 % was also observed both by sedimentation and through gas emission. To complete field data analyses we examined the ability of vertical one dimensional (1DV) numerical models (Aquasim biogeochemical model coupled with k-ɛ mixing model) to reproduce the main biogeochemical cycles in the Cointzio reservoir. The model can describe all the mineralization processes both in the water column and in the sediment. The values of the entire mass balance of nutrients and of the mineralization rates (denitrification and aerobic benthic mineralization) calculated from the model

  5. Analyzing the ecosystem carbon and hydrologic characteristics of forested wetland using a biogeochemical process model

    Science.gov (United States)

    Jianbo Cui; Changsheng Li; Carl Trettin

    2005-01-01

    A comprehensive biogeochemical model, Wetland-DNDC, was applied to analyze the carbon and hydrologic characteristics of forested wetland ecosystem at Minnesota (MN) and Florida (FL) sites. The model simulates the flows of carbon, energy, and water in forested wetlands. Modeled carbon dynamics depends on physiological plant factors, the size of plant pools,...

  6. SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

    Science.gov (United States)

    Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

    2015-08-01

    SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently

  7. Long-term controls on ocean phosphorus and oxygen in a global biogeochemical model

    NARCIS (Netherlands)

    Palastanga, V.; Slomp, C.P.; Heinze, C.

    2011-01-01

    In this study, we use a biogeochemical ocean general circulation model (HAMOCC), originally developed for the carbon and silicon cycles, and expand it with a description of the sedimentary phosphorus (P) cycle. The model simulates the release of reactive P by aerobic and anaerobic degradation of

  8. Biogeochemical modelling of dissolved oxygen in a changing ocean

    Science.gov (United States)

    Andrews, Oliver; Buitenhuis, Erik; Le Quéré, Corinne; Suntharalingam, Parvadha

    2017-08-01

    Secular decreases in dissolved oxygen concentration have been observed within the tropical oxygen minimum zones (OMZs) and at mid- to high latitudes over the last approximately 50 years. Earth system model projections indicate that a reduction in the oxygen inventory of the global ocean, termed ocean deoxygenation, is a likely consequence of on-going anthropogenic warming. Current models are, however, unable to consistently reproduce the observed trends and variability of recent decades, particularly within the established tropical OMZs. Here, we conduct a series of targeted hindcast model simulations using a state-of-the-art global ocean biogeochemistry model in order to explore and review biases in model distributions of oceanic oxygen. We show that the largest magnitude of uncertainty is entrained into ocean oxygen response patterns due to model parametrization of pCO2-sensitive C : N ratios in carbon fixation and imposed atmospheric forcing data. Inclusion of a pCO2-sensitive C : N ratio drives historical oxygen depletion within the ocean interior due to increased organic carbon export and subsequent remineralization. Atmospheric forcing is shown to influence simulated interannual variability in ocean oxygen, particularly due to differences in imposed variability of wind stress and heat fluxes. This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

  9. Biogeochemical modelling of dissolved oxygen in a changing ocean.

    Science.gov (United States)

    Andrews, Oliver; Buitenhuis, Erik; Le Quéré, Corinne; Suntharalingam, Parvadha

    2017-09-13

    Secular decreases in dissolved oxygen concentration have been observed within the tropical oxygen minimum zones (OMZs) and at mid- to high latitudes over the last approximately 50 years. Earth system model projections indicate that a reduction in the oxygen inventory of the global ocean, termed ocean deoxygenation, is a likely consequence of on-going anthropogenic warming. Current models are, however, unable to consistently reproduce the observed trends and variability of recent decades, particularly within the established tropical OMZs. Here, we conduct a series of targeted hindcast model simulations using a state-of-the-art global ocean biogeochemistry model in order to explore and review biases in model distributions of oceanic oxygen. We show that the largest magnitude of uncertainty is entrained into ocean oxygen response patterns due to model parametrization of p CO 2 -sensitive C : N ratios in carbon fixation and imposed atmospheric forcing data. Inclusion of a p CO 2 -sensitive C : N ratio drives historical oxygen depletion within the ocean interior due to increased organic carbon export and subsequent remineralization. Atmospheric forcing is shown to influence simulated interannual variability in ocean oxygen, particularly due to differences in imposed variability of wind stress and heat fluxes.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

  10. Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP

    Directory of Open Access Journals (Sweden)

    J. C. Orr

    2017-06-01

    Full Text Available The Ocean Model Intercomparison Project (OMIP focuses on the physics and biogeochemistry of the ocean component of Earth system models participating in the sixth phase of the Coupled Model Intercomparison Project (CMIP6. OMIP aims to provide standard protocols and diagnostics for ocean models, while offering a forum to promote their common assessment and improvement. It also offers to compare solutions of the same ocean models when forced with reanalysis data (OMIP simulations vs. when integrated within fully coupled Earth system models (CMIP6. Here we detail simulation protocols and diagnostics for OMIP's biogeochemical and inert chemical tracers. These passive-tracer simulations will be coupled to ocean circulation models, initialized with observational data or output from a model spin-up, and forced by repeating the 1948–2009 surface fluxes of heat, fresh water, and momentum. These so-called OMIP-BGC simulations include three inert chemical tracers (CFC-11, CFC-12, SF6 and biogeochemical tracers (e.g., dissolved inorganic carbon, carbon isotopes, alkalinity, nutrients, and oxygen. Modelers will use their preferred prognostic BGC model but should follow common guidelines for gas exchange and carbonate chemistry. Simulations include both natural and total carbon tracers. The required forced simulation (omip1 will be initialized with gridded observational climatologies. An optional forced simulation (omip1-spunup will be initialized instead with BGC fields from a long model spin-up, preferably for 2000 years or more, and forced by repeating the same 62-year meteorological forcing. That optional run will also include abiotic tracers of total dissolved inorganic carbon and radiocarbon, CTabio and 14CTabio, to assess deep-ocean ventilation and distinguish the role of physics vs. biology. These simulations will be forced by observed atmospheric histories of the three inert gases and CO2 as well as carbon isotope ratios of CO2. OMIP-BGC simulation

  11. Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)

    Science.gov (United States)

    Orr, James C.; Najjar, Raymond G.; Aumont, Olivier; Bopp, Laurent; Bullister, John L.; Danabasoglu, Gokhan; Doney, Scott C.; Dunne, John P.; Dutay, Jean-Claude; Graven, Heather; Griffies, Stephen M.; John, Jasmin G.; Joos, Fortunat; Levin, Ingeborg; Lindsay, Keith; Matear, Richard J.; McKinley, Galen A.; Mouchet, Anne; Oschlies, Andreas; Romanou, Anastasia; Schlitzer, Reiner; Tagliabue, Alessandro; Tanhua, Toste; Yool, Andrew

    2017-06-01

    The Ocean Model Intercomparison Project (OMIP) focuses on the physics and biogeochemistry of the ocean component of Earth system models participating in the sixth phase of the Coupled Model Intercomparison Project (CMIP6). OMIP aims to provide standard protocols and diagnostics for ocean models, while offering a forum to promote their common assessment and improvement. It also offers to compare solutions of the same ocean models when forced with reanalysis data (OMIP simulations) vs. when integrated within fully coupled Earth system models (CMIP6). Here we detail simulation protocols and diagnostics for OMIP's biogeochemical and inert chemical tracers. These passive-tracer simulations will be coupled to ocean circulation models, initialized with observational data or output from a model spin-up, and forced by repeating the 1948-2009 surface fluxes of heat, fresh water, and momentum. These so-called OMIP-BGC simulations include three inert chemical tracers (CFC-11, CFC-12, SF6) and biogeochemical tracers (e.g., dissolved inorganic carbon, carbon isotopes, alkalinity, nutrients, and oxygen). Modelers will use their preferred prognostic BGC model but should follow common guidelines for gas exchange and carbonate chemistry. Simulations include both natural and total carbon tracers. The required forced simulation (omip1) will be initialized with gridded observational climatologies. An optional forced simulation (omip1-spunup) will be initialized instead with BGC fields from a long model spin-up, preferably for 2000 years or more, and forced by repeating the same 62-year meteorological forcing. That optional run will also include abiotic tracers of total dissolved inorganic carbon and radiocarbon, CTabio and 14CTabio, to assess deep-ocean ventilation and distinguish the role of physics vs. biology. These simulations will be forced by observed atmospheric histories of the three inert gases and CO2 as well as carbon isotope ratios of CO2. OMIP-BGC simulation protocols are

  12. Modeling anticipated climate change impact on biogeochemical cycles of an acidified headwater catchment

    Czech Academy of Sciences Publication Activity Database

    Benčoková, A.; Hruška, Jakub; Krám, P.

    2011-01-01

    Roč. 26, S (2011), S6-S8 ISSN 0883-2927 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073 Institutional research plan: CEZ:AV0Z60870520 Keywords : modeling anticipated * climate change * biogeochemical cycles * acidified headwater catchment Subject RIV: DD - Geochemistry Impact factor: 2.176, year: 2011

  13. Use of combined biogeochemical model approaches and empirical data to assess critical loads of nitrogen

    Science.gov (United States)

    Mark Fenn; Charles Driscoll; Quingtao Zhou; Leela Rao; Thomas Meixner; Edith Allen; Fengming Yuan; Timothy Sullivan

    2015-01-01

    Empirical and dynamic biogeochemical modelling are complementary approaches for determining the critical load (CL) of atmospheric nitrogen (N) or other constituent deposition that an ecosystem can tolerate without causing ecological harm. The greatest benefits are obtained when these approaches are used in combination. Confounding environmental factors can complicate...

  14. Biogeochemical validation of an interannual simulation of the ROMS-PISCES coupled model in the Southeast Pacific

    Directory of Open Access Journals (Sweden)

    Dante Espinoza-Morriberon

    2016-08-01

    Full Text Available Currently biogeochemical models are used to understand and quantify key biogeochemical processes in the ocean. The objective of the present study was to validate predictive ability of a regional configuration of the PISCES biogeochemical model on main biogeochemical variables in Humboldt Current Large Marine Ecosystem (HCLME. The statistical indicators used to evaluate the model were the bias, root-mean-square error, correlation coefficient and, graphically, the Taylor’s diagram. The results showed that the model reproduces the dynamics of the main biogeochemical variables (chlorophyll, dissolved oxygen and nutrients; in particular, the impact of El Niño 1997-1998 in the chlorophyll (decrease and oxygen minimum zone depth (increase. However, it is necessary to carry out sensitivity studies of the PISCES model with different key parameters values to obtain a more accurate representation of the properties of the Ocean.

  15. HYDROBIOGEOCHEM: A coupled model of HYDROlogic transport and mixed BIOGEOCHEMical kinetic/equilibrium reactions in saturated-unsaturated media

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, G.T.; Salvage, K.M. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Civil and Environmental Engineering; Gwo, J.P. [Oak Ridge National Lab., TN (United States); Zachara, J.M.; Szecsody, J.E. [Pacific Northwest National Lab., Richland, WA (United States)

    1998-07-01

    The computer program HYDROBIOGEOCHEM is a coupled model of HYDROlogic transport and BIOGEOCHEMical kinetic and/or equilibrium reactions in saturated/unsaturated media. HYDROBIOGEOCHEM iteratively solves the two-dimensional transport equations and the ordinary differential and algebraic equations of mixed biogeochemical reactions. The transport equations are solved for all aqueous chemical components and kinetically controlled aqueous species. HYDROBIOGEOCHEM is designed for generic application to reactive transport problems affected by both microbiological and geochemical reactions in subsurface media. Input to the program includes the geometry of the system, the spatial distribution of finite elements and nodes, the properties of the media, the potential chemical and microbial reactions, and the initial and boundary conditions. Output includes the spatial distribution of chemical and microbial concentrations as a function of time and space, and the chemical speciation at user-specified nodes.

  16. Implications of a More Comprehensive Nitrogen Cycle in a Global Biogeochemical Ocean Model

    Science.gov (United States)

    Six, K. D.; Ilyina, T.

    2016-02-01

    Nitrogen plays a crucial role for nearly all living organisms in the Earth system. Changes in the marine nitrogen cycle not only alter the marine biota, but will also have an impact on the marine carbon cycle and, in turn, on climate due to the close coupling of the carbon-nitrogen cycle. The understanding of processes and controls of the marine nitrogen cycle is therefore a prerequisite to reduce uncertainties in the prediction of future climate. Nevertheless, most ocean biogeochemical components of modern Earth system models have a rather simplistic representation of marine N-cycle mainly focusing on nitrate. Here we present results of the HAMburg Ocean Carbon Cycle model (HAMOCC) as part of the MPI-ESM which was extended by a prognostic representation of ammonium and nitrite to resolve important processes of the marine N-cycle such as nitrification and anaerobic ammonium oxidation (anammox). Additionally, we updated the production of nitrous oxide, an important greenhouse gas, allowing for two sources from oxidation of ammonium (nitrification) and from reduction of nitrite (nitrifier-denitrification) at low oxygen concentrations. Besides an extended model data comparison we discuss the following aspects of the N-cycle by model means: (1) contribution of anammox to the loss of fixed nitrogen, and (2) production and emission of marine nitrous oxide.

  17. Modeling biogeochemical reactive transport in a fracture zone

    International Nuclear Information System (INIS)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing; Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-01

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters

  18. How well can we assess impacts of agricultural land management changes on the total greenhouse gas balance (CO2, CH4 and N2O) of tropical rice-cropping systems with biogeochemical models?

    Science.gov (United States)

    Kraus, David; Weller, Sebastian; Janz, Baldur; Klatt, Steffen; Santabárbara, Ignacio; Haas, Edwin; Werner, Christian; Wassmann, Reiner; Kiese, Ralf; Butterbach-Bahl, Klaus

    2016-04-01

    Paddy rice cultivation is increasingly challenged by physical and economic irrigation water scarcity. This already results in the trend of converting paddy rice to upland crop cultivation (e.g., maize, aerobic rice) in large parts of South East Asia. Such land management change from flooded lowland systems to well-aerated upland systems drastically affects soil C and N cycling and related emissions of greenhouse gases. Emissions of methane (CH4) are expected to decrease, while emissions of nitrous oxide (N2O) will most likely increase. In addition to such fast evolving 'pollution swapping' it is expected that on longer time scales significant amounts of soil organic carbon (SOC) stocks will be lost in form of carbon dioxide (CO2). Within the DFG-funded research unit ICON (Introducing non-flooded crops in rice-dominated landscapes: Impact on carbon, nitrogen and water cycles), we investigated environmental impacts of land management change from historical paddy rice cultivation to the upland crops maize and aerobic rice at experimental sites at the International Rice Research Institute (IRRI), the Philippines. To present, more than three years of continuous measurement data of CH4 and N2O emissions under different fertilization regimes have been collected. In addition, measurements of SOC contents and bulk densities in different soil horizons allow for an overall very good characterization of the environmental impacts of mentioned land management change. In this contribution we will show how well mentioned land management change effects in tropical agricultural systems can be represented and thus better understood by the help of process-based biogeochemical models. Seasonal emissions of CH4 and N2O are simulated with r2 values of 0.85 and 0.78 and average underestimations of 15 and 14 %, respectively. These underestimations predominantly originate from treatments in which no fertilizer is applied (CH4) as well as uncertainties of soil hydrology (N2O). Long

  19. Introducing mixotrophy into a biogeochemical model describing an eutrophied coastal ecosystem: The Southern North Sea

    Science.gov (United States)

    Ghyoot, Caroline; Lancelot, Christiane; Flynn, Kevin J.; Mitra, Aditee; Gypens, Nathalie

    2017-09-01

    Most biogeochemical/ecological models divide planktonic protists between phototrophs (phytoplankton) and heterotrophs (zooplankton). However, a large number of planktonic protists are able to combine several mechanisms of carbon and nutrient acquisition. Not representing these multiple mechanisms in biogeochemical/ecological models describing eutrophied coastal ecosystems can potentially lead to different conclusions regarding ecosystem functioning, especially regarding the success of harmful algae, which are often reported as mixotrophic. This modelling study investigates the implications for trophic dynamics of including 3 contrasting forms of mixotrophy, namely osmotrophy (using alkaline phosphatase activity, APA), non-constitutive mixotrophy (acquired phototrophy by microzooplankton) and also constitutive mixotrophy. The application is in the Southern North Sea, an ecosystem that faced, between 1985 and 2005, a significant increase in the nutrient supply N:P ratio (from 31 to 81 mol N:P). The comparison with a traditional model shows that, when the winter N:P ratio in the Southern North Sea is above 22 molN molP-1 (as occurred from mid-1990s), APA allows a 3-32% increase of annual gross primary production (GPP). In result of the higher GPP, the annual sedimentation increases as well as the bacterial production. By contrast, APA does not affect the export of matter to higher trophic levels because the increased GPP is mainly due to Phaeocystis colonies, which are not grazed by copepods. Under high irradiance, non-constitutive mixotrophy appreciably increases annual GPP, transfer to higher trophic levels, sedimentation, and nutrient remineralisation. In this ecosystem, non-constitutive mixotrophy is also observed to have an indirect stimulating effect on diatoms. Constitutive mixotrophy in nanoflagellates appears to have little influence on this ecosystem functioning. An important conclusion from this work is that contrasting forms of mixotrophy have different

  20. A Unified Multi-scale Model for Cross-Scale Evaluation and Integration of Hydrological and Biogeochemical Processes

    Science.gov (United States)

    Liu, C.; Yang, X.; Bailey, V. L.; Bond-Lamberty, B. P.; Hinkle, C.

    2013-12-01

    Mathematical representations of hydrological and biogeochemical processes in soil, plant, aquatic, and atmospheric systems vary with scale. Process-rich models are typically used to describe hydrological and biogeochemical processes at the pore and small scales, while empirical, correlation approaches are often used at the watershed and regional scales. A major challenge for multi-scale modeling is that water flow, biogeochemical processes, and reactive transport are described using different physical laws and/or expressions at the different scales. For example, the flow is governed by the Navier-Stokes equations at the pore-scale in soils, by the Darcy law in soil columns and aquifer, and by the Navier-Stokes equations again in open water bodies (ponds, lake, river) and atmosphere surface layer. This research explores whether the physical laws at the different scales and in different physical domains can be unified to form a unified multi-scale model (UMSM) to systematically investigate the cross-scale, cross-domain behavior of fundamental processes at different scales. This presentation will discuss our research on the concept, mathematical equations, and numerical execution of the UMSM. Three-dimensional, multi-scale hydrological processes at the Disney Wilderness Preservation (DWP) site, Florida will be used as an example for demonstrating the application of the UMSM. In this research, the UMSM was used to simulate hydrological processes in rooting zones at the pore and small scales including water migration in soils under saturated and unsaturated conditions, root-induced hydrological redistribution, and role of rooting zone biogeochemical properties (e.g., root exudates and microbial mucilage) on water storage and wetting/draining. The small scale simulation results were used to estimate effective water retention properties in soil columns that were superimposed on the bulk soil water retention properties at the DWP site. The UMSM parameterized from smaller

  1. Modeling biogeochemical processes of phosphorus for global food supply.

    Science.gov (United States)

    Dumas, Marion; Frossard, Emmanuel; Scholz, Roland W

    2011-08-01

    Harvests of crops, their trade and consumption, soil erosion, fertilization and recycling of organic waste generate fluxes of phosphorus in and out of the soil that continuously change the worldwide spatial distribution of total phosphorus in arable soils. Furthermore, due to variability in the properties of the virgin soils and the different histories of agricultural practices, on a planetary scale, the distribution of total soil phosphorus is very heterogeneous. There are two key relationships that determine how this distribution and its change over time affect crop yields. One is the relationship between total soil phosphorus and bioavailable soil phosphorus and the second is the relationship between bioavailable soil phosphorus and yields. Both of these depend on environmental variables such as soil properties and climate. We propose a model in which these relationships are described probabilistically and integrated with the dynamic feedbacks of P cycling in the human ecosystem. The model we propose is a first step towards evaluating the large-scale effects of different nutrient management scenarios. One application of particular interest is to evaluate the vulnerability of different regions to an increased scarcity in P mineral fertilizers. Another is to evaluate different regions' deficiency in total soil phosphorus compared with the level at which they could sustain their maximum potential yield without external mineral inputs of phosphorus but solely by recycling organic matter to close the nutrient cycle. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Biogeochemical dynamics of Flores Island aquatic systems, Azores

    Science.gov (United States)

    Aguiar, P.; Antunes, P.; Raposeiro, P.; Mestre, R.; Costa, A.; Cruz, V.

    2009-04-01

    The present work was developed during the 2009 Flores and Corvo expedition organized by the Department of Biology, University of the Azores. The main goal was to conduct a robust ecosystem analysis in which the microbial community composition assessment of the lakes water column and of the adjacent bottom sediments was integrated with the environmental characterization of specific Flores Island freshwater habitats. For this, three lake systems and three mineral springs were studied. Water and sediment samples were collected at each site. Additionally, microbial biofilm samples were also collected where detected and the community was studied using a culture independent integrated approach. The Azores archipelago is located within the North Atlantic, between the boundary of three tectonic plates (American, Eurasia, and African plates), and it is composed of nine volcanic islands spread along a general WNW-ESSE direction, between 37° to 40° N and 25° to 31° W. The islands correspond to the emerged portions of the Azores plateau defined by the 2000 m bathimetry line Flores and Corvo form the western islands group, with Flores being the western most island of the archipelago. These islands genesis would have started during the Miocenico Flores island subaereal phase is dated of 0.7 M BP and the island volcanic actividade is thought to stop around 3000 years A.C. All lakes included in the study are of volcanic origins and are subject to vulcanic contamination. Hydrogeochemical studies can be used as an insight to the volcanic systems since vulcanic gases condensation and/or thermal fluids mixing can occur at these sites. Most microbial community studies within azorean freshwater systems were restricted to phytoplanktonic community studies or were conducted at hydrothermal sites solely. This is the first work that integrates microbial community composition studies of the lakes water column (phytoplankton as well as bacterioplankton) and of the adjacent bottom

  3. Quantifying the Variability of CH4 Emissions from Pan-Arctic Lakes with Lake Biogeochemical and Landscape Evolution Models

    Science.gov (United States)

    Tan, Z.; Zhuang, Q.

    2014-12-01

    Recent studies in the arctic and subarctic show that CH4 emissions from pan-arctic lakes are playing much more significant roles in the regional carbon cycling than previously estimated. Permafrost thawing due to pronounced warming at northern high latitudes affects lake morphology, changing its CH4 emissions. Thermokarst can enlarge the extent of artic lakes, exposing stable ancient carbon buried in the permafrost zone for degradation and changing a previously known carbon sink to a large carbon source. In some areas, the thawing of subarctic discontinuous and isolated permafrost can diminish thermokarst lakes. To date, few models have considered these important hydrological and biogeochemical processes to provide adequate estimation of CH4 emissions from these lakes. To fill this gap, we have developed a process-based climate-sensitive lake biogeochemical model and a landscape evolution model, which have been applied to quantify the state and variability of CH4 emissions from this freshwater system. Site-level experiments show the models are capable to capture the spatial and temporal variability of CH4 emissions from lakes across Siberia and Alaska. With the lake biogeochemical model solely, we estimate that the magnitude of CH4 emissions from lakes is 13.2 Tg yr-1 in the north of 60 ºN at present, which is on the same order of CH4 emissions from northern high-latitude wetlands. The maximum increment is 11.8 Tg CH4 yr-1 by the end of the 21st century when the worst warming scenario is assumed. We expect the landscape evolution model will improve the existing estimates.

  4. Impact of satellite data assimilation in a coupled physical-biogeochemical model of the North Atlantic

    Science.gov (United States)

    Berline, L.; Brankart, J.-M.; Brasseur, P.

    The general objective of this work is to examine how the assimilation of data in a circulation model can improve the biological response simulated by a coupled physical-ecosystem model. In this work, the focus will be on the impact of altimetric, SST and SSS data assimilation in an eddy-permitting coupled model of the North Atlantic. The physical model is a z-coordinate, rigid lid, primitive-equation model based on the OPA code [Madec et al, 1998]. The horizontal resolution is 1/3° and there are 43 vertical levels with refinement near the surface. The biogeochemical model is the P3ZD biogeochemical model [Aumont et al., 1998] that describes the cycling of carbon, silica and calcium. The simulations are performed using realistic forcings during 1998. The assimilation method is based on a Kalman filter with reduced order error covariance matrix, known as the SEEK filter [ Pham et al., 1998]. The sequential scheme has been modified recently using the concept of "incremental analysis update" to enforce temporal continuity of the assimilation run. In order to evaluate how the assimilation can improve the representation of the biological fields, comparisons are made between free runs and simulations with assimilation. A first comparison with the assimilation run obtained using the scheme developed by Testut et al. [2003] indicates the excessive supply of nutrients in the euphotic zone through spurious mixing and advection mechanisms. This can be partly attributed to several factors, e.g. the statistical method which is unable to maintain the model constraint of hydrostatic stability, the discontinuous nature of the sequential algorithm, or the lack of consistent corrections between the physical and biological components of the state vector. Several variants of the assimilation algorithm are implemented in order to improve the representation of the model dynamics and its subsequent impact on the biological variables. A comparison between the assimilation runs obtained

  5. PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies

    Directory of Open Access Journals (Sweden)

    O. Aumont

    2015-08-01

    of marine ecosystems (phytoplankton, microzooplankton and mesozooplankton and the biogeochemical cycles of carbon and of the main nutrients (P, N, Fe, and Si. The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual and long-term (climate change, paleoceanography analyses. There are 24 prognostic variables (tracers including two phytoplankton compartments (diatoms and nanophytoplankton, two zooplankton size classes (microzooplankton and mesozooplankton and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod–quota formalism. On the one hand, stoichiometry of C / N / P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicon quotas are variable and the growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting, for instance, the complexity of iron chemistry or the description of particulate organic materials. So far, PISCES-v2 has been coupled to the Nucleus for European Modelling of the Ocean (NEMO and Regional Ocean Modeling System (ROMS systems. A full description of PISCES-v2 and of its optional functionalities is provided here. The results of a quasi-steady-state simulation are presented and evaluated against diverse observational and satellite-derived data. Finally, some of the new functionalities of PISCES-v2 are tested in a series of sensitivity experiments.

  6. Water, Energy, and Biogeochemical Model (WEBMOD), user’s manual, version 1

    Science.gov (United States)

    Webb, Richard M.T.; Parkhurst, David L.

    2017-02-08

    The Water, Energy, and Biogeochemical Model (WEBMOD) uses the framework of the U.S. Geological Survey (USGS) Modular Modeling System to simulate fluxes of water and solutes through watersheds. WEBMOD divides watersheds into model response units (MRU) where fluxes and reactions are simulated for the following eight hillslope reservoir types: canopy; snowpack; ponding on impervious surfaces; O-horizon; two reservoirs in the unsaturated zone, which represent preferential flow and matrix flow; and two reservoirs in the saturated zone, which also represent preferential flow and matrix flow. The reservoir representing ponding on impervious surfaces, currently not functional (2016), will be implemented once the model is applied to urban areas. MRUs discharge to one or more stream reservoirs that flow to the outlet of the watershed. Hydrologic fluxes in the watershed are simulated by modules derived from the USGS Precipitation Runoff Modeling System; the National Weather Service Hydro-17 snow model; and a topography-driven hydrologic model (TOPMODEL). Modifications to the standard TOPMODEL include the addition of heterogeneous vertical infiltration rates; irrigation; lateral and vertical preferential flows through the unsaturated zone; pipe flow draining the saturated zone; gains and losses to regional aquifer systems; and the option to simulate baseflow discharge by using an exponential, parabolic, or linear decrease in transmissivity. PHREEQC, an aqueous geochemical model, is incorporated to simulate chemical reactions as waters evaporate, mix, and react within the various reservoirs of the model. The reactions that can be specified for a reservoir include equilibrium reactions among water; minerals; surfaces; exchangers; and kinetic reactions such as kinetic mineral dissolution or precipitation, biologically mediated reactions, and radioactive decay. WEBMOD also simulates variations in the concentrations of the stable isotopes deuterium and oxygen-18 as a result of

  7. Dynamic modeling of nitrogen losses in river networks unravels the coupled effects of hydrological and biogeochemical processes

    Science.gov (United States)

    Alexander, Richard B.; Böhlke, John Karl; Boyer, Elizabeth W.; David, Mark B.; Harvey, Judson W.; Mulholland, Patrick J.; Seitzinger, Sybil P.; Tobias, Craig R.; Tonitto, Christina; Wollheim, Wilfred M.

    2009-01-01

    The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal in the river networks of two watersheds having widely differing levels of nitrate enrichment but nearly identical discharges. Stream denitrification is estimated by regression as a nonlinear function of nitrate concentration, streamflow, and temperature, using more than 300 published measurements from a variety of US streams. These relations are used in the stream transport model to characterize nitrate dynamics related to denitrification at a monthly time scale in the stream reaches of the two watersheds. Results indicate that the nitrate removal efficiency of streams, as measured by the percentage of the stream nitrate flux removed via denitrification per unit length of channel, is appreciably reduced during months with high discharge and nitrate flux and increases during months of low-discharge and flux. Biogeochemical factors, including land use, nitrate inputs, and stream concentrations, are a major control on reach-scale denitrification, evidenced by the disproportionately lower nitrate removal efficiency in streams of the highly nitrate-enriched watershed as compared with that in similarly sized streams in the less nitrate-enriched watershed. Sensitivity analyses reveal that these important biogeochemical factors and physical hydrological factors contribute nearly

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

    Science.gov (United States)

    Wu, Y.; Blodau, C.

    2013-08-01

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

  9. Parameter estimation and uncertainty quantification in a biogeochemical model using optimal experimental design methods

    Science.gov (United States)

    Reimer, Joscha; Piwonski, Jaroslaw; Slawig, Thomas

    2016-04-01

    The statistical significance of any model-data comparison strongly depends on the quality of the used data and the criterion used to measure the model-to-data misfit. The statistical properties (such as mean values, variances and covariances) of the data should be taken into account by choosing a criterion as, e.g., ordinary, weighted or generalized least squares. Moreover, the criterion can be restricted onto regions or model quantities which are of special interest. This choice influences the quality of the model output (also for not measured quantities) and the results of a parameter estimation or optimization process. We have estimated the parameters of a three-dimensional and time-dependent marine biogeochemical model describing the phosphorus cycle in the ocean. For this purpose, we have developed a statistical model for measurements of phosphate and dissolved organic phosphorus. This statistical model includes variances and correlations varying with time and location of the measurements. We compared the obtained estimations of model output and parameters for different criteria. Another question is if (and which) further measurements would increase the model's quality at all. Using experimental design criteria, the information content of measurements can be quantified. This may refer to the uncertainty in unknown model parameters as well as the uncertainty regarding which model is closer to reality. By (another) optimization, optimal measurement properties such as locations, time instants and quantities to be measured can be identified. We have optimized such properties for additional measurement for the parameter estimation of the marine biogeochemical model. For this purpose, we have quantified the uncertainty in the optimal model parameters and the model output itself regarding the uncertainty in the measurement data using the (Fisher) information matrix. Furthermore, we have calculated the uncertainty reduction by additional measurements depending on time

  10. Modeling distinct vertical biogeochemical structure of the Black Sea: Dynamical coupling of the oxic, suboxic, and anoxic layers

    Science.gov (United States)

    Oguz, Temel; Ducklow, Hugh W.; Malanotte-Rizzoli, Paola

    2000-12-01

    A one-dimensional, vertically resolved, physical-biogeochemical model is used to provide a unified representation of the dynamically coupled oxic-suboxic-anoxic system for the interior Black Sea. The model relates the annual cycle of plankton production in the form of a series of successive phytoplankton, mesozooplankton, and higher consumer blooms to organic matter generation and to the remineralization-ammonification-nitrification-denitrification chain of the nitrogen cycle as well as to anaerobic sulfide oxidation in the suboxic-anoxic interface zone. The simulations indicate that oxygen consumption during remineralization and nitrification, together with a lack of ventilation of subsurface waters due to the presence of strong stratification, are the two main factors limiting aerobic biogeochemical activity to the upper ˜75 m of the water column, which approximately corresponds to the level of nitrate maximum. The position of the upper boundary and thus the thickness of the suboxic layer are controlled by upper layer biological processes. The quasi-permanent character of this layer and the stability of the suboxic-anoxic interface within the last several decades are maintained by a constant rate of nitrate supply from the nitrate maximum zone. Nitrate is consumed to oxidize sinking particulate organic matter as well as hydrogen sulfide and ammonium transported upward from deeper levels.

  11. Simulation of glacial ocean biogeochemical tracer and isotope distributions based on the PMIP3 suite of climate models

    Science.gov (United States)

    Khatiwala, Samar; Muglia, Juan; Kvale, Karin; Schmittner, Andreas

    2016-04-01

    In the present climate system, buoyancy forced convection at high-latitudes together with internal mixing results in a vigorous overturning circulation whose major component is North Atlantic Deep Water. One of the key questions of climate science is whether this "mode" of circulation persisted during glacial periods, and in particular at the Last Glacial Maximum (LGM; 21000 years before present). Resolving this question is both important for advancing our understanding of the climate system, as well as a critical test of numerical models' ability to reliably simulate different climates. The observational evidence, based on interpreting geochemical tracers archived in sediments, is conflicting, as are simulations carried out with state-of-the-art climate models (e.g., as part of the PMIP3 suite), which, due to the computational cost involved, do not by and large include biogeochemical and isotope tracers that can be directly compared with proxy data. Here, we apply geochemical observations to evaluate the ability of several realisations of an ocean model driven by atmospheric forcing from the PMIP3 suite of climate models to simulate global ocean circulation during the LGM. This results in a wide range of circulation states that are then used to simulate biogeochemical tracer and isotope (13C, 14C and Pa/Th) distributions using an efficient, "offline" computational scheme known as the transport matrix method (TMM). One of the key advantages of this approach is the use of a uniform set of biogeochemical and isotope parameterizations across all the different circulations based on the PMIP3 models. We compare these simulated distributions to both modern observations and data from LGM ocean sediments to identify similarities and discrepancies between model and data. We find, for example, that when the ocean model is forced with wind stress from the PMIP3 models the radiocarbon age of the deep ocean is systematically younger compared with reconstructions. Changes in

  12. Useless arithmetic or useful scientific tools? Evaluation of the current state and future perspectives of aquatic biogeochemical modeling

    Science.gov (United States)

    Arhonditsis, G.

    2009-04-01

    What is the capacity of the current models to simulate the dynamics of environmental systems? How carefully do modelers develop their models? Which model features primarily determine our decision to utilize a specific model? How rigorously do we assess what a model can or cannot predict? The first part of my presentation is to answer some of these questions by reviewing the state of aquatic biogeochemical modeling; a research tool that has been extensively used for understanding and quantitatively describing aquatic ecosystems. Mechanistic aquatic biogeochemical models have form the scientific basis for environmental management decisions by providing a predictive link between management actions and ecosystem response; they have provided an important tool for elucidating the interactions between climate variability and plankton communities, and thus for addressing questions regarding the pace and impacts of climate change. The sizable number of aquatic ecosystem modeling studies which successfully passed the scrutiny of the peer-review process along with the experience gained from addressing a breadth of management problems can objectively reveal the systematic biases, methodological inconsistencies, and common misconceptions characterizing the modeling practice in environmental science. My arguments are that (i) models are not always developed in a consistent manner, clearly stated purpose, and predetermined acceptable model performance level, (ii) the potential "customers" select models without properly assessing their technical value, and (iii) oceanic modeling is a dynamic area of the current modeling practice whereas, model application for addressing environmental management issues on a local scale faces challenges as a scientific tool. The second part of my presentation argues that (i) the development of novel methods for rigorously assessing the uncertainty underlying model predictions should be a top priority of the modeling community, and (ii) the model

  13. A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

    Science.gov (United States)

    Shapiro, B.; Jin, Q.

    2015-12-01

    Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

  14. Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models

    Energy Technology Data Exchange (ETDEWEB)

    Sarmiento, Jorge L. [Princeton Univ., NJ (United States); Gnanadesikan, Anand [Princeton Univ., NJ (United States); Gruber, Nicolas [Univ. of California, Los Angeles, CA (United States); Jin, Xin [Univ. of California, Los Angeles, CA (United States); Armstrong, Robert [State Univ. of New York (SUNY), Plattsburgh, NY (United States)

    2007-06-21

    This final report summarizes research undertaken collaboratively between Princeton University, the NOAA Geophysical Fluid Dynamics Laboratory on the Princeton University campus, the State University of New York at Stony Brook, and the University of California, Los Angeles between September 1, 2000, and November 30, 2006, to do fundamental research on ocean iron fertilization as a means to enhance the net oceanic uptake of CO2 from the atmosphere. The approach we proposed was to develop and apply a suite of coupled physical-ecological-biogeochemical models in order to (i) determine to what extent enhanced carbon fixation from iron fertilization will lead to an increase in the oceanic uptake of atmospheric CO2 and how long this carbon will remain sequestered (efficiency), and (ii) examine the changes in ocean ecology and natural biogeochemical cycles resulting from iron fertilization (consequences). The award was funded in two separate three-year installments: September 1, 2000 to November 30, 2003, for a project entitled “Ocean carbon sequestration by fertilization: An integrated biogeochemical assessment.” A final report was submitted for this at the end of 2003 and is included here as Appendix 1; and, December 1, 2003 to November 30, 2006, for a follow-on project under the same grant number entitled “Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models.” This report focuses primarily on the progress we made during the second period of funding subsequent to the work reported on in Appendix 1. When we began this project, we were thinking almost exclusively in terms of long-term fertilization over large regions of the ocean such as the Southern Ocean, with much of our focus being on how ocean circulation and biogeochemical cycling would interact to control the response to a given fertilization scenario. Our research on these types of scenarios, which was carried out largely during the

  15. Volume reduction outweighs biogeochemical processes in controlling phosphorus treatment in aged detention systems

    Science.gov (United States)

    Shukla, Asmita; Shukla, Sanjay; Annable, Michael D.; Hodges, Alan W.

    2017-08-01

    Stormwater detention areas (SDAs) play an important role in treating end-of-the-farm runoff in phosphorous (P) limited agroecosystems. Phosphorus transport from the SDAs, including those through subsurface pathways, are not well understood. The prevailing understanding of these systems assumes that biogeochemical processes play the primary treatment role and that subsurface losses can be neglected. Water and P fluxes from a SDA located in a row-crop farm were measured for two years (2009-2011) to assess the SDA's role in reducing downstream P loads. The SDA treated 55% (497 kg) and 95% (205 kg) of the incoming load during Year 1 (Y1, 09-10) and Year 2 (Y2, 10-11), respectively. These treatment efficiencies were similar to surface water volumetric retention (49% in Y1 and 84% in Y2) and varied primarily with rainfall. Similar water volume and P retentions indicate that volume retention is the main process controlling P loads. A limited role of biogeochemical processes was supported by low to no remaining soil P adsorption capacity due to long-term drainage P input. The fact that outflow P concentrations (Y1 = 368.3 μg L- 1, Y2 = 230.4 μg L- 1) could be approximated by using a simple mixing of rainfall and drainage P input further confirmed the near inert biogeochemical processes. Subsurface P losses through groundwater were 304 kg (27% of inflow P) indicating that they are an important source for downstream P. Including subsurface P losses reduces the treatment efficiency to 35% (from 61%). The aboveground biomass in the SDA contained 42% (240 kg) of the average incoming P load suggesting that biomass harvesting could be a cost-effective alternative for reviving the role of biogeochemical processes to enhance P treatment in aged, P-saturated SDAs. The 20-year present economic value of P removal through harvesting was estimated to be 341,000, which if covered through a cost share or a payment for P treatment services program could be a positive outcome for both

  16. Numerical modeling of watershed-scale radiocesium transport coupled with biogeochemical cycling in forests

    Science.gov (United States)

    Mori, K.; Tada, K.; Tawara, Y.; Tosaka, H.; Ohno, K.; Asami, M.; Kosaka, K.

    2015-12-01

    Since the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident, intensive monitoring and modeling works on radionuclide transfer in environment have been carried out. Although Cesium (Cs) concentration has been attenuating due to both physical and environmental half-life (i.e., wash-off by water and sediment), the attenuation rate depends clearly on the type of land use and land cover. In the Fukushima case, studying the migration in forest land use is important for predicting the long-term behavior of Cs because most of the contaminated region is covered by forests. Atmospheric fallout is characterized by complicated behavior in biogeochemical cycle in forests which can be described by biotic/abiotic interactions between many components. In developing conceptual and mathematical model on Cs transfer in forest ecosystem, defining the dominant components and their interactions are crucial issues (BIOMASS, 1997-2001). However, the modeling of fate and transport in geosphere after Cs exports from the forest ecosystem is often ignored. An integrated watershed modeling for simulating spatiotemporal redistribution of Cs that includes the entire region from source to mouth and surface to subsurface, has been recently developed. Since the deposited Cs can migrate due to water and sediment movement, the different species (i.e., dissolved and suspended) and their interactions are key issues in the modeling. However, the initial inventory as source-term was simplified to be homogeneous and time-independent, and biogeochemical cycle in forests was not explicitly considered. Consequently, it was difficult to evaluate the regionally-inherent characteristics which differ according to land uses, even if the model was well calibrated. In this study, we combine the different advantages in modeling of forest ecosystem and watershed. This enable to include more realistic Cs deposition and time series of inventory can be forced over the land surface. These processes are integrated

  17. One-dimensional model for biogeochemical interactions and permeability reduction in soils during leachate permeation

    Science.gov (United States)

    Singhal, Naresh; Islam, Jahangir

    2008-02-01

    This paper uses the findings from a column study to develop a reactive model for exploring the interactions occurring in leachate-contaminated soils. The changes occurring in the concentrations of acetic acid, sulphate, suspended and attached biomass, Fe(II), Mn(II), calcium, carbonate ions, and pH in the column are assessed. The mathematical model considers geochemical equilibrium, kinetic biodegradation, precipitation-dissolution reactions, bacterial and substrate transport, and permeability reduction arising from bacterial growth and gas production. A two-step sequential operator splitting method is used to solve the coupled transport and biogeochemical reaction equations. The model gives satisfactory fits to experimental data and the simulations show that the transport of metals in soil is controlled by multiple competing biotic and abiotic reactions. These findings suggest that bioaccumulation and gas formation, compared to chemical precipitation, have a larger influence on hydraulic conductivity reduction.

  18. Study of the seasonal cycle of the biogeochemical processes in the Ligurian Sea using a 1D interdisciplinary model

    NARCIS (Netherlands)

    Raick, C.; Delhez, E.J.M.; Soetaert, K.E.R.; Grégoire, M.

    2005-01-01

    A one-dimensional coupled physical–biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version 1D) developed at the GeoHydrodynamics and Environmental Laboratory (GHER) of the University of

  19. Insight from Genomics on Biogeochemical Cycles in a Shallow-Sea Hydrothermal System

    Science.gov (United States)

    Lu, G. S.; Amend, J.

    2015-12-01

    Shallow-sea hydrothermal ecosystems are dynamic, high-energy systems influenced by sunlight and geothermal activity. They provide accessible opportunities for investigating thermophilic microbial biogeochemical cycles. In this study, we report biogeochemical data from a shallow-sea hydrothermal system offshore Paleochori Bay, Milos, Greece, which is characterized by a central vent covered by white microbial mats with hydrothermally influenced sediments extending into nearby sea grass area. Geochemical analysis and deep sequencing provide high-resolution information on the geochemical patterns, microbial diversity and metabolic potential in a two-meter transect. The venting fluid is elevated in temperature (~70oC), low in pH (~4), and enriched in reduced species. The geochemical pattern shows that the profile is affected by not only seawater dilution but also microbial regulation. The microbial community in the deepest section of vent core (10-12 cm) is largely dominated by thermophilic archaea, including a methanogen and a recently described Crenarcheon. Mid-core (6-8 cm), the microbial community in the venting area switches to the hydrogen utilizer Aquificae. Near the sediment-water interface, anaerobic Firmicutes and Actinobacteria dominate, both of which are commonly associated with subsurface and hydrothermal sites. All other samples are dominated by diverse Proteobacteria. The sulfate profile is strongly correlated with the population size of delta- and episilon-proteobactia. The dramatic decrease in concentrations of As and Mn in pore fluids as a function of distance from the vent suggests that in addition to seawater dilution, microorganisms are likely transforming these and other ions through a combination of detoxification and catabolism. In addition, high concentrations of dissolved Fe are only measurable in the shallow sea grass area, suggesting that iron-transforming microorganisms are controlling Fe mobility, and promoting biomineralization. Taken

  20. Biogeochemical modelling vs. tree-ring data - comparison of forest ecosystem productivity estimates

    Science.gov (United States)

    Zorana Ostrogović Sever, Maša; Barcza, Zoltán; Hidy, Dóra; Paladinić, Elvis; Kern, Anikó; Marjanović, Hrvoje

    2017-04-01

    Forest ecosystems are sensitive to environmental changes as well as human-induce disturbances, therefore process-based models with integrated management modules represent valuable tool for estimating and forecasting forest ecosystem productivity under changing conditions. Biogeochemical model Biome-BGC simulates carbon, nitrogen and water fluxes, and it is widely used for different terrestrial ecosystems. It was modified and parameterised by many researchers in the past to meet the specific local conditions. In this research, we used recently published improved version of the model Biome-BGCMuSo (BBGCMuSo), with multilayer soil module and integrated management module. The aim of our research is to validate modelling results of forest ecosystem productivity (NPP) from BBGCMuSo model with observed productivity estimated from an extensive dataset of tree-rings. The research was conducted in two distinct forest complexes of managed Pedunculate oak in SE Europe (Croatia), namely Pokupsko basin and Spačva basin. First, we parameterized BBGCMuSo model at a local level using eddy-covariance (EC) data from Jastrebarsko EC site. Parameterized model was used for the assessment of productivity on a larger scale. Results of NPP assessment with BBGCMuSo are compared with NPP estimated from tree ring data taken from trees on over 100 plots in both forest complexes. Keywords: Biome-BGCMuSo, forest productivity, model parameterization, NPP, Pedunculate oak

  1. Integrating "Omics" Data Into A Biogeochemical Model: A New Model Scheme To Predict Climate Feedbacks From Microbial Function In Tropical Ecosystems

    Science.gov (United States)

    Song, Y.; Yao, Q.; Wang, G.; Yang, X.; Pan, C.; Johnston, E.; Kim, M.; Konstantinidis, K.; Hazen, T.; Mayes, M. A.

    2016-12-01

    Soil microorganisms and their activities, which play a significant role in regulating carbon (C) and nutrient biogeochemical cycles, are highly responsive to changes in climate. The diversity of microorganisms, however, complicates the explicit representation of microbial and enzymatic processes in biogeochemical or earth system models. Uncertainties in accounting for microbial diversity therefore limits our ability to incorporate microbial functions into models. However, `omics technology provides abundant information to identify the structure and function of the microbial community and strengthens our ability to understand microbially-mediated C and nutrient cycles and their climate feedbacks. We collected soils from control and phosphorus (P) fertilized plots at the Gigante Peninsula long-term fertilization experiment at the Smithsonian Tropical Research Institute in Panama, an ecosystem where P limitation constrains primary productivity and microbial activities. We monitored effects P addition on soil carbon decomposition with respiration measurements and investigated the responsible microbial mechanisms with metagenomics, metatranscriptomics, metaproteomics, and enzyme activity assays. We integrated the P dynamics into the C-N coupled Microbial Enzyme Decomposition (MEND) model. We integrated the `omics data with the new microbially-enabled C-N-P model to examine the mechanistic responses of soil microbial activity and heterotrophic respiration to P availability. Our finding indicates that increases in soil P availability can alter both the abundance and activity of enzymes related to soil carbon decomposition and P mineralization in the tropical soil, leading to increased CO2 emissions to the atmosphere. Integrating the `omics data into the biogeochemical model enabled scaling of complex ecosystem functions from genes to functional groups to enable predictions of microbial controls on C, N and P cycles.

  2. Characterization of mixing errors in a coupled physical biogeochemical model of the North Atlantic: implications for nonlinear estimation using Gaussian anamorphosis

    Directory of Open Access Journals (Sweden)

    D. Béal

    2010-02-01

    Full Text Available In biogeochemical models coupled to ocean circulation models, vertical mixing is an important physical process which governs the nutrient supply and the plankton residence in the euphotic layer. However, vertical mixing is often poorly represented in numerical simulations because of approximate parameterizations of sub-grid scale turbulence, wind forcing errors and other mis-represented processes such as restratification by mesoscale eddies. Getting a sufficient knowledge of the nature and structure of these errors is necessary to implement appropriate data assimilation methods and to evaluate if they can be controlled by a given observation system.

    In this paper, Monte Carlo simulations are conducted to study mixing errors induced by approximate wind forcings in a three-dimensional coupled physical-biogeochemical model of the North Atlantic with a 1/4° horizontal resolution. An ensemble forecast involving 200 members is performed during the 1998 spring bloom, by prescribing perturbations of the wind forcing to generate mixing errors. The biogeochemical response is shown to be rather complex because of nonlinearities and threshold effects in the coupled model. The response of the surface phytoplankton depends on the region of interest and is particularly sensitive to the local stratification. In addition, the statistical relationships computed between the various physical and biogeochemical variables reflect the signature of the non-Gaussian behaviour of the system. It is shown that significant information on the ecosystem can be retrieved from observations of chlorophyll concentration or sea surface temperature if a simple nonlinear change of variables (anamorphosis is performed by mapping separately and locally the ensemble percentiles of the distributions of each state variable on the Gaussian percentiles. The results of idealized observational updates (performed with perfect observations and neglecting horizontal correlations

  3. Development of Advanced Eco-hydrologic and Biogeochemical Coupling Model to Re-evaluate Greenhouse Gas Budget of Biosphere

    Science.gov (United States)

    Nakayama, T.; Maksyutov, S. S.

    2015-12-01

    Inland waters including rivers, lakes, and groundwater are suggested to act as a transport pathway for water and dissolved substances, and play some role in continental biogeochemical cycling (Cole et al., 2007; Battin et al., 2009). The authors have developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (2014, 2015, etc.), which includes feedback between hydrologic-geomorphic-ecological processes. In this study, NICE was further developed to couple with various biogeochemical cycle models in biosphere, those for water quality in aquatic ecosystems, and those for carbon weathering. The NICE-biogeochemical coupling model incorporates connectivity of the biogeochemical cycle accompanied by hydrologic cycle between surface water and groundwater, hillslopes and river networks, and other intermediate regions. The model also includes reaction between inorganic and organic carbons, and its relation to nitrogen and phosphorus in terrestrial-aquatic continuum. The coupled model showed to improve the accuracy of inundation stress mechanism such as photosynthesis and primary production, which attributes to improvement of CH4 flux in wetland sensitive to fluctuations of shallow groundwater. The model also simulated CO2 evasion from inland water in global scale, and was relatively in good agreement in empirical relation (Aufdenkampe et al., 2011) which has relatively an uncertainty in the calculated flux because of pCO2 data missing in some region and effect of small tributaries, etc. Further, the model evaluated how the expected CO2 evasion might change as inland waters become polluted with nutrients and eutrophication increases from agriculture and urban areas (Pacheco et al., 2013). This advanced eco-hydrologic and biogeochemical coupling model would play important role to re-evaluate greenhouse gas budget of the biosphere, and to bridge gap between top-down and bottom-up approaches (Battin et al., 2009; Regnier et al., 2013).

  4. Small pores in soils: Is the physico-chemical environment accurately reflected in biogeochemical models ?

    Science.gov (United States)

    Weber, Tobias K. D.; Riedel, Thomas

    2015-04-01

    Free water is a prerequesite to chemical reactions and biological activity in earth's upper crust essential to life. The void volume between the solid compounds provides space for water, air, and organisms that thrive on the consumption of minerals and organic matter thereby regulating soil carbon turnover. However, not all water in the pore space in soils and sediments is in its liquid state. This is a result of the adhesive forces which reduce the water activity in small pores and charged mineral surfaces. This water has a lower tendency to react chemically in solution as this additional binding energy lowers its activity. In this work, we estimated the amount of soil pore water that is thermodynamically different from a simple aqueous solution. The quantity of soil pore water with properties different to liquid water was found to systematically increase with increasing clay content. The significance of this is that the grain size and surface area apparently affects the thermodynamic state of water. This implies that current methods to determine the amount of water content, traditionally determined from bulk density or gravimetric water content after drying at 105°C overestimates the amount of free water in a soil especially at higher clay content. Our findings have consequences for biogeochemical processes in soils, e.g. nutrients may be contained in water which is not free which could enhance preservation. From water activity measurements on a set of various soils with 0 to 100 wt-% clay, we can show that 5 to 130 mg H2O per g of soil can generally be considered as unsuitable for microbial respiration. These results may therefore provide a unifying explanation for the grain size dependency of organic matter preservation in sedimentary environments and call for a revised view on the biogeochemical environment in soils and sediments. This could allow a different type of process oriented modelling.

  5. Links between contaminant hotspots in low flow estuarine systems and altered sediment biogeochemical processes

    Science.gov (United States)

    Sutherland, Michael D.; Dafforn, Katherine A.; Scanes, Peter; Potts, Jaimie; Simpson, Stuart L.; Sim, Vivian X. Y.; Johnston, Emma L.

    2017-11-01

    The urbanisation of coastal zones is a major threat to the health of global estuaries and has been linked to increased contamination (e.g. metals) and excess organic matter. Urban stormwater networks collect and funnel contaminants into waterways at point sources (e.g. stormdrains). Under dry, low flow conditions, these stormwater contaminants can accumulate in sediments over time and result in modifications to benthic sediment biogeochemical processes. To quantify these processes, this field study measured differences in benthic metabolism (CR, GPP, NEM) and sediment-water nutrient fluxes (NH3, NOx, PO4) associated with stormdrains (0 m, 200 m and 1000 m away) and increased water-retention (embayments vs channels). Significant changes to benthic metabolism were detected with distance from stormdrains, and with differences in water-retention rates, above natural spatial and temporal variation. Oxygen consumption was ∼50% higher at stormdrains (0 m) compared to 1000 m away and >70% higher at stormdrains (0 m) located in embayments compared to channels. Oxygen production also appeared to decrease with distance from stormdrains in embayments, but patterns were variable. These changes to benthic metabolism were of a magnitude expected to influence benthic nutrient cycling, but NH3, NOx and PO4 fluxes were generally low, and highly spatially and temporally variable. Overall, metal (Cu) contamination explained most of the variation in sediment biogeochemical processes between embayments and channels, while sediment grain size explained differences in fluxes with distance from stormdrains. Importantly, although there was evidence of increased productivity associated with stormdrains, we also detected evidence of early hypoxia suggesting that systems with legacy stormwater contaminants exist on a tipping point. Future work should investigate changes to sediment processes after a major rainfall event, when large and sudden inputs of potentially toxic contaminants occur

  6. MOPS-1.0: towards a model for the regulation of the global oceanic nitrogen budget by marine biogeochemical processes

    Directory of Open Access Journals (Sweden)

    I. Kriest

    2015-09-01

    Analysis of the model misfit with respect to observed biogeochemical tracer distributions and fluxes suggests a particle flux profile close to the one suggested by Martin et al. (1987. Simulated pelagic denitrification best agrees with the lower values between 59 and 84 Tg N yr−1 recently estimated by other authors.

  7. Performance and results of the high-resolution biogeochemical model PELAGOS025 within NEMO

    Science.gov (United States)

    Epicoco, I.; Mocavero, S.; Macchia, F.; Vichi, M.; Lovato, T.; Masina, S.; Aloisio, G.

    2015-12-01

    The present work aims at evaluating the scalability performance of a high-resolution global ocean biogeochemistry model (PELAGOS025) on massive parallel architectures and the benefits in terms of the time-to-solution reduction. PELAGOS025 is an on-line coupling between the physical ocean model NEMO and the BFM biogeochemical model. Both the models use a parallel domain decomposition along the horizontal dimension. The parallelisation is based on the message passing paradigm. The performance analysis has been done on two parallel architectures, an IBM BlueGene/Q at ALCF (Argonne Leadership Computing Facilities) and an IBM iDataPlex with Sandy Bridge processors at CMCC (Euro Mediterranean Center on Climate Change). The outcome of the analysis demonstrated that the lack of scalability is due to several factors such as the I/O operations, the memory contention, the load unbalancing due to the memory structure of the BFM component and, for the BlueGene/Q, the absence of a hybrid parallelisation approach.

  8. Variably Saturated Flow and Multicomponent Biogeochemical Reactive Transport Modeling of a Uranium Bioremediation Field Experiment

    International Nuclear Information System (INIS)

    Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.; Murray, Christopher J.; Ward, Anderson L.; Dayvault, Richard; Waichler, Scott R.; Newcomer, Darrell R.; Spane, Frank A.; Long, Philip E.

    2011-01-01

    Field experiments at a former uranium mill tailings site have identified the potential for stimulating indigenous bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. This effectively removes uranium from solution resulting in groundwater concentrations below actionable standards. Three-dimensional, coupled variably-saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport rates and biogeochemical reaction rates that determine the location and magnitude of key reaction products. A comprehensive reaction network, developed largely through previous 1-D modeling studies, was used to simulate the impacts on uranium behavior of pulsed acetate amendment, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. A principal challenge is the mechanistic representation of biologically-mediated terminal electron acceptor process (TEAP) reactions whose products significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. In general, these simulations of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado confirmed previously identified behaviors including (1) initial dominance by iron reducing bacteria that concomitantly reduce aqueous U(VI), (2) sulfate reducing bacteria that become dominant after ∼30 days and outcompete iron reducers for the acetate electron donor, (3) continuing iron-reducer activity and U(VI) bioreduction during dominantly sulfate reducing conditions, and (4) lower apparent U(VI) removal from groundwater during dominantly sulfate reducing conditions. New knowledge on simultaneously active metal and sulfate reducers has been

  9. A Hydrological Concept including Lateral Water Flow Compatible with the Biogeochemical Model ForSAFE

    Directory of Open Access Journals (Sweden)

    Giuliana Zanchi

    2016-03-01

    Full Text Available The study presents a hydrology concept developed to include lateral water flow in the biogeochemical model ForSAFE. The hydrology concept was evaluated against data collected at Svartberget in the Vindeln Research Forest in Northern Sweden. The results show that the new concept allows simulation of a saturated and an unsaturated zone in the soil as well as water flow that reaches the stream comparable to measurements. The most relevant differences compared to streamflow measurements are that the model simulates a higher base flow in winter and lower flow peaks after snowmelt. These differences are mainly caused by the assumptions made to regulate the percolation at the bottom of the simulated soil columns. The capability for simulating lateral flows and a saturated zone in ForSAFE can greatly improve the simulation of chemical exchange in the soil and export of elements from the soil to watercourses. Such a model can help improve the understanding of how environmental changes in the forest landscape will influence chemical loads to surface waters.

  10. Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model

    Science.gov (United States)

    Dutkiewicz, S.; Hickman, A. E.; Jahn, O.; Gregg, W. W.; Mouw, C. B.; Follows, M. J.

    2015-07-01

    We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemical-ecosystem component in a dynamic three-dimensional physical framework. The radiative transfer component resolves the penetration of spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (different phytoplankton functional types; detrital particles; and coloured dissolved organic matter, CDOM). The model is evaluated against in situ-observed and satellite-derived products. In particular we compare to concurrently measured biogeochemical, ecosystem, and optical data along a meridional transect of the Atlantic Ocean. The simulation captures the patterns and magnitudes of these data, and estimates surface upwelling irradiance analogous to that observed by ocean colour satellite instruments. We find that incorporating the different optically important constituents explicitly and including spectral irradiance was crucial to capture the variability in the depth of the subsurface chlorophyll a (Chl a) maximum. We conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, as well as the crucial feedbacks between the light field, the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at attenuating light at short wavelengths and in more productive waters, phytoplankton absorption is relatively more important at the subsurface Chl a maximum, and water molecules have the greatest contribution when concentrations of other constituents are low, such as in the oligotrophic gyres. Scattering had less effect on attenuation, but since it is important for the amount and type of upwelling irradiance, it is crucial for setting sea surface reflectance. Strikingly, sensitivity experiments in which absorption by any of the

  11. CMS: Simulated Physical-Biogeochemical Data, SABGOM Model, Gulf of Mexico, 2005-2010

    Data.gov (United States)

    National Aeronautics and Space Administration — This dataset contains monthly mean ocean surface physical and biogeochemical data for the Gulf of Mexico simulated by the South Atlantic Bight and Gulf of Mexico...

  12. Biogeochemical response of tropical coastal systems to present and past environmental change

    Science.gov (United States)

    Jennerjahn, Tim C.

    2012-08-01

    Global climate and environmental change affect the biogeochemistry and ecology of aquatic systems mostly due to a combination of natural and anthropogenic factors. The latter became more and more important during the past few thousand years and particularly during the 'Anthropocene'. However, although they are considered important in this respect as yet much less is known from tropical than from high latitude coasts. Tropical coasts receive the majority of river inputs into the ocean, they harbor a variety of diverse ecosystems and a majority of the population lives there and economically depends on their natural resources. This review delineates the biogeochemical response of coastal systems to environmental change and the interplay of natural and anthropogenic control factors nowadays and in the recent geological past with an emphasis on tropical regions. Weathering rates are higher in low than in high latitude regions with a maximum in the SE Asia/Western Pacific region. On a global scale the net effect of increasing erosion due to deforestation and sediment retention behind dams is a reduced sediment input into the oceans during the Anthropocene. However, an increase was observed in the SE Asia/Western Pacific region. Nitrogen and phosphorus inputs into the ocean have trebled between the 1970s and 1990s due to human activities. As a consequence of increased nutrient inputs and a change in the nutrient mix excessive algal blooms and changes in the phytoplankton community composition towards non-biomineralizing species have been observed in many regions. This has implications for foodwebs and biogeochemical cycles of coastal seas including the release of greenhouse gases. Examples from tropical coasts with high population density and extensive agriculture, however, display deviations from temperate and subtropical regions in this respect. According to instrumental records and observations the present-day biogeochemical and ecological response to environmental

  13. Improving National Capability in Biogeochemical Flux Modelling: the UK Environmental Virtual Observatory (EVOp)

    Science.gov (United States)

    Johnes, P.; Greene, S.; Freer, J. E.; Bloomfield, J.; Macleod, K.; Reaney, S. M.; Odoni, N. A.

    2012-12-01

    The best outcomes from watershed management arise where policy and mitigation efforts are underpinned by strong science evidence, but there are major resourcing problems associated with the scale of monitoring needed to effectively characterise the sources rates and impacts of nutrient enrichment nationally. The challenge is to increase national capability in predictive modelling of nutrient flux to waters, securing an effective mechanism for transferring knowledge and management tools from data-rich to data-poor regions. The inadequacy of existing tools and approaches to address these challenges provided the motivation for the Environmental Virtual Observatory programme (EVOp), an innovation from the UK Natural Environment Research Council (NERC). EVOp is exploring the use of a cloud-based infrastructure in catchment science, developing an exemplar to explore N and P fluxes to inland and coastal waters in the UK from grid to catchment and national scale. EVOp is bringing together for the first time national data sets, models and uncertainty analysis into cloud computing environments to explore and benchmark current predictive capability for national scale biogeochemical modelling. The objective is to develop national biogeochemical modelling capability, capitalising on extensive national investment in the development of science understanding and modelling tools to support integrated catchment management, and supporting knowledge transfer from data rich to data poor regions, The AERC export coefficient model (Johnes et al., 2007) has been adapted to function within the EVOp cloud environment, and on a geoclimatic basis, using a range of high resolution, geo-referenced digital datasets as an initial demonstration of the enhanced national capacity for N and P flux modelling using cloud computing infrastructure. Geoclimatic regions are landscape units displaying homogenous or quasi-homogenous functional behaviour in terms of process controls on N and P cycling

  14. Glacial-interglacial variability in ocean oxygen and phosphorus in a global biogeochemical model

    Directory of Open Access Journals (Sweden)

    V Palastanga

    2013-02-01

    Full Text Available Increased transfer of particulate matter from continental shelves to the open ocean during glacials may have had a major impact on the biogeochemistry of the ocean. Here, we assess the response of the coupled oceanic cycles of oxygen, carbon, phosphorus, and iron to the input of particulate organic carbon and reactive phosphorus from shelves. We use a biogeochemical ocean model and specifically focus on the Last Glacial Maximum (LGM. When compared to an interglacial reference run, our glacial scenario with shelf input shows major increases in ocean productivity and phosphorus burial, while mean deep-water oxygen concentrations decline. There is a downward expansion of the oxygen minimum zones (OMZs in the Atlantic and Indian Ocean, while the extension of the OMZ in the Pacific is slightly reduced. Oxygen concentrations below 2000 m also decline but bottom waters do not become anoxic. The model simulations show when shelf input of particulate organic matter and particulate reactive P is considered, low oxygen areas in the glacial ocean expand, but concentrations are not low enough to generate wide scale changes in sediment biogeochemistry and sedimentary phosphorus recycling. Increased reactive phosphorus burial in the open ocean during the LGM in the model is related to dust input, notably over the southwest Atlantic and northwest Pacific, whereas input of material from shelves explains higher burial fluxes in continental slope and rise regions. Our model results are in qualitative agreement with available data and reproduce the strong spatial differences in the response of phosphorus burial to glacial-interglacial change. Our model results also highlight the need for additional sediment core records from all ocean basins to allow further insight into changes in phosphorus, carbon and oxygen dynamics in the ocean on glacial-interglacial timescales.

  15. Constraining denitrification in permeable wave-influenced marine sediment using linked hydrodynamic and biogeochemical modeling

    Science.gov (United States)

    Cardenas, M. B.; Cook, P. L.; Jiang, H.; Traykovski, P.

    2009-12-01

    Permeable marine sediment are ubiquitous complex environments, the biogeochemistry of which are strongly coupled to hydrodynamic process above and within the sediment. The biogeochemical processes in these settings have global scale implications but are poorly understood and challenging to quantify. We present the first simulation of linked turbulent oscillatory flow of the water column, porous media flow, and solute transport in the sediment with oxygen consumption, nitrification, denitrification, and ammonification, informed by field- and/ or experimentally-derived parameters. Nitrification and denitrification were significantly impacted by advective pore water exchange between the sediment and the water column. Denitrification rates showed a maximum at intermediate permeabilities, and were negligible at high permeabilities. Denitrification rates were low, with only ~15% of total N mineralized being denitrified, although this may be increased temporarily following sediment resuspension events. Our model-estimated denitrification rates are about half of previous estimates which do not consider solute advection through the sediment. Given the critical role of sediment permeability, topography, and bottom currents in controlling denitrification rates, an improved knowledge of these factors is vital for obtaining better estimates of denitrification taking place on shelf sediment. Broad application of our approach to myriad conditions will lead to improved predictive capacity, better informed experimental and sampling design, and more holistic understanding of the biogeochemistry of permeable sediment.

  16. Nutrient dynamics, transfer and retention along the aquatic continuum from land to ocean: towards integration of ecological and biogeochemical models

    Directory of Open Access Journals (Sweden)

    A. F. Bouwman

    2013-01-01

    Full Text Available In river basins, soils, groundwater, riparian zones and floodplains, streams, rivers, lakes and reservoirs act as successive filters in which the hydrology, ecology and biogeochemical processing are strongly coupled and together act to retain a significant fraction of the nutrients transported. This paper compares existing river ecology concepts with current approaches to describe river biogeochemistry, and assesses the value of these concepts and approaches for understanding the impacts of interacting global change disturbances on river biogeochemistry. Through merging perspectives, concepts, and modeling techniques, we propose integrated model approaches that encompass both aquatic and terrestrial components in heterogeneous landscapes. In this model framework, existing ecological and biogeochemical concepts are extended with a balanced approach for assessing nutrient and sediment delivery, on the one hand, and nutrient in-stream retention on the other hand.

  17. Modelling of transport and biogeochemical processes in pollution plumes: Vejen landfill, Denmark

    DEFF Research Database (Denmark)

    Brun, A.; Engesgaard, Peter Knudegaard; Christensen, Thomas Højlund

    2002-01-01

    A biogeochemical transport code is used to simulate leachate attenuation. biogeochemical processes. and development of redox zones in a pollution plume downstream of the Vejen landfill in Denmark. Calibration of the degradation parameters resulted in a good agreement with the observed distribution...... redox zone were determined giving DOC half-lives ranging from 100 to 1-2 days going from the methanogenic to the aerobic zone. The order of decrease in DOC half-lives from the anaerobic to the aerobic zone corresponds to findings at other landfills. (C) 2002 Elsevier Science B.V. All rights reserved....

  18. Development of an advanced eco-hydrologic and biogeochemical coupling model aimed at clarifying the missing role of inland water in the global biogeochemical cycle

    Science.gov (United States)

    Nakayama, Tadanobu

    2017-04-01

    Recent research showed that inland water including rivers, lakes, and groundwater may play some role in carbon cycling, although its contribution has remained uncertain due to limited amount of reliable data available. In this study, the author developed an advanced model coupling eco-hydrology and biogeochemical cycle (National Integrated Catchment-based Eco-hydrology (NICE)-BGC). This new model incorporates complex coupling of hydrologic-carbon cycle in terrestrial-aquatic linkages and interplay between inorganic and organic carbon during the whole process of carbon cycling. The model could simulate both horizontal transports (export from land to inland water 2.01 ± 1.98 Pg C/yr and transported to ocean 1.13 ± 0.50 Pg C/yr) and vertical fluxes (degassing 0.79 ± 0.38 Pg C/yr, and sediment storage 0.20 ± 0.09 Pg C/yr) in major rivers in good agreement with previous researches, which was an improved estimate of carbon flux from previous studies. The model results also showed global net land flux simulated by NICE-BGC (-1.05 ± 0.62 Pg C/yr) decreased carbon sink a little in comparison with revised Lund-Potsdam-Jena Wetland Hydrology and Methane (-1.79 ± 0.64 Pg C/yr) and previous materials (-2.8 to -1.4 Pg C/yr). This is attributable to CO2 evasion and lateral carbon transport explicitly included in the model, and the result suggests that most previous researches have generally overestimated the accumulation of terrestrial carbon and underestimated the potential for lateral transport. The results further implied difference between inverse techniques and budget estimates suggested can be explained to some extent by a net source from inland water. NICE-BGC would play an important role in reevaluation of greenhouse gas budget of the biosphere, quantification of hot spots, and bridging the gap between top-down and bottom-up approaches to global carbon budget.

  19. Reconstructing the Nd oceanic cycle using a coupled dynamical – biogeochemical model

    Directory of Open Access Journals (Sweden)

    T. Arsouze

    2009-12-01

    Full Text Available The decoupled behaviour observed between Nd isotopic composition (Nd IC, also referred as εNd and Nd concentration cycles has led to the notion of a "Nd paradox". While εNd behaves in a quasi-conservative way in the open ocean, leading to its broad use as a water-mass tracer, Nd concentration displays vertical profiles that increase with depth, together with a deep-water enrichment along the global thermohaline circulation. This non-conservative behaviour is typical of nutrients affected by scavenging in surface waters and remineralisation at depth. In addition, recent studies suggest the only way to reconcile both concentration and Nd IC oceanic budgets, is to invoke a "Boundary Exchange" process (BE, defined as the co-occurrence of transfer of elements from the margin to the sea with removal of elements from the sea by Boundary Scavenging as a source-sink term. However, these studies do not simulate the input/output fluxes of Nd to the ocean, and therefore prevents from crucial information that limits our understanding of Nd decoupling. To investigate this paradox on a global scale, this study uses for the first time a fully prognostic coupled dynamical/biogeochemical model with an explicit representation of Nd sources and sinks to simulate the Nd oceanic cycle. Sources considered include dissolved river fluxes, atmospheric dusts and margin sediment re-dissolution. Sinks are scavenging by settling particles. This model simulates the global features of the Nd oceanic cycle well, and produces a realistic distribution of Nd concentration (correct order of magnitude, increase with depth and along the conveyor belt, 65% of the simulated values fit in the ±10 pmol/kg envelop when compared to the data and isotopic composition (inter-basin gradient, characterization of the main water-masses, more than 70% of the simulated values fit in the ±3 εNd envelop when compared to the data, though a slight overestimation of

  20. Understanding system disturbance and ecosystem services in restored saltmarshes: Integrating physical and biogeochemical processes

    Science.gov (United States)

    Spencer, K. L.; Harvey, G. L.

    2012-06-01

    Coastal saltmarsh ecosystems occupy only a small percentage of Earth's land surface, yet contribute a wide range of ecosystem services that have significant global economic and societal value. These environments currently face significant challenges associated with climate change, sea level rise, development and water quality deterioration and are consequently the focus of a range of management schemes. Increasingly, soft engineering techniques such as managed realignment (MR) are being employed to restore and recreate these environments, driven primarily by the need for habitat (re)creation and sustainable coastal flood defence. Such restoration schemes also have the potential to provide additional ecosystem services including climate regulation and waste processing. However, these sites have frequently been physically impacted by their previous land use and there is a lack of understanding of how this 'disturbance' impacts the delivery of ecosystem services or of the complex linkages between ecological, physical and biogeochemical processes in restored systems. Through the exploration of current data this paper determines that hydrological, geomorphological and hydrodynamic functioning of restored sites may be significantly impaired with respects to natural 'undisturbed' systems and that links between morphology, sediment structure, hydrology and solute transfer are poorly understood. This has consequences for the delivery of seeds, the provision of abiotic conditions suitable for plant growth, the development of microhabitats and the cycling of nutrients/contaminants and may impact the delivery of ecosystem services including biodiversity, climate regulation and waste processing. This calls for a change in our approach to research in these environments with a need for integrated, interdisciplinary studies over a range of spatial and temporal scales incorporating both intensive and extensive research design.

  1. Regional impacts of iron-light colimitation in a global biogeochemical model

    Directory of Open Access Journals (Sweden)

    E. D. Galbraith

    2010-03-01

    Full Text Available Laboratory and field studies have revealed that iron has multiple roles in phytoplankton physiology, with particular importance for light-harvesting cellular machinery. However, although iron-limitation is explicitly included in numerous biogeochemical/ecosystem models, its implementation varies, and its effect on the efficiency of light harvesting is often ignored. Given the complexity of the ocean environment, it is difficult to predict the consequences of applying different iron limitation schemes. Here we explore the interaction of iron and nutrient cycles in an ocean general circulation model using a new, streamlined model of ocean biogeochemistry. Building on previously published parameterizations of photoadaptation and export production, the Biogeochemistry with Light Iron Nutrients and Gasses (BLING model is constructed with only four explicit tracers but including macronutrient and micronutrient limitation, light limitation, and an implicit treatment of community structure. The structural simplicity of this computationally-inexpensive model allows us to clearly isolate the global effect that iron availability has on maximum light-saturated photosynthesis rates vs. the effect iron has on photosynthetic efficiency. We find that the effect on light-saturated photosynthesis rates is dominant, negating the importance of photosynthetic efficiency in most regions, especially the cold waters of the Southern Ocean. The primary exceptions to this occur in iron-rich regions of the Northern Hemisphere, where high light-saturated photosynthesis rates allow photosynthetic efficiency to play a more important role. In other words, the ability to efficiently harvest photons has little effect in regions where light-saturated growth rates are low. Additionally, we speculate that the phytoplankton cells dominating iron-limited regions tend to have relatively high photosynthetic efficiency, due to reduced packaging effects. If this speculation is correct

  2. Soil engineering in vivo: harnessing natural biogeochemical systems for sustainable, multi-functional engineering solutions.

    Science.gov (United States)

    DeJong, Jason T; Soga, Kenichi; Banwart, Steven A; Whalley, W Richard; Ginn, Timothy R; Nelson, Douglas C; Mortensen, Brina M; Martinez, Brian C; Barkouki, Tammer

    2011-01-06

    Carbon sequestration, infrastructure rehabilitation, brownfields clean-up, hazardous waste disposal, water resources protection and global warming-these twenty-first century challenges can neither be solved by the high-energy consumptive practices that hallmark industry today, nor by minor tweaking or optimization of these processes. A more radical, holistic approach is required to develop the sustainable solutions society needs. Most of the above challenges occur within, are supported on, are enabled by or grown from soil. Soil, contrary to conventional civil engineering thought, is a living system host to multiple simultaneous processes. It is proposed herein that 'soil engineering in vivo', wherein the natural capacity of soil as a living ecosystem is used to provide multiple solutions simultaneously, may provide new, innovative, sustainable solutions to some of these great challenges of the twenty-first century. This requires a multi-disciplinary perspective that embraces the science of biology, chemistry and physics and applies this knowledge to provide multi-functional civil and environmental engineering designs for the soil environment. For example, can native soil bacterial species moderate the carbonate cycle in soils to simultaneously solidify liquefiable soil, immobilize reactive heavy metals and sequester carbon-effectively providing civil engineering functionality while clarifying the ground water and removing carbon from the atmosphere? Exploration of these ideas has begun in earnest in recent years. This paper explores the potential, challenges and opportunities of this new field, and highlights one biogeochemical function of soil that has shown promise and is developing rapidly as a new technology. The example is used to propose a generalized approach in which the potential of this new field can be fully realized.

  3. Simulating anchovy's full life cycle in the northern Aegean Sea (eastern Mediterranean): A coupled hydro-biogeochemical-IBM model

    Science.gov (United States)

    Politikos, D.; Somarakis, S.; Tsiaras, K. P.; Giannoulaki, M.; Petihakis, G.; Machias, A.; Triantafyllou, G.

    2015-11-01

    A 3-D full life cycle population model for the North Aegean Sea (NAS) anchovy stock is presented. The model is two-way coupled with a hydrodynamic-biogeochemical model (POM-ERSEM). The anchovy life span is divided into seven life stages/age classes. Embryos and early larvae are passive particles, but subsequent stages exhibit active horizontal movements based on specific rules. A bioenergetics model simulates the growth in both the larval and juvenile/adult stages, while the microzooplankton and mesozooplankton fields of the biogeochemical model provide the food for fish consumption. The super-individual approach is adopted for the representation of the anchovy population. A dynamic egg production module, with an energy allocation algorithm, is embedded in the bioenergetics equation and produces eggs based on a new conceptual model for anchovy vitellogenesis. A model simulation for the period 2003-2006 with realistic initial conditions reproduced well the magnitude of population biomass and daily egg production estimated from acoustic and daily egg production method (DEPM) surveys, carried out in the NAS during June 2003-2006. Model simulated adult and egg habitats were also in good agreement with observed spatial distributions of acoustic biomass and egg abundance in June. Sensitivity simulations were performed to investigate the effect of different formulations adopted for key processes, such as reproduction and movement. The effect of the anchovy population on plankton dynamics was also investigated, by comparing simulations adopting a two-way or a one-way coupling of the fish with the biogeochemical model.

  4. Compilation of a global N{sub 2}O emission inventory for tropical rainforest soils using a detailed biogeochemical model

    Energy Technology Data Exchange (ETDEWEB)

    Werner, C.

    2007-09-15

    Nitrous oxide (N{sub 2}O) is a potent trace gas contributing to approximately 6% to the observed anthropogenic global warming. Soils have been identified to be the major source of atmospheric N{sub 2}O and tropical rainforest soils are thought to account for the largest part. Furthermore, various studies have shown that the magnitude of N{sub 2}O emissions from tropical rainforest soil is highly variable on spatial and temporal scales. Detailed, process-based models coupled to Geographic Information Systems (GIS) are considered promising tools for the calculation of N{sub 2}O emission inventories. This methodology explicitly accounts for the governing microbial processes as well as the environmental controls. Moreover, mechanistic biogeochemical models operating in daily time-steps (e.g. ForestDNDC-tropica) have been shown to capture the observed intra- and inter-annual variations of N{sub 2}O emissions. However, detailed N{sub 2}O emission datasets are required for model calibration and testing, but are currently few in numbers. In this study an automated measurement system was used to derive detailed datasets of N{sub 2}O, methane (CH{sub 4}) and carbon dioxide (CO{sub 2}) soil-atmosphere exchange and important environmental parameters from tropical rainforest soils in Kenya and Southwest China. Distinct differences were identified in the magnitude of the C and N soil-atmosphere exchange at the investigated sites and forest types. However, common features such as N{sub 2}O pulse emissions after dry season or the pronounced soil moisture dependency of N{sub 2}O emissions were observed at both sites. The derived datasets are unique for these tropical regions as so far no information about the source strength of these regions was available and, for the first time, the N{sub 2}O, CH{sub 4} and CO{sub 2} soil-atmosphere exchange was recorded in sub-daily resolution. The datasets were utilized in conjunction with available high-resolution datasets from Australian

  5. Nitrous oxide emissions from cropland: a procedure for calibrating the DayCent biogeochemical model using inverse modelling

    Science.gov (United States)

    Rafique, Rashad; Fienen, Michael N.; Parkin, Timothy B.; Anex, Robert P.

    2013-01-01

    DayCent is a biogeochemical model of intermediate complexity widely used to simulate greenhouse gases (GHG), soil organic carbon and nutrients in crop, grassland, forest and savannah ecosystems. Although this model has been applied to a wide range of ecosystems, it is still typically parameterized through a traditional “trial and error” approach and has not been calibrated using statistical inverse modelling (i.e. algorithmic parameter estimation). The aim of this study is to establish and demonstrate a procedure for calibration of DayCent to improve estimation of GHG emissions. We coupled DayCent with the parameter estimation (PEST) software for inverse modelling. The PEST software can be used for calibration through regularized inversion as well as model sensitivity and uncertainty analysis. The DayCent model was analysed and calibrated using N2O flux data collected over 2 years at the Iowa State University Agronomy and Agricultural Engineering Research Farms, Boone, IA. Crop year 2003 data were used for model calibration and 2004 data were used for validation. The optimization of DayCent model parameters using PEST significantly reduced model residuals relative to the default DayCent parameter values. Parameter estimation improved the model performance by reducing the sum of weighted squared residual difference between measured and modelled outputs by up to 67 %. For the calibration period, simulation with the default model parameter values underestimated mean daily N2O flux by 98 %. After parameter estimation, the model underestimated the mean daily fluxes by 35 %. During the validation period, the calibrated model reduced sum of weighted squared residuals by 20 % relative to the default simulation. Sensitivity analysis performed provides important insights into the model structure providing guidance for model improvement.

  6. A Coupled Ocean General Circulation, Biogeochemical, and Radiative Model of the Global Oceans: Seasonal Distributions of Ocean Chlorophyll and Nutrients

    Science.gov (United States)

    Gregg, Watson W.; Busalacchi, Antonio (Technical Monitor)

    2000-01-01

    A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability. and the interactions among three functional phytoplankton groups (diatoms. chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (greater than 1000 km) model chlorophyll results are in overall agreement with CZCS pigments in many global regions. Seasonal variability observed in the CZCS is also represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are generally in conformance although occasional departures are apparent. Model nitrate distributions agree with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicates that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent many aspects of the great diversity of physical, biological, chemical, and radiative environments encountered in the global oceans.

  7. Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef

    Science.gov (United States)

    Jones, Emlyn M.; Baird, Mark E.; Mongin, Mathieu; Parslow, John; Skerratt, Jenny; Lovell, Jenny; Margvelashvili, Nugzar; Matear, Richard J.; Wild-Allen, Karen; Robson, Barbara; Rizwi, Farhan; Oke, Peter; King, Edward; Schroeder, Thomas; Steven, Andy; Taylor, John

    2016-12-01

    Skillful marine biogeochemical (BGC) models are required to understand a range of coastal and global phenomena such as changes in nitrogen and carbon cycles. The refinement of BGC models through the assimilation of variables calculated from observed in-water inherent optical properties (IOPs), such as phytoplankton absorption, is problematic. Empirically derived relationships between IOPs and variables such as chlorophyll-a concentration (Chl a), total suspended solids (TSS) and coloured dissolved organic matter (CDOM) have been shown to have errors that can exceed 100 % of the observed quantity. These errors are greatest in shallow coastal regions, such as the Great Barrier Reef (GBR), due to the additional signal from bottom reflectance. Rather than assimilate quantities calculated using IOP algorithms, this study demonstrates the advantages of assimilating quantities calculated directly from the less error-prone satellite remote-sensing reflectance (RSR). To assimilate the observed RSR, we use an in-water optical model to produce an equivalent simulated RSR and calculate the mismatch between the observed and simulated quantities to constrain the BGC model with a deterministic ensemble Kalman filter (DEnKF). The traditional assumption that simulated surface Chl a is equivalent to the remotely sensed OC3M estimate of Chl a resulted in a forecast error of approximately 75 %. We show this error can be halved by instead using simulated RSR to constrain the model via the assimilation system. When the analysis and forecast fields from the RSR-based assimilation system are compared with the non-assimilating model, a comparison against independent in situ observations of Chl a, TSS and dissolved inorganic nutrients (NO3, NH4 and DIP) showed that errors are reduced by up to 90 %. In all cases, the assimilation system improves the simulation compared to the non-assimilating model. Our approach allows for the incorporation of vast quantities of remote-sensing observations

  8. Biogeochemical impact of a model western iron source in the Pacific Equatorial Undercurrent

    OpenAIRE

    Slemons, L.; Gorgues, T.; Aumont, Olivier; Menkès, Christophe; Murray, J. W.

    2009-01-01

    Trace element distributions in the source waters of the Pacific Equatorial Undercurrent (EUC) show the existence of elevated total acid-soluble iron concentrations. This region has been suggested to contribute enough bioavailable iron to regulate interannual and interglacial variability in biological productivity downstream in the high-nitrate low-chlorophyll upwelling zone of the eastern equatorial Pacific. We investigated the advection and first-order biogeochemical impact of an imposed, da...

  9. Simulating temporal variations of nitrogen losses in river networks with a dynamic transport model unravels the coupled effects of hydrological and biogeochemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Mulholland, Patrick J [ORNL; Alexander, Richard [U.S. Geological Survey; Bohlke, John [U.S. Geological Survey; Boyer, Elizabeth [Pennsylvania State University; Harvey, Judson [U.S. Geological Survey; Seitzinger, Sybil [Rutgers University; Tobias, Craig [University of North Carolina, Wilmington; Tonitto, Christina [Cornell University; Wollheim, Wilfred [University of New Hampshire

    2009-01-01

    The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal in the river networks of two watersheds having widely differing levels of nitrate enrichment but nearly identical discharges. Stream denitrification is estimated by regression as a nonlinear function of nitrate concentration, streamflow, and temperature, using more than 300 published measurements from a variety of US streams. These relations are used in the stream transport model to characterize nitrate dynamics related to denitrification at a monthly time scale in the stream reaches of the two watersheds. Results indicate that the nitrate removal efficiency of streams, as measured by the percentage of the stream nitrate flux removed via denitrification per unit length of channel, is appreciably reduced during months with high discharge and nitrate flux and increases during months of low-discharge and flux. Biogeochemical factors, including land use, nitrate inputs, and stream concentrations, are a major control on reach-scale denitrification, evidenced by the disproportionately lower nitrate removal efficiency in streams of the highly nitrate-enriched watershed as compared with that in similarly sized streams in the less nitrate-enriched watershed. Sensitivity analyses reveal that these important biogeochemical factors and physical hydrological factors contribute nearly

  10. Biogeochemical-Argo: achievements, challenges for the future and potential synergies with other components of ocean observation systems

    Science.gov (United States)

    Claustre, Hervé; Johnson, Ken

    2017-04-01

    The recently launched Biogeochemical-Argo (BGC-Argo) program aims at developing a global network of biogeochemical sensors on Argo profiling floats for acquiring long-term high-quality time-series of oceanic properties. BGC-Argo is in particular poised to address a number of challenges in ocean science (e.g. hypoxia, carbon uptake, ocean acidification, biological-carbon pump and phytoplankton communities), topics that are difficult, if not impossible, to address with our present observing assets. Presently six variables are considered as core BGC-Argo variables (O2, NO3, pH, Chla, suspended particles and downwelling irradiance). Historically, BGC-Argo has been initiated through small-scale "showcase" projects progressively scaling up into regional case studies essentially addressing key biological pump-related questions in specific regions (e.g. sub-tropical gyres, North Atlantic, Southern Ocean). Now BGC-Argo is transitioning towards a global and sustained observation system thanks to progressive international coordination of national contributions and to increasingly mature and efficient data management and distribution systems. In this presentation, we will highlight a variety of results derived from BGC-Argo observations and encompassing a wide range of topics related to ocean biogeochemistry. Challenges for the future and long-term sustainability of the system will be addressed in particular with respect to maintaining a high-quality and interoperable dataset over long-term. Part of this can be achieved through a tight interaction with programs (e.g. GOSHIP) and their historical databases, which should constitute a corner stone to assess data quality. Example on the interplay between BGC-Argo and GlodapV2 databases will be particularly exemplified in this context. Furthermore, we will illustrate the potential synergies between synoptically measured surface satellite-quantities and their vertically resolved (BGC-Argo) counterparts into the development of 3D

  11. Using satellite-derived backscattering coefficients in addition to chlorophyll data to constrain a simple marine biogeochemical model

    Directory of Open Access Journals (Sweden)

    H. Kettle

    2009-08-01

    Full Text Available Biogeochemical models of the ocean carbon cycle are frequently validated by, or tuned to, satellite chlorophyll data. However, ocean carbon cycle models are required to accurately model the movement of carbon, not chlorophyll, and due to the high variability of the carbon to chlorophyll ratio in phytoplankton, chlorophyll is not a robust proxy for carbon. Using inherent optical property (IOP inversion algorithms it is now possible to also derive the amount of light backscattered by the upper ocean (bb which is related to the amount of particulate organic carbon (POC present. Using empirical relationships between POC and bb, a 1-D marine biogeochemical model is used to simulate bb at 490 nm thereby allowing the model to be compared with both remotely-sensed chlorophyll or bb data. Here I investigate the possibility of using bb in conjunction with chlorophyll data to help constrain the parameters in a simple 1-D NPZD model. The parameters of the biogeochemical model are tuned with a genetic algorithm, so that the model is fitted to either chlorophyll data or to both chlorophyll and bb data at three sites in the Atlantic with very different characteristics. Several inherent optical property (IOP algorithms are available for estimating bb, three of which are used here. The effect of the different bb datasets on the behaviour of the tuned model is examined to ascertain whether the uncertainty in bb is significant. The results show that the addition of bb data does not consistently alter the same model parameters at each site and in fact can lead to some parameters becoming less well constrained, implying there is still much work to be done on the mechanisms relating chlorophyll to POC and bb within the model. However, this study does indicate that

  12. Net primary productivity estimates and environmental variables in the Arctic Ocean: An assessment of coupled physical-biogeochemical models

    Science.gov (United States)

    Lee, Younjoo J.; Matrai, Patricia A.; Friedrichs, Marjorie A. M.; Saba, Vincent S.; Aumont, Olivier; Babin, Marcel; Buitenhuis, Erik T.; Chevallier, Matthieu; de Mora, Lee; Dessert, Morgane; Dunne, John P.; Ellingsen, Ingrid H.; Feldman, Doron; Frouin, Robert; Gehlen, Marion; Gorgues, Thomas; Ilyina, Tatiana; Jin, Meibing; John, Jasmin G.; Lawrence, Jon; Manizza, Manfredi; Menkes, Christophe E.; Perruche, Coralie; Le Fouest, Vincent; Popova, Ekaterina E.; Romanou, Anastasia; Samuelsen, Annette; Schwinger, Jörg; Séférian, Roland; Stock, Charles A.; Tjiputra, Jerry; Tremblay, L. Bruno; Ueyoshi, Kyozo; Vichi, Marcello; Yool, Andrew; Zhang, Jinlun

    2016-12-01

    The relative skill of 21 regional and global biogeochemical models was assessed in terms of how well the models reproduced observed net primary productivity (NPP) and environmental variables such as nitrate concentration (NO3), mixed layer depth (MLD), euphotic layer depth (Zeu), and sea ice concentration, by comparing results against a newly updated, quality-controlled in situ NPP database for the Arctic Ocean (1959-2011). The models broadly captured the spatial features of integrated NPP (iNPP) on a pan-Arctic scale. Most models underestimated iNPP by varying degrees in spite of overestimating surface NO3, MLD, and Zeu throughout the regions. Among the models, iNPP exhibited little difference over sea ice condition (ice-free versus ice-influenced) and bottom depth (shelf versus deep ocean). The models performed relatively well for the most recent decade and toward the end of Arctic summer. In the Barents and Greenland Seas, regional model skill of surface NO3 was best associated with how well MLD was reproduced. Regionally, iNPP was relatively well simulated in the Beaufort Sea and the central Arctic Basin, where in situ NPP is low and nutrients are mostly depleted. Models performed less well at simulating iNPP in the Greenland and Chukchi Seas, despite the higher model skill in MLD and sea ice concentration, respectively. iNPP model skill was constrained by different factors in different Arctic Ocean regions. Our study suggests that better parameterization of biological and ecological microbial rates (phytoplankton growth and zooplankton grazing) are needed for improved Arctic Ocean biogeochemical modeling.

  13. Towards Next Generation Ocean Models: Novel Discontinuous Galerkin Schemes for 2D Unsteady Biogeochemical Models

    Science.gov (United States)

    2009-09-01

    FVCOM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 2.7 ICOM ...coastal re- gions featured with complex irregular geometry and steep bottom topography. ICOM Imperial College Ocean Model FEM (CG and DG) using...the ICOM group. This code is written in C. Finel was also developed by the same group, and it is a three-dimensional non- hydrostatic finite element

  14. Spatial patterns in soil biogeochemical process rates along a Louisiana wetland salinity gradient in the Barataria Bay estuarine system

    Science.gov (United States)

    Roberts, B. J.; Rich, M. W.; Sullivan, H. L.; Bledsoe, R.; Dawson, M.; Donnelly, B.; Marton, J. M.

    2014-12-01

    Louisiana has the highest rates of coastal wetland loss in the United States. In addition to being lost, Louisiana wetlands experience numerous other environmental stressors including changes in salinity regime (both increases from salt water intrusion and decreases from the creation of river diversions) and climate change induced changes in vegetation (e.g. the northward expansion of Avicennia germinans (black mangrove) into salt marshes). In this study, we examined how these changes might influence biogeochemical process rates important in regulating carbon balance and the cycling, retention, and removal of nutrients in Louisiana wetlands. Specifically, we measured net soil greenhouse gas fluxes and collected cores for the determination of rates of greenhouse gas production, denitrification potential, nitrification potential, iron reduction, and phosphorus sorption from surface (0-5cm) and subsurface (10-15cm) depths for three plots in each of 4 sites along the salinity gradient: a freshwater marsh site, a brackish (7 ppt) marsh site, a salt marsh (17 ppt), and a Avicennia germinans stand (17 ppt; adjacent to salt marsh site) in the Barataria Bay estuarine system. Most biogeochemical processes displayed similar spatial patterns with salt marsh rates being lower than rates in freshwater and/or brackish marsh sites and not having significantly different rates than in Avicennia germinans stands. Rates in surface soils were generally higher than in subsurface soils. These patterns were generally consistent with spatial patterns in soil properties with soil water content, organic matter quantity and quality, and extractable nutrients generally being higher in freshwater and brackish marsh sites than salt marsh and Avicennia germinans sites, especially in surface soils. These spatial patterns suggest that the ability of coastal wetlands to retain and remove nutrients might change significantly in response to future climate changes in the region and that these

  15. Seasonal Distributions of Global Ocean Chlorophyll and Nutrients: Analysis with a Coupled Ocean General Circulation Biogeochemical, and Radiative Model

    Science.gov (United States)

    Gregg, Watson W.

    1999-01-01

    A coupled general ocean circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. The model is driven by climatological meteorological conditions, cloud cover, and sea surface temperature. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability, and the interactions among three functional phytoplankton groups (diatoms, chorophytes, and picoplankton) and three nutrient groups (nitrate, ammonium, and silicate). Phytoplankton groups are initialized as homogeneous fields horizontally and vertically, and allowed to distribute themselves according to the prevailing conditions. Basin-scale model chlorophyll results are in very good agreement with CZCS pigments in virtually every global region. Seasonal variability observed in the CZCS is also well represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are also in good conformance, although occasional departures are apparent. Agreement of nitrate distributions with in situ data is even better, including seasonal dynamics, except for the equatorial Atlantic. The good agreement of the model with satellite and in situ data sources indicates that the model dynamics realistically simulate phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization, and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent the great diversity of physical, biological

  16. Regional application of process based biogeochemical model DNDC in Godavari Sub-basin

    Directory of Open Access Journals (Sweden)

    A Biswal

    2016-12-01

    Full Text Available The denitrification decomposition (DNDC model is a process-based computer simulation model of soil carbon and nitrogen biogeochemistry. The DNDC model is one of the few process-based bio-geo chemical crop simulation models for which both a site-specific mode and a regional mode were developed. For regional mode, a region is presented in a typical Geographic Information System (GIS consisting of many polygons or grid cells. The database consists of spatially differentiated information of location, climate, soil properties, cropping systems, and farm management practices for each polygon or grid cell for the entire modeled region. An attempt was made to establish the methodology for the estimation of soil greenhouse gas fluxes like CH4, CO2 and N2O on a sub-basin scale.

  17. An Analytical Particle Biogeochemical Sensor Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Evaluation of the technical and scientific feasibility of developing a model and sensor for the analytical optical determination of particle biogeochemical...

  18. Carbon, nitrogen, oxygen and sulfide budgets in the Black Sea : a biogeochemical model of the whole water column coupling the oxic and anoxic parts

    NARCIS (Netherlands)

    Grégoire, M.; Soetaert, K.E.R.

    2010-01-01

    Carbon, nitrogen, oxygen and sulfide budgets are derived for the Black Sea water column from a coupled physical–biogeochemical model. The model is applied in the deep part of the sea and simulates processes over the whole water column including the anoxic layer that extends from similar, equals115 m

  19. Constraining parameters in state-of-the-art marine pelagic biogeochemical models. Is it sufficient to use typical observations of standing-stocks?

    Science.gov (United States)

    Loeptien, Ulrike; Dietze, Heiner

    2014-05-01

    In order to constrain potential feedbacks in the climate system, simple pelagic biogeochemical models (BGCMs) are coupled to 3-dimensional ocean-atmosphere models. These so-called earth system models are frequently applied to calculate climate projections. All BGCs rely on a set of rather uncertain parameters. Among them are generally the Michaelis Menten (MM) constants, utilized in the hyperbolic MM- formulation (which specifies the limiting effect of light and nutrients on carbon assimilation by autotrophic phytoplankton). All model parameters are typically tuned in rather subjective trial-and-error exercises where the parameters are changed manually until a "reasonable" similarity with observed standing stocks is achieved. In the present study, we explore with twin experiments (or synthetic ``observations") the demands on observations that would allow for a more objective estimation of model parameters. These parameter retrieval experiments are based on ``perfect" (synthetic) observations which we, step by step, distort to approach realistic conditions. Finally, we confirm our findings with real-world observations. In summary, we find that even modest noise (10%) inherent to observations may hinder the parameter retrieval already. Particularly, the MM constants are hard to constrain. This is of concern since the MM parameters are key to the model`s sensitivity to anticipated changes of the external conditions.

  20. Stream biogeochemical resilience in the age of Anthropocene

    Science.gov (United States)

    Dong, H.; Creed, I. F.

    2017-12-01

    Recent evidence indicates that biogeochemical cycles are being pushed beyond the tolerance limits of the earth system in the age of the Anthropocene placing terrestrial and aquatic ecosystems at risk. Here, we explored the question: Is there empirical evidence of global atmospheric changes driving losses in stream biogeochemical resilience towards a new normal? Stream biogeochemical resilience is the process of returning to equilibrium conditions after a disturbance and can be measured using three metrics: reactivity (the highest initial response after a disturbance), return rate (the rate of return to equilibrium condition after reactive changes), and variance of the stationary distribution (the signal to noise ratio). Multivariate autoregressive models were used to derive the three metrics for streams along a disturbance gradient - from natural systems where global drivers would dominate, to relatively managed or modified systems where global and local drivers would interact. We observed a loss of biogeochemical resilience in all streams. The key biogeochemical constituent(s) that may be driving loss of biogeochemical resilience were identified from the time series of the stream biogeochemical constituents. Non-stationary trends (detected by Mann-Kendall analysis) and stationary cycles (revealed through Morlet wavelet analysis) were removed, and the standard deviation (SD) of the remaining residuals were analyzed to determine if there was an increase in SD over time that would indicate a pending shift towards a new normal. We observed that nitrate-N and total phosphorus showed behaviours indicative of a pending shift in natural and managed forest systems, but not in agricultural systems. This study provides empirical support that stream ecosystems are showing signs of exceeding planetary boundary tolerance levels and shifting towards a "new normal" in response to global changes, which can be exacerbated by local management activities. Future work will consider

  1. Optical Remote Sensing Algorithm Validation using High-Frequency Underway Biogeochemical Measurements in Three Large Global River Systems

    Science.gov (United States)

    Kuhn, C.; Richey, J. E.; Striegl, R. G.; Ward, N.; Sawakuchi, H. O.; Crawford, J.; Loken, L. C.; Stadler, P.; Dornblaser, M.; Butman, D. E.

    2017-12-01

    More than 93% of the world's river-water volume occurs in basins impacted by large dams and about 43% of river water discharge is impacted by flow regulation. Human land use also alters nutrient and carbon cycling and the emission of carbon dioxide from inland reservoirs. Increased water residence times and warmer temperatures in reservoirs fundamentally alter the physical settings for biogeochemical processing in large rivers, yet river biogeochemistry for many large systems remains undersampled. Satellite remote sensing holds promise as a methodology for responsive regional and global water resources management. Decades of ocean optics research has laid the foundation for the use of remote sensing reflectance in optical wavelengths (400 - 700 nm) to produce satellite-derived, near-surface estimates of phytoplankton chlorophyll concentration. Significant improvements between successive generations of ocean color sensors have enabled the scientific community to document changes in global ocean productivity (NPP) and estimate ocean biomass with increasing accuracy. Despite large advances in ocean optics, application of optical methods to inland waters has been limited to date due to their optical complexity and small spatial scale. To test this frontier, we present a study evaluating the accuracy and suitability of empirical inversion approaches for estimating chlorophyll-a, turbidity and temperature for the Amazon, Columbia and Mississippi rivers using satellite remote sensing. We demonstrate how riverine biogeochemical measurements collected at high frequencies from underway vessels can be used as in situ matchups to evaluate remotely-sensed, near-surface temperature, turbidity, chlorophyll-a derived from the Landsat 8 (NASA) and Sentinel 2 (ESA) satellites. We investigate the use of remote sensing water reflectance to infer trophic status as well as tributary influences on the optical characteristics of the Amazon, Mississippi and Columbia rivers.

  2. Modelling ecosystem functions and properties at different time and spatial scales in shallow coastal lagoons: An application of the LOICZ biogeochemical model

    Science.gov (United States)

    Giordani, Gianmarco; Austoni, Martina; Zaldívar, José M.; Swaney, Dennis P.; Viaroli, Pierluigi

    2008-04-01

    The Land-Ocean Interactions in the Coastal Zone (LOICZ) biogeochemical model (LBM) was applied at different temporal and spatial scales in 17 Italian lagoons of the LaguNet network ( http://www.dsa.unipr.it/lagunet). A series of alternative assumptions taking into account benthic vegetation and sedimentary fluxes were introduced and compared with the classical LBM approach at various time scales. The reliability of the LBM application to the seventeen Italian lagoons was tested by comparison to a pool of shallow coastal systems from the global LOICZ database with comparable depths and sizes. The nutrient loads of the Italian sites can be considered relatively low, particularly for dissolved inorganic phosphorus (DIP). Although the median values of estimated internal transformations (source-sink) of both dissolved inorganic phosphorous and nitrogen at the LaguNet sites were comparable with the selected LOICZ sites, the positive and negative extreme values were one order of magnitude lower. Overall, the LBM applications to the Italian sites gave good quality budgets for shallow systems subjected to relatively low nutrient inputs and with a wide range of primary producer communities, including seagrass, macroalgae and phytoplankton. Furthermore, stoichiometry of Carbon:Nitrogen:Phosphorous for the different primary producer groups allowed the integration of previous studies by identifying a series of relationships between nutrient loads and ecosystem functions. To some extent, the LBM application at monthly and seasonal time scales, as shown for the Sacca di Goro lagoon, can simulate the internal variability affected by the life cycle of the dominant primary producers. Therefore, the LBM not only allows the assessment of net ecological metabolism but seems, also, capable of representing the wide range of trophic conditions associated with shallow coastal systems. Overall, the application of alternative assumptions supports the robustness of the classical LBM, although

  3. Modeling the nitrogen fluxes in the Black Sea using a 3D coupledhydrodynamical-biogeochemical model: transport versus biogeochemicalprocesses, exchanges across the shelf break and comparison of the shelf anddeep sea ecodynamics

    Directory of Open Access Journals (Sweden)

    M. Grégoire

    2004-01-01

    Full Text Available A 6-compartment biogeochemical model of nitrogen cycling and plankton productivity has been coupled with a 3D general circulation model in an enclosed environment (the Black Sea so as to quantify and compare, on a seasonal and annual scale, the typical internal biogeochemical functioning of the shelf and of the deep sea as well as to estimate the nitrogen and water exchanges at the shelf break. Model results indicate that the annual nitrogen net export to the deep sea roughly corresponds to the annual load of nitrogen discharged by the rivers on the shelf. The model estimated vertically integrated gross annual primary production is 130gCm-2yr-1 for the whole basin, 220gCm-2yr-1 for the shelf and 40gCm-2yr-1 for the central basin. In agreement with sediment trap observations, model results indicate a rapid and efficient recycling of particulate organic matter in the sub-oxic portion of the water column (60-80m of the open sea. More than 95% of the PON produced in the euphotic layer is recycled in the upper 100m of the water column, 87% in the upper 80 m and 67% in the euphotic layer. The model estimates the annual export of POC towards the anoxic layer to 4 1010molyr-1. This POC is definitely lost for the system and represents 2% of the annual primary production of the open sea.

  4. Evaluation of additional biogeochemical impacts on mitigation pathways in an energy sytem integrated assessment model.

    Science.gov (United States)

    Dessens, O.

    2017-12-01

    Within the last IPCC AR5 a large and systematic sensitivity study around available technologies and timing of policies applied in IAMs to achieve the 2°C target has been conducted. However the simple climate representations included in IAMs are generally tuned to the results of ensemble means. This may result in hiding within the ensemble mean results possible challenging mitigation pathways for the economy or the technology future scenarios. This work provides new insights on the sensitivity of the socio-economic response to different climate factors under a 2°C climate change target in order to help guide future efforts to reduce uncertainty in the climate mitigation decisions. The main objective is to understand and bring new insights on how future global warming will affect the natural biochemical feedbacks on the climate system and what could be the consequences of these feedbacks on the anthropogenic emission pathways with a specific focus on the energy-economy system. It specifically focuses on three issues of the climate representation affecting the energy system transformation and GHG emissions pathways: 1- Impacts of the climate sensitivity (or TCR); 2- Impacts of warming on the radiative forcing (cloudiness,...); 3- Impacts of warming on the carbon cycle (carbon cycle feedback). We use the integrated assessment model TIAM-UCL to examine the mitigation pathways compatible with the 2C target depending on assumptions regarding the 3 issues of the climate representation introduced above. The following key conclusions drawn from this study are that mitigation to 2°C is still possible under strong climate sensitivity (TCR), strong carbon cycle amplification or positive radiative forcing feedback. However, this level of climate mitigation will require a significant transformation in the way we produce and consume energy. Carbon capture and sequestration on electricity generation, industry and biomass is part of the technology pool needed to achieve this

  5. Development of a 3D coupled physical-biogeochemical model for the Marseille coastal area (NW Mediterranean Sea: what complexity is required in the coastal zone?

    Directory of Open Access Journals (Sweden)

    Marion Fraysse

    Full Text Available Terrestrial inputs (natural and anthropogenic from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C and nitrogen (N cycles and a second model that also considers the phosphorus (P cycle. Realistic simulations were performed for a period of 5 years (2007-2011. The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model.

  6. Evaluation of the transport matrix method for simulation of ocean biogeochemical tracers

    Science.gov (United States)

    Kvale, Karin F.; Khatiwala, Samar; Dietze, Heiner; Kriest, Iris; Oschlies, Andreas

    2017-06-01

    Conventional integration of Earth system and ocean models can accrue considerable computational expenses, particularly for marine biogeochemical applications. Offline numerical schemes in which only the biogeochemical tracers are time stepped and transported using a pre-computed circulation field can substantially reduce the burden and are thus an attractive alternative. One such scheme is the transport matrix method (TMM), which represents tracer transport as a sequence of sparse matrix-vector products that can be performed efficiently on distributed-memory computers. While the TMM has been used for a variety of geochemical and biogeochemical studies, to date the resulting solutions have not been comprehensively assessed against their online counterparts. Here, we present a detailed comparison of the two. It is based on simulations of the state-of-the-art biogeochemical sub-model embedded within the widely used coarse-resolution University of Victoria Earth System Climate Model (UVic ESCM). The default, non-linear advection scheme was first replaced with a linear, third-order upwind-biased advection scheme to satisfy the linearity requirement of the TMM. Transport matrices were extracted from an equilibrium run of the physical model and subsequently used to integrate the biogeochemical model offline to equilibrium. The identical biogeochemical model was also run online. Our simulations show that offline integration introduces some bias to biogeochemical quantities through the omission of the polar filtering used in UVic ESCM and in the offline application of time-dependent forcing fields, with high latitudes showing the largest differences with respect to the online model. Differences in other regions and in the seasonality of nutrients and phytoplankton distributions are found to be relatively minor, giving confidence that the TMM is a reliable tool for offline integration of complex biogeochemical models. Moreover, while UVic ESCM is a serial code, the TMM can

  7. Evaluation of the transport matrix method for simulation of ocean biogeochemical tracers

    Directory of Open Access Journals (Sweden)

    K. F. Kvale

    2017-06-01

    Full Text Available Conventional integration of Earth system and ocean models can accrue considerable computational expenses, particularly for marine biogeochemical applications. Offline numerical schemes in which only the biogeochemical tracers are time stepped and transported using a pre-computed circulation field can substantially reduce the burden and are thus an attractive alternative. One such scheme is the transport matrix method (TMM, which represents tracer transport as a sequence of sparse matrix–vector products that can be performed efficiently on distributed-memory computers. While the TMM has been used for a variety of geochemical and biogeochemical studies, to date the resulting solutions have not been comprehensively assessed against their online counterparts. Here, we present a detailed comparison of the two. It is based on simulations of the state-of-the-art biogeochemical sub-model embedded within the widely used coarse-resolution University of Victoria Earth System Climate Model (UVic ESCM. The default, non-linear advection scheme was first replaced with a linear, third-order upwind-biased advection scheme to satisfy the linearity requirement of the TMM. Transport matrices were extracted from an equilibrium run of the physical model and subsequently used to integrate the biogeochemical model offline to equilibrium. The identical biogeochemical model was also run online. Our simulations show that offline integration introduces some bias to biogeochemical quantities through the omission of the polar filtering used in UVic ESCM and in the offline application of time-dependent forcing fields, with high latitudes showing the largest differences with respect to the online model. Differences in other regions and in the seasonality of nutrients and phytoplankton distributions are found to be relatively minor, giving confidence that the TMM is a reliable tool for offline integration of complex biogeochemical models. Moreover, while UVic ESCM is a serial

  8. Contrasting biogeochemical responses of ENSO induced upwelling variability in the Humboldt Current System

    Science.gov (United States)

    Franco, Ana C.; Gruber, Nicolas; Münnich, Matthias

    2017-04-01

    The Humboldt Current System (HCS) is one of the most productive ecosystems in the world. This high productivity is supported by a large input of nutrients from the subsurface layers to the surface due to year-round upwelling. However, upwelling also supplies waters with low pH and low aragonite saturation state potentially affecting many organisms, especially those that calcify. The influence, extent and source of upwelled water vary substantially on interannual timescales in association with the El Niño/Southern Oscillation (ENSO) phenomenon, generating natural contrasting responses on the biogeochemistry of this system. Here we analyze these responses using an eddy resolving, basin-scale ocean model that covers the whole Pacific Ocean with high resolution (4 km) on the west coast of South America. We performed a simulation of the last 30 years (hindcast simulation) that allows us to investigate the influence of at least eight El Niño episodes and eight La Niña episodes on productivity variations and changes in oxygen concentration and aragonite saturation state. An absolute change in surface omega aragonite of almost 2 units, as well as an absolute change of the aragonite saturation depth of 200 m result from the change of an El Niño phase to a La Niña phase. This variability is on the same order of magnitude as the projected change in the aragonite saturation state in a centennial timescale. During La Niña events, a lower aragonite saturation state values and reduced oxygen concentration in the surface layer are a direct consequence of enhanced upwelling and increased net primary productivity. The opposite is true during El Niño events, where high values of omega aragonite occur in concordance with extraordinarily low net primary productivity values.

  9. Using annually-resolved bivalve records and biogeochemical models to understand and predict climate impacts in coastal oceans

    Science.gov (United States)

    Holmes, Sarah

    2017-04-01

    It is more important than ever to study the oceans and especially the shelf seas, which are disproportionately productive, sustaining over 90% of global fisheries . The economic and societal significance of these shallow oceans, as the interface through which society interacts with the marine environment, makes them highly relevant to the decisions of policy-makers and stakeholders. These decision-makers rely upon empirical data informed by consistent and extensive monitoring and assessment from experts in the field, yet long-term, spatially-extensive datasets of the marine environment do not exist or are of poor quality. Modelling the shelf seas with biogeochemical models can provide valuable data, allowing scientists to look at both past and future scenarios to estimate ecosystem response to change. In particular, the European Regional Sea Ecosystem Model or ERSEM combines not only the complex hydrographical aspects of the North West European shelf, but also vast numbers of biological and chemical parameters. Though huge efforts across the modelling community are invested into developing and ultimately increasing the reliability of models such as the ERSEM, this is typically achieved by looking at relationships with aforementioned observed datasets, restricting model accuracy and our understanding of ecosystem processes. It is for this reason that proxy data of the marine environment is so valuable. Of all marine proxies available, sclerochronology, the study of the growth bands on long-lived marine molluscs, is the only proven to provide novel, high resolution, multi-centennial, annually-resolved, absolutely-dated archives of past ocean environment, analogous to dendrochronology. For the first time, this PhD project will combine the proxy data of sclerochronology with model hindcast data from the ERSEM with the aim to better understand the North West European shelf sea environment and potentially improve predictions of future climate change in this region and

  10. Data-model integration to interpret connectivity between biogeochemical cycling, and vegetation phenology and productivity in mountainous ecosystems under changing hydrologic regimes

    Science.gov (United States)

    Brodie, E.; Arora, B.; Beller, H. R.; Bill, M.; Bouskill, N.; Chakraborty, R.; Conrad, M. E.; Dafflon, B.; Enquist, B. J.; Falco, N.; Henderson, A.; Karaoz, U.; Polussa, A.; Sorensen, P.; Steltzer, H.; Wainwright, H. M.; Wang, S.; Williams, K. H.; Wilmer, C.; Wu, Y.

    2017-12-01

    In mountainous systems, snow-melt is associated with a large pulse of nutrients that originates from under-snow microbial mineralization of organic matter and microbial biomass turnover. Vegetation phenology in these systems is regulated by environmental cues such as air temperature ranges and photoperiod, such that, under typical conditions, vegetation greening and nutrient uptake occur in sync with microbial biomass turnover and nutrient release, closing nutrient cycles and enhancing nutrient retention. However, early snow-melt has been observed with increasing frequency in the mountainous west and is hypothesized to disrupt coupled plant-microbial behavior, potentially resulting in a temporal discontinuity between microbial nutrient release and vegetation greening. As part of the Watershed Function Scientific Focus Area (SFA) at Berkeley Lab we are quantifying below-ground biogeochemistry and above-ground phenology and vegetation chemistry and their relationships to hydrologic events at a lower montane hillslope in the East River catchment, Crested Butte, CO. This presentation will focus on data-model integration to interpret connectivity between biogeochemical cycling of nitrogen and vegetation nitrogen demand. Initial model results suggest that early snow-melt will result in an earlier accumulation and leaching loss of nitrate from the upper soil depths but that vegetation productivity may not decline as traits such as greater rooting depth and resource allocation to stems are favored.

  11. Feedbacks of CO2 dependent dissolved organic carbon production on atmospheric CO2 in an ocean biogeochemical model

    Science.gov (United States)

    Bordelon-Katrynski, L. A.; Schneider, B.

    2012-07-01

    We use an ocean biogeochemical model to test whether a potential CO2 dependence of dissolved organic carbon (DOC) production may have an influence on marine carbon sequestration via particle aggregation and so may represent a potentially larger ocean sink for anthropogenic CO2. The hypothesis is based on mesocosm experiments that have shown enhanced carbon uptake by phytoplankton when more CO2 is available, and where the extra carbon was probably directly routed into DOC instead of the particulate phase. Sensitivity experiments are carried out where phytoplankton exudation of DOC is systematically increased with and without a parallel rise in atmospheric CO2. We find that under a fourfold increase of the DOC formation rate, there is a slight reduction of global particle export, which results in a shallower turnover of nutrients and carbon. As a consequence, a positive feedback loop develops, such that the ocean becomes a weak source of CO2 to the atmosphere. The effect is amplified under high CO2 conditions due to the decreased CO2 buffer capacity of the ocean, however, it is rather low compared to the total anthropogenic perturbation. The positive feedback is in contrast to a very similar study, where a slight stimulation of particle export was found. Therefore, we conclude that the sign of the feedback depends on the actual pathway the extra carbon is taking and on the overall background conditions of marine primary production and ocean circulation.

  12. The Effects of Chlorophyll Assimilation on Carbon Fluxes in a Global Biogeochemical Model. [Technical Report Series on Global Modeling and Data Assimilation

    Science.gov (United States)

    Koster, Randal D. (Editor); Rousseaux, Cecile Severine; Gregg, Watson W.

    2014-01-01

    In this paper, we investigated whether the assimilation of remotely-sensed chlorophyll data can improve the estimates of air-sea carbon dioxide fluxes (FCO2). Using a global, established biogeochemical model (NASA Ocean Biogeochemical Model, NOBM) for the period 2003-2010, we found that the global FCO2 values produced in the free-run and after assimilation were within -0.6 mol C m(sup -2) y(sup -1) of the observations. The effect of satellite chlorophyll assimilation was assessed in 12 major oceanographic regions. The region with the highest bias was the North Atlantic. Here the model underestimated the fluxes by 1.4 mol C m(sup -2) y(sup -1) whereas all the other regions were within 1 mol C m(sup -2) y(sup -1) of the data. The FCO2 values were not strongly impacted by the assimilation, and the uncertainty in FCO2 was not decreased, despite the decrease in the uncertainty in chlorophyll concentration. Chlorophyll concentrations were within approximately 25% of the database in 7 out of the 12 regions, and the assimilation improved the chlorophyll concentration in the regions with the highest bias by 10-20%. These results suggest that the assimilation of chlorophyll data does not considerably improve FCO2 estimates and that other components of the carbon cycle play a role that could further improve our FCO2 estimates.

  13. PnET-BGC: Modeling Biogeochemical Processes in a Northern Hardwood Forest Ecosystem

    Data.gov (United States)

    National Aeronautics and Space Administration — This archived model product contains the directions, executables, and procedures for running PnET-BGC to recreate the results of: Gbondo-Tugbawa, S.S., C.T. Driscoll...

  14. PnET-BGC: Modeling Biogeochemical Processes in a Northern Hardwood Forest Ecosystem

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This archived model product contains the directions, executables, and procedures for running PnET-BGC to recreate the results of: Gbondo-Tugbawa, S.S.,...

  15. Parameter sensitivity and identifiability for a biogeochemical model of hypoxia in the northern Gulf of Mexico

    Science.gov (United States)

    Local sensitivity analyses and identifiable parameter subsets were used to describe numerical constraints of a hypoxia model for bottom waters of the northern Gulf of Mexico. The sensitivity of state variables differed considerably with parameter changes, although most variables ...

  16. Nutrients, oxygen and biogeochemical processes in the Humboldt upwelling current system off Peru

    Directory of Open Access Journals (Sweden)

    Michelle I. Graco

    2013-04-01

    Full Text Available The upwelling system of the Humboldt Current, is considered among the most productive systems in the world, extending along the eastern South Pacific off Chile and Peru. In particular the coastal waters off Peru attracted considerable interest for being among the most fertile and productive the world, highlighting fisheries, such as anchovy, which represent one of the pillars of the economy of Peru.

  17. Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms

    Science.gov (United States)

    Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; Yang, Ziming; Graham, David E.; Gu, Baohua; Painter, Scott L.; Thornton, Peter E.

    2016-09-01

    Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe the observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.

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

    Science.gov (United States)

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

    2011-04-01

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

  19. Mechanistic site-based emulation of a global ocean biogeochemical model (MEDUSA 1.0 for parametric analysis and calibration: an application of the Marine Model Optimization Testbed (MarMOT 1.1

    Directory of Open Access Journals (Sweden)

    J. C. P. Hemmings

    2015-03-01

    Full Text Available Biogeochemical ocean circulation models used to investigate the role of plankton ecosystems in global change rely on adjustable parameters to capture the dominant biogeochemical dynamics of a complex biological system. In principle, optimal parameter values can be estimated by fitting models to observational data, including satellite ocean colour products such as chlorophyll that achieve good spatial and temporal coverage of the surface ocean. However, comprehensive parametric analyses require large ensemble experiments that are computationally infeasible with global 3-D simulations. Site-based simulations provide an efficient alternative but can only be used to make reliable inferences about global model performance if robust quantitative descriptions of their relationships with the corresponding 3-D simulations can be established. The feasibility of establishing such a relationship is investigated for an intermediate complexity biogeochemistry model (MEDUSA coupled with a widely used global ocean model (NEMO. A site-based mechanistic emulator is constructed for surface chlorophyll output from this target model as a function of model parameters. The emulator comprises an array of 1-D simulators and a statistical quantification of the uncertainty in their predictions. The unknown parameter-dependent biogeochemical environment, in terms of initial tracer concentrations and lateral flux information required by the simulators, is a significant source of uncertainty. It is approximated by a mean environment derived from a small ensemble of 3-D simulations representing variability of the target model behaviour over the parameter space of interest. The performance of two alternative uncertainty quantification schemes is examined: a direct method based on comparisons between simulator output and a sample of known target model "truths" and an indirect method that is only partially reliant on knowledge of the target model output. In general, chlorophyll

  20. Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model

    Directory of Open Access Journals (Sweden)

    S. Dutkiewicz

    2015-07-01

    This new model that captures bio-optical feedbacks will be important for improving our understanding of the role of light and optical constituents on ocean biogeochemistry, especially in a changing environment. Further, resolving surface upwelling irradiance will make it easier to connect to satellite-derived products in the future.

  1. Modeling biogeochemical processes and isotope fractionation of enhanced in situ biodenitrification in a fractured aquifer

    NARCIS (Netherlands)

    Rodríguez-Escales, Paula; Folch, Albert; Vidal-Gavilan, Georgina; van Breukelen, B.M.

    2016-01-01

    Enhanced in situ biodenitrification (EIB) is a feasible technology to clean nitrate-polluted groundwater and reach
    drinking water standards. Aimed at enabling a better monitoring and management of the technology at the field
    scale, we developed a two-dimensional reactive transport model

  2. Reactive transport modeling of biogeochemical dynamics in subterranean estuaries: Implications for submarine groundwater discharge of nutrients

    NARCIS (Netherlands)

    Spiteri, C.

    2007-01-01

    The quality of groundwater, in particular in coastal areas, is increasingly deteriorating due to the input of nutrients (NO3-, NH4+ and PO4) from septic systems and agricultural leaching. The discharge of groundwater to coastal waters, termed submarine groundwater discharge (SGD), is now recognized

  3. Improving Representation of the Nitrous Oxide Cycle in Ocean Biogeochemical Models

    Science.gov (United States)

    Suntharalingam, P.; Buitenhuis, E.; Le Quere, C.; O'Meara, S.; Nevison, C. D.; Bange, H. W.; Butler, J. H.; Elkins, J. W.

    2011-12-01

    The processes governing the marine nitrous oxide cycle, oceanic distribution, and flux to the atmosphere display distinct heterogeneity. The primary pathway for N2O production in the oxygenated open ocean is believed to be nitrification during the oxidation of ammonium to nitrate. However, mechanisms of marine N2O production and consumption display significant sensitivity to local oxygen concentration. Oxygen minimum zones such as the Arabian Sea and Eastern Equatorial Pacific are characterized by large gradients in sub-surface N2O, and high rates of N2O turnover that significantly exceed those observed in the open ocean. A range of processes is believed to govern N2O formation in these regions, including enhanced nitrification, and a coupling of nitrification and denitrification pathways. N2O is also depleted via denitrification in anoxic zones. This spatial heterogeneity presents challenges to the development of effective model parameterizations for ocean N2O; i.e., parameterizations that also display reliable predictive capability under conditions of changing ocean circulation, productivity, and oxygen distribution. In this analysis we use the ocean biogeochemistry model NEMO-PlankTOM to evaluate a range of recent empirical parameterizations for marine N2O formation. We contrast these parameterizations with a recently developed process-based model of oceanic N2O. Simulations are evaluated using a global database of oceanic N2O measurements. Evaluation metrics include surface concentrations, depth profiles, and regional averages. We also discuss the challenges of developing a successful representation of the marine N2O cycle, given specific limitations of the present generation of global ocean biogeochemistry models.

  4. Ecotoxicological, ecophysiological, and biogeochemical fundamentals of risk assessment

    International Nuclear Information System (INIS)

    Bashkin, V.N.; Kozlov, M.Ya.; Evstafjeva, E.V.

    1993-01-01

    Risk assessment (RA) influenced by different factors in radionuclide polluted regions is carried out by determining the biogeochemical structure of a region. Consequently, ecological-biogeochemical regionalization, ecotoxicological and ecophysiological monitoring of human population health are the important approach to RA. These criteria should conjugate with LCA of various industrial and agricultural products. Given fundamentals and approaches are needed for areas where traditional pollutants (heavy metals, pesticides, fertilizers, POPs etc) are enforced sharply by radioactive pollution. For RA of these complex pollutants, the methods of human adaptability to a polluted environment have been carried out. These techniques include biogeochemical, ecotoxicological, and ecophysiological analyses of risk factors as well as quantitative analysis of uncertainties using expert-modeling systems. Furthermore, the modern statistical methods are used for quantitative assessment of human adaptability to radioactive and nonradioactive pollutants. The results obtained in Chernobyl regions show the acceptability of these methods for risk assessment

  5. Mapping and modeling the biogeochemical cycling of turf grasses in the United States.

    Science.gov (United States)

    Milesi, Cristina; Running, Steven W; Elvidge, Christopher D; Dietz, John B; Tuttle, Benjamin T; Nemani, Ramakrishna R

    2005-09-01

    Turf grasses are ubiquitous in the urban landscape of the United States and are often associated with various types of environmental impacts, especially on water resources, yet there have been limited efforts to quantify their total surface and ecosystem functioning, such as their total impact on the continental water budget and potential net ecosystem exchange (NEE). In this study, relating turf grass area to an estimate of fractional impervious surface area, it was calculated that potentially 163,800 km2 (+/- 35,850 km2) of land are cultivated with turf grasses in the continental United States, an area three times larger than that of any irrigated crop. Using the Biome-BGC ecosystem process model, the growth of warm-season and cool-season turf grasses was modeled at a number of sites across the 48 conterminous states under different management scenarios, simulating potential carbon and water fluxes as if the entire turf surface was to be managed like a well-maintained lawn. The results indicate that well-watered and fertilized turf grasses act as a carbon sink. The potential NEE that could derive from the total surface potentially under turf (up to 17 Tg C/yr with the simulated scenarios) would require up to 695 to 900 liters of water per person per day, depending on the modeled water irrigation practices, suggesting that outdoor water conservation practices such as xeriscaping and irrigation with recycled waste-water may need to be extended as many municipalities continue to face increasing pressures on freshwater.

  6. High-resolution mineralogical characterization and biogeochemical modeling of uranium reaction pathways at the NABIR field-research center

    International Nuclear Information System (INIS)

    Chen Zhu

    2006-01-01

    High-Resolution Mineralogical Characterization and Biogeochemical Modeling of Uranium Reduction Pathways at the Oak Ridge Field-Research Center (FRC) Chen Zhu, Indiana University, David R. Veblen, Johns Hopkins University We have successfully completed a proof-of-concept, one-year grant on a three-year proposal from the former NABIR program, and here we seek additional two-year funding to complete and publish the research. Using a state-of-the-art 300-kV, atomic resolution, Field Emission Gun Transmission Electron Microscope (TEM), we have successfully identified three categories of mineral hosts for uranium in contaminated soils: (1) iron oxides; (2) mixed manganese-iron oxides; and (3) uranium phosphates. Method development using parallel electron energy loss spectroscopy (EELS) associated with the TEM shows great promise for characterizing the valence states of immobilized U during bioremediation. We have also collected 27 groundwater samples from two push-pull field biostimulation tests, which form two time series from zero to approximately 600 hours. The temporal evolution in major cations, anions, trace elements, and the stable isotopes 34S, 18O in sulfate, 15N in nitrate, and 13C in dissolved inorganic carbon (DIC) clearly show that biostimulation resulted in reduction of nitrate, Mn(IV), Fe(III), U(VI), sulfate, and Tc(VII), and these reduction reactions were intimately coupled with a complex network of inorganic reactions evident from alkalinity, pH, Na, K, Mg, and Ca concentrations. From these temporal trends, apparent zero order rates were regressed. However, our extensive suite of chemical and isotopic data sets, perhaps the first and only comprehensive data set available at the FRC, show that the derived rates from these field biostimulation experiments are composite and lump-sum rates. There were several reactions that were occurring at the same time but were masked by these pseudo-zero order rates. A reaction-path model comprising a total of nine

  7. Modelling biogeochemical processes in sediments from the north-western Adriatic Sea: response to enhanced particulate organic carbon fluxes

    Science.gov (United States)

    Brigolin, Daniele; Rabouille, Christophe; Bombled, Bruno; Colla, Silvia; Vizzini, Salvatrice; Pastres, Roberto; Pranovi, Fabio

    2018-03-01

    This work presents the result of a study carried out in the north-western Adriatic Sea, by combining two different types of biogeochemical models with field sampling efforts. A longline mussel farm was taken as a local source of perturbation to the natural particulate organic carbon (POC) downward flux. This flux was first quantified by means of a pelagic model of POC deposition coupled to sediment trap data, and its effects on sediment bioirrigation capacity and organic matter (OM) degradation pathways were investigated constraining an early diagenesis model by using original data collected in sediment porewater. The measurements were performed at stations located inside and outside the area affected by mussel farm deposition. Model-predicted POC fluxes showed marked spatial and temporal variability, which was mostly associated with the dynamics of the farming cycle. Sediment trap data at the two sampled stations (inside and outside of the mussel farm) showed average POC background flux of 20.0-24.2 mmol C m-2 d-1. The difference of organic carbon (OC) fluxes between the two stations was in agreement with model results, ranging between 3.3 and 14.2 mmol C m-2 d-1, and was primarily associated with mussel physiological conditions. Although restricted, these changes in POC fluxes induced visible effects on sediment biogeochemistry. Observed oxygen microprofiles presented a 50 % decrease in oxygen penetration depth (from 2.3 to 1.4 mm), accompanied by an increase in the O2 influx at the station below the mussel farm (19-31 versus 10-12 mmol O2 m-2 d-1) characterised by higher POC flux. Dissolved inorganic carbon (DIC) and NH4+ concentrations showed similar behaviour, with a more evident effect of bioirrigation underneath the farm. This was confirmed through constraining the early diagenesis model, of which calibration leads to an estimation of enhanced and shallower bioirrigation underneath the farm: bioirrigation rates of 40 yr-1 and irrigation depth of 15 cm were

  8. Estimates of fire emissions from an active deforestation region in the southern Amazon based on satellite data and biogeochemical modelling

    Science.gov (United States)

    van der Werf, G. R.; Morton, D. C.; Defries, R. S.; Giglio, L.; Randerson, J. T.; Collatz, G. J.; Kasibhatla, P. S.

    2009-02-01

    Tropical deforestation contributes to the build-up of atmospheric carbon dioxide in the atmosphere. Within the deforestation process, fire is frequently used to eliminate biomass in preparation for agricultural use. Quantifying these deforestation-induced fire emissions represents a challenge, and current estimates are only available at coarse spatial resolution with large uncertainty. Here we developed a biogeochemical model using remote sensing observations of plant productivity, fire activity, and deforestation rates to estimate emissions for the Brazilian state of Mato Grosso during 2001-2005. Our model of DEforestation CArbon Fluxes (DECAF) runs at 250-m spatial resolution with a monthly time step to capture spatial and temporal heterogeneity in fire dynamics in our study area within the ''arc of deforestation'', the southern and eastern fringe of the Amazon tropical forest where agricultural expansion is most concentrated. Fire emissions estimates from our modelling framework were on average 90 Tg C year-1, mostly stemming from fires associated with deforestation (74%) with smaller contributions from fires from conversions of Cerrado or pastures to cropland (19%) and pasture fires (7%). In terms of carbon dynamics, about 80% of the aboveground living biomass and litter was combusted when forests were converted to pasture, and 89% when converted to cropland because of the highly mechanized nature of the deforestation process in Mato Grosso. The trajectory of land use change from forest to other land uses often takes more than one year, and part of the biomass that was not burned in the dry season following deforestation burned in consecutive years. This led to a partial decoupling of annual deforestation rates and fire emissions, and lowered interannual variability in fire emissions. Interannual variability in the region was somewhat dampened as well because annual emissions from fires following deforestation and from maintenance fires did not covary, although

  9. Estimates of fire emissions from an active deforestation region in the southern Amazon based on satellite data and biogeochemical modelling

    Directory of Open Access Journals (Sweden)

    G. R. van der Werf

    2009-02-01

    Full Text Available Tropical deforestation contributes to the build-up of atmospheric carbon dioxide in the atmosphere. Within the deforestation process, fire is frequently used to eliminate biomass in preparation for agricultural use. Quantifying these deforestation-induced fire emissions represents a challenge, and current estimates are only available at coarse spatial resolution with large uncertainty. Here we developed a biogeochemical model using remote sensing observations of plant productivity, fire activity, and deforestation rates to estimate emissions for the Brazilian state of Mato Grosso during 2001–2005. Our model of DEforestation CArbon Fluxes (DECAF runs at 250-m spatial resolution with a monthly time step to capture spatial and temporal heterogeneity in fire dynamics in our study area within the ''arc of deforestation'', the southern and eastern fringe of the Amazon tropical forest where agricultural expansion is most concentrated. Fire emissions estimates from our modelling framework were on average 90 Tg C year−1, mostly stemming from fires associated with deforestation (74% with smaller contributions from fires from conversions of Cerrado or pastures to cropland (19% and pasture fires (7%. In terms of carbon dynamics, about 80% of the aboveground living biomass and litter was combusted when forests were converted to pasture, and 89% when converted to cropland because of the highly mechanized nature of the deforestation process in Mato Grosso. The trajectory of land use change from forest to other land uses often takes more than one year, and part of the biomass that was not burned in the dry season following deforestation burned in consecutive years. This led to a partial decoupling of annual deforestation rates and fire emissions, and lowered interannual variability in fire emissions. Interannual variability in the region was somewhat dampened as well because annual emissions from fires following deforestation

  10. [Utilization of a biogeochemical model in dendroecology. Application to the Cembro pine].

    Science.gov (United States)

    Rathgeber, C; Guiot, J; Edouard, J L

    2000-05-01

    Dendroecology, which is based on annual growth variable measurements, is in possession of data particularly well adapted to analyse the impact of global change on vegetation production. But the classical statistical methods of quantification of tree ring-climate relationship cannot take into account the effect of CO2 increase. Therefore, a biogeochemistry model (BIOME3) has been adapted to these data and then validated on Pinus cembra. The results indicate that the production is reduced by 14% if only the climatic changes are taken into account. If both climatic changes and CO2 increase are taken into account the production is increased by 62%. The direct fertilisation effect of CO2 increase will have more influence on the productivity than the indirect climatic effect.

  11. Importance of biogeochemical processes in modeling stream chemistry in two watersheds in the Sierra Nevada, California

    Science.gov (United States)

    Meixner, Thomas; Brown, Aaron; Bales, Roger C.

    1998-11-01

    Two small (0.22 and 0.48 ha) alpine watersheds in the Sierra Nevada of California were studied during the 1992 and 1993 snowmelt seasons to evaluate the importance of soil properties and processes on chemical concentrations in the discharges from each watershed. Watershed 1 was surveyed as having 26% soil cover, whereas watershed 2 was 10% soil covered. Watershed 2 had greater H+ and nitrogen consumption than watershed 1 but similar cation and sulfate concentrations despite having one fourth the surveyed soil volume per unit area as watershed 1. Daily stream concentrations simulated with the Alpine Hydrochemical Model (AHM) matched the data well, after a systematic model calibration with a subset of the data. We found that the structure of the AHM and the hydrologic parameters developed for the nearby 1.2 km2 Emerald Lake watershed could be applied to these watersheds with only small adjustments; chemical parameters required considerably more adjustment, reflecting a greater degree of chemical versus physical heterogeneity at this scale. Calibration for watershed 2 gave a higher percent base saturation (19 versus 4%) and lower streamversus 10-2.6 atm) than for watershed 1 and three times the soil reactivity (expected) of a field survey. Areas mapped as exposed bedrock in the catchments apparently contributed cations and alkalinity to stream water to a greater extent than did neighboring areas of soil. Areas of exposed bedrock were a larger nitrogen sink than the adjoining areas of soil. The pH and acid-neutralizing capacity of surface runoff in both catchments were less sensitive to changes in atmospheric deposition than at the nearby Emerald Lake watershed. This decreased sensitivity was due to (1) a less pronounced ionic pulse, (2) less retention of sulfate in the soil, and (3) greater nitrate retention.

  12. Preferential flow systems amended with biogeochemical components: imaging of a two-dimensional study

    Science.gov (United States)

    Pales, Ashley R.; Li, Biting; Clifford, Heather M.; Kupis, Shyla; Edayilam, Nimisha; Montgomery, Dawn; Liang, Wei-zhen; Dogan, Mine; Tharayil, Nishanth; Martinez, Nicole; Moysey, Stephen; Powell, Brian; Darnault, Christophe J. G.

    2018-04-01

    The vadose zone is a highly interactive heterogeneous system through which water enters the subsurface system by infiltration. This paper details the effects of simulated plant exudate and soil component solutions upon unstable flow patterns in a porous medium (ASTM silica sand; US Silica, Ottawa, IL, USA) through the use of two-dimensional tank light transmission method (LTM). The contact angle (θ) and surface tension (γ) of two simulated plant exudate solutions (i.e., oxalate and citrate) and two soil component solutions (i.e., tannic acid and Suwannee River natural organic matter, SRNOM) were analyzed to determine the liquid-gas and liquid-solid interface characteristics of each. To determine if the unstable flow formations were dependent on the type and concentration of the simulated plant exudates and soil components, the analysis of the effects of the simulated plant exudate and soil component solutions were compared to a control solution (Hoagland nutrient solution with 0.01 M NaCl). Fingering flow patterns, vertical and horizontal water saturation profiles, water saturation at the fingertips, finger dimensions and velocity, and number of fingers were obtained using the light transmission method. Significant differences in the interface properties indicated a decrease between the control and the plant exudate and soil component solutions tested; specifically, the control (θ = 64.5° and γ = 75.75 mN m-1) samples exhibited a higher contact angle and surface tension than the low concentration of citrate (θ = 52.6° and γ = 70.8 mN m-1). Wetting front instability and fingering flow phenomena were reported in all infiltration experiments. The results showed that the plant exudates and soil components influenced the soil infiltration as differences in finger geometries, velocities, and water saturation profiles were detected when compared to the control. Among the tested solutions and concentrations of soil components, the largest finger width (10.19 cm

  13. A critical review of selenium biogeochemical behavior in soil-plant system with an inference to human health.

    Science.gov (United States)

    Natasha; Shahid, Muhammad; Niazi, Nabeel Khan; Khalid, Sana; Murtaza, Behzad; Bibi, Irshad; Rashid, Muhammad Imtiaz

    2018-03-01

    Selenium (Se) is an essential trace element for humans and animals, although controversial for different plant species. There exists a narrow line between essential, beneficial and toxic levels of Se to living organisms which greatly varies with Se speciation, as well as the type of living organisms. Therefore, it is crucial to monitor its solid- and solution-phase speciation, exposure levels and pathways to living organisms. Consumption of Se-laced food (cereals, vegetables, legumes and pulses) is the prime source of Se exposure to humans. Thus, it is imperative to assess the biogeochemical behavior of Se in soil-plant system with respect to applied levels and speciation, which ultimately affect Se status in humans. Based on available relevant literature, this review traces a plausible link among (i) Se levels, sources, speciation, bioavailability, and effect of soil chemical properties on selenium bioavailability/speciation in soil; (ii) role of different protein transporters in soil-root-shoot transfer of Se; and (iii) speciation, metabolism, phytotoxicity and detoxification of Se inside plants. The toxic and beneficial effects of Se to plants have been discussed with respect to speciation and toxic/deficient concentration of Se. We highlight the significance of various enzymatic (catalase, peroxidase, superoxide dismutase, ascorbate peroxidase, glutathione peroxidase) and non-enzymatic (phytochelatins and glutathione) antioxidants which help combat Se-induced overproduction of reactive oxygen species (ROS). The review also delineates Se accumulation in edible plant parts from soils containing low or high Se levels; elucidates associated health disorders or risks due to the consumption of Se-deficient or Se-rich foods; discusses the potential role of Se in different human disorders/diseases. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Freshwater and its role in the Arctic Marine System: Sources, disposition, storage, export, and physical and biogeochemical consequences in the Arctic and global oceans

    Science.gov (United States)

    Carmack, E. C.; Yamamoto-Kawai, M.; Haine, T. W. N.; Bacon, S.; Bluhm, B. A.; Lique, C.; Melling, H.; Polyakov, I. V.; Straneo, F.; Timmermans, M.-L.; Williams, W. J.

    2016-03-01

    The Arctic Ocean is a fundamental node in the global hydrological cycle and the ocean's thermohaline circulation. We here assess the system's key functions and processes: (1) the delivery of fresh and low-salinity waters to the Arctic Ocean by river inflow, net precipitation, distillation during the freeze/thaw cycle, and Pacific Ocean inflows; (2) the disposition (e.g., sources, pathways, and storage) of freshwater components within the Arctic Ocean; and (3) the release and export of freshwater components into the bordering convective domains of the North Atlantic. We then examine physical, chemical, or biological processes which are influenced or constrained by the local quantities and geochemical qualities of freshwater; these include stratification and vertical mixing, ocean heat flux, nutrient supply, primary production, ocean acidification, and biogeochemical cycling. Internal to the Arctic the joint effects of sea ice decline and hydrological cycle intensification have strengthened coupling between the ocean and the atmosphere (e.g., wind and ice drift stresses, solar radiation, and heat and moisture exchange), the bordering drainage basins (e.g., river discharge, sediment transport, and erosion), and terrestrial ecosystems (e.g., Arctic greening, dissolved and particulate carbon loading, and altered phenology of biotic components). External to the Arctic freshwater export acts as both a constraint to and a necessary ingredient for deep convection in the bordering subarctic gyres and thus affects the global thermohaline circulation. Geochemical fingerprints attained within the Arctic Ocean are likewise exported into the neighboring subarctic systems and beyond. Finally, we discuss observed and modeled functions and changes in this system on seasonal, annual, and decadal time scales and discuss mechanisms that link the marine system to atmospheric, terrestrial, and cryospheric systems.

  15. Division of Biogeochemical Ecology FY-1985 highlights

    International Nuclear Information System (INIS)

    Anon.

    1985-01-01

    The primary goal of the Division is to understand the various biogeochemical processes, both in aquatic and terrestrial systems, that occur in the southeastern United States, including the Savannah River Plant. Both applied and basic approaches are being used to enhance understanding of the biogeochemical cycles of certain elements and trace contaminants, either in inorganic or organic states, and in stable or radioactive forms. Specific examples of studies conducted during the past year include: (1) ecosystem modeling and implementation of a computer model to predict the fate, behavior and transport of heavy metals and radionuclides in SRP streams, (2) laboratory and greenhouse studies on the environmental chemistry of an organo-borate in the soil-plant system, (3) research on the behavior and fate of actinide elements and other long-lived radioisotopes in terrestrial and aquatic ecosystems, and (4) responses of pine plantations to organic waste fertilization. Major findings of these studies are summarized. The chemical speciation-transport model MEXAMS (Metal Exposure Analysis Modeling System) was implemented to provide predictive capabilities for the transport of heavy metals and radionuclides in SRP aquatic systems. The basic components of the model are the geochemical model MINTEQ, and an aquatic exposure assessment model, EXAMS. The interfacing of these two models provides information on the complex chemistry and behavior of metals, as well as the transport processes influencing their migration and ultimate fate in aquatic systems. Test simulations for Cd, Cu, and Ni speciation in various SRP streams were conducted. The results indicated that the MEXAMS model will be a useful tool in predicting the transport and fate of metals in SRP streams

  16. Modelling biogeochemical processes in sediments from the north-western Adriatic Sea: response to enhanced particulate organic carbon fluxes

    Directory of Open Access Journals (Sweden)

    D. Brigolin

    2018-03-01

    Full Text Available This work presents the result of a study carried out in the north-western Adriatic Sea, by combining two different types of biogeochemical models with field sampling efforts. A longline mussel farm was taken as a local source of perturbation to the natural particulate organic carbon (POC downward flux. This flux was first quantified by means of a pelagic model of POC deposition coupled to sediment trap data, and its effects on sediment bioirrigation capacity and organic matter (OM degradation pathways were investigated constraining an early diagenesis model by using original data collected in sediment porewater. The measurements were performed at stations located inside and outside the area affected by mussel farm deposition. Model-predicted POC fluxes showed marked spatial and temporal variability, which was mostly associated with the dynamics of the farming cycle. Sediment trap data at the two sampled stations (inside and outside of the mussel farm showed average POC background flux of 20.0–24.2 mmol C m−2 d−1. The difference of organic carbon (OC fluxes between the two stations was in agreement with model results, ranging between 3.3 and 14.2 mmol C m−2 d−1, and was primarily associated with mussel physiological conditions. Although restricted, these changes in POC fluxes induced visible effects on sediment biogeochemistry. Observed oxygen microprofiles presented a 50 % decrease in oxygen penetration depth (from 2.3 to 1.4 mm, accompanied by an increase in the O2 influx at the station below the mussel farm (19–31 versus 10–12 mmol O2 m−2 d−1 characterised by higher POC flux. Dissolved inorganic carbon (DIC and NH4+ concentrations showed similar behaviour, with a more evident effect of bioirrigation underneath the farm. This was confirmed through constraining the early diagenesis model, of which calibration leads to an estimation of enhanced and shallower bioirrigation underneath the farm

  17. Constraining a complex biogeochemical model for CO2 and N2O emission simulations from various land uses by model-data fusion

    Science.gov (United States)

    Houska, Tobias; Kraus, David; Kiese, Ralf; Breuer, Lutz

    2017-07-01

    This study presents the results of a combined measurement and modelling strategy to analyse N2O and CO2 emissions from adjacent arable land, forest and grassland sites in Hesse, Germany. The measured emissions reveal seasonal patterns and management effects, including fertilizer application, tillage, harvest and grazing. The measured annual N2O fluxes are 4.5, 0.4 and 0.1 kg N ha-1 a-1, and the CO2 fluxes are 20.0, 12.2 and 3.0 t C ha-1 a-1 for the arable land, grassland and forest sites, respectively. An innovative model-data fusion concept based on a multicriteria evaluation (soil moisture at different depths, yield, CO2 and N2O emissions) is used to rigorously test the style="" class="text">LandscapeDNDC biogeochemical model. The model is run in a Latin-hypercube-based uncertainty analysis framework to constrain model parameter uncertainty and derive behavioural model runs. The results indicate that the model is generally capable of predicting trace gas emissions, as evaluated with RMSE as the objective function. The model shows a reasonable performance in simulating the ecosystem C and N balances. The model-data fusion concept helps to detect remaining model errors, such as missing (e.g. freeze-thaw cycling) or incomplete model processes (e.g. respiration rates after harvest). This concept further elucidates the identification of missing model input sources (e.g. the uptake of N through shallow groundwater on grassland during the vegetation period) and uncertainty in the measured validation data (e.g. forest N2O emissions in winter months). Guidance is provided to improve the model structure and field measurements to further advance landscape-scale model predictions.

  18. Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minjing [School; Qian, Wei-jun [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Shi, Liang [School; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; School

    2017-09-28

    The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates

  19. Iron-light colimitation in a global ocean biogeochemical model and the sensitivity of oceanic CO2 uptake to dust deposition

    Science.gov (United States)

    Nickelsen, L.; Oschlies, A.

    2012-12-01

    The iron hypothesis of glacial-interglacial cycles states that glacial increases in the deposition of dust enhanced the concentrations of the micronutrient iron in the ocean where it triggered phytoplankton growth and thus CO2 uptake. Indeed, iron fertilization experiments find that phytoplankton needs iron in particular for nitrate uptake, light harvesting, synthesis of chlorophyll and in the electron transport chain of photosynthesis. Previous global biogeochemical models used to extrapolate results from local culture and field experiments have suggested that the sensitivity of ocean biogeochemistry to changes in dust deposition is too low to account for the observed glacial-interglacial changes of atmospheric CO2 concentrations. Here we show that this sensitivity is increased significantly when iron-light colimitation, i.e. the impact of iron on light harvesting capabilities and chlorophyll synthesis, is explicitly considered in a global biogeochemical ocean model. Iron-light colimitation increases the shift of export production to higher latitudes at high dust deposition and amplifies iron limitation at low dust deposition. Our results suggest that iron fertilization by increased dust deposition may explain a substantially larger portion of the observed past CO2 variability than thought previously. Our results emphasize the role of iron as a key limiting nutrient for phytoplankton in the ocean, with a high potential for changes in oceanic iron supply affecting the global carbon cycle and climate.

  20. Towards an assessment of riverine dissolved organic carbon in surface waters of the western Arctic Ocean based on remote sensing and biogeochemical modeling

    Science.gov (United States)

    Le Fouest, Vincent; Matsuoka, Atsushi; Manizza, Manfredi; Shernetsky, Mona; Tremblay, Bruno; Babin, Marcel

    2018-03-01

    Future climate warming of the Arctic could potentially enhance the load of terrigenous dissolved organic carbon (tDOC) of Arctic rivers due to increased carbon mobilization within watersheds. A greater flux of tDOC might impact the biogeochemical processes of the coastal Arctic Ocean (AO) and ultimately its capacity to absorb atmospheric CO2. In this study, we show that sea-surface tDOC concentrations simulated by a physical-biogeochemical coupled model in the Canadian Beaufort Sea for 2003-2011 compare favorably with estimates retrieved by satellite imagery. Our results suggest that, over spring-summer, tDOC of riverine origin contributes to 35 % of primary production and that an equivalent of ˜ 10 % of tDOC is exported westwards with the potential of fueling the biological production of the eastern Alaskan nearshore waters. The combination of model and satellite data provides promising results to extend this work to the entire AO so as to quantify, in conjunction with in situ data, the expected changes in tDOC fluxes and their potential impact on the AO biogeochemistry at basin scale.

  1. MEDUSA-2.0: an intermediate complexity biogeochemical model of the marine carbon cycle for climate change and ocean acidification studies

    Directory of Open Access Journals (Sweden)

    A. Yool

    2013-10-01

    Full Text Available MEDUSA-1.0 (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification was developed as an "intermediate complexity" plankton ecosystem model to study the biogeochemical response, and especially that of the so-called "biological pump", to anthropogenically driven change in the World Ocean (Yool et al., 2011. The base currency in this model was nitrogen from which fluxes of organic carbon, including export to the deep ocean, were calculated by invoking fixed C:N ratios in phytoplankton, zooplankton and detritus. However, due to anthropogenic activity, the atmospheric concentration of carbon dioxide (CO2 has significantly increased above its natural, inter-glacial background. As such, simulating and predicting the carbon cycle in the ocean in its entirety, including ventilation of CO2 with the atmosphere and the resulting impact of ocean acidification on marine ecosystems, requires that both organic and inorganic carbon be afforded a more complete representation in the model specification. Here, we introduce MEDUSA-2.0, an expanded successor model which includes additional state variables for dissolved inorganic carbon, alkalinity, dissolved oxygen and detritus carbon (permitting variable C:N in exported organic matter, as well as a simple benthic formulation and extended parameterizations of phytoplankton growth, calcification and detritus remineralisation. A full description of MEDUSA-2.0, including its additional functionality, is provided and a multi-decadal spin-up simulation (1860–2005 is performed. The biogeochemical performance of the model is evaluated using a diverse range of observational data, and MEDUSA-2.0 is assessed relative to comparable models using output from the Coupled Model Intercomparison Project (CMIP5.

  2. ENSO-Modulation of Plankton Production in the Northern Gulf of Mexico: A High-Resolution Ocean-Biogeochemical Model Study

    Science.gov (United States)

    Gomez, F. A.; Lee, S. K.; Liu, Y.; Hernandez, F., Jr.; Lamkin, J. T.

    2017-12-01

    Previous studies have suggested that El Nino-Southern Oscillation (ENSO) plays a role in modulating phytoplankton biomass and the reproductive success of marine species in the Gulf of Mexico (GoM). However, characterizations of ENSO-related ecosystem responses such as plankton production have not been fully addressed for the region. Here we examine ENSO impacts on biogeochemical processes within coastal and open ocean domains in the GoM, using a three dimensional high-resolution ocean-biogeochemical model, forced with historical surface fluxes and river run-off for 1979 - 2014. Enhanced precipitation across southern US during El Nino winter increases freshwater discharge and nutrient load into the GoM mainly via the Mississippi-Atchafalaya River. Those anomalies lead to reduced salinity and greater concentration of dissolved inorganic nitrogen and plankton production in the northern shelf especially during winter. In addition, the frequency of northerly wind anomalies that cool the upper ocean increases during El Nino. The negative surface heat flux anomalies further decrease vertical thermal stratification and thus increase phytoplankton production during early spring in the northern deep GoM.

  3. Disturbance decouples biogeochemical cycles across forests of the southeastern US

    Science.gov (United States)

    Ashley D. Keiser; Jennifer D. Knoepp; Mark A. Bradford

    2016-01-01

    Biogeochemical cycles are inherently linked through the stoichiometric demands of the organisms that cycle the elements. Landscape disturbance can alter element availability and thus the rates of biogeochemical cycling. Nitrification is a fundamental biogeochemical process positively related to plant productivity and nitrogen loss from soils to aquatic systems, and the...

  4. Impact of urban effluents on summer hypoxia in the highly turbid Gironde Estuary, applying a 3D model coupling hydrodynamics, sediment transport and biogeochemical processes

    Science.gov (United States)

    Lajaunie-Salla, Katixa; Wild-Allen, Karen; Sottolichio, Aldo; Thouvenin, Bénédicte; Litrico, Xavier; Abril, Gwenaël

    2017-10-01

    Estuaries are increasingly degraded due to coastal urban development and are prone to hypoxia problems. The macro-tidal Gironde Estuary is characterized by a highly concentrated turbidity maximum zone (TMZ). Field observations show that hypoxia occurs in summer in the TMZ at low river flow and a few days after the spring tide peak. In situ data highlight lower dissolved oxygen (DO) concentrations around the city of Bordeaux, located in the upper estuary. Interactions between multiple factors limit the understanding of the processes controlling the dynamics of hypoxia. A 3D biogeochemical model was developed, coupled with hydrodynamics and a sediment transport model, to assess the contribution of the TMZ and the impact of urban effluents through wastewater treatment plants (WWTPs) and sewage overflows (SOs) on hypoxia. Our model describes the transport of solutes and suspended material and the biogeochemical mechanisms impacting oxygen: primary production, degradation of all organic matter (i.e. including phytoplankton respiration, degradation of river and urban watershed matter), nitrification and gas exchange. The composition and the degradation rates of each variable were characterized by in situ measurements and experimental data from the study area. The DO model was validated against observations in Bordeaux City. The simulated DO concentrations show good agreement with field observations and satisfactorily reproduce the seasonal and neap-spring time scale variations around the city of Bordeaux. Simulations show a spatial and temporal correlation between the formation of summer hypoxia and the location of the TMZ, with minimum DO centered in the vicinity of Bordeaux. To understand the contribution of the urban watershed forcing, different simulations with the presence or absence of urban effluents were compared. Our results show that in summer, a reduction of POC from SO would increase the DO minimum in the vicinity of Bordeaux by 3% of saturation. Omitting

  5. Biogeochemical speciation of Fe in ocean water

    NARCIS (Netherlands)

    Hiemstra, T.; Riemsdijk, van W.H.

    2006-01-01

    The biogeochemical speciation of Fe in seawater has been evaluated using the consistent Non-Ideal Competitive Adsorption model (NICA¿Donnan model). Two types of data sets were used, i.e. Fe-hydroxide solubility data and competitive ligand equilibration/cathodic stripping voltammetry (CLE/CSV) Fe

  6. Subsurface Uranium Fate and Transport: Integrated Experiments and Modeling of Coupled Biogeochemical Mechanisms of Nanocrystalline Uraninite Oxidation by Fe(III)-(hydr)oxides - Project Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Peyton, Brent M. [Montana State Univ., Bozeman, MT (United States); Timothy, Ginn R. [Univ. of California, Davis, CA (United States); Sani, Rajesh K. [South Dakota School of Mines and Technology, Rapid City, SD (United States)

    2013-08-14

    citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO2 reoxidation as Fe(III) oxidizes HS– preferentially over UO2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network.

  7. Using a Hydrodynamic and Biogeochemical Model to Investigate the Effects of Nutrient Loading from a Wastewater Treatment Plant into Lake Michigan

    Science.gov (United States)

    Khazaei, B.; Bravo, H.; Bootsma, H.

    2017-12-01

    There is clear evidence that excessive nutrient, in particular phosphorus (P), loading into Lake Michigan has produced significant problems, such as algal blooms, hypoxia, and reduced water quality. Addressing those problems requires understanding the transport and fate of P in the lake. The dominance of mixing and dispersion processes on the P transport has been demonstrated, yet recent research has shown the remarkable influence of dreissenid mussels and Cladophora on water clarity and the P budget. Since mussels and Cladophora tend to concentrate near the coastlines, nearshore-offshore P exchange is of a big importance. In this research, a computer model was developed to simulate the P cycle by incorporating the biogeochemical processes relevant to the transport of P into a 3D high-resolution hydrodynamic model. The near-bottom biogeochemical model consists of three linked modules: Cladophora, mussel, and sediment storage modules. The model was applied to the Milwaukee Metropolitan Sewerage District South Shore Wastewater Treatment Plant, between June and October of 2013 and 2015, as a case study. The plant outfall introduces a point source of P into the study domain—the nearshore zone of Lake Michigan adjacent to Milwaukee County. The model was validated against field observations of water temperature, dissolved phosphorus (DP), particulate phosphorus (PP), Cladophora biomass, and P content. The model simulations showed reasonably good agreement with field measurements. Model results showed a) different temporal patterns in 2013 and 2015, b) a larger range of fluctuations in DP than that in PP, and c) that the effects of mussels and Cladophora could explain the differences in patterns and ranges. PP concentrations showed more frequent spikes of concentration in 2013 due to resuspension events during that year because of stronger winds. The model is being applied as a management tool to test scenarios of nutrient loading to determine effluent P limits for the

  8. Constraining a complex biogeochemical model for CO2 and N2O emission simulations from various land uses by model–data fusion

    Directory of Open Access Journals (Sweden)

    T. Houska

    2017-07-01

    Full Text Available This study presents the results of a combined measurement and modelling strategy to analyse N2O and CO2 emissions from adjacent arable land, forest and grassland sites in Hesse, Germany. The measured emissions reveal seasonal patterns and management effects, including fertilizer application, tillage, harvest and grazing. The measured annual N2O fluxes are 4.5, 0.4 and 0.1 kg N ha−1 a−1, and the CO2 fluxes are 20.0, 12.2 and 3.0 t C ha−1 a−1 for the arable land, grassland and forest sites, respectively. An innovative model–data fusion concept based on a multicriteria evaluation (soil moisture at different depths, yield, CO2 and N2O emissions is used to rigorously test the LandscapeDNDC biogeochemical model. The model is run in a Latin-hypercube-based uncertainty analysis framework to constrain model parameter uncertainty and derive behavioural model runs. The results indicate that the model is generally capable of predicting trace gas emissions, as evaluated with RMSE as the objective function. The model shows a reasonable performance in simulating the ecosystem C and N balances. The model–data fusion concept helps to detect remaining model errors, such as missing (e.g. freeze–thaw cycling or incomplete model processes (e.g. respiration rates after harvest. This concept further elucidates the identification of missing model input sources (e.g. the uptake of N through shallow groundwater on grassland during the vegetation period and uncertainty in the measured validation data (e.g. forest N2O emissions in winter months. Guidance is provided to improve the model structure and field measurements to further advance landscape-scale model predictions.

  9. Biogeochemical aspects of aquifer thermal energy storage

    NARCIS (Netherlands)

    Brons, H.J.

    1992-01-01

    During the process of aquifer thermal energy storage the in situ temperature of the groundwater- sediment system may fluctuate significantly. As a result the groundwater characteristics can be considerably affected by a variety of chemical, biogeochemical and microbiological

  10. Use of remotely-sensed observations and a data assimilating marine biogeochemical model to determine water quality on the Great Barrier Reef.

    Science.gov (United States)

    Baird, Mark; Jones, Emlyn; Wozniak, Monika; Mongin, Mathieu; Skerratt, Jennifer; Margvelashvilli, Nugzar; Wild-Allen, Karen; Robson, Barbara; Rizwi, Farhan; Schroeder, Thomas; Steven, Andy

    2017-04-01

    The health of the Great Barrier Reef is presently assessed using the water column concentration of chlorophyll and suspended solids, and measured light penetration. Quantifying these water column properties over 2,000 km of often cloud-covered, sparsely sampled, and highly variable coastal waters is problematic. To provide the best estimate of water quality, we assimilating satellite remote-sensing reflectance (the ratio of water-leaving radiance versus water-entering irradiance) using an in-water optical model to produce an equivalent simulated remote-sensing reflectance, and calculate the mis-match between the observed and simulated quantities to constrain a complex biogeochemical model (eReefs) with a Deterministic Ensemble Kalman Filter (DEnKF). We compare the water quality properties of the data assimilating model with in-situ observations, as well as with withheld remote-sensed observations. As a final step, we consider whether withheld observations can be combined with the data-assimilation generated chlorophyll fields to provide the best estimate of the chlorophyll concentration given all the available information.

  11. A hybrid ensemble-OI Kalman filter for efficient data assimilation into a 3-D biogeochemical model of the Mediterranean

    KAUST Repository

    Tsiaras, Kostas P.

    2017-04-20

    A hybrid ensemble data assimilation scheme (HYBRID), combining a flow-dependent with a static background covariance, was developed and implemented for assimilating satellite (SeaWiFS) Chl-a data into a marine ecosystem model of the Mediterranean. The performance of HYBRID was assessed against a model free-run, the ensemble-based singular evolutive interpolated Kalman (SEIK) and its variant with static covariance (SFEK), with regard to the assimilated variable (Chl-a) and non-assimilated variables (dissolved inorganic nutrients). HYBRID was found more efficient than both SEIK and SFEK, reducing the Chl-a error by more than 40% in most areas, as compared to the free-run. Data assimilation had a positive overall impact on nutrients, except for a deterioration of nitrates simulation by SEIK in the most productive area (Adriatic). This was related to SEIK pronounced update in this area and the phytoplankton limitation on phosphate that lead to a built up of excess nitrates. SEIK was found more efficient in productive and variable areas, where its ensemble exhibited important spread. SFEK had an effect mostly on Chl-a, performing better than SEIK in less dynamic areas, adequately described by the dominant modes of its static covariance. HYBRID performed well in all areas, due to its “blended” covariance. Its flow-dependent component appears to track changes in the system dynamics, while its static covariance helps maintaining sufficient spread in the forecast. HYBRID sensitivity experiments showed that an increased contribution from the flow-dependent covariance results in a deterioration of nitrates, similar to SEIK, while the improvement of HYBRID with increasing flow-dependent ensemble size quickly levels off.

  12. A hybrid ensemble-OI Kalman filter for efficient data assimilation into a 3-D biogeochemical model of the Mediterranean

    Science.gov (United States)

    Tsiaras, Kostas P.; Hoteit, Ibrahim; Kalaroni, Sofia; Petihakis, George; Triantafyllou, George

    2017-06-01

    A hybrid ensemble data assimilation scheme (HYBRID), combining a flow-dependent with a static background covariance, was developed and implemented for assimilating satellite (SeaWiFS) Chl-a data into a marine ecosystem model of the Mediterranean. The performance of HYBRID was assessed against a model free-run, the ensemble-based singular evolutive interpolated Kalman (SEIK) and its variant with static covariance (SFEK), with regard to the assimilated variable (Chl-a) and non-assimilated variables (dissolved inorganic nutrients). HYBRID was found more efficient than both SEIK and SFEK, reducing the Chl-a error by more than 40% in most areas, as compared to the free-run. Data assimilation had a positive overall impact on nutrients, except for a deterioration of nitrates simulation by SEIK in the most productive area (Adriatic). This was related to SEIK pronounced update in this area and the phytoplankton limitation on phosphate that lead to a built up of excess nitrates. SEIK was found more efficient in productive and variable areas, where its ensemble exhibited important spread. SFEK had an effect mostly on Chl-a, performing better than SEIK in less dynamic areas, adequately described by the dominant modes of its static covariance. HYBRID performed well in all areas, due to its "blended" covariance. Its flow-dependent component appears to track changes in the system dynamics, while its static covariance helps maintaining sufficient spread in the forecast. HYBRID sensitivity experiments showed that an increased contribution from the flow-dependent covariance results in a deterioration of nitrates, similar to SEIK, while the improvement of HYBRID with increasing flow-dependent ensemble size quickly levels off.

  13. Estimating the potential of energy saving and carbon emission mitigation of cassava-based fuel ethanol using life cycle assessment coupled with a biogeochemical process model.

    Science.gov (United States)

    Jiang, Dong; Hao, Mengmeng; Fu, Jingying; Tian, Guangjin; Ding, Fangyu

    2017-09-14

    Global warming and increasing concentration of atmospheric greenhouse gas (GHG) have prompted considerable interest in the potential role of energy plant biomass. Cassava-based fuel ethanol is one of the most important bioenergy and has attracted much attention in both developed and developing countries. However, the development of cassava-based fuel ethanol is still faced with many uncertainties, including raw material supply, net energy potential, and carbon emission mitigation potential. Thus, an accurate estimation of these issues is urgently needed. This study provides an approach to estimate energy saving and carbon emission mitigation potentials of cassava-based fuel ethanol through LCA (life cycle assessment) coupled with a biogeochemical process model-GEPIC (GIS-based environmental policy integrated climate) model. The results indicate that the total potential of cassava yield on marginal land in China is 52.51 million t; the energy ratio value varies from 0.07 to 1.44, and the net energy surplus of cassava-based fuel ethanol in China is 92,920.58 million MJ. The total carbon emission mitigation from cassava-based fuel ethanol in China is 4593.89 million kgC. Guangxi, Guangdong, and Fujian are identified as target regions for large-scale development of cassava-based fuel ethanol industry. These results can provide an operational approach and fundamental data for scientific research and energy planning.

  14. The ocean response to volcanic iron fertilisation after the eruption of Kasatochi volcano: a regional-scale biogeochemical ocean model study

    Directory of Open Access Journals (Sweden)

    A. Lindenthal

    2013-06-01

    Full Text Available In high-nutrient–low-chlorophyll regions, phytoplankton growth is limited by the availability of water-soluble iron. The eruption of Kasatochi volcano in August 2008 led to ash deposition into the iron-limited NE Pacific Ocean. Volcanic ash released iron upon contact with seawater and generated a massive phytoplankton bloom. Here we investigate this event with a one-dimensional ocean biogeochemical column model to illuminate the ocean response to iron fertilisation by volcanic ash. The results indicate that the added iron triggered a phytoplankton bloom in the summer of 2008. Associated with this bloom, macronutrient concentrations such as nitrate and silicate decline and zooplankton biomass is enhanced in the ocean mixed layer. The simulated development of the drawdown of carbon dioxide and increase of pH in surface seawater is in good agreement with available observations. Sensitivity studies with different supply dates of iron to the ocean emphasise the favourable oceanic conditions in the NE Pacific to generate massive phytoplankton blooms in particular during July and August in comparison to other months. By varying the amount of volcanic ash and associated bio-available iron supplied to the ocean, model results demonstrate that the NE Pacific Ocean has higher, but limited capabilities to consume CO2 after iron fertilisation than those observed after the volcanic eruption of Kasatochi.

  15. A biogeochemical model of Lake Pusiano (North Italy and its use in the predictability of phytoplankton blooms: first preliminary results

    Directory of Open Access Journals (Sweden)

    Alessandro OGGIONI

    2006-02-01

    Full Text Available This study reports the first preliminary results of the DYRESM-CAEDYM model application to a mid size sub-alpine lake (Lake Pusiano North Italy. The in-lake modelling is a part of a more general project called Pusiano Integrated Lake/Catchment project (PILE whose final goal is to understand the hydrological and trophic relationship between lake and catchment, supporting the restoration plan of the lake through field data analysis and numerical models. DYRESM is a 1D-3D hydrodynamics model for predicting the vertical profile of temperature, salinity and density. CAEDYM is multi-component ecological model, used here as a phytoplankton-zooplankton processes based model, which includes algorithms to simulate the nutrient cycles within the water column as well as the air-water gas exchanges and the water-sediments fluxes. The first results of the hydrodynamics simulations underline the capability of the model to accurately simulate the surface temperature seasonal trend and the thermal gradient whereas, during summer stratification, the model underestimates the bottom temperature of around 2 °C. The ecological model describes the epilimnetic reactive phosphorus (PO4 depletion (due to the phytoplankton uptake and the increase in PO4 concentrations in the deepest layers of the lake (due to the mineralization processes and the sediments release. In terms of phytoplankton dynamics the model accounts for the Planktothrix rubescens dominance during the whole season, whereas it seems to underestimate the peak in primary production related to both the simulated algal groups (P. rubescens and the rest of the other species aggregated in a single class. The future aims of the project are to complete the model parameterization and to connect the in-lake and the catchment modelling in order to gain an integrated view of the lake-catchment ecosystem as well as to develop a three dimensional model of the lake.

  16. Full uncertainty quantification of N2O and NO emissions using the biogeochemical model LandscapeDNDC on site and regional scale

    Science.gov (United States)

    Haas, Edwin; Santabarbara, Ignacio; Kiese, Ralf; Butterbach-Bahl, Klaus

    2017-04-01

    Numerical simulation models are increasingly used to estimate greenhouse gas emissions at site to regional / national scale and are outlined as the most advanced methodology (Tier 3) in the framework of UNFCCC reporting. Process-based models incorporate the major processes of the carbon and nitrogen cycle of terrestrial ecosystems and are thus thought to be widely applicable at various conditions and spatial scales. Process based modelling requires high spatial resolution input data on soil properties, climate drivers and management information. The acceptance of model based inventory calculations depends on the assessment of the inventory's uncertainty (model, input data and parameter induced uncertainties). In this study we fully quantify the uncertainty in modelling soil N2O and NO emissions from arable, grassland and forest soils using the biogeochemical model LandscapeDNDC. We address model induced uncertainty (MU) by contrasting two different soil biogeochemistry modules within LandscapeDNDC. The parameter induced uncertainty (PU) was assessed by using joint parameter distributions for key parameters describing microbial C and N turnover processes as obtained by different Bayesian calibration studies for each model configuration. Input data induced uncertainty (DU) was addressed by Bayesian calibration of soil properties, climate drivers and agricultural management practices data. For the MU, DU and PU we performed several hundred simulations each to contribute to the individual uncertainty assessment. For the overall uncertainty quantification we assessed the model prediction probability, followed by sampled sets of input datasets and parameter distributions. Statistical analysis of the simulation results have been used to quantify the overall full uncertainty of the modelling approach. With this study we can contrast the variation in model results to the different sources of uncertainties for each ecosystem. Further we have been able to perform a fully

  17. Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Stegen, James C.

    2017-11-01

    Much research has focused on improving ecosystem models by incorporating microbial regulation of biogeochemistry. However, models still struggle to predict biogeochemical function in future scenarios linked to accelerating global environmental change. Ecological mechanisms may influence the relationship between microbial communities and biogeochemistry, and here, we show that stochastic dispersal processes (e.g., wind-driven or hydrologic transport) can suppress biogeochemical function. Microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the balance of these two processes is hypothesized to influence how microbial communities correspond to biogeochemical function. We explore the theoretical basis for this hypothesis and use ecological simulation models to demonstrate potential influences of assembly processes on ecosystem function. We assemble ‘receiving’ communities under different levels of dispersal from a source community (selection-only, moderate dispersal, and homogenizing dispersal). We then calculate the degree to which assembled individuals are adapted to their environment and relate the level of adaptation to biogeochemical function. We also use ecological null models to further link assembly the level of deterministic assembly to function. We find that dispersal can decrease biogeochemical function by increasing the proportion of maladapted taxa, outweighing selection. The niche breadth of taxa is also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Together, our results highlight the importance of considering ecological assembly processes to reduce uncertainty in predictions of biogeochemical cycles under future environmental scenarios.

  18. Impact of vegetation and ecosystems on chlorine(-36) cycling and its modeling: from simplified approaches towards more complex biogeochemical tools

    Science.gov (United States)

    Thiry, Yves; Redon, Paul-Olivier; Gustafsson, Malin; Marang, Laura; Bastviken, David

    2013-04-01

    al., 2012), average Cl residence time in forest soils calculated for Clin and Clorg together was 5-fold higher that the residence time estimated for Clin alone (Redon et al., 2011), locally, Cl amount taken up by certain vegetation types can be larger than annual atmospheric deposits, the Cl in excess being recycled mainly by throughfall (Thiry, 2010), root uptake and chlorine transformation rates in soils are essential to calibrate dynamic compartment models since those processes control the persistence of chlorine in the whole system but data are still deficient for different land uses (Van den Hoof & Thiry, 2012). References: Bastviken, D., Thomsen, F., Svensson, T., Karlsson, S., Sandén, P., Shaw, G., Matucha, M., and Öberg, G. (2007). Chloride retention in forest soil by microbial uptake and by natural chlorination of organic matter. Geochim. Cosmochim. Acta, 71: 3182-3192. Gustavsson, M., Karlsson, S.,Öberg, G.,Sandén, P.,Svensson, T.,Valinia, S.,Thiry, Y. and Bastviken, D. (2012). Organic matter chlorination rates in different boreal soils: the role of soil organic matter content. Environmental Science & Technology, 46 (3): 1504-1510 Thiry, Y., 2010. Contribution à l'étude du cycle biogéochimique du chlore en écosystème forestier: cas d'un peuplement de pin sylvestre. Rapport Andra n° ENV.NT.ASTR.10.0068. IAEA (2010). Handbook of parameter values for the prediction of radionuclide transfer to humans in terrestrial and freshwater environments. Technical Report Series n° 472, Vienna, Austria. Öberg, G. (1998). Chloride and organic chlorine in soil. Acta hydrochimica et hydrobiologica, 26 (3): 137-144. Redon, P-O., Abdelouas, A., Bastviken, D., Cecchini, S. Nicolas, M. and Thiry, Y. (2011). Chloride and organic chlorine in forest soils: storage, residence times, and influence of ecological conditions. Environmental Science & Technology, 45: 7202-7208. Redon, P-O., Jolivet, C., Saby, N., Abdelouas, A.and Thiry, Y. (2012). Occurrence of natural organic

  19. Biogeochemical Modeling of In Situ U(VI) Reduction and Immobilization with Emulsified Vegetable Oil as the Electron Donor at a Field Site in Oak Ridge, Tennessee

    Science.gov (United States)

    Tang, G.; Parker, J.; Wu, W.; Schadt, C. W.; Watson, D. B.; Brooks, S. C.; Orifrc Team

    2011-12-01

    A comprehensive biogeochemical model was developed to quantitatively describe the coupled hydrologic, geochemical and microbiological processes that occurred following injection of emulsified vegetable oil (EVO) as the electron donor to immobilize U(VI) at the Oak Ridge Integrated Field Research Challenge site (ORIFRC) in Tennessee. The model couples the degradation of EVO, production and oxidation of long-chain fatty acids (LCFA), glycerol, hydrogen and acetate, reduction of nitrate, manganese, ferrous iron, sulfate and uranium, and methanoganesis with growth of multiple microbial groups. The model describes the evolution of geochemistry and microbial populations not only in the aqueous phase as typically observed, but also in the mineral phase and therefore enables us to evaluate the applicability of rates from the literature for field scale assessment, estimate the retention and degradation rates of EVO and LCFA, and assess the influence of the coupled processes on fate and transport of U(VI). Our results suggested that syntrophic bacteria or metal reducers might catalyze LCFA oxidation in the downstream locations when sulfate was consumed, and competition between methanogens and others for electron donors and slow growth of methanogen might contribute to the sustained reducing condition. Among the large amount of hydrologic, geochemical and microbiological parameter values, the initial biomass, and the interactions (e.g., inhibition) of the microbial functional groups, and the rate and extent of Mn and Fe oxide reduction appear as the major sources of uncertainty. Our model provides a platform to conduct numerical experiments to study these interactions, and could be useful for further iterative experimental and modeling investigations into the bioreductive immobiliztion of radionuclide and metal contaminants in the subsurface.

  20. Potential environmental impact of tidal energy extraction in the Pentland Firth at large spatial scales: results of a biogeochemical model

    NARCIS (Netherlands)

    van der Molen, J.; Ruardij, P.; Greenwood, N.

    2016-01-01

    A model study was carried out of the potentiallarge-scale (> 100 km) effects of marine renewabletidal energy generation in the Pentland Firth, using the 3-D hydrodynamics–biogeochemistry model GETM-ERSEMBFM.A realistic 800MW scenario and a high-impact scenariowith massive expansion of tidal energy

  1. Estimating the potential of energy saving and carbon emission mitigation of cassava-based fuel ethanol using life cycle assessment coupled with a biogeochemical process model

    Science.gov (United States)

    Jiang, Dong; Hao, Mengmeng; Fu, Jingying; Tian, Guangjin; Ding, Fangyu

    2017-09-01

    Global warming and increasing concentration of atmospheric greenhouse gas (GHG) have prompted considerable interest in the potential role of energy plant biomass. Cassava-based fuel ethanol is one of the most important bioenergy and has attracted much attention in both developed and developing countries. However, the development of cassava-based fuel ethanol is still faced with many uncertainties, including raw material supply, net energy potential, and carbon emission mitigation potential. Thus, an accurate estimation of these issues is urgently needed. This study provides an approach to estimate energy saving and carbon emission mitigation potentials of cassava-based fuel ethanol through LCA (life cycle assessment) coupled with a biogeochemical process model—GEPIC (GIS-based environmental policy integrated climate) model. The results indicate that the total potential of cassava yield on marginal land in China is 52.51 million t; the energy ratio value varies from 0.07 to 1.44, and the net energy surplus of cassava-based fuel ethanol in China is 92,920.58 million MJ. The total carbon emission mitigation from cassava-based fuel ethanol in China is 4593.89 million kgC. Guangxi, Guangdong, and Fujian are identified as target regions for large-scale development of cassava-based fuel ethanol industry. These results can provide an operational approach and fundamental data for scientific research and energy planning.

  2. Parameterization of biogeochemical sediment-water fluxes using in-situ measurements and a steady-state diagenetic model

    Science.gov (United States)

    Diagenetic processes are important drivers of water column biogeochemistry in coastal areas. For example, sediment oxygen consumption can be a significant contributor to oxygen depletion in hypoxic systems, and sediment–water nutrient fluxes support primary productivity in ...

  3. The influence of winter convection on primary production: A parameterisation using a hydrostatic three-dimensional biogeochemical model

    DEFF Research Database (Denmark)

    Grosse, Fabian; Lindemann, Christian; Pätch, Johannes

    2014-01-01

    organic carbon. The carbon export during late winter/early spring significantly exceeded the export of the reference run. Furthermore, a non-hydrostatic convection model was used to evaluate the major assumption of the presented parameterisation which implies the matching of the mixed layer depth...

  4. Calibration of Daycent biogeochemical model for rice paddies in three agro-ecological zones in Peninsular India to optimize cropping practices and predict GHG emissions

    Science.gov (United States)

    Rajan, S.; Kritee, K.; Keough, C.; Parton, W. J.; Ogle, S. M.

    2014-12-01

    Rice is a staple for nearly half of the world population with irrigated and rainfed lowland rice accounting for about 80% of the worldwide harvested rice area. Increased atmospheric CO2 and rising temperatures are expected to adversely affect rice yields by the end of the 21st century. In addition, different crop management practices affect methane and nitrous oxide emissions from rice paddies antagonistically warranting a review of crop management practices such that farmers can adapt to the changing climate and also help mitigate climate change. The Daily DayCent is a biogeochemical model that operates on a daily time step, driven by four ecological drivers, i.e. climate, soil, vegetation, and management practices. The model is widely used to simulate daily fluxes of various gases, plant productivity, nutrient availability, and other ecosystem parameters in response to changes in land management and climate. We employed the DayCent model as a tool to optimize rice cropping practices in Peninsular India so as to develop a set of farming recommendations to ensure a triple win (i.e. higher yield, higher profit and lower GHG emissions). We applied the model to simulate both N2O and CH4 emissions, and crop yields from four rice paddies in three different agro-ecological zones under different management practices, and compared them with measured GHG and yield data from these plots. We found that, like all process based models, the biggest constraint in using the model was input data acquisition. Lack of accurate documentation of historic land use and management practices, missing historical daily weather data, and difficulty in obtaining digital records of soil and crop/vegetation parameters related to our experimental plots came in the way of our execution of this model. We will discuss utilization of estimates based on available literature, or knowledge-based values in lieu of missing measured parameters in our simulations with DayCent which could prove to be a

  5. The submarine hydrothermal system of Panarea (Southern Italy: biogeochemical processes at the thermal fluids - sea bottom interface

    Directory of Open Access Journals (Sweden)

    T. Maugeri

    2006-06-01

    Full Text Available Among the submarine hydrothermal systems located offshore the volcanic archipelago of the Aeolian Islands (Southern Italy, the most active is located off the coasts of Panarea island. Thermal waters, gases and sulfur deposits coexist at the sea bottom where hydrothermal fluids are released from both shallow and deep vents. The chemical and isotopic composition of the fluid phase shows the presence of a significant magmatic component and the physico-chemical conditions of the geothermal reservoir allow the release of reduced chemical species that are microbially mediated towards the production of organic carbon as a form of biochemical energy. Microorganisms inhabiting this environment possess nutritional requirements and overall metabolic pathways ideally suited to such ecosystem that represents a clear example of the close connection between geosphere and biosphere. Microscopic examination of the white mat attached to rock surfaces showed the presence of Thiothrix-like filamentous bacteria. Moderately thermophilic heterotrophic isolates were identified as strains of the genus Bacillus. Although the hydrothermal system of Panarea has to be considered a “shallow” system, it shows many characteristics that make it similar to the “deep” oceanic systems, giving a unique opportunity for improving our knowledge on such an unexplored world by working at this easily accessible site.

  6. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    Science.gov (United States)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

    2015-12-01

    Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

  7. Quantification of terrestrial ecosystem carbon dynamics in the conterminous United States combining a process-based biogeochemical model and MODIS and AmeriFlux data

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Min; Zhuang, Qianlai; Cook, D.; Coulter, Richard L.; Pekour, Mikhail S.; Scott, Russell L.; Munger, J. W.; Bible, Ken

    2011-08-31

    Satellite remote sensing provides continuous temporal and spatial information of terrestrial ecosystems. Using these remote sensing data and eddy flux measurements and biogeochemical models, such as the Terrestrial Ecosystem Model (TEM), should provide a more adequate quantification of carbon dynamics of terrestrial ecosystems. Here we use Moderate Resolution Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI), Land Surface Water Index (LSWI) and carbon flux data of AmeriFlux to conduct such a study. We first modify the gross primary production (GPP) modeling in TEM by incorporating EVI and LSWI to account for the effects of the changes of canopy photosynthetic capacity, phenology and water stress. Second, we parameterize and verify the new version of TEM with eddy flux data. We then apply the model to the conterminous United States over the period 2000-2005 at a 0.05-0.05 spatial resolution. We find that the new version of TEM made improvement over the previous version and generally captured the expected temporal and spatial patterns of regional carbon dynamics. We estimate that regional GPP is between 7.02 and 7.78 PgC yr{sup -1} and net primary production (NPP) ranges from 3.81 to 4.38 Pg Cyr{sup -1} and net ecosystem production (NEP) varies within 0.08- 0.73 PgC yr{sup -1} over the period 2000-2005 for the conterminous United States. The uncertainty due to parameterization is 0.34, 0.65 and 0.18 PgC yr{sup -1} for the regional estimates of GPP, NPP and NEP, respectively. The effects of extreme climate and disturbances such as severe drought in 2002 and destructive Hurricane Katrina in 2005 were captured by the model. Our study provides a new independent and more adequate measure of carbon fluxes for the conterminous United States, which will benefit studies of carbon-climate feedback and facilitate policy-making of carbon management and climate.

  8. Quantification of Terrestrial Ecosystem Carbon Dynamics in the Conterminous United States Combining a Process-Based Biogeochemical Model and MODIS and AmeriFlux data

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Min; Zhuang, Qianlai; Cook, David R.; Coulter, Richard L.; Pekour, Mikhail S.; Scott, Russell L.; Munger, J. W.; Bible, Ken

    2011-09-21

    Satellite remote sensing provides continuous temporal and spatial information of terrestrial 24 ecosystems. Using these remote sensing data and eddy flux measurements and biogeochemical 25 models, such as the Terrestrial Ecosystem Model (TEM), should provide a more adequate 26 quantification of carbon dynamics of terrestrial ecosystems. Here we use Moderate Resolution 27 Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI), Land Surface Water Index 28 (LSWI) and carbon flux data of AmeriFlux to conduct such a study. We first modify the gross primary 29 production (GPP) modeling in TEM by incorporating EVI and LSWI to account for the effects of the 30 changes of canopy photosynthetic capacity, phenology and water stress. Second, we parameterize and 31 verify the new version of TEM with eddy flux data. We then apply the model to the conterminous 32 United States over the period 2000-2005 at a 0.05o ×0.05o spatial resolution. We find that the new 33 version of TEM generally captured the expected temporal and spatial patterns of regional carbon 34 dynamics. We estimate that regional GPP is between 7.02 and 7.78 Pg C yr-1 and net primary 35 production (NPP) ranges from 3.81 to 4.38 Pg C yr-1 and net ecosystem production (NEP) varies 36 within 0.08-0.73 Pg C yr-1 over the period 2000-2005 for the conterminous United States. The 37 uncertainty due to parameterization is 0.34, 0.65 and 0.18 Pg C yr-1 for the regional estimates of GPP, 38 NPP and NEP, respectively. The effects of extreme climate and disturbances such as severe drought in 39 2002 and destructive Hurricane Katrina in 2005 were captured by the model. Our study provides a 40 new independent and more adequate measure of carbon fluxes for the conterminous United States, 41 which will benefit studies of carbon-climate feedback and facilitate policy-making of carbon 42 management and climate.

  9. Quantification of terrestrial ecosystem carbon dynamics in the conterminous United States combining a process-based biogeochemical model and MODIS and AmeriFlux data

    Directory of Open Access Journals (Sweden)

    M. Chen

    2011-09-01

    Full Text Available Satellite remote sensing provides continuous temporal and spatial information of terrestrial ecosystems. Using these remote sensing data and eddy flux measurements and biogeochemical models, such as the Terrestrial Ecosystem Model (TEM, should provide a more adequate quantification of carbon dynamics of terrestrial ecosystems. Here we use Moderate Resolution Imaging Spectroradiometer (MODIS Enhanced Vegetation Index (EVI, Land Surface Water Index (LSWI and carbon flux data of AmeriFlux to conduct such a study. We first modify the gross primary production (GPP modeling in TEM by incorporating EVI and LSWI to account for the effects of the changes of canopy photosynthetic capacity, phenology and water stress. Second, we parameterize and verify the new version of TEM with eddy flux data. We then apply the model to the conterminous United States over the period 2000–2005 at a 0.05° × 0.05° spatial resolution. We find that the new version of TEM made improvement over the previous version and generally captured the expected temporal and spatial patterns of regional carbon dynamics. We estimate that regional GPP is between 7.02 and 7.78 Pg C yr−1 and net primary production (NPP ranges from 3.81 to 4.38 Pg C yr−1 and net ecosystem production (NEP varies within 0.08–0.73 Pg C yr−1 over the period 2000–2005 for the conterminous United States. The uncertainty due to parameterization is 0.34, 0.65 and 0.18 Pg C yr−1 for the regional estimates of GPP, NPP and NEP, respectively. The effects of extreme climate and disturbances such as severe drought in 2002 and destructive Hurricane Katrina in 2005 were captured by the model. Our study provides a new independent and more adequate measure of carbon fluxes for the conterminous United States, which will benefit studies of carbon-climate feedback and facilitate policy-making of carbon management and climate.

  10. Biogeochemical processes controlling the mobility of major ions and trace metals in aquitard sediments beneath an oil sand tailing pond: Laboratory studies and reactive transport modeling

    Science.gov (United States)

    Holden, A. A.; Haque, S. E.; Mayer, K. U.; Ulrich, A. C.

    2013-08-01

    Increased production and expansion of the oil sand industry in Alberta are of great benefit to the economy, but they carry major environmental challenges. The volume of fluid fine tailings requiring storage is 840 × 106 m3 and growing, making it imperative that we better understand the fate and transport of oil sand process-affected water (OSPW) seepage from these facilities. Accordingly, the current study seeks to characterize both a) the potential for major ion and trace element release, and b) the principal biogeochemical processes involved, as tailing pond OSPW infiltrates into, and interacts with, underlying glacial till sediments prior to reaching down gradient aquifers or surface waters. Objectives were addressed through a series of aqueous and solid phase experiments, including radial diffusion cells, an isotope analysis, X-ray diffraction, and sequential extractions. The diffusion cells were also simulated in a reactive transport framework to elucidate key reaction processes. The experiments indicate that the ingress and interaction of OSPW with the glacial till sediment-pore water system will result in: a mitigation of ingressing Na (retardation), displacement and then limited precipitation of exchangeable Ca and Mg (as carbonates), sulfate reduction and subsequent precipitation of the produced sulfides, as well as biodegradation of organic carbon. High concentrations of ingressing Cl (~ 375 mg L- 1) and Na (~ 575 mg L- 1) (even though the latter is delayed, or retarded) are expected to migrate through the till and into the underlying sand channel. Trace element mobility was influenced by ion exchange, oxidation-reduction, and mineral phase reactions including reductive dissolution of metal oxyhydroxides — in accordance with previous observations within sandy aquifer settings. Furthermore, although several trace elements showed the potential for release (Al, B, Ba, Cd, Mn, Pb, Si, Sr), large-scale mobilization is not supported. Thus, the present

  11. Spectral induced polarization as a tool to map subsurface biogeochemical hot spots: a first laboratory evaluation in the Fe-S system

    Science.gov (United States)

    Nordsiek, Sven; Gilfedder, Ben; Frei, Sven

    2017-04-01

    Zones of intense biogeochemical reactivity (hot spots) arise in the saturated subsurface at the interface between regions with oxidizing and reducing conditions. Hot spots are both sinks and sources of different chemical compounds, thus they are of particular importance for element cycling in the subsurface. However, the investigation of hot spot structures is difficult, because they are not directly identifiable from the surface and can only be investigated by invasive methods in the subsurface. Additionally, they often form in sensitive wetland ecosystems where only non-destructive measurements are applicable to avoid significant degradation of these sensitive environments. Under these circumstances, geophysical methods may provide useful tools to identify biogeochemically active regions. One of the most important biogeochemical reactions in wetlands is the reduction of sulphate and formation and accumulation of FexSy minerals (where x and y delineate mineral stoichiometry). These reactions only occur in specific hot spots where specific chemical and microbial conditions are met. Within a research project concerning biogeochemical transformations and turnover in wetlands, we investigate the applicability of the geoelectrical method of spectral induced polarization (SIP) to locate and monitor regions containing polarizing FexSy particles as indicator for biogeochemical hot spots. After developing and testing a sample holder and a set of non-polarizing electrodes for laboratory SIP measurements, we performed experiments on natural soil samples taken from the hyporheic zone of a local river channel. The collected material originates from a location known for biogeochemical activity. The sample contains a high percentage of dark grayish/black sediment interpreted as FexSy, and possibly pyrite (FeS2). The material was homogenized and split into four samples. The FexSy concentration was adjusted to three different levels by oxidation using H2O2. For all samples we

  12. Mangrove forests: a potent nexus of coastal biogeochemical cycling

    Science.gov (United States)

    Barr, J. G.; Fuentes, J. D.; Shoemaker, B.; O'Halloran, T. L.; Lin, G., Sr.; Engel, V. C.

    2014-12-01

    Mangrove forests cover just 0.1% of the Earth's terrestrial surface, yet they provide a disproportionate source (~10 % globally) of terrestrially derived, refractory dissolved organic carbon to the oceans. Mangrove forests are biogeochemical reactors that convert biomass into dissolved organic and inorganic carbon at unusually high rates, and many studies recognize the value of mangrove ecosystems for the substantial amounts of soil carbon storage they produce. However, questions remain as to how mangrove forest ecosystem services should be valuated and quantified. Therefore, this study addresses several objectives. First, we demonstrate that seasonal and annual net ecosystem carbon exchange in three selected mangrove forests, derived from long-term eddy covariance measurements, represent key quantities in defining the magnitude of biogeochemical cycling and together with other information on carbon cycle parameters serves as a proxy to estimate ecosystem services. Second, we model ecosystem productivity across the mangrove forests of Everglades National Park and southern China by relating net ecosystem exchange values to remote sensing data. Finally, we develop a carbon budget for the mangrove forests in the Everglades National Park for the purposes of demonstrating that these forests and adjacent estuaries are sites of intense biogeochemical cycling. One conclusion from this study is that much of the carbon entering from the atmosphere as net ecosystem exchange (~1000 g C m-2 yr-1) is not retained in the net ecosystem carbon balance. Instead, a substantial fraction of the carbon entering the system as net ecosystem exchange is ultimately exported to the oceans or outgassed as reaction products within the adjacent estuary.

  13. Greenland's glacial fjords and their role in regional biogeochemical dynamics.

    Science.gov (United States)

    Crosby, J.; Arndt, S.

    2017-12-01

    Greenland's coastal fjords serve as important pathways that connect the Greenland Ice Sheet (GrIS) and the surrounding oceans. They export seasonal glacial meltwater whilst being significant sites of primary production. These fjords are home to some of the most productive ecosystems in the world and possess high socio-economic value via fisheries. A growing number of studies have proposed the GrIS as an underappreciated yet significant source of nutrients to surrounding oceans. Acting as both transfer routes and sinks for glacial nutrient export, fjords have the potential to act as significant biogeochemical processors, yet remain underexplored. Critically, an understanding of the quantitative contribution of fjords to carbon and nutrient budgets is lacking, with large uncertainties associated with limited availability of field data and the lack of robust upscaling approaches. To close this knowledge gap we developed a coupled 2D physical-biogeochemical model of the Godthåbsfjord system, a sub-Arctic sill fjord in southwest Greenland, to quantitatively assess the impact of nutrients exported from the GrIS on fjord primary productivity and biogeochemical dynamics. Glacial meltwater is found to be a key driver of fjord-scale circulation patterns, whilst tracer simulations reveal the relative nutrient contributions from meltwater-driven upwelling and meltwater export from the GrIS. Hydrodynamic circulation patterns and freshwater transit times are explored to provide a first understanding of the glacier-fjord-ocean continuum, demonstrating the complex pattern of carbon and nutrient cycling at this critical land-ocean interface.

  14. Formation of methane-related authigenic carbonates in a highly dynamic biogeochemical system in the Krishna–Godavari Basin, Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Kocherla, M.; Teichert, B.M.A.; Pillai, S.; Satyanarayan, M.; Ramamurty, P.B.; Patil, D.J.; Rao, A.N.

    (2) During both biogeochemical processes bicarbonate [HCO3-] is being produced and thus pore water alkalinity increases. This will lead together with seawater calcium to the precipitation of authigenic carbonate minerals (equation 3). Ca2+ + 2...). This is also the zone where methane-related authigenic carbonates will form due to the production of bicarbonate and increase in alkalinity. Characteristic low carbon isotope ratios of methane-related carbonates have been identified at Sites 1, 5, 8, 9, 12...

  15. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

    Science.gov (United States)

    Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

    2016-08-01

    Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Biogeochemical processes controlling the mobility of major ions and trace metals in aquitard sediments beneath an oil sand tailing pond: laboratory studies and reactive transport modeling.

    Science.gov (United States)

    Holden, A A; Haque, S E; Mayer, K U; Ulrich, A C

    2013-08-01

    Increased production and expansion of the oil sand industry in Alberta are of great benefit to the economy, but they carry major environmental challenges. The volume of fluid fine tailings requiring storage is 840×10(6) m(3) and growing, making it imperative that we better understand the fate and transport of oil sand process-affected water (OSPW) seepage from these facilities. Accordingly, the current study seeks to characterize both a) the potential for major ion and trace element release, and b) the principal biogeochemical processes involved, as tailing pond OSPW infiltrates into, and interacts with, underlying glacial till sediments prior to reaching down gradient aquifers or surface waters. Objectives were addressed through a series of aqueous and solid phase experiments, including radial diffusion cells, an isotope analysis, X-ray diffraction, and sequential extractions. The diffusion cells were also simulated in a reactive transport framework to elucidate key reaction processes. The experiments indicate that the ingress and interaction of OSPW with the glacial till sediment-pore water system will result in: a mitigation of ingressing Na (retardation), displacement and then limited precipitation of exchangeable Ca and Mg (as carbonates), sulfate reduction and subsequent precipitation of the produced sulfides, as well as biodegradation of organic carbon. High concentrations of ingressing Cl (~375 mg L(-1)) and Na (~575 mg L(-1)) (even though the latter is delayed, or retarded) are expected to migrate through the till and into the underlying sand channel. Trace element mobility was influenced by ion exchange, oxidation-reduction, and mineral phase reactions including reductive dissolution of metal oxyhydroxides - in accordance with previous observations within sandy aquifer settings. Furthermore, although several trace elements showed the potential for release (Al, B, Ba, Cd, Mn, Pb, Si, Sr), large-scale mobilization is not supported. Thus, the present

  17. The computational future for climate and Earth system models: on the path to petaflop and beyond.

    Science.gov (United States)

    Washington, Warren M; Buja, Lawrence; Craig, Anthony

    2009-03-13

    The development of the climate and Earth system models has had a long history, starting with the building of individual atmospheric, ocean, sea ice, land vegetation, biogeochemical, glacial and ecological model components. The early researchers were much aware of the long-term goal of building the Earth system models that would go beyond what is usually included in the climate models by adding interactive biogeochemical interactions. In the early days, the progress was limited by computer capability, as well as by our knowledge of the physical and chemical processes. Over the last few decades, there has been much improved knowledge, better observations for validation and more powerful supercomputer systems that are increasingly meeting the new challenges of comprehensive models. Some of the climate model history will be presented, along with some of the successes and difficulties encountered with present-day supercomputer systems.

  18. A biogeochemical cycle for aluminium?

    Science.gov (United States)

    Exley, Christopher

    2003-09-15

    The elaboration of biogeochemical cycles for elements which are known to be essential for life has enabled a broad appreciation of the homeostatic mechanisms which underlie element essentiality. In particular they can be used effectively to identify any part played by human activities in element cycling and to predict how such activities might impact upon the lithospheric and biospheric availability of an element in the future. The same criteria were the driving force behind the construction of a biogeochemical cycle for aluminium, a non-essential element which is a known ecotoxicant and a suspected health risk in humans. The purpose of this exercise was to examine the concept of a biogeochemical cycle for aluminium and not to review the biogeochemistry of this element. The cycle as presented is rudimentary and qualitative though, even in this nascent form, it is informative and predictive and, for these reasons alone, it is deserving of future quantification. A fully fledged biogeochemical cycle for aluminium should explain the biospheric abundance of this element and whether we should expect its (continued) active involvement in biochemical evolution.

  19. Engineering Pseudomonas stutzeri as a biogeochemical biosensor

    Science.gov (United States)

    Boynton, L.; Cheng, H. Y.; Del Valle, I.; Masiello, C. A.; Silberg, J. J.

    2016-12-01

    Biogeochemical cycles are being drastically altered as a result of anthropogenic activities, such as the burning of fossil fuels and the industrial production of ammonia. We know microbes play a major part in these cycles, but the extent of their biogeochemical roles remains largely uncharacterized due to inadequacies with culturing and measurement. While metagenomics and other -omics methods offer ways to reconstruct microbial communities, these approaches can only give an indication of the functional roles of microbes in a community. These -omics approaches are rapidly being expanded to the point of outpacing our knowledge of functional genes, which highlights an inherent need for analytical methods that non-invasively monitor Earth's processes in real time. Here we aim to exploit synthetic biology methods in order to engineer a ubiquitous denitrifying microbe, Pseudomonas stutzeri that can act as a biosensor in soil and marine environments. By using an easily cultivated microbe that is also common in many environments, we hope to develop a tool that allows us to zoom in on specific aspects of the nitrogen cycle. In order to monitor processes occurring at the genetic level in environments that cannot be resolved with fluorescence-based methods, such as soils, we have developed a system that instead relies on gas production by engineered microbial biosensors. P. stutzeri has been successfully engineered to release a gas, methyl bromide, which can continuously and non-invasively be measured by GC-MS. Similar to using Green Fluorescent Protein, GFP, in the biological sciences, the gene controlling gas production can be linked to those involved in denitrification, thereby creating a quantifiable gas signal that is correlated with microbial activity in the soil. Synthetically engineered microbial biosensors could reveal key aspects of metabolism in soil systems and offer a tool for characterizing the scope and degree of microbial impact on major biogeochemical cycles.

  20. Research priorities in land use and land-cover change for the Earth System and Integrated Assessment Modelling

    NARCIS (Netherlands)

    Hibbard, K.; Janetos, A.; Vuuren, van D.; Pongratz, J.; Rose, S.; Betts, R.; Herold, M.; Feddema, J.

    2010-01-01

    This special issue has highlighted recent and innovative methods and results that integrate observations and modelling analyses of regional to global aspect of biophysical and biogeochemical interactions of land-cover change with the climate system. Both the Earth System and the Integrated

  1. Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments

    Energy Technology Data Exchange (ETDEWEB)

    Kenwell, Amy [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Navarre-Sitchler, Alexis, E-mail: asitchle@mines.edu [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Prugue, Rodrigo [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Spear, John R. [Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Hering, Amanda S. [Department of Applied Mathematics and Statistics, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Maxwell, Reed M. [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Carroll, Rosemary W.H. [Desert Research Institute, Division of Hydrologic Sciences, 2215 Raggio Parkway, Reno, NV 89512 (United States); Williams, Kenneth H. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

    2016-09-01

    A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This study develops a methodology to predict potential elevated rates of biogeochemical activity (microbial “hotspots”) in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments. Multiple linear regression models of simulated precipitation leachate, HCl and hydroxylamine extractable iron and manganese, total organic carbon (TOC), and microbial community structure were used to identify sample characteristics indicative of biogeochemical hotspots within fluvially-derived aquifer sediments and overlying soils. The method has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 16 alluvial samples were taken from 8 sediment cores, and at the East River, 46 soil/sediment samples were collected across and perpendicular to 3 active meanders and an oxbow meander. Regression models using TOC and TOC combined with extractable iron and manganese results were determined to be the best fitting statistical models of microbial DNA (via 16S rRNA gene analysis). Fitting these models to observations in both contaminated and natural floodplain deposits, and their associated alluvial aquifers, demonstrates the broad applicability of the geochemical indicator based approach. - Highlights: • Biogeochemical characterization of alluvial floodplain soils and sediments was performed to investigate parameters that may indicate microbial hot spot formation. • A correlation between geochemical parameters (total organic carbon and

  2. Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments

    International Nuclear Information System (INIS)

    Kenwell, Amy; Navarre-Sitchler, Alexis; Prugue, Rodrigo; Spear, John R.; Hering, Amanda S.; Maxwell, Reed M.; Carroll, Rosemary W.H.; Williams, Kenneth H.

    2016-01-01

    A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This study develops a methodology to predict potential elevated rates of biogeochemical activity (microbial “hotspots”) in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments. Multiple linear regression models of simulated precipitation leachate, HCl and hydroxylamine extractable iron and manganese, total organic carbon (TOC), and microbial community structure were used to identify sample characteristics indicative of biogeochemical hotspots within fluvially-derived aquifer sediments and overlying soils. The method has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 16 alluvial samples were taken from 8 sediment cores, and at the East River, 46 soil/sediment samples were collected across and perpendicular to 3 active meanders and an oxbow meander. Regression models using TOC and TOC combined with extractable iron and manganese results were determined to be the best fitting statistical models of microbial DNA (via 16S rRNA gene analysis). Fitting these models to observations in both contaminated and natural floodplain deposits, and their associated alluvial aquifers, demonstrates the broad applicability of the geochemical indicator based approach. - Highlights: • Biogeochemical characterization of alluvial floodplain soils and sediments was performed to investigate parameters that may indicate microbial hot spot formation. • A correlation between geochemical parameters (total organic carbon and

  3. Predictive Understanding of Mountainous Watershed Hydro-Biogeochemical Function and Response to Perturbations

    Science.gov (United States)

    Hubbard, S. S.; Williams, K. H.; Agarwal, D.; Banfield, J. F.; Beller, H. R.; Bouskill, N.; Brodie, E.; Maxwell, R. M.; Nico, P. S.; Steefel, C. I.; Steltzer, H.; Tokunaga, T. K.; Wainwright, H. M.; Dwivedi, D.; Newcomer, M. E.

    2017-12-01

    Recognizing the societal importance, vulnerability and complexity of mountainous watersheds, the `Watershed Function' project is developing a predictive understanding of how mountainous watersheds retain and release downgradient water, nutrients, carbon, and metals. In particular, the project is exploring how early snowmelt, drought, floods and other disturbances will influence mountainous watershed dynamics at seasonal to decadal timescales. Located in the 300km2 East River headwater catchment of the Upper Colorado River Basin, the project is guided by several constructs. First, the project considers the integrated role of surface and subsurface flow and biogeochemical reactions - from bedrock to the top of the vegetative canopy, from terrestrial through aquatic compartments, and from summit to receiving waters. The project takes a system-of-systems perspective, focused on developing new methods to quantify the cumulative watershed hydrobiogeochemical response to perturbations based on information from select subsystems within the watershed, each having distinct vegetation-subsurface biogeochemical-hydrological characteristics. A `scale-adaptive' modeling capability, in development using adaptive mesh refinement methods, serves as the organizing framework for the SFA. The scale-adaptive approach is intended to permit simulation of system-within-systems behavior - and aggregation of that behavior - from genome through watershed scales. This presentation will describe several early project discoveries and advances made using experimental, observational and numerical approaches. Among others, examples may include:quantiying how seasonal hydrological perturbations drive biogeochemical responses across critical zone compartments, with a focus on N and C transformations; metagenomic documentation of the spatial variability in floodplain meander microbial ecology; 3D reactive transport simulations of couped hydrological-biogeochemical behavior in the hyporheic zone; and

  4. Uncertainty in Earth System Models: Benchmarks for Ocean Model Performance and Validation

    Science.gov (United States)

    Ogunro, O. O.; Elliott, S.; Collier, N.; Wingenter, O. W.; Deal, C.; Fu, W.; Hoffman, F. M.

    2017-12-01

    The mean ocean CO2 sink is a major component of the global carbon budget, with marine reservoirs holding about fifty times more carbon than the atmosphere. Phytoplankton play a significant role in the net carbon sink through photosynthesis and drawdown, such that about a quarter of anthropogenic CO2 emissions end up in the ocean. Biology greatly increases the efficiency of marine environments in CO2 uptake and ultimately reduces the impact of the persistent rise in atmospheric concentrations. However, a number of challenges remain in appropriate representation of marine biogeochemical processes in Earth System Models (ESM). These threaten to undermine the community effort to quantify seasonal to multidecadal variability in ocean uptake of atmospheric CO2. In a bid to improve analyses of marine contributions to climate-carbon cycle feedbacks, we have developed new analysis methods and biogeochemistry metrics as part of the International Ocean Model Benchmarking (IOMB) effort. Our intent is to meet the growing diagnostic and benchmarking needs of ocean biogeochemistry models. The resulting software package has been employed to validate DOE ocean biogeochemistry results by comparison with observational datasets. Several other international ocean models contributing results to the fifth phase of the Coupled Model Intercomparison Project (CMIP5) were analyzed simultaneously. Our comparisons suggest that the biogeochemical processes determining CO2 entry into the global ocean are not well represented in most ESMs. Polar regions continue to show notable biases in many critical biogeochemical and physical oceanographic variables. Some of these disparities could have first order impacts on the conversion of atmospheric CO2 to organic carbon. In addition, single forcing simulations show that the current ocean state can be partly explained by the uptake of anthropogenic emissions. Combined effects of two or more of these forcings on ocean biogeochemical cycles and ecosystems

  5. PFLOTRAN: Recent Developments Facilitating Massively-Parallel Reactive Biogeochemical Transport

    Science.gov (United States)

    Hammond, G. E.

    2015-12-01

    With the recent shift towards modeling carbon and nitrogen cycling in support of climate-related initiatives, emphasis has been placed on incorporating increasingly mechanistic biogeochemistry within Earth system models to more accurately predict the response of terrestrial processes to natural and anthropogenic climate cycles. PFLOTRAN is an open-source subsurface code that is specialized for simulating multiphase flow and multicomponent biogeochemical transport on supercomputers. The object-oriented code was designed with modularity in mind and has been coupled with several third-party simulators (e.g. CLM to simulate land surface processes and E4D for coupled hydrogeophysical inversion). Central to PFLOTRAN's capabilities is its ability to simulate tightly-coupled reactive transport processes. This presentation focuses on recent enhancements to the code that enable the solution of large parameterized biogeochemical reaction networks with numerous chemical species. PFLOTRAN's "reaction sandbox" is described, which facilitates the implementation of user-defined reaction networks without the need for a comprehensive understanding of PFLOTRAN software infrastructure. The reaction sandbox is written in modern Fortran (2003-2008) and leverages encapsulation, inheritance, and polymorphism to provide the researcher with a flexible workspace for prototyping reactions within a massively parallel flow and transport simulation framework. As these prototypical reactions mature into well-accepted implementations, they can be incorporated into PFLOTRAN as native biogeochemistry capability. Users of the reaction sandbox are encouraged to upload their source code to PFLOTRAN's main source code repository, including the addition of simple regression tests to better ensure the long-term code compatibility and validity of simulation results.

  6. Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models: FINAL REPORT of grant Grant No. DE-FG02-04ER63726

    Energy Technology Data Exchange (ETDEWEB)

    Sarmiento, Jorge L; Gnanadesikan, Anand; Gruber, Nicolas

    2007-06-21

    This final report summarizes research undertaken collaboratively between Princeton University, the NOAA Geophysical Fluid Dynamics Laboratory on the Princeton University campus, the State University of New York at Stony Brook, and the University of California, Los Angeles between September 1, 2000, and November 30, 2006, to do fundamental research on ocean iron fertilization as a means to enhance the net oceanic uptake of CO2 from the atmosphere. The approach we proposed was to develop and apply a suite of coupled physical-ecologicalbiogeochemical models in order to (i) determine to what extent enhanced carbon fixation from iron fertilization will lead to an increase in the oceanic uptake of atmospheric CO2 and how long this carbon will remain sequestered (efficiency), and (ii) examine the changes in ocean ecology and natural biogeochemical cycles resulting from iron fertilization (consequences). The award was funded in two separate three-year installments: • September 1, 2000 to November 30, 2003, for a project entitled “Ocean carbon sequestration by fertilization: An integrated biogeochemical assessment.” A final report was submitted for this at the end of 2003 and is included here as Appendix 1. • December 1, 2003 to November 30, 2006, for a follow-on project under the same grant number entitled “Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models.” This report focuses primarily on the progress we made during the second period of funding subsequent to the work reported on in Appendix 1. When we began this project, we were thinking almost exclusively in terms of long-term fertilization over large regions of the ocean such as the Southern Ocean, with much of our focus being on how ocean circulation and biogeochemical cycling would interact to control the response to a given fertilization scenario. Our research on these types of scenarios, which was carried out largely during

  7. Inverse modeling of pan-Arctic methane emissions at high spatial resolution: what can we learn from assimilating satellite retrievals and using different process-based wetland and lake biogeochemical models?

    Directory of Open Access Journals (Sweden)

    Z. Tan

    2016-10-01

    Full Text Available Understanding methane emissions from the Arctic, a fast-warming carbon reservoir, is important for projecting future changes in the global methane cycle. Here we optimized methane emissions from north of 60° N (pan-Arctic regions using a nested-grid high-resolution inverse model that assimilates both high-precision surface measurements and column-average SCanning Imaging Absorption spectroMeter for Atmospheric CHartogrphY (SCIAMACHY satellite retrievals of methane mole fraction. For the first time, methane emissions from lakes were integrated into an atmospheric transport and inversion estimate, together with prior wetland emissions estimated with six biogeochemical models. In our estimates, in 2005, global methane emissions were in the range of 496.4–511.5 Tg yr−1, and pan-Arctic methane emissions were in the range of 11.9–28.5 Tg yr−1. Methane emissions from pan-Arctic wetlands and lakes were 5.5–14.2 and 2.4–14.2 Tg yr−1, respectively. Methane emissions from Siberian wetlands and lakes are the largest and also have the largest uncertainty. Our results indicate that the uncertainty introduced by different wetland models could be much larger than the uncertainty of each inversion. We also show that assimilating satellite retrievals can reduce the uncertainty of the nested-grid inversions. The significance of lake emissions cannot be identified across the pan-Arctic by high-resolution inversions, but it is possible to identify high lake emissions from some specific regions. In contrast to global inversions, high-resolution nested-grid inversions perform better in estimating near-surface methane concentrations.

  8. Modeling of System Families

    National Research Council Canada - National Science Library

    Feiler, Peter

    2007-01-01

    .... The Society of Automotive Engineers (SAE) Architecture Analysis & Design Language (AADL) is an industry-standard, architecture-modeling notation specifically designed to support a component- based approach to modeling embedded systems...

  9. Modelling Railway Interlocking Systems

    DEFF Research Database (Denmark)

    Lindegaard, Morten Peter; Viuf, P.; Haxthausen, Anne Elisabeth

    2000-01-01

    In this report we present a model of interlocking systems, and describe how the model may be validated by simulation. Station topologies are modelled by graphs in which the nodes denote track segments, and the edges denote connectivity for train traÆc. Points and signals are modelled by annotatio...

  10. Diel biogeochemical processes in terrestrial waters

    Science.gov (United States)

    Nimick, David A.; Gammons, Christopher H.

    2011-01-01

    scientists typically do not encompass the wide diversity and range of processes that produce diel cycles, and (3) the logistics of making field measurements for 24-h periods has limited recognition and understanding of these important cycles. Thus, the topical session brought together hydrologists, biologists, geochemists, and ecologists to discuss field studies, laboratory experiments, theoretical modeling, and measurement techniques related to diel cycling. Hopefully with the cross-disciplinary synergy developed at the session as well as by this special issue, a more comprehensive understanding of the interrelationships between the diel processes will be developed. Needless to say, understanding diel processes is critical for regulatory agencies and the greater scientific community. And perhaps more importantly, expanded knowledge of biogeochemical cycling may lead to better predictions of how aquatic ecosystems might react to changing conditions of contaminant loading, eutrophication, climate change, drought, industrialization, development, and other variables.

  11. Simulation of anthropogenic CO2 uptake in the CCSM3.1 ocean circulation-biogeochemical model: comparison with data-based estimates

    Science.gov (United States)

    Wang, S.; Moore, J. K.; Primeau, F. W.; Khatiwala, S.

    2012-04-01

    The global ocean has taken up a large fraction of the CO2 released by human activities since the industrial revolution. Quantifying the oceanic anthropogenic carbon (Cant) inventory and its variability is important for predicting the future global carbon cycle. The detailed comparison of data-based and model-based estimates is essential for the validation and continued improvement of our prediction capabilities. So far, three global estimates of oceanic Cant inventory that are "data-based" and independent of global ocean circulation models have been produced: one based on the Δ C* method, and two that are based on constraining surface-to-interior transport of tracers, the TTD method and a maximum entropy inversion method (GF). The GF method, in particular, is capable of reconstructing the history of Cant inventory through the industrial era. In the present study we use forward model simulations of the Community Climate System Model (CCSM3.1) to estimate the Cant inventory and compare the results with the data-based estimates. We also use the simulations to test several assumptions of the GF method, including the assumption of constant climate and circulation, which is common to all the data-based estimates. Though the integrated estimates of global Cant inventories are consistent with each other, the regional estimates show discrepancies up to 50 %. The CCSM3 model underestimates the total Cant inventory, in part due to weak mixing and ventilation in the North Atlantic and Southern Ocean. Analyses of different simulation results suggest that key assumptions about ocean circulation and air-sea disequilibrium in the GF method are generally valid on the global scale, but may introduce errors in Cant estimates on regional scales. The GF method should also be used with caution when predicting future oceanic anthropogenic carbon uptake.

  12. Low-frequency variability in North Sea and Baltic Sea identified through simulations with the 3-D coupled physical–biogeochemical model ECOSMO

    Directory of Open Access Journals (Sweden)

    U. Daewel

    2017-09-01

    Full Text Available Here we present results from a long-term model simulation of the 3-D coupled ecosystem model ECOSMO II for a North Sea and Baltic Sea set-up. The model allows both multi-decadal hindcast simulation of the marine system and specific process studies under controlled environmental conditions. Model results have been analysed with respect to long-term multi-decadal variability in both physical and biological parameters with the help of empirical orthogonal function (EOF analysis. The analysis of a 61-year (1948–2008 hindcast reveals a quasi-decadal variation in salinity, temperature and current fields in the North Sea in addition to singular events of major changes during restricted time frames. These changes in hydrodynamic variables were found to be associated with changes in ecosystem productivity that are temporally aligned with the timing of reported regime shifts in the areas. Our results clearly indicate that for analysing ecosystem productivity, spatially explicit methods are indispensable. Especially in the North Sea, a correlation analysis between atmospheric forcing and primary production (PP reveals significant correlations between PP and the North Atlantic Oscillation (NAO and wind forcing for the central part of the region, while the Atlantic Multi-decadal Oscillation (AMO and air temperature are correlated to long-term changes in PP in the southern North Sea frontal areas. Since correlations cannot serve to identify causal relationship, we performed scenario model runs perturbing the temporal variability in forcing condition to emphasize specifically the role of solar radiation, wind and eutrophication. The results revealed that, although all parameters are relevant for the magnitude of PP in the North Sea and Baltic Sea, the dominant impact on long-term variability and major shifts in ecosystem productivity was introduced by modulations of the wind fields.

  13. Simulation of anthropogenic CO2 uptake in the CCSM3.1 ocean circulation-biogeochemical model: comparison with data-based estimates

    Directory of Open Access Journals (Sweden)

    S. Khatiwala

    2012-04-01

    Full Text Available The global ocean has taken up a large fraction of the CO2 released by human activities since the industrial revolution. Quantifying the oceanic anthropogenic carbon (Cant inventory and its variability is important for predicting the future global carbon cycle. The detailed comparison of data-based and model-based estimates is essential for the validation and continued improvement of our prediction capabilities. So far, three global estimates of oceanic Cant inventory that are "data-based" and independent of global ocean circulation models have been produced: one based on the Δ C* method, and two that are based on constraining surface-to-interior transport of tracers, the TTD method and a maximum entropy inversion method (GF. The GF method, in particular, is capable of reconstructing the history of Cant inventory through the industrial era. In the present study we use forward model simulations of the Community Climate System Model (CCSM3.1 to estimate the Cant inventory and compare the results with the data-based estimates. We also use the simulations to test several assumptions of the GF method, including the assumption of constant climate and circulation, which is common to all the data-based estimates. Though the integrated estimates of global Cant inventories are consistent with each other, the regional estimates show discrepancies up to 50 %. The CCSM3 model underestimates the total Cant inventory, in part due to weak mixing and ventilation in the North Atlantic and Southern Ocean. Analyses of different simulation results suggest that key assumptions about ocean circulation and air-sea disequilibrium in the GF method are generally valid on the global scale, but may introduce errors in Cant estimates on regional scales. The GF method should also be used with caution when predicting future oceanic anthropogenic carbon uptake.

  14. Neotropical peatland methane emissions along a vegetation and biogeochemical gradient.

    Science.gov (United States)

    Winton, R Scott; Flanagan, Neal; Richardson, Curtis J

    2017-01-01

    Tropical wetlands are thought to be the most important source of interannual variability in atmospheric methane (CH4) concentrations, yet sparse data prevents them from being incorporated into Earth system models. This problem is particularly pronounced in the neotropics where bottom-up models based on water table depth are incongruent with top-down inversion models suggesting unaccounted sinks or sources of CH4. The newly documented vast areas of peatlands in the Amazon basin may account for an important unrecognized CH4 source, but the hydrologic and biogeochemical controls of CH4 dynamics from these systems remain poorly understood. We studied three zones of a peatland in Madre de Dios, Peru, to test whether CH4 emissions and pore water concentrations varied with vegetation community, soil chemistry and proximity to groundwater sources. We found that the open-canopy herbaceous zone emitted roughly one-third as much CH4 as the Mauritia flexuosa palm-dominated areas (4.7 ± 0.9 and 14.0 ± 2.4 mg CH4 m-2 h-1, respectively). Emissions decreased with distance from groundwater discharge across the three sampling sites, and tracked changes in soil carbon chemistry, especially increased soil phenolics. Based on all available data, we calculate that neotropical peatlands contribute emissions of 43 ± 11.9 Tg CH4 y-1, however this estimate is subject to geographic bias and will need revision once additional studies are published.

  15. Neotropical peatland methane emissions along a vegetation and biogeochemical gradient.

    Directory of Open Access Journals (Sweden)

    R Scott Winton

    Full Text Available Tropical wetlands are thought to be the most important source of interannual variability in atmospheric methane (CH4 concentrations, yet sparse data prevents them from being incorporated into Earth system models. This problem is particularly pronounced in the neotropics where bottom-up models based on water table depth are incongruent with top-down inversion models suggesting unaccounted sinks or sources of CH4. The newly documented vast areas of peatlands in the Amazon basin may account for an important unrecognized CH4 source, but the hydrologic and biogeochemical controls of CH4 dynamics from these systems remain poorly understood. We studied three zones of a peatland in Madre de Dios, Peru, to test whether CH4 emissions and pore water concentrations varied with vegetation community, soil chemistry and proximity to groundwater sources. We found that the open-canopy herbaceous zone emitted roughly one-third as much CH4 as the Mauritia flexuosa palm-dominated areas (4.7 ± 0.9 and 14.0 ± 2.4 mg CH4 m-2 h-1, respectively. Emissions decreased with distance from groundwater discharge across the three sampling sites, and tracked changes in soil carbon chemistry, especially increased soil phenolics. Based on all available data, we calculate that neotropical peatlands contribute emissions of 43 ± 11.9 Tg CH4 y-1, however this estimate is subject to geographic bias and will need revision once additional studies are published.

  16. Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history

    Science.gov (United States)

    Goldman, Amy E.; Graham, Emily B.; Crump, Alex R.; Kennedy, David W.; Romero, Elvira B.; Anderson, Carolyn G.; Dana, Karl L.; Resch, Charles T.; Fredrickson, Jim K.; Stegen, James C.

    2017-09-01

    , the microbial community adapts to saturation by shifting composition, and the CO2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. Extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.

  17. Using Coupled Models to Study the Effects of River Discharge on Biogeochemical Cycling and Hypoxia in the Northern Gulf of Mexico

    Science.gov (United States)

    Penta, Bradley; Ko, D.; Gould, Richard W.; Arnone, Robert A.; Greene, R.; Lehrter, J.; Hagy, James; Schaeffer, B.; Murrell, M.; Kurtz, J.; hide

    2009-01-01

    We describe emerging capabilities to understand physical processes and biogeoehemical cycles in coastal waters through the use of satellites, numerical models, and ship observations. Emerging capabilities provide significantly improved ability to model ecological systems and the impact of environmental management actions on them. The complex interaction of physical and biogeoehemical processes responsible for hypoxic events requires an integrated approach to research, monitoring, and modeling in order to fully define the processes leading to hypoxia. Our efforts characterizes the carbon cycle associated with river plumes and the export of organic matter and nutrients form coastal Louisiana wetlands and embayments in a spatially and temporally intensive manner previously not possible. Riverine nutrients clearly affect ecosystems in the northern Gulf of Mexico as evidenced in the occurrence of regional hypoxia events. Less known and largely unqualified is the export of organic matter and nutrients from the large areas of disappearing coastal wetlands and large embayments adjacent to the Louisiana Continental Shelf. This project provides new methods to track the river plume along the shelf and to estimate the rate of export of suspended inorganic and organic paniculate matter and dissolved organic matter form coastal habitats of south Louisiana.

  18. CH4 and N2O Emissions from Rice Paddy Soils in Vietnam - Identifying Regional Hotspots and Quantifying the Total Emission Strength using a Biogeochemical Model

    Science.gov (United States)

    Werner, C.; Kraus, D.; Mai, T. V.; Butterbach-Bahl, K.

    2016-12-01

    Agriculture is the economic backbone for over two thirds of Vietnam's population, providing food security, employment and income. However, agriculture in Vietnam is challenged by climate change and climate extremes and at the same time, agriculture remains a key source of greenhouse gas (GHG) emissions. The first bi-annual update report (BUR1), published in 2014 indicated that while the proportion of GHG emissions from agriculture had fallen from 43.1% to 33.2% from 2000 to 2010, the emission total increased from 65.1 mio to 88.4 mio t CO2e. Reducing GHG emissions from agriculture has thus become a key issue within the national strategy of GHG emission management. Here we present first data using IPCC Tier 3 modeling for quantifying the source strength of rice based crop systems for CH4 and N2O. We used LandscapeDNDC and linked it to a newly developed spatial landuse and land management database (climate, soil properties, and detailed field management data). Site application showed good agreement of simulated biomass, yield and GHG emissions with field observations, providing confidence for model use at national scale. Our results also show good agreement with national yield data and total annual emissions of the simulated period (2006-2015) ranged from 1060 - 1502 kt CH4 and 6.2 - 7.7 kt N2O, respectively. The dominating emission hotspot for CH4 is the Mekong Delta region with its double and triple rice cropping systems (819 kt CH4/yr, Fig. 1). With regard to N2O, emission hotspots have been identified to be closely related to regions with high fertilizer use and single to double rice cropping systems (Fig. 1). Though, our emission estimates are likely representing the best of current knowledge on national GHG emissions from rice based systems in Vietnam, the uncertainty is significant as information on rice system management remains vague. Sensitivity studies show that changes in field management affecting the soil organic carbon dynamics (duration of flooding

  19. The NEON Aquatic Network: Expanding the Availability of Biogeochemical Data

    Science.gov (United States)

    Vance, J. M.; Bohall, C.; Fitzgerald, M.; Utz, R.; Parker, S. M.; Roehm, C. L.; Goodman, K. J.; McLaughlin, B.

    2013-12-01

    Aquatic ecosystems are facing unprecedented pressure from climate change and land-use practices. Invasive species, whether plant, animal, insect or microbe present additional threat to aquatic ecosystem services. There are significant scientific challenges to understanding how these forces will interact to affect aquatic ecosystems, as the flow of energy and materials in the environment is driven by multivariate and non-linear biogeochemical cycles. The National Ecological Observatory Network (NEON) will collect and provide observational data across multiple scales. Sites were selected to maximize representation of major North American ecosystems using a multivariate geographic clustering method that partitioned the continental US, AK, HI, and Puerto Rico into 20 eco-climatic domains. The NEON data collection systems and methods are designed to yield standardized, near real-time data subjected to rigorous quality controls prior to public dissemination through an online data portal. NEON will collect data for 30 years to facilitate spatial-temporal analysis of environmental responses and drivers of ecosystem change, ranging from local through continental scales. Here we present the NEON Aquatic Network, a multi-parameter network consisting of a combination of in situ sensor and observational data. This network will provide data to examine biogeochemical, biological, hydrologic and geomorphic metrics at 36 sites, which are a combination of small 1st/2nd order wadeable streams, large rivers and lakes. A typical NEON Aquatic site will host up to two in-stream sensor sets designed to collect near-continuous water quality data (e.g. pH/ORP, temperature, conductivity, dissolved oxygen, CDOM) along with up to 8 shallow groundwater monitoring wells (level, temp., cond.), and a local meteorological station (e.g. 2D wind speed, PAR, barometric pressure, temperature, net radiation). These coupled sensor suites will be complemented by observational data (e.g. water

  20. Biogeochemical reactive-transport modelling of the interactions of medium activity long-lived nuclear waste in fractured argillite and the effect on redox conditions

    International Nuclear Information System (INIS)

    Small, J.S.; Steele, H.; Kwong, S.; Albrecht, A.

    2010-01-01

    Document available in extended abstract form only. The role of anaerobic microbial processes in mediating gas generation and redox reactions in organic (cellulose) containing low level activity nuclear wastes (LLW) is well established through monitoring of operational near-surface LLW disposal sites and municipal waste disposal sites. Modelling approaches based on Monod kinetic growth models to represent the complex suite of anaerobic processes have been developed and these models are able to reproduce the evolving biogeochemistry and gas generation of large scale and long term (10 year) experiments on cellulose waste degradation. In the case of geological disposal of medium activity long-lived nuclear waste (MAVL) microbial processes have the potential to exploit metabolic energy sources present in the waste, engineered barriers and host geological formation and as a consequence influence redox potential. Several electron donors and electron acceptors may be present in MAVL. Electron donors include; hydrogen (resulting from radiolysis and anaerobic corrosion of metals), and hydrolysis products of organic waste materials. Sulphate, nitrate and Fe(III) containing minerals and corrosion products are examples of electron acceptors present in intermediate level wastes. Significant amounts of organic matter, sulphate and iron minerals may also be present in host geological formations and have the potential to act as microbial energy sources once the system is perturbed by electron donors/acceptors from the waste. The construction of a geological disposal facility will physically disturb the host formation, potentially causing fracturing of the excavation damage zone (EDZ). The EDZ may thus provide environmental conditions, such as space and free water that together with nutrient and energy sources to promote microbial activity. In this study the Generalised Repository Model (GRM) developed to simulate the coupled microbiological, chemical and transport processes in near

  1. RSMASS system model development

    International Nuclear Information System (INIS)

    Marshall, A.C.; Gallup, D.R.

    1998-01-01

    RSMASS system mass models have been used for more than a decade to make rapid estimates of space reactor power system masses. This paper reviews the evolution of the RSMASS models and summarizes present capabilities. RSMASS has evolved from a simple model used to make rough estimates of space reactor and shield masses to a versatile space reactor power system model. RSMASS uses unique reactor and shield models that permit rapid mass optimization calculations for a variety of space reactor power and propulsion systems. The RSMASS-D upgrade of the original model includes algorithms for the balance of the power system, a number of reactor and shield modeling improvements, and an automatic mass optimization scheme. The RSMASS-D suite of codes cover a very broad range of reactor and power conversion system options as well as propulsion and bimodal reactor systems. Reactor choices include in-core and ex-core thermionic reactors, liquid metal cooled reactors, particle bed reactors, and prismatic configuration reactors. Power conversion options include thermoelectric, thermionic, Stirling, Brayton, and Rankine approaches. Program output includes all major component masses and dimensions, efficiencies, and a description of the design parameters for a mass optimized system. In the past, RSMASS has been used as an aid to identify and select promising concepts for space power applications. The RSMASS modeling approach has been demonstrated to be a valuable tool for guiding optimization of the power system design; consequently, the model is useful during system design and development as well as during the selection process. An improved in-core thermionic reactor system model RSMASS-T is now under development. The current development of the RSMASS-T code represents the next evolutionary stage of the RSMASS models. RSMASS-T includes many modeling improvements and is planned to be more user-friendly. RSMASS-T will be released as a fully documented, certified code at the end of

  2. Assessment of the sea-ice carbon pump: Insights from a three-dimensional ocean-sea-ice biogeochemical model (NEMO-LIM-PISCES

    Directory of Open Access Journals (Sweden)

    Sébastien Moreau

    2016-08-01

    Full Text Available Abstract The role of sea ice in the carbon cycle is minimally represented in current Earth System Models (ESMs. Among potentially important flaws, mentioned by several authors and generally overlooked during ESM design, is the link between sea-ice growth and melt and oceanic dissolved inorganic carbon (DIC and total alkalinity (TA. Here we investigate whether this link is indeed an important feature of the marine carbon cycle misrepresented in ESMs. We use an ocean general circulation model (NEMO-LIM-PISCES with sea-ice and marine carbon cycle components, forced by atmospheric reanalyses, adding a first-order representation of DIC and TA storage and release in/from sea ice. Our results suggest that DIC rejection during sea-ice growth releases several hundred Tg C yr−1 to the surface ocean, of which < 2% is exported to depth, leading to a notable but weak redistribution of DIC towards deep polar basins. Active carbon processes (mainly CaCO3 precipitation but also ice-atmosphere CO2 fluxes and net community production increasing the TA/DIC ratio in sea-ice modified ocean-atmosphere CO2 fluxes by a few Tg C yr−1 in the sea-ice zone, with specific hemispheric effects: DIC content of the Arctic basin decreased but DIC content of the Southern Ocean increased. For the global ocean, DIC content increased by 4 Tg C yr−1 or 2 Pg C after 500 years of model run. The simulated numbers are generally small compared to the present-day global ocean annual CO2 sink (2.6 ± 0.5 Pg C yr−1. However, sea-ice carbon processes seem important at regional scales as they act significantly on DIC redistribution within and outside polar basins. The efficiency of carbon export to depth depends on the representation of surface-subsurface exchanges and their relationship with sea ice, and could differ substantially if a higher resolution or different ocean model were used.

  3. Systemic resilience model

    International Nuclear Information System (INIS)

    Lundberg, Jonas; Johansson, Björn JE

    2015-01-01

    It has been realized that resilience as a concept involves several contradictory definitions, both for instance resilience as agile adjustment and as robust resistance to situations. Our analysis of resilience concepts and models suggest that beyond simplistic definitions, it is possible to draw up a systemic resilience model (SyRes) that maintains these opposing characteristics without contradiction. We outline six functions in a systemic model, drawing primarily on resilience engineering, and disaster response: anticipation, monitoring, response, recovery, learning, and self-monitoring. The model consists of four areas: Event-based constraints, Functional Dependencies, Adaptive Capacity and Strategy. The paper describes dependencies between constraints, functions and strategies. We argue that models such as SyRes should be useful both for envisioning new resilience methods and metrics, as well as for engineering and evaluating resilient systems. - Highlights: • The SyRes model resolves contradictions between previous resilience definitions. • SyRes is a core model for envisioning and evaluating resilience metrics and models. • SyRes describes six functions in a systemic model. • They are anticipation, monitoring, response, recovery, learning, self-monitoring. • The model describes dependencies between constraints, functions and strategies

  4. Selected System Models

    Science.gov (United States)

    Schmidt-Eisenlohr, F.; Puñal, O.; Klagges, K.; Kirsche, M.

    Apart from the general issue of modeling the channel, the PHY and the MAC of wireless networks, there are specific modeling assumptions that are considered for different systems. In this chapter we consider three specific wireless standards and highlight modeling options for them. These are IEEE 802.11 (as example for wireless local area networks), IEEE 802.16 (as example for wireless metropolitan networks) and IEEE 802.15 (as example for body area networks). Each section on these three systems discusses also at the end a set of model implementations that are available today.

  5. Towards a community Earth System Model

    Science.gov (United States)

    Blackmon, M.

    2003-04-01

    The Community Climate System Model, version 2 (CCSM2), was released in June 2002. CCSM2 has several new components and features, which I will discuss briefly. I will also show a few results from a multi-century equilibrium run with this model, emphasizing the improvements over the earlier simulation using the original CSM. A few flaws and inadequacies in CCSM2 have been identified. I will also discuss briefly work underway to improve the model and present results, if available. CCSM2, with improvements, will be the basis for the development of a Community Earth System Model (CESM). The highest priority for expansion of the model involves incorporation of biogeosciences into the coupled model system, with emphasis given to the carbon, nitrogen and iron cycles. The overall goal of the biogeosciences project within CESM is to understand the regulation of planetary energetics, planetary ecology, and planetary metabolism through exchanges of energy, momentum, and materials among atmosphere, land, and ocean, and the response of the climate system through these processes to changes in land cover and land use. In particular, this research addresses how biogeochemical coupling of carbon, nitrogen, and iron cycles affects climate and how human perturbations of these cycles alter climate. To accomplish these goals, the Community Land Model, the land component of CCSM2, is being developed to include river routing, carbon and nitrogen cycles, emissions of mineral aerosols and biogenic volatile organic compounds, dry deposition of various gases, and vegetation dynamics. The carbon and nitrogen cycles are being implemented using parameterizations developed as part of a state-of-the-art ecosystem biogeochemistry model. The primary goal of this research is to provide an accurate net flux of CO2 between the land and the atmosphere so that CESM can be used to study the dynamics of the coupled climate-carbon system. Emissions of biogenic volatile organic compounds are also based on a

  6. A biogeochemical assessment of the Tono site, Japan

    Science.gov (United States)

    Baker, Steven J.; West, Julia M.; Metcalfe, Richard; Noy, David J.; Yoshida, H.; Aoki, K.

    1998-12-01

    When designing investigations of microbial populations in the subsurface, it is extremely valuable to undertake scoping calculations to estimate the likely microbial abundances and evaluate the effects of contamination during sampling. A biogeochemical assessment of the groundwater and lithologies of the Tono mine, Japan, has been made using the BGS/NAGRA computer code BGSE (Bacterial Growth in Subsurface Environments). This code enables an assessment to be made of the maximum microbial growth rates that may be achieved in ideal circumstances, based on availability of nutrients and energy calculated from mineralogical and groundwater analyses. The effect of drilling fluid/groundwater mixing on biomass was assessed using a hypothetical drilling fluid composition. The results of modelling the mixing between groundwater and drilling fluid shows that the addition of only small concentrations of drilling fluid (<1% (v/v)) to the groundwater gives rise to significant microbial growth rates for the systems studied. Maximum growth rates were observed at ratios of 50:50 (v/v) (groundwater: drilling fluid) for the Akeyo and Toki lower groundwaters, and ratios of 90:10 (v/v) (groundwater:drilling fluid) for the Toki upper and Granite groundwaters. At low ratios of drilling fluid (<1% (v/v)) the limiting factor in each system was the availability of an energy source. This reflects the fact that the system is approaching pristine conditions. However, there was sufficient energy to permit a significant growth rate to be observed.

  7. Evaluating the Terrestrial Biogeochemical Responses and Feedbacks of Stratospheric Geoengineering Strategies

    Science.gov (United States)

    Yang, C. E.; Hoffman, F. M.; Fu, J. S.

    2017-12-01

    Stratospheric aerosol geoengineering options, involving injection of sulfur dioxide (SO2) aerosols into the stratosphere, are being proposed to reduce the heating effects of increasing anthropogenic atmospheric carbon dioxide (CO2). While the impacts of stratospheric aerosol geoengineering on climate changes, such as stratospheric ozone depletion and weakened monsoons, have been extensively investigated in the past few decades, few studies have considered the biogeochemical (BGC) responses and feedbacks on land. Previous Earth system model (ESM) simulations incorporating stratospheric aerosol geoengineering scenarios primarily focused on the atmospheric radiative forcing and temperature response in the absence of ocean and land responses. The land model setup in these simulations did not incorporate the carbon-nitrogen cycles and effects on the hydrological cycle considering vegetation responses. Since ESMs simulated very different aerosol distributions for the G3 and G4 scenarios in the Geoengineering Model Intercomparison Project (GeoMIP), we instead adopted the G4SSA scenario to simulate the BGC responses and feedbacks on land due to stratospheric aerosol geoengineering using the Community Earth System Model with active biogeochemical dynamic variations enabled. Implications for the terrestrial carbon cycle and hydrological responses will be presented.

  8. Landscape Conservation of Aquatic Habitats Promotes Watershed-scale Biological, Biogeochemical, and Hydrological Functions

    Science.gov (United States)

    Wetlands are exceptionally productive landscape features that provide critical habitat for endemic species, threatened/endangered and migratory animals, store floodwaters and maintain baseflows in stream systems, recharge groundwaters, and biogeochemically and physically affect n...

  9. Modeling cellular systems

    CERN Document Server

    Matthäus, Franziska; Pahle, Jürgen

    2017-01-01

    This contributed volume comprises research articles and reviews on topics connected to the mathematical modeling of cellular systems. These contributions cover signaling pathways, stochastic effects, cell motility and mechanics, pattern formation processes, as well as multi-scale approaches. All authors attended the workshop on "Modeling Cellular Systems" which took place in Heidelberg in October 2014. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.

  10. Hydrological and associated biogeochemical consequences of rapid global warming during the Paleocene-Eocene Thermal Maximum

    Science.gov (United States)

    Carmichael, Matthew J.; Inglis, Gordon N.; Badger, Marcus P. S.; Naafs, B. David A.; Behrooz, Leila; Remmelzwaal, Serginio; Monteiro, Fanny M.; Rohrssen, Megan; Farnsworth, Alexander; Buss, Heather L.; Dickson, Alexander J.; Valdes, Paul J.; Lunt, Daniel J.; Pancost, Richard D.

    2017-10-01

    The Paleocene-Eocene Thermal Maximum (PETM) hyperthermal, 56 million years ago (Ma), is the most dramatic example of abrupt Cenozoic global warming. During the PETM surface temperatures increased between 5 and 9 °C and the onset likely took < 20 kyr. The PETM provides a case study of the impacts of rapid global warming on the Earth system, including both hydrological and associated biogeochemical feedbacks, and proxy data from the PETM can provide constraints on changes in warm climate hydrology simulated by general circulation models (GCMs). In this paper, we provide a critical review of biological and geochemical signatures interpreted as direct or indirect indicators of hydrological change at the PETM, explore the importance of adopting multi-proxy approaches, and present a preliminary model-data comparison. Hydrological records complement those of temperature and indicate that the climatic response at the PETM was complex, with significant regional and temporal variability. This is further illustrated by the biogeochemical consequences of inferred changes in hydrology and, in fact, changes in precipitation and the biogeochemical consequences are often conflated in geochemical signatures. There is also strong evidence in many regions for changes in the episodic and/or intra-annual distribution of precipitation that has not widely been considered when comparing proxy data to GCM output. Crucially, GCM simulations indicate that the response of the hydrological cycle to the PETM was heterogeneous - some regions are associated with increased precipitation - evaporation (P - E), whilst others are characterised by a decrease. Interestingly, the majority of proxy data come from the regions where GCMs predict an increase in PETM precipitation. We propose that comparison of hydrological proxies to GCM output can be an important test of model skill, but this will be enhanced by further data from regions of model-simulated aridity and simulation of extreme precipitation

  11. Methods for biogeochemical studies of sea ice: The state of the art, caveats, and recommendations

    Directory of Open Access Journals (Sweden)

    Lisa A. Miller

    2015-01-01

    Full Text Available Abstract Over the past two decades, with recognition that the ocean’s sea-ice cover is neither insensitive to climate change nor a barrier to light and matter, research in sea-ice biogeochemistry has accelerated significantly, bringing together a multi-disciplinary community from a variety of fields. This disciplinary diversity has contributed a wide range of methodological techniques and approaches to sea-ice studies, complicating comparisons of the results and the development of conceptual and numerical models to describe the important biogeochemical processes occurring in sea ice. Almost all chemical elements, compounds, and biogeochemical processes relevant to Earth system science are measured in sea ice, with published methods available for determining biomass, pigments, net community production, primary production, bacterial activity, macronutrients, numerous natural and anthropogenic organic compounds, trace elements, reactive and inert gases, sulfur species, the carbon dioxide system parameters, stable isotopes, and water-ice-atmosphere fluxes of gases, liquids, and solids. For most of these measurements, multiple sampling and processing techniques are available, but to date there has been little intercomparison or intercalibration between methods. In addition, researchers collect different types of ancillary data and document their samples differently, further confounding comparisons between studies. These problems are compounded by the heterogeneity of sea ice, in which even adjacent cores can have dramatically different biogeochemical compositions. We recommend that, in future investigations, researchers design their programs based on nested sampling patterns, collect a core suite of ancillary measurements, and employ a standard approach for sample identification and documentation. In addition, intercalibration exercises are most critically needed for measurements of biomass, primary production, nutrients, dissolved and particulate

  12. Ocean fronts drive marine fishery production and biogeochemical cycling.

    Science.gov (United States)

    Woodson, C Brock; Litvin, Steven Y

    2015-02-10

    Long-term changes in nutrient supply and primary production reportedly foreshadow substantial declines in global marine fishery production. These declines combined with current overfishing, habitat degradation, and pollution paint a grim picture for the future of marine fisheries and ecosystems. However, current models forecasting such declines do not account for the effects of ocean fronts as biogeochemical hotspots. Here we apply a fundamental technique from fluid dynamics to an ecosystem model to show how fronts increase total ecosystem biomass, explain fishery production, cause regime shifts, and contribute significantly to global biogeochemical budgets by channeling nutrients through alternate trophic pathways. We then illustrate how ocean fronts affect fishery abundance and yield, using long-term records of anchovy-sardine regimes and salmon abundances in the California Current. These results elucidate the fundamental importance of biophysical coupling as a driver of bottom-up vs. top-down regulation and high productivity in marine ecosystems.

  13. Marginal Ice Zone: Biogeochemical Sampling with Gliders

    Science.gov (United States)

    2015-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Marginal Ice Zone: Biogeochemical Sampling with Gliders...under the ice and in the marginal ice zone. The project specific goals are to develop biogeochemical and optical proxies for glider optics; to use the...water, in the marginal ice zone, and under the ice; to use glider optical measurements to compute fields of rates of photosynthetic carbon fixation

  14. Modelling of wastewater systems

    DEFF Research Database (Denmark)

    Bechmann, Henrik

    Oxygen Demand) flux and SS flux in the inlet to the WWTP. COD is measured by means of a UV absorption sensor while SS is measured by a turbidity sensor. These models include a description of the deposit of COD and SS amounts, respectively, in the sewer system, and the models can thus be used to quantify......In this thesis, models of pollution fluxes in the inlet to 2 Danish wastewater treatment plants (WWTPs) as well as of suspended solids (SS) concentrations in the aeration tanks of an alternating WWTP and in the effluent from the aeration tanks are developed. The latter model is furthermore used...... to analyze and quantify the effect of the Aeration Tank Settling (ATS) operating mode, which is used during rain events. Furthermore, the model is used to propose a control algorithm for the phase lengths during ATS operation. The models are mainly formulated as state space model in continuous time...

  15. The Community Earth System Model: A Framework for Collaborative Research

    Energy Technology Data Exchange (ETDEWEB)

    Hurrell, Jim; Holland, Marika M.; Gent, Peter R.; Ghan, Steven J.; Kay, Jennifer; Kushner, P.; Lamarque, J.-F.; Large, William G.; Lawrence, David M.; Lindsay, Keith; Lipscomb, William; Long , Matthew; Mahowald, N.; Marsh, D.; Neale, Richard; Rasch, Philip J.; Vavrus, Steven J.; Vertenstein, Mariana; Bader, David C.; Collins, William D.; Hack, James; Kiehl, J. T.; Marshall, Shawn

    2013-09-30

    The Community Earth System Model (CESM) is a flexible and extensible community tool used to investigate a diverse set of earth system interactions across multiple time and space scales. This global coupled model is a natural evolution from its predecessor, the Community Climate System Model, following the incorporation of new earth system capabilities. These include the ability to simulate biogeochemical cycles, atmospheric chemistry, ice sheets, and a high-top atmosphere. These and other new model capabilities are enabling investigations into a wide range of pressing scientific questions, providing new predictive capabilities and increasing our collective knowledge about the behavior and interactions of the earth system. Simulations with numerous configurations of the CESM have been provided to the Coupled Model Intercomparison Project Phase 5 (CMIP5) and are being analyzed by the broader community of scientists. Additionally, the model source code and associated documentation are freely available to the scientific community to use for earth system studies, making it a true community tool. Here we describe this earth modeling system, its various possible configurations, and illustrate its capabilities with a few science highlights.

  16. Biotic and Biogeochemical Feedbacks to Climate Change

    Science.gov (United States)

    Torn, M. S.; Harte, J.

    2002-12-01

    Feedbacks to paleoclimate change are evident in ice core records showing correlations of temperature with carbon dioxide, nitrous oxide, and methane. Such feedbacks may be explained by plant and microbial responses to climate change, and are likely to occur under impending climate warming, as evidenced by results of ecosystem climate manipulation experiments and biometeorological observations along ecological and climate gradients. Ecosystems exert considerable influence on climate, by controlling the energy and water balance of the land surface as well as being sinks and sources of greenhouse gases. This presentation will focus on biotic and biogeochemical climate feedbacks on decadal to century time scales, emphasizing carbon storage and energy exchange. In addition to the direct effects of climate on decomposition rates and of climate and CO2 on plant productivity, climate change can alter species composition; because plant species differ in their surface properties, productivity, phenology, and chemistry, climate-induced changes in plant species composition can exert a large influence on the magnitude and sign of climate feedbacks. We discuss the effects of plant species on ecosystem carbon storage that result from characteristic differences in plant biomass and lifetime, allocation to roots vs. leaves, litter quality, microclimate for decomposition and the ultimate stabilization of soil organic matter. We compare the effect of species transitions on transpiration, albedo, and other surface properties, with the effect of elevated CO2 and warming on single species' surface exchange. Global change models and experiments that investigate the effect of climate only on existing vegetation may miss the biggest impacts of climate change on biogeochemical cycling and feedbacks. Quantification of feedbacks will require understanding how species composition and long-term soil processes will change under global warming. Although no single approach, be it experimental

  17. Modeling Complex Systems

    CERN Document Server

    Boccara, Nino

    2010-01-01

    Modeling Complex Systems, 2nd Edition, explores the process of modeling complex systems, providing examples from such diverse fields as ecology, epidemiology, sociology, seismology, and economics. It illustrates how models of complex systems are built and provides indispensable mathematical tools for studying their dynamics. This vital introductory text is useful for advanced undergraduate students in various scientific disciplines, and serves as an important reference book for graduate students and young researchers. This enhanced second edition includes: . -recent research results and bibliographic references -extra footnotes which provide biographical information on cited scientists who have made significant contributions to the field -new and improved worked-out examples to aid a student’s comprehension of the content -exercises to challenge the reader and complement the material Nino Boccara is also the author of Essentials of Mathematica: With Applications to Mathematics and Physics (Springer, 2007).

  18. Modeling Complex Systems

    International Nuclear Information System (INIS)

    Schreckenberg, M

    2004-01-01

    This book by Nino Boccara presents a compilation of model systems commonly termed as 'complex'. It starts with a definition of the systems under consideration and how to build up a model to describe the complex dynamics. The subsequent chapters are devoted to various categories of mean-field type models (differential and recurrence equations, chaos) and of agent-based models (cellular automata, networks and power-law distributions). Each chapter is supplemented by a number of exercises and their solutions. The table of contents looks a little arbitrary but the author took the most prominent model systems investigated over the years (and up until now there has been no unified theory covering the various aspects of complex dynamics). The model systems are explained by looking at a number of applications in various fields. The book is written as a textbook for interested students as well as serving as a comprehensive reference for experts. It is an ideal source for topics to be presented in a lecture on dynamics of complex systems. This is the first book on this 'wide' topic and I have long awaited such a book (in fact I planned to write it myself but this is much better than I could ever have written it!). Only section 6 on cellular automata is a little too limited to the author's point of view and one would have expected more about the famous Domany-Kinzel model (and more accurate citation!). In my opinion this is one of the best textbooks published during the last decade and even experts can learn a lot from it. Hopefully there will be an actualization after, say, five years since this field is growing so quickly. The price is too high for students but this, unfortunately, is the normal case today. Nevertheless I think it will be a great success! (book review)

  19. A test of the hierarchical model of litter decomposition

    NARCIS (Netherlands)

    Bradford, Mark A.; Veen, Ciska G.F.; Bonis, Anne; Bradford, Ella M.; Classen, Aimee T.; Cornelissen, J.H.C.; Crowther, T.W.; Long, de Jonathan R.; Freschet, Gregoire T.; Kardol, Paul; Manrubia-Freixa, Marta; Maynard, Daniel S.; Newman, Gregory S.; Logtestijn, Richard S.P.; Viketoft, Maria; Wardle, David A.; Wieder, William R.; Wood, Stephen A.; Putten, van der Wim H.

    2017-01-01

    Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle–climate feedbacks therefore depends on accurate knowledge about the controls

  20. A test of the hierarchical model of litter decomposition

    NARCIS (Netherlands)

    Bradford, Mark A.; Ciska, G. F.; Bonis, Anne; Bradford, Ella M.; Classen, Aimee T.; Cornelissen, J. Hans C.; Crowther, Thomas W.; De Long, Jonathan R.; Freschet, Gregoire T.; Kardol, Paul; Manrubia-Freixa, Marta; Maynard, Daniel S.; Newman, Gregory S.; Logtestijn, Richard S.P.; Viketoft, Maria; Wardle, David A.; Wieder, William R.; Wood, Stephen A.; Van Der Putten, Wim H.

    2017-01-01

    Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle-climate feedbacks therefore depends on accurate knowledge about the controls

  1. Modeling the earth system

    Energy Technology Data Exchange (ETDEWEB)

    Ojima, D. [ed.

    1992-12-31

    The 1990 Global Change Institute (GCI) on Earth System Modeling is the third of a series organized by the Office for Interdisciplinary Earth Studies to look in depth at particular issues critical to developing a better understanding of the earth system. The 1990 GCI on Earth System Modeling was organized around three themes: defining critical gaps in the knowledge of the earth system, developing simplified working models, and validating comprehensive system models. This book is divided into three sections that reflect these themes. Each section begins with a set of background papers offering a brief tutorial on the subject, followed by working group reports developed during the institute. These reports summarize the joint ideas and recommendations of the participants and bring to bear the interdisciplinary perspective that imbued the institute. Since the conclusion of the 1990 Global Change Institute, research programs, nationally and internationally, have moved forward to implement a number of the recommendations made at the institute, and many of the participants have maintained collegial interactions to develop research projects addressing the needs identified during the two weeks in Snowmass.

  2. Nutrient transports in the Baltic Sea - results from a 30-year physical-biogeochemical reanalysis

    Science.gov (United States)

    Liu, Ye; Meier, H. E. Markus; Eilola, Kari

    2017-04-01

    Long-term oxygen and nutrient transports in the Baltic Sea are reconstructed using the Swedish Coastal and Ocean Biogeochemical model (SCOBI) coupled to the Rossby Centre Ocean model (RCO). Two simulations with and without data assimilation covering the period 1970-1999 are carried out. Here, the weakly coupled scheme with the Ensemble Optimal Interpolation (EnOI) method is adopted to assimilate observed profiles in the reanalysis system. The reanalysis shows considerable improvement in the simulation of both oxygen and nutrient concentrations relative to the free run. Further, the results suggest that the assimilation of biogeochemical observations has a significant effect on the simulation of the oxygen-dependent dynamics of biogeochemical cycles. From the reanalysis, nutrient transports between sub-basins, between the coastal zone and the open sea, and across latitudinal and longitudinal cross sections are calculated. Further, the spatial distributions of regions with nutrient import or export are examined. Our results emphasize the important role of the Baltic proper for the entire Baltic Sea, with large net transport (export minus import) of nutrients from the Baltic proper into the surrounding sub-basins (except the net phosphorus import from the Gulf of Riga and the net nitrogen import from the Gulf of Riga and Danish Straits). In agreement with previous studies, we found that the Bothnian Sea imports large amounts of phosphorus from the Baltic proper that are retained in this sub-basin. For the calculation of sub-basin budgets, the location of the lateral borders of the sub-basins is crucial, because net transports may change sign with the location of the border. Although the overall transport patterns resemble the results of previous studies, our calculated estimates differ in detail considerably.

  3. Biogeochemical and isotopic gradients in a BTEX/PAH contaminant plume: Model-based interpretation of a high-resolution field data set

    DEFF Research Database (Denmark)

    Prommer, H.; Anneser, B.; Rolle, Massimo

    2009-01-01

    A high spatial resolution data set documenting carbon and sulfur isotope fractionation at a tar oil-contaminated, sulfate-reducing field site was analyzed with a reactive transport model. Within a comprehensive numerical model, the study links the distinctive observed isotope depth profiles...... with the degradation of various monoaromatic and polycyclic aromatic hydrocarbon compounds (BTEX/PAHs) under sulfate-reducing conditions. In the numerical model, microbial dynamics were simulated explicitly and isotope fractionation was directly linked to the differential microbial uptake of lighter and heavier carbon...... of toluene, which is the most rapidly degrading compound and the most important reductant at the site. The resulting depth profiles at the observation well show distinct differences between the small isotopic enrichment in the contaminant plume core and the much stronger enrichment of up to 3.3 parts per...

  4. Developing a Terrestrial Biogeochemical Cycle Modeling System to Support the Management of Fort Benning and its Surrounding Areas

    Science.gov (United States)

    2010-12-01

    prescribed fire is essential to maintain and restore longleaf pine ecosystem and associated biodiversity . However, it also substantially alters...Legends are the same as in Figure 26. -46 - SOC (sum of carbon in humus, particulate matters, soil microbes , and soil fungi) changed from about

  5. Developing a Spatially Distributed Terrestrial Biogeochemical Cycle Modeling System to Support the Management of Fort Benning and its Surrounding Areas

    Science.gov (United States)

    2010-12-01

    Cyclic prescribed fire is essential to maintain and restore longleaf pine ecosystem and associated biodiversity . However, it also substantially...stock (d). Legends are the same as in Figure 26. -46 - SOC (sum of carbon in humus, particulate matters, soil microbes , and soil fungi) changed

  6. Dramatic variability of the carbonate system at a temperate coastal ocean site (Beaufort, North Carolina, USA is regulated by physical and biogeochemical processes on multiple timescales.

    Directory of Open Access Journals (Sweden)

    Zackary I Johnson

    Full Text Available Increasing atmospheric carbon dioxide (CO2 from anthropogenic sources is acidifying marine environments resulting in potentially dramatic consequences for the physical, chemical and biological functioning of these ecosystems. If current trends continue, mean ocean pH is expected to decrease by ~0.2 units over the next ~50 years. Yet, there is also substantial temporal variability in pH and other carbon system parameters in the ocean resulting in regions that already experience change that exceeds long-term projected trends in pH. This points to short-term dynamics as an important layer of complexity on top of long-term trends. Thus, in order to predict future climate change impacts, there is a critical need to characterize the natural range and dynamics of the marine carbonate system and the mechanisms responsible for observed variability. Here, we present pH and dissolved inorganic carbon (DIC at time intervals spanning 1 hour to >1 year from a dynamic, coastal, temperate marine system (Beaufort Inlet, Beaufort NC USA to characterize the carbonate system at multiple time scales. Daily and seasonal variation of the carbonate system is largely driven by temperature, alkalinity and the balance between primary production and respiration, but high frequency change (hours to days is further influenced by water mass movement (e.g. tides and stochastic events (e.g. storms. Both annual (~0.3 units and diurnal (~0.1 units variability in coastal ocean acidity are similar in magnitude to 50 year projections of ocean acidity associated with increasing atmospheric CO2. The environmental variables driving these changes highlight the importance of characterizing the complete carbonate system rather than just pH. Short-term dynamics of ocean carbon parameters may already exert significant pressure on some coastal marine ecosystems with implications for ecology, biogeochemistry and evolution and this shorter term variability layers additive effects and

  7. Factors driving the biogeochemical budget of the Amazon River and its statistical modelling Facteurs denext term contrôle du bilan biogéochimique previous termdenext term l'Amazone et modélisation statistique associée

    OpenAIRE

    Bustillo , Vincent; Victoria , Reynaldo Luiz; Sousa De Moura , Jose Mauro; De Castro Victoria , Daniel; Toledo , Andrade; Collicchio , Erich

    2011-01-01

    International audience; The seasonal and interannual fluctuations of the biogeochemical budget (solutes, suspended matter, isotopes) of the Amazon River basin were analyzed, with a special focus on 44 physicochemical parameters monitored over the period 1982-1984 during the Carbon in the AMazon River Experiment (CAMREX) project. The relevant factors driving this variability were identified and sorted through the implementation of a statistical-regressive model coupled to variance analysis. Ba...

  8. Evolution of Earth-like Extrasolar Planetary Atmospheres: Assessing the Atmospheres and Biospheres of Early Earth Analog Planets with a Coupled Atmosphere Biogeochemical Model

    Science.gov (United States)

    Gebauer, S.; Grenfell, J. L.; Stock, J. W.; Lehmann, R.; Godolt, M.; von Paris, P.; Rauer, H.

    2017-01-01

    Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models. In this work, we present results from our newly developed Coupled Atmosphere Biogeochemistry model in which atmospheric O2 concentrations are fixed to values inferred by geological evidence. Applying a unique tool (Pathway Analysis Program), ours is the first quantitative analysis of catalytic cycles that governed O2 in early Earth's atmosphere near the Great Oxidation Event. Complicated oxidation pathways play a key role in destroying O2, whereas in the upper atmosphere, most O2 is formed abiotically via CO2 photolysis. The O2 bistability found by Goldblatt et al. (2006) is not observed in our calculations likely due to our detailed CH4 oxidation scheme. We calculate increased CH4 with increasing O2 during the Great Oxidation Event. For a given atmospheric surface flux, different atmospheric states are possible; however, the net primary productivity of the biosphere that produces O2 is unique. Mixing, CH4 fluxes, ocean solubility, and mantle/crust properties strongly affect net primary productivity and surface O2 fluxes. Regarding exoplanets, different "states" of O2 could exist for similar biomass output. Strong geological activity could lead to false negatives for life (since our analysis suggests that reducing gases remove O2 that

  9. Evolution of Earth-like Extrasolar Planetary Atmospheres: Assessing the Atmospheres and Biospheres of Early Earth Analog Planets with a Coupled Atmosphere Biogeochemical Model.

    Science.gov (United States)

    Gebauer, S; Grenfell, J L; Stock, J W; Lehmann, R; Godolt, M; von Paris, P; Rauer, H

    2017-01-01

    Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models. In this work, we present results from our newly developed Coupled Atmosphere Biogeochemistry model in which atmospheric O 2 concentrations are fixed to values inferred by geological evidence. Applying a unique tool (Pathway Analysis Program), ours is the first quantitative analysis of catalytic cycles that governed O 2 in early Earth's atmosphere near the Great Oxidation Event. Complicated oxidation pathways play a key role in destroying O 2 , whereas in the upper atmosphere, most O 2 is formed abiotically via CO 2 photolysis. The O 2 bistability found by Goldblatt et al. ( 2006 ) is not observed in our calculations likely due to our detailed CH 4 oxidation scheme. We calculate increased CH 4 with increasing O 2 during the Great Oxidation Event. For a given atmospheric surface flux, different atmospheric states are possible; however, the net primary productivity of the biosphere that produces O 2 is unique. Mixing, CH 4 fluxes, ocean solubility, and mantle/crust properties strongly affect net primary productivity and surface O 2 fluxes. Regarding exoplanets, different "states" of O 2 could exist for similar biomass output. Strong geological activity could lead to false negatives for life (since our analysis suggests that reducing gases

  10. Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses

    Science.gov (United States)

    Ogawa, Diogo M. O.; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R. B.; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

    2014-01-01

    We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing

  11. Building a high level sample processing and quality assessment model for biogeochemical measurements: a case study from the ocean acidification community

    Science.gov (United States)

    Thomas, R.; Connell, D.; Spears, T.; Leadbetter, A.; Burger, E. F.

    2016-12-01

    The scientific literature heavily features small-scale studies with the impact of the results extrapolated to regional/global importance. There are on-going initiatives (e.g. OA-ICC, GOA-ON, GEOTRACES, EMODNet Chemistry) aiming to assemble regional to global-scale datasets that are available for trend or meta-analyses. Assessing the quality and comparability of these data requires information about the processing chain from "sampling to spreadsheet". This provenance information needs to be captured and readily available to assess data fitness for purpose. The NOAA Ocean Acidification metadata template was designed in consultation with domain experts for this reason; the core carbonate chemistry variables have 23-37 metadata fields each and for scientists generating these datasets there could appear to be an ever increasing amount of metadata expected to accompany a dataset. While this provenance metadata should be considered essential by those generating or using the data, for those discovering data there is a sliding scale between what is considered discovery metadata (title, abstract, contacts, etc.) versus usage metadata (methodology, environmental setup, lineage, etc.), the split depending on the intended use of data. As part of the OA-ICC's activities, the metadata fields from the NOAA template relevant to the sample processing chain and QA criteria have been factored to develop profiles for, and extensions to, the OM-JSON encoding supported by the PROV ontology. While this work started focused on carbonate chemistry variable specific metadata, the factorization could be applied within the O&M model across other disciplines such as trace metals or contaminants. In a linked data world with a suitable high level model for sample processing and QA available, tools and support can be provided to link reproducible units of metadata (e.g. the standard protocol for a variable as adopted by a community) and simplify the provision of metadata and subsequent discovery.

  12. Information Systems Efficiency Model

    Directory of Open Access Journals (Sweden)

    Milos Koch

    2017-07-01

    Full Text Available This contribution discusses the basic concept of creating a new model for the efficiency and effectiveness assessment of company information systems. The present trends in this field are taken into account, and the attributes are retained of measuring the optimal solutions for a company’s ICT (the implementation, functionality, service, innovations, safety, relationships, costs, etc.. The proposal of a new model of assessment comes from our experience with formerly implemented and employed methods, methods which we have modified in time and adapted to companies’ needs but also to the necessaries of our research that has been done through the ZEFIS portal. The most noteworthy of them is the HOS method that we have discussed in a number of forums. Its main feature is the fact that it respects the complexity of an information system in correlation with the balanced state of its individual parts.

  13. Biogeochemical reactive transport of carbon, nitrogen and iron in the hyporheic zone

    Science.gov (United States)

    Dwivedi, D.; Steefel, C. I.; Newcomer, M. E.; Arora, B.; Spycher, N.; Hammond, G. E.; Moulton, J. D.; Fox, P. M.; Nico, P. S.; Williams, K. H.; Dafflon, B.; Carroll, R. W. H.

    2017-12-01

    To understand how biogeochemical processes in the hyporheic zone influence carbon and nitrogen cycling as well as stream biogeochemistry, we developed a biotic and abiotic reaction network and integrated it into a reactive transport simulator - PFLOTRAN. Three-dimensional reactive flow and transport simulations were performed to describe the hyporheic exchange of fluxes from and within an intra-meander region encompassing two meanders of East River in the East Taylor watershed, Colorado. The objectives of this study were to quantify (1) the effect of transience on the export of carbon, nitrogen, and iron; and (2) the biogeochemical transformation of nitrogen and carbon species as a function of the residence time. The model was able to capture reasonably well the observed trends of nitrate and dissolved oxygen values that decreased as well as iron (Fe (II)) values that increased along the meander centerline away from the stream. Hyporheic flow paths create lateral redox zonation within intra-meander regions, which considerably impact nitrogen export into the stream system. Simulation results further demonstrated that low water conditions lead to higher levels of dissolved iron in groundwater, which (Fe (II)> 80%) is exported to the stream on the downstream side during high water conditions. An important conclusion from this study is that reactive transport models representing spatial and temporal heterogeneities are required to identify important factors that contribute to the redox gradients at riverine scales.

  14. Establishment of quantitative hydrological indexes for studies of hydro-biogeochemical interactions at the subsurface.

    Science.gov (United States)

    Alves Meira Neto, A.; Sengupta, A.; Wang, Y.; Volkmann, T.; Chorover, J.; Troch, P. A. A.

    2017-12-01

    Advances in the understanding of processes in the critical zone (CZ) are dependent on studies coupling the fields of hydrology, microbiology, geochemistry and soil development. At the same time, better insights are needed to integrate hydrologic information into biogeochemical analysis of subsurface environments. This study investigated potential hydrological indexes that help explaining spatiotemporal biogeochemical patterns. The miniLEO is a 2 m3, 10 degree sloping lysimeter located at Biosphere 2 - University of Arizona. The lysimeter was initially filled with pristine basaltic soil and subject to intermittent rainfall applications throughout the period of 18 months followed by its excavation, resulting in a grid-based sample collection at 324 locations. As a result, spatially distributed microbiological and geochemical patterns as well as soil physical properties were obtained. A hydrologic model was then developed in order to simulate the history of the system until the excavation. After being calibrated against sensor data to match its observed input-state-output behavior, the resulting distributed fields of flow velocities and moisture states were retrieved. These results were translated into several hydrological indexes to be used in with distributed microbiological and geochemical signatures. Our study attempts at conciliating sound hydrological modelling with an investigation of the subsurface biological signatures, thus providing a unique opportunity for understanding of fine-scale hydro-biological interactions.

  15. Hyporheic zone as a bioreactor: sediment heterogeneity influencing biogeochemical processes

    Science.gov (United States)

    Perujo, Nuria; Romani, Anna M.; Sanchez-Vila, Xavier

    2017-04-01

    Mediterranean fluvial systems are characterized by frequent periods of low flow or even drought. During low flow periods, water from wastewater treatment plants (WWTPs) is proportionally large in fluvial systems. River water might be vertically transported through the hyporheic zone, and then porous medium acts as a complementary treatment system since, as water infiltrates, a suite of biogeochemical processes occurs. Subsurface sediment heterogeneity plays an important role since it influences the interstitial fluxes of the medium and drives biomass growing, determining biogeochemical reactions. In this study, WWTP water was continuously infiltrated for 3 months through two porous medium tanks: one consisting of 40 cm of fine sediment (homogeneous); and another comprised of two layers of different grain size sediments (heterogeneous), 20 cm of coarse sediment in the upper part and 20 cm of fine one in the bottom. Several hydrological, physicochemical and biological parameters were measured periodically (weekly at the start of the experiment and biweekly at the end). Analysed parameters include dissolved nitrogen, phosphorus, organic carbon, and oxygen all measured at the surface, and at 5, 20 and 40 cm depth. Variations in hydraulic conductivity with time were evaluated. Sediment samples were also analysed at three depths (surface, 20 and 40 cm) to determine bacterial density, chlorophyll content, extracellular polymeric substances, and biofilm function (extracellular enzyme activities and carbon substrate utilization profiles). Preliminary results suggest hydraulic conductivity to be the main driver of the differences in the biogeochemical processes occurring in the subsurface. At the heterogeneous tank, a low nutrient reduction throughout the whole medium is measured. In this medium, high hydraulic conductivity allows for a large amount of infiltrating water, but with a small residence time. Since some biological processes are largely time-dependent, small water

  16. Novel Insights Linking Ecological Health to Biogeochemical Hotspots across the Groundwater-Surface Water Interface in Mixed Land Use Stream Systems

    Science.gov (United States)

    McKnight, U. S.; Sonne, A. T.; Rasmussen, J. J.; Rønde, V.; Traunspurger, W.; Höss, S.; Bjerg, P. L.

    2017-12-01

    Increasing modifications in land use and water management have resulted in multiple stressors impacting freshwater ecosystems globally. Chemicals with the potential to impact aquatic habitats are still often evaluated individually for their adverse effects on ecosystem health. This may lead to critical underestimations of the combined impact caused by interactions occurring between stressors not typically evaluated together, e.g. xenobiotic groundwater pollutants and trace metals. To address this issue, we identified sources and levels of chemical stressors along a 16-km groundwater-fed stream corridor (Grindsted, Denmark), representative for a mixed land use stream system. Potential pollution sources included two contaminated sites (factory, landfill), aquaculture, wastewater/industrial discharges, and diffuse sources from agriculture and urban areas. Ecological status was determined by monitoring meiobenthic and macrobenthic invertebrate communities.The stream was substantially impaired by both geogenic and anthropogenic sources of metals throughout the investigated corridor, with concentrations close to or above threshold values for barium, copper, lead, nickel and zinc in the stream water, hyporheic zone and streambed sediment. The groundwater plume from the factory site caused elevated concentrations of chlorinated ethenes, benzene and pharmaceuticals in both the hyporheic zone and stream, persisting for several km downstream. Impaired ecological conditions, represented by a lower abundance of meiobenthic individuals, were found in zones where the groundwater plume discharges to the stream. The effect was only pronounced in areas characterized by high xenobiotic organic concentrations and elevated dissolved iron and arsenic levels - linked to the dissolution of iron hydroxides caused by the degradation of xenobiotic compounds in the plume. The results thus provide ecological evidence for the interaction of organic and inorganic chemical stressors, which may

  17. Final Project Report - Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloriethylene Co-Metabolism: Co-Metabolic Enzyme Activity Probes and Modeling Co-Metabolism and Attenuation

    Energy Technology Data Exchange (ETDEWEB)

    Starr, Robert C; Orr, Brennon R; Lee, M Hope; Delwiche, Mark

    2010-02-26

    Trichloroethene (TCE) (also known as trichloroethylene) is a common contaminant in groundwater. TCE is regulated in drinking water at a concentration of 5 µg/L, and a small mass of TCE has the potential to contaminant large volumes of water. The physical and chemical characteristics of TCE allow it to migrate quickly in most subsurface environments, and thus large plumes of contaminated groundwater can form from a single release. The migration and persistence of TCE in groundwater can be limited by biodegradation. TCE can be biodegraded via different processes under either anaerobic or aerobic conditions. Anaerobic biodegradation is widely recognized, but aerobic degradation is less well recognized. Under aerobic conditions, TCE can be oxidized to non hazardous conditions via cometabolic pathways. This study applied enzyme activity probes to demonstrate that cometabolic degradation of TCE occurs in aerobic groundwater at several locations, used laboratory microcosm studies to determine aerobic degradation rates, and extrapolated lab-measured rates to in situ rates based on concentrations of microorganisms with active enzymes involved in cometabolic TCE degradation. Microcosms were constructed using basalt chips that were inoculated with microorganisms to groundwater at the Idaho National Laboratory Test Area North TCE plume by filling a set of Flow-Through In Situ Reactors (FTISRs) with chips and placing the FTISRs into the open interval of a well for several months. A parametric study was performed to evaluate predicted degradation rates and concentration trends using a competitive inhibition kinetic model, which accounts for competition for enzyme active sites by both a growth substrate and a cometabolic substrate. The competitive inhibition kinetic expression was programmed for use in the RT3D reactive transport package. Simulations of TCE plume evolution using both competitive inhibition kinetics and first order decay were performed.

  18. Biogeochemical cycling of radionuclides in the environment

    International Nuclear Information System (INIS)

    Livens, F.R.

    1990-01-01

    The biogeochemical cycling of radionuclides with other components such as nutrients around ecosystems is discussed. In particular the behaviour of cesium in freshwater ecosystems since the Chernobyl accident and the behaviour of technetium in the form of pertechnetate anions, TcO 4 , in marine ecosystems is considered. (UK)

  19. Manganese Oxidation by Bacteria: Biogeochemical Aspects

    Digital Repository Service at National Institute of Oceanography (India)

    Sujith, P.P.; LokaBharathi, P.A.

    to oxygen in the aquatic environment and therefore control the fate of several elements. Mn oxidizing bacteria have a suit of enzymes that not only help to scavenge Mn but also other associated elements, thus playing a crucial role in biogeochemical cycles...

  20. Development of a system emulating the global carbon cycle in Earth system models

    Directory of Open Access Journals (Sweden)

    K. Tachiiri

    2010-08-01

    Full Text Available Recent studies have indicated that the uncertainty in the global carbon cycle may have a significant impact on the climate. Since state of the art models are too computationally expensive for it to be possible to explore their parametric uncertainty in anything approaching a comprehensive fashion, we have developed a simplified system for investigating this problem. By combining the strong points of general circulation models (GCMs, which contain detailed and complex processes, and Earth system models of intermediate complexity (EMICs, which are quick and capable of large ensembles, we have developed a loosely coupled model (LCM which can represent the outputs of a GCM-based Earth system model, using much smaller computational resources. We address the problem of relatively poor representation of precipitation within our EMIC, which prevents us from directly coupling it to a vegetation model, by coupling it to a precomputed transient simulation using a full GCM. The LCM consists of three components: an EMIC (MIROC-lite which consists of a 2-D energy balance atmosphere coupled to a low resolution 3-D GCM ocean (COCO including an ocean carbon cycle (an NPZD-type marine ecosystem model; a state of the art vegetation model (Sim-CYCLE; and a database of daily temperature, precipitation, and other necessary climatic fields to drive Sim-CYCLE from a precomputed transient simulation from a state of the art AOGCM. The transient warming of the climate system is calculated from MIROC-lite, with the global temperature anomaly used to select the most appropriate annual climatic field from the pre-computed AOGCM simulation which, in this case, is a 1% pa increasing CO2 concentration scenario.

    By adjusting the effective climate sensitivity (equivalent to the equilibrium climate sensitivity for an energy balance model of MIROC-lite, the transient warming of the LCM could be adjusted to closely follow the low sensitivity (with an equilibrium

  1. Biogeochemical stability and reactions of iron-organic carbon complexes

    Science.gov (United States)

    Yang, Y.; Adhikari, D.; Zhao, Q.; Dunham-Cheatham, S.; Das, K.; Mejia, J.; Huang, R.; Wang, X.; Poulson, S.; Tang, Y.; Obrist, D.; Roden, E. E.

    2017-12-01

    Our core hypothesis is that the degradation rate of soil organic carbon (OC) is governed by the amount of iron (Fe)-bound OC, and the ability of microbial communities to utilize OC as an energy source and electron shuttle for Fe reduction that in turn stimulates reductive release of Fe-bound labile dissolved OC. This hypothesis is being systematically evaluated using model Fe-OC complexes, natural soils, and microcosm system. We found that hematite-bound aliphatic C was more resistant to reduction release, although hematite preferred to sorb more aromatic C. Resistance to reductive release represents a new mechanism that aliphatic soil OC was stabilized by association with Fe oxide. In other studies, pyrogenic OC was found to facilitate the reduction of hematite, by enhancing extracellular electron transport and sorbing Fe(II). For ferrihydrite-OC co-precipitates, the reduction of Fe and release of OC was closely governed by the C/Fe ratio in the system. Based on the XPS, XANES and XAFS analysis, the transformation of Fe speciation was heterogeneous, depending on the conformation and composition of Fe-OC complexes. For natural soils, we investigated the quantity, characteristics, and reactivity of Fe-bound OC in soils collected from 14 forests in the United States. Fe-bound OC contributed up to 57.8% of total OC in the forest soils. Under the anaerobic conditions, the reduction of Fe was positively correlated to the electron accepting capacity of OC. Our findings highlight the closely coupled dynamics of Fe and OC, with broad implications on the turnover of OC and biogeochemical cycles of Fe.

  2. Global Change: A Biogeochemical Perspective

    Science.gov (United States)

    Mcelroy, M.

    1983-01-01

    A research program that is designed to enhance our understanding of the Earth as the support system for life is described. The program change, both natural and anthropogenic, that might affect the habitability of the planet on a time scale roughly equal to that of a human life is studied. On this time scale the atmosphere, biosphere, and upper ocean are treated as a single coupled system. The need for understanding the processes affecting the distribution of essential nutrients--carbon, nitrogen, phosphorous, sulfur, and water--within this coupled system is examined. The importance of subtle interactions among chemical, biological, and physical effects is emphasized. The specific objectives are to define the present state of the planetary life-support system; to ellucidate the underlying physical, chemical, and biological controls; and to provide the body of knowledge required to assess changes that might impact the future habitability of the Earth.

  3. Predicting marine physical-biogeochemical variabilities in the Gulf of Mexico and southeastern U.S. shelf sea

    Science.gov (United States)

    He, R.; Zong, H.; Xue, Z. G.; Fennel, K.; Tian, H.; Cai, W. J.; Lohrenz, S. E.

    2017-12-01

    An integrated terrestrial-ocean ecosystem modeling system is developed and used to investigate marine physical-biogeochemical variabilities in the Gulf of Mexico and southeastern US shelf sea. Such variabilities stem from variations in the shelf circulation, boundary current dynamics, impacts of climate variability, as well as growing population and associated land use practices on transport of carbon and nutrients within terrestrial systems and their delivery to the coastal ocean. We will report our efforts in evaluating the performance of the coupled modeling system via extensive model and data comparisons, as well as findings from a suite of case studies and scenario simulations. Long-term model simulation results are used to quantify regional ocean circulation dynamics, nitrogen budget and carbon fluxes. Their corresponding sub-regional differences are also characterized and contrasted.

  4. Modelling Holocene carbon accumulation and methane emissions of boreal wetlands – an Earth system model approach

    Directory of Open Access Journals (Sweden)

    R. J. Schuldt

    2013-03-01

    Full Text Available Since the Last Glacial Maximum, boreal wetlands have accumulated substantial amounts of peat, estimated at 180–621 Pg of carbon. Wetlands have significantly affected the atmospheric greenhouse gas composition in the past and will play a significant role in future changes of atmospheric CO2 and CH4 concentrations. In order to investigate those changes with an Earth system model, biogeochemical processes in boreal wetlands need to be accounted for. Thus, a model of peat accumulation and decay was developed and included in the land surface model JSBACH of the Max Planck Institute Earth System Model (MPI-ESM. Here we present the evaluation of model results from 6000 yr BP to the pre-industrial period. Over this period of time, 240 Pg of peat carbon accumulated in the model in the areas north of 40° N. Simulated peat accumulation rates agree well with those reported for boreal wetlands. The model simulates CH4 emissions of 49.3 Tg CH4 yr−1 for 6000 yr BP and 51.5 Tg CH4 yr−1 for pre-industrial times. This is within the range of estimates in the literature, which range from 32 to 112 Tg CH4 yr−1 for boreal wetlands. The modelled methane emission for the West Siberian Lowlands and Hudson Bay Lowlands agree well with observations. The rising trend of methane emissions over the last 6000 yr is in agreement with measurements of Antarctic and Greenland ice cores.

  5. The integrated Earth System Model Version 1: formulation and functionality

    Energy Technology Data Exchange (ETDEWEB)

    Collins, William D.; Craig, Anthony P.; Truesdale, John E.; Di Vittorio, Alan; Jones, Andrew D.; Bond-Lamberty, Benjamin; Calvin, Katherine V.; Edmonds, James A.; Kim, Son H.; Thomson, Allison M.; Patel, Pralit L.; Zhou, Yuyu; Mao, Jiafu; Shi, Xiaoying; Thornton, Peter E.; Chini, Louise M.; Hurtt, George C.

    2015-07-23

    The integrated Earth System Model (iESM) has been developed as a new tool for pro- jecting the joint human/climate system. The iESM is based upon coupling an Integrated Assessment Model (IAM) and an Earth System Model (ESM) into a common modeling in- frastructure. IAMs are the primary tool for describing the human–Earth system, including the sources of global greenhouse gases (GHGs) and short-lived species, land use and land cover change, and other resource-related drivers of anthropogenic climate change. ESMs are the primary scientific tools for examining the physical, chemical, and biogeochemical impacts of human-induced changes to the climate system. The iESM project integrates the economic and human dimension modeling of an IAM and a fully coupled ESM within a sin- gle simulation system while maintaining the separability of each model if needed. Both IAM and ESM codes are developed and used by large communities and have been extensively applied in recent national and international climate assessments. By introducing heretofore- omitted feedbacks between natural and societal drivers, we can improve scientific under- standing of the human–Earth system dynamics. Potential applications include studies of the interactions and feedbacks leading to the timing, scale, and geographic distribution of emissions trajectories and other human influences, corresponding climate effects, and the subsequent impacts of a changing climate on human and natural systems. This paper de- scribes the formulation, requirements, implementation, testing, and resulting functionality of the first version of the iESM released to the global climate community.

  6. Global Biogeochemical Fluxes Program for the Ocean Observatories Initiative: A Proposal. (Invited)

    Science.gov (United States)

    Ulmer, K. M.; Taylor, C.

    2010-12-01

    The overarching emphasis of the Global Biogeochemical Flux Ocean Observatories Initiative is to assess the role of oceanic carbon, both living and non-, in the Earth climate system. Modulation of atmospheric CO2 and its influence on global climate is a function of the quantitative capacity of the oceans to sequester organic carbon into deep waters. Critical to our understanding of the role of the oceans in the global cycling of carbon are the quantitative dynamics in both time and space of the fixation of CO2 into organic matter by surface ocean primary production and removal of this carbon to deep waters via the “biological pump”. To take the next major step forward in advancing our understanding of the oceanic biological pump, a global observation program is required that: (i) greatly improves constraints on estimates of global marine primary production (PP), a critical factor in understanding the global CO2 cycle and for developing accurate estimates of export production (EP); (ii) explores the spatiotemporal links between PP, EP and the biogeochemical processes that attenuate particulate organic carbon (POC) flux; (iii) characterizes microbial community structure and dynamics both in the surface and deep ocean; (iv) develops a comprehensive picture of the chemical and biological processes that take place from the surface ocean to the sea floor; (v) provides unique time-series samples for detailed laboratory-based chemical and biological characterization and tracer studies that will enable connections to be made between the operation of the biological pump at present and in the geologic past. The primary goal is to provide high quality biological and biogeochemical observational data for the modeling and prediction efforts of the global CO2 cycle research community. Crucial to the realization of the GBF-OOI is the development of reliable, long-term, time-series ocean observation platforms capable of precise and controlled placement of sophisticated

  7. Biogeochemical prospecting for uranium in Nova Scotia

    International Nuclear Information System (INIS)

    Brooks, R.R.; Holzbecher, J.; Ryan, D.E.

    1981-01-01

    Ashed twigs of Picea rubens (red spruce) collected over an area of uranium mineralization in central Nova Scotia were analyzed for uranium in the course of biogeochemical prospecting for this element. Uranium levels in background samples were significantly lower than in those collected from areas with mineralization either at depth or on the surface. Scintillometric data were useful only to differentiate background and surface mineralization. Uranium levels in soils showed no correlation whatsoever with mineralization or with radiometry. There was a very high degree of correlation between the scintillometric data and uranium concentrations in ashed twigs and it is considered that twigs of Picea rubens might be successfully used for biogeochemical prospecting for uranium in this area. (Auth.)

  8. Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

    Science.gov (United States)

    Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan; Bailey, Vanessa L.

    2017-11-01

    Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

  9. Application of a hybrid multiscale approach to simulate hydrologic and biogeochemical processes in the river-groundwater interaction zone.

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, Glenn Edward; Yang, Xiaofan; Song, Xuehang; Song, Hyun-Seob; Hou, Zhangshuan; Chen, Xingyuan; Liu, Yuanyuan; Scheibe, Tim

    2017-03-01

    The groundwater-surface water interaction zone (GSIZ) plays an important role in riverine and watershed ecosystems as the exchange of waters of variable composition and temperature (hydrologic exchange flows) stimulate microbial activity and associated biogeochemical reactions. Variable temporal and spatial scales of hydrologic exchange flows, heterogeneity of the subsurface environment, and complexity of biogeochemical reaction networks in the GSIZ present challenges to incorporation of fundamental process representations and model parameterization across a range of spatial scales (e.g. from pore-scale to field scale). This paper presents a novel hybrid multiscale simulation approach that couples hydrologic-biogeochemical (HBGC) processes between two distinct length scales of interest.

  10. Biogeochemical gradients above a coal tar DNAPL

    Energy Technology Data Exchange (ETDEWEB)

    Scherr, Kerstin E., E-mail: kerstin.brandstaetter-scherr@boku.ac.at [University of Natural Resources and Life Sciences Vienna (BOKU), Department IFA-Tulln, Institute for Environmental Biotechnology, Konrad Lorenz Strasse 20, 3430 Tulln (Austria); Backes, Diana [University of Natural Resources and Life Sciences Vienna (BOKU), Department IFA-Tulln, Institute for Environmental Biotechnology, Konrad Lorenz Strasse 20, 3430 Tulln (Austria); Scarlett, Alan G. [University of Plymouth, Petroleum and Environmental Geochemistry Group, Biogeochemistry Research Centre, Drake Circus, Plymouth, Devon PL4 8AA (United Kingdom); Lantschbauer, Wolfgang [Government of Upper Austria, Directorate for Environment and Water Management, Division for Environmental Protection, Kärntner Strasse 10-12, 4021 Linz (Austria); Nahold, Manfred [GUT Gruppe Umwelt und Technik GmbH, Ingenieurbüro für Technischen Umweltschutz, Plesching 15, 4040 Linz (Austria)

    2016-09-01

    Naturally occurring distribution and attenuation processes can keep hydrocarbon emissions from dense non aqueous phase liquids (DNAPL) into the adjacent groundwater at a minimum. In a historically coal tar DNAPL-impacted site, the de facto absence of a plume sparked investigations regarding the character of natural attenuation and DNAPL resolubilization processes at the site. Steep vertical gradients of polycyclic aromatic hydrocarbons, microbial community composition, secondary water quality and redox-parameters were found to occur between the DNAPL-proximal and shallow waters. While methanogenic and mixed-electron acceptor conditions prevailed close to the DNAPL, aerobic conditions and very low dissolved contaminant concentrations were identified in three meters vertical distance from the phase. Comprehensive two-dimensional gas chromatography–mass spectrometry (GC × GC–MS) proved to be an efficient tool to characterize the behavior of the present complex contaminant mixture. Medium to low bioavailability of ferric iron and manganese oxides of aquifer samples was detected via incubation with Shewanella alga and evidence for iron and manganese reduction was collected. In contrast, 16S rDNA phylogenetic analysis revealed the absence of common iron reducing bacteria. Aerobic hydrocarbon degraders were abundant in shallow horizons, while nitrate reducers were dominating in deeper aquifer regions, in addition to a low relative abundance of methanogenic archaea. Partial Least Squares – Canonical Correspondence Analysis (PLS-CCA) suggested that nitrate and oxygen concentrations had the greatest impact on aquifer community structure in on- and offsite wells, which had a similarly high biodiversity (H’ and Chao1). Overall, slow hydrocarbon dissolution from the DNAPL appears to dominate natural attenuation processes. This site may serve as a model for developing legal and technical strategies for the treatment of DNAPL-impacted sites where contaminant plumes are

  11. Benthic contributions to Adriatic and Mediterranean biogeochemical cycles

    Science.gov (United States)

    Capet, Arthur; Lazzari, Paolo; Spagnoli, Federico; Bolzon, Giorgio; Solidoro, Cosimo

    2017-04-01

    The 3D biogeochemical BFM-OGSTM implementation currently exploited operationally in the Copernicus Marine Environment Monitoring Services Mediterranean Sea Monitoring and Forecasting Centre (CMEMS-Med-MFC; Lazzari et al., 2010) has been complemented with a benthic component. The approach followed that of (Capet et al 2016) and involved a vertically integrated benthic module accounting for the effect of environmental bottom conditions on diagenetic rates (aerobic mineralization, denitrification, nitrification) through transfer functions as well as the effect of waves and bottom currents on sediment deposition and resuspension. A balanced climatological year is simulated for various values of the resuspension parameters, using specifically calibrated transfer functions for the Adriatic Sea and generic formulations for the rest of the Mediterranean basin. The results serves the mapping of distinct provinces of the Adriatic Sea based on the benthic contributions biogeochemical budgets and the seasonal variability of benthic-pelagic fluxes. The differences with the non-benthic reference simulation are highlighted in details regarding the Adriatic, and more generally for the entire Mediterranean Sea. Lazzari, P., Teruzzi, A., Salon, S., Campagna, S., Calonaci, C., Colella, S., Tonani, M., Crise, A. (2010). Pre-operational short-term forecasts for Mediterranean Sea biogeochemistry. Ocean Science, 6(1), 25-39. Capet, A., Meysman, F. J., Akoumianaki, I., Soetaert, K., & Grégoire, M. (2016). Integrating sediment biogeochemistry into 3D oceanic models: A study of benthic-pelagic coupling in the Black Sea. Ocean Modelling, 101, 83-100.

  12. Beyond best management practices: pelagic biogeochemical dynamics in urban stormwater ponds.

    Science.gov (United States)

    Williams, Clayton J; Frost, Paul C; Xenopoulos, Marguerite A

    2013-09-01

    Urban stormwater ponds are considered to be a best management practice for flood control and the protection of downstream aquatic ecosystems from excess suspended solids and other contaminants. Following this, urban ponds are assumed to operate as unreactive settling basins, whereby their overall effectiveness in water treatment is strictly controlled by physical processes. However, pelagic microbial biogeochemical dynamics could be significant contributors to nutrient and carbon cycling in these small, constructed aquatic systems. In the present study, we examined pelagic biogeochemical dynamics in 26 stormwater ponds located in southern Ontario, Canada, during late summer. Initially, we tested to see if total suspended solids (TSS) concentration, which provides a measure of catchment disturbance, landscape stability, and pond performance, could be used as an indirect predictor of plankton stocks in stormwater ponds. Structural equation modeling (SEM) using TSS as a surrogate for external loading suggested that TSS was an imperfect predictor. TSS masked plankton-nutrient relationships and appeared to reflect autochthonous production moreso than external forces. When TSS was excluded, the SEM model explained a large amount of the variation in dissolved organic matter (DOM) characteristics (55-75%) but a small amount of the variation in plankton stocks (3-38%). Plankton stocks were correlated positively with particulate nutrients and extracellular enzyme activities, suggesting rapid recycling of the fixed nutrient and carbon pool with consequential effects on DOM. DOM characteristics across the ponds were mainly of autochthonous origin. Humic matter from the watershed formed a larger part of the DOM pool only in ponds with low productivity and low dissolved organic carbon concentrations. Our results suggest that in these small, high nutrient systems internal processes might outweigh the impact of the landscape on carbon cycles. Hence, the overall benefit that

  13. A biogeochemical paradigm for reconstruction of past shelf sea regimes

    Science.gov (United States)

    Jago, C. F.; Jones, S. E.

    2003-04-01

    signatures in the sediments across the Celtic Sea front. In addition, there are gradients in dinoflagellate cyst assemblages which reflect the overlying water column structure. Such proxies, when suitably calibrated, can be used to interpret biogeochemical regimes of the past. Linked to biogeochemical and ecosystem models, they provide the potential for reconstruction of ecologically important parameters of past shelf regimes.

  14. Modeling and estimating system availability

    International Nuclear Information System (INIS)

    Gaver, D.P.; Chu, B.B.

    1976-11-01

    Mathematical models to infer the availability of various types of more or less complicated systems are described. The analyses presented are probabilistic in nature and consist of three parts: a presentation of various analytic models for availability; a means of deriving approximate probability limits on system availability; and a means of statistical inference of system availability from sparse data, using a jackknife procedure. Various low-order redundant systems are used as examples, but extension to more complex systems is not difficult

  15. Effects of ozone-vegetation coupling on surface ozone air quality via biogeochemical and meteorological feedbacks

    Science.gov (United States)

    Sadiq, Mehliyar; Tai, Amos P. K.; Lombardozzi, Danica; Martin, Maria Val

    2017-02-01

    Tropospheric ozone is one of the most hazardous air pollutants as it harms both human health and plant productivity. Foliage uptake of ozone via dry deposition damages photosynthesis and causes stomatal closure. These foliage changes could lead to a cascade of biogeochemical and biogeophysical effects that not only modulate the carbon cycle, regional hydrometeorology and climate, but also cause feedbacks onto surface ozone concentration itself. In this study, we implement a semi-empirical parameterization of ozone damage on vegetation in the Community Earth System Model to enable online ozone-vegetation coupling, so that for the first time ecosystem structure and ozone concentration can coevolve in fully coupled land-atmosphere simulations. With ozone-vegetation coupling, present-day surface ozone is simulated to be higher by up to 4-6 ppbv over Europe, North America and China. Reduced dry deposition velocity following ozone damage contributes to ˜ 40-100 % of those increases, constituting a significant positive biogeochemical feedback on ozone air quality. Enhanced biogenic isoprene emission is found to contribute to most of the remaining increases, and is driven mainly by higher vegetation temperature that results from lower transpiration rate. This isoprene-driven pathway represents an indirect, positive meteorological feedback. The reduction in both dry deposition and transpiration is mostly associated with reduced stomatal conductance following ozone damage, whereas the modification of photosynthesis and further changes in ecosystem productivity are found to play a smaller role in contributing to the ozone-vegetation feedbacks. Our results highlight the need to consider two-way ozone-vegetation coupling in Earth system models to derive a more complete understanding and yield more reliable future predictions of ozone air quality.

  16. Molecular biogeochemical provinces in the Atlantic Surface Ocean

    Science.gov (United States)

    Koch, B. P.; Flerus, R.; Schmitt-Kopplin, P.; Lechtenfeld, O. J.; Bracher, A.; Cooper, W.; Frka, S.; Gašparović, B.; Gonsior, M.; Hertkorn, N.; Jaffe, R.; Jenkins, A.; Kuss, J.; Lara, R. J.; Lucio, M.; McCallister, S. L.; Neogi, S. B.; Pohl, C.; Roettgers, R.; Rohardt, G.; Schmitt, B. B.; Stuart, A.; Theis, A.; Ying, W.; Witt, M.; Xie, Z.; Yamashita, Y.; Zhang, L.; Zhu, Z. Y.; Kattner, G.

    2010-12-01

    One of the most important aspects to understand marine organic carbon fluxes is to resolve the molecular mechanisms which convert fresh, labile biomolecules into semi-labile and refractory dissolved and particulate organic compounds in the ocean. In this interdisciplinary project, which was performed on a cruise with RV Polarstern, we carried out a detailed molecular characterisation of dissolved organic matter (DOM) on a North-South transect in the Atlantic surface ocean in order to relate the data to different biological, climatic, oceanographic, and meteorological regimes as well as to terrestrial input from riverine and atmospheric sources. Our goal was to achieve a high resolution data set for the biogeochemical characterisation of the sources and reactivity of DOM. We applied ultrahigh resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS), nutrient, trace element, amino acid, and lipid analyses and other biogeochemical measurements for 220 samples from the upper water column (0-200m) and eight deep profiles. Various spectroscopic techniques were applied continuously in a constant sample water flow supplied by a fish system and the moon pool. Radiocarbon dating enabled assessing DOC residence time. Bacterial abundance and production provided a metabolic context for the DOM characterization work and pCO2 concentrations. Combining molecular organic techniques and inductively coupled plasma mass spectrometry (ICP-MS) established an important link between organic and inorganic biogeochemical studies. Multivariate statistics, primarily based on FT-ICR-MS data for 220 samples, allowed identifying geographical clusters which matched ecological provinces proposed previously by Longhurst (2007). Our study demonstrated that marine DOM carries molecular information reflecting the “history” of ocean water masses. This information can be used to define molecular biogeochemical provinces and to improve our understanding of element fluxes in

  17. Next generation framework for aquatic modeling of the Earth System

    Science.gov (United States)

    Fekete, B. M.; Wollheim, W. M.; Wisser, D.; Vörösmarty, C. J.

    2009-03-01

    Earth System model development is becoming an increasingly complex task. As scientists attempt to represent the physical and bio-geochemical processes and various feedback mechanisms in unprecedented detail, the models themselves are becoming increasingly complex. At the same time, the complexity of the surrounding IT infrastructure is growing as well. Earth System models must manage a vast amount of data in heterogeneous computing environments. Numerous development efforts are on the way to ease that burden and offer model development platforms that reduce IT challenges and allow scientists to focus on their science. While these new modeling frameworks (e.g. FMS, ESMF, CCA, OpenMI) do provide solutions to many IT challenges (performing input/output, managing space and time, establishing model coupling, etc.), they are still considerably complex and often have steep learning curves. The Next generation Framework for Aquatic Modeling of the Earth System (NextFrAMES, a revised version of FrAMES) have numerous similarities to those developed by other teams, but represents a novel model development paradigm. NextFrAMES is built around a modeling XML that lets modelers to express the overall model structure and provides an API for dynamically linked plugins to represent the processes. The model XML is executed by the NextFrAMES run-time engine that parses the model definition, loads the module plugins, performs the model I/O and executes the model calculations. NextFrAMES has a minimalistic view representing spatial domains and treats every domain (regardless of its layout such as grid, network tree, individual points, polygons, etc.) as vector of objects. NextFrAMES performs computations on multiple domains and interactions between different spatial domains are carried out through couplers. NextFrAMES allows processes to operate at different frequencies by providing rudimentary aggregation and disaggregation facilities. NextFrAMES was designed primarily for

  18. Biogeochemical Hotspots: Role of Small Wetlands in Nutrient Processing at the Watershed Scale

    Science.gov (United States)

    Cheng, F. Y.; Basu, N. B.

    2016-12-01

    Increased loading of nutrients (nitrogen N and phosphorus P) from agricultural and urban intensification in the Anthropocene has led to severe degradation of inland and coastal waters. Amongst aquatic ecosystems, wetlands receive and retain significant quantities of nutrients and thus are important regulators of nutrient transport in watersheds. While the factors controlling N and P retention in wetlands is relatively well known, there is a lack of quantitative understanding on the relative contributions of the different factors on nutrient retention. There is also a deficiency in knowledge of how these processes behave across system size and type. In our study, we synthesized nutrient retention data from wetlands, lakes, and reservoirs to gain insight on the relationship between hydrologic and biogeochemical controls on nutrient retention. Our results indicated that the first-order reaction rate constant, k [T-1], is inversely proportional to the hydraulic residence time, τ, across six orders of magnitude in residence time for total nitrogen, total phosphorus, nitrate and phosphate. We hypothesized that the consistency of the relationship across constituent and system types points to the strong hydrologic control on biogeochemical processing. The hypothesis was tested using a two-compartment mechanistic model that links the nutrient removal processes (denitrification for N and sedimentation for P) with the system size. Finally, the k-τ relationships were upscaled with a regional size-frequency distribution to demonstrate the disproportionately large role of small wetlands in watershed-scale nutrient processing. Our results highlight the importance of hydrological controls as the dominant modifiers of nutrient removal mechanisms and the need for a stronger focus on small lentic ecosystems like wetlands as major nutrient sinks in the landscape.

  19. Modelling of reverberation enhancement systems

    OpenAIRE

    ROUCH , Jeremy; Schmich , Isabelle; Galland , Marie-Annick

    2012-01-01

    International audience; Electroacoustic enhancement systems are increasingly specified by acoustic consultants to address the requests for a multi-purpose use of performance halls. However, there is still a lack of simple models to predict the effect induced by these systems on the acoustic field. Two models are introduced to establish the impulse responses of a room equipped with a reverberation enhancement system. These models are based on passive impulse responses according to the modified...

  20. MODELLING OF MATERIAL FLOW SYSTEMS

    OpenAIRE

    PÉTER TELEK

    2012-01-01

    Material flow systems are in generally very complex processes. During design, building and operation of complex systems there are many different problems. If these complex processes can be described in a simple model, the tasks will be clearer, better adaptable and easier solvable. As the material flow systems are very different, so using models is a very important aid to create uniform methods and solutions. This paper shows the details of the application possibilities of modelling in the ma...

  1. Dynamic Modeling of ALS Systems

    Science.gov (United States)

    Jones, Harry

    2002-01-01

    The purpose of dynamic modeling and simulation of Advanced Life Support (ALS) systems is to help design them. Static steady state systems analysis provides basic information and is necessary to guide dynamic modeling, but static analysis is not sufficient to design and compare systems. ALS systems must respond to external input variations and internal off-nominal behavior. Buffer sizing, resupply scheduling, failure response, and control system design are aspects of dynamic system design. We develop two dynamic mass flow models and use them in simulations to evaluate systems issues, optimize designs, and make system design trades. One model is of nitrogen leakage in the space station, the other is of a waste processor failure in a regenerative life support system. Most systems analyses are concerned with optimizing the cost/benefit of a system at its nominal steady-state operating point. ALS analysis must go beyond the static steady state to include dynamic system design. All life support systems exhibit behavior that varies over time. ALS systems must respond to equipment operating cycles, repair schedules, and occasional off-nominal behavior or malfunctions. Biological components, such as bioreactors, composters, and food plant growth chambers, usually have operating cycles or other complex time behavior. Buffer sizes, material stocks, and resupply rates determine dynamic system behavior and directly affect system mass and cost. Dynamic simulation is needed to avoid the extremes of costly over-design of buffers and material reserves or system failure due to insufficient buffers and lack of stored material.

  2. Modeling soft interface dominated systems

    NARCIS (Netherlands)

    Lamorgese, A.; Mauri, R.; Sagis, L.M.C.

    2017-01-01

    The two main continuum frameworks used for modeling the dynamics of soft multiphase systems are the Gibbs dividing surface model, and the diffuse interface model. In the former the interface is modeled as a two dimensional surface, and excess properties such as a surface density, or surface energy

  3. Validation of systems biology models

    NARCIS (Netherlands)

    Hasdemir, D.

    2015-01-01

    The paradigm shift from qualitative to quantitative analysis of biological systems brought a substantial number of modeling approaches to the stage of molecular biology research. These include but certainly are not limited to nonlinear kinetic models, static network models and models obtained by the

  4. From Numeric Models to Granular System Modeling

    Directory of Open Access Journals (Sweden)

    Witold Pedrycz

    2015-03-01

    To make this study self-contained, we briefly recall the key concepts of granular computing and demonstrate how this conceptual framework and its algorithmic fundamentals give rise to granular models. We discuss several representative formal setups used in describing and processing information granules including fuzzy sets, rough sets, and interval calculus. Key architectures of models dwell upon relationships among information granules. We demonstrate how information granularity and its optimization can be regarded as an important design asset to be exploited in system modeling and giving rise to granular models. With this regard, an important category of rule-based models along with their granular enrichments is studied in detail.

  5. Advancement of Global-scale River Hydrodynamics Modelling and Its Potential Applications to Earth System Models

    Science.gov (United States)

    Yamazaki, D.

    2015-12-01

    Global river routine models have been developed for representing freshwater discharge from land to ocean in Earth System Models. At the beginning, global river models had simulated river discharge along a prescribed river network map by using a linear-reservoir assumption. Recently, in parallel with advancement of remote sensing and computational powers, many advanced global river models have started to represent floodplain inundation assuming sub-grid floodplain topography. Some of them further pursue physically-appropriate representation of river and floodplain dynamics, and succeeded to utilize "hydrodynamic flow equations" to realistically simulate channel/floodplain and upstream/downstream interactions. State-of-the-art global river hydrodynamic models can well reproduce flood stage (e.g. inundated areas and water levels) in addition to river discharge. Flood stage simulation by global river models can be potentially coupled with land surface processes in Earth System Models. For example, evaporation from inundated water area is not negligible for land-atmosphere interactions in arid areas (such as the Niger River). Surface water level and ground water level are correlated each other in flat topography, and this interaction could dominate wetting and drying of many small lakes in flatland and could also affect biogeochemical processes in these lakes. These land/surface water interactions had not been implemented in Earth System Models but they have potential impact on the global climate and carbon cycle. In the AGU presentation, recent advancements of global river hydrodynamic modelling, including super-high resolution river topography datasets, will be introduces. The potential applications of river and surface water modules within Earth System Models will be also discussed.

  6. Coastal Modeling System Advanced Topics

    Science.gov (United States)

    2012-06-18

    22 June 2012 - Day 5  Debugging and Problem solving  Model Calibration  Post-processing Coastal and Hydraulics Laboratory Focus of...Efficiently: • The setup process is fast and without wasted time or effort 3 Coastal and Hydraulics Laboratory 4 Coastal Modeling System (CMS) What...is the CMS? Integrated wave, current, and morphology change model in the Surface- water Modeling System (SMS). Why CMS? Operational at 10

  7. Understanding why the volume of suboxic waters does not increase over centuries of global warming in an Earth System Model

    OpenAIRE

    A. Gnanadesikan; J. P. Dunne; J. John

    2012-01-01

    Global warming is expected to reduce oxygen solubility and vertical exchange in the ocean, changes which would be expected to result in an increase in the volume of hypoxic waters. A simulation made with a full Earth System model with dynamical atmosphere, ocean, sea ice and biogeochemical cycling (the Geophysical Fluid Dynamics Laboratory's Earth System Model 2.1) shows that this holds true if the condition for hypoxia is set relatively high. However, the volume of the most hypoxic (i.e., su...

  8. Safeguards system effectiveness modeling

    International Nuclear Information System (INIS)

    Bennett, H.A.; Boozer, D.D.; Chapman, L.D.; Daniel, S.L.; Engi, D.; Hulme, B.L.; Varnado, G.B.

    1976-01-01

    A general methodology for the comparative evaluation of physical protection system effectiveness at nuclear facilities is presently under development. The approach is applicable to problems of sabotage or theft at fuel cycle facilities. The overall methodology and the primary analytic techniques used to assess system effectiveness are briefly outlined

  9. Safeguards system effectiveness modeling

    International Nuclear Information System (INIS)

    Bennett, H.A.; Boozer, D.D.; Chapman, L.D.; Daniel, S.L.; Engi, D.; Hulme, B.L.; Varnado, G.B.

    1976-01-01

    A general methodology for the comparative evaluation of physical protection system effectiveness at nuclear facilities is presently under development. The approach is applicable to problems of sabotage or theft at fuel cycle facilities. In this paper, the overall methodology and the primary analytic techniques used to assess system effectiveness are briefly outlined

  10. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minjing [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Qian, Wei-Jun [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Shi, Liang [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nelson, William C. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nicora, Carrie D. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Resch, Charles T. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Thompson, Christopher [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Yan, Sen [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Fredrickson, James K. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Zachara, John M. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People' s Republic of China

    2017-07-13

    Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

  11. Carbon isotopes in the ocean model of the Community Earth System Model (CESM1)

    Science.gov (United States)

    Jahn, A.; Lindsay, K.; Giraud, X.; Gruber, N.; Otto-Bliesner, B. L.; Liu, Z.; Brady, E. C.

    2015-08-01

    Carbon isotopes in the ocean are frequently used as paleoclimate proxies and as present-day geochemical ocean tracers. In order to allow a more direct comparison of climate model results with this large and currently underutilized data set, we added a carbon isotope module to the ocean model of the Community Earth System Model (CESM), containing the cycling of the stable isotope 13C and the radioactive isotope 14C. We implemented the 14C tracer in two ways: in the "abiotic" case, the 14C tracer is only subject to air-sea gas exchange, physical transport, and radioactive decay, while in the "biotic" version, the 14C additionally follows the 13C tracer through all biogeochemical and ecological processes. Thus, the abiotic 14C tracer can be run without the ecosystem module, requiring significantly fewer computational resources. The carbon isotope module calculates the carbon isotopic fractionation during gas exchange, photosynthesis, and calcium carbonate formation, while any subsequent biological process such as remineralization as well as any external inputs are assumed to occur without fractionation. Given the uncertainty associated with the biological fractionation during photosynthesis, we implemented and tested three parameterizations of different complexity. Compared to present-day observations, the model is able to simulate the oceanic 14C bomb uptake and the 13C Suess effect reasonably well compared to observations and other model studies. At the same time, the carbon isotopes reveal biases in the physical model, for example, too sluggish ventilation of the deep Pacific Ocean.

  12. Carbon isotopes in the ocean model of the Community Earth System Model (CESM1

    Directory of Open Access Journals (Sweden)

    A. Jahn

    2015-08-01

    Full Text Available Carbon isotopes in the ocean are frequently used as paleoclimate proxies and as present-day geochemical ocean tracers. In order to allow a more direct comparison of climate model results with this large and currently underutilized data set, we added a carbon isotope module to the ocean model of the Community Earth System Model (CESM, containing the cycling of the stable isotope 13C and the radioactive isotope 14C. We implemented the 14C tracer in two ways: in the "abiotic" case, the 14C tracer is only subject to air–sea gas exchange, physical transport, and radioactive decay, while in the "biotic" version, the 14C additionally follows the 13C tracer through all biogeochemical and ecological processes. Thus, the abiotic 14C tracer can be run without the ecosystem module, requiring significantly fewer computational resources. The carbon isotope module calculates the carbon isotopic fractionation during gas exchange, photosynthesis, and calcium carbonate formation, while any subsequent biological process such as remineralization as well as any external inputs are assumed to occur without fractionation. Given the uncertainty associated with the biological fractionation during photosynthesis, we implemented and tested three parameterizations of different complexity. Compared to present-day observations, the model is able to simulate the oceanic 14C bomb uptake and the 13C Suess effect reasonably well compared to observations and other model studies. At the same time, the carbon isotopes reveal biases in the physical model, for example, too sluggish ventilation of the deep Pacific Ocean.

  13. The Jena Diversity Model: Towards a Richer Representation of the Terrestrial Biosphere for Earth System Modelling

    Science.gov (United States)

    Pavlick, R.; Reu, B.; Bohn, K.; Dyke, J.; Kleidon, A.

    2010-12-01

    The terrestrial biosphere is a complex, self-organizing system which is continually both adapting to and altering its global environment. It also exhibits a vast diversity of vegetation forms and functioning. However, the terrestrial biosphere components within current state-of-the-art Earth System Models abstract this diversity in to a handful of relatively static plant functional types. These coarse and static representations of functional diversity might contribute to overly pessimistic projections regarding terrestrial ecosystem responses to scenarios of global change (e.g. Amazonian and boreal forest diebacks). In the Jena Diversity (JeDi) model, we introduce a new approach to vegetation modelling with a richer representation of functional diversity, based not on plant functional types, but on unavoidable plant ecophysiological trade-offs, which we hypothesize should be more stable in time. The JeDi model tests a large number of plant growth strategies. Each growth strategy is simulated using a set of randomly generated parameter values, which characterize its functioning in terms of carbon allocation, ecophysiology, and phenology, which are then linked to the growing conditions at the land surface. The model is constructed in such a way that these parameters inherently lead to ecophysiological trade-offs, which determine whether a growth strategy is able to survive and reproduce under the prevalent climatic conditions. Kleidon and Mooney (2000) demonstrated that this approach is capable of reproducing the geographic distribution of species richness. More recently, we have shown the JeDi model can explain other biogeographical phenomena including the present-day global pattern of biomes (Reu et al., accepted), ecosystem evenness (Kleidon et al. 2009), and possible mechanisms for biome shifts and biodiversity changes under scenarios of global warming (Reu et al., submitted). We have also evaluated the simulated biogeochemical fluxes from JeDi against a variety

  14. Effects of Solar UV Radiation and Climate Change on Biogeochemical Cycling: Interactions and Feedbacks

    Science.gov (United States)

    Solar UV radiation, climate and other drivers of global change are undergoing significant changes and models forecast that these changes will continue for the remainder of this century. Here we assess the effects of solar UV radiation on biogeochemical cycles and the interactions...

  15. Biogeochemical research priorities for sustainable biofuel and bioenergy feedstock production in the Americas

    Science.gov (United States)

    Hero T. Gollany; Brian D. Titus; D. Andrew Scott; Heidi Asbjornsen; Sigrid C. Resh; Rodney A. Chimner; Donald J. Kaczmarek; Luiz F.C. Leite; Ana C.C. Ferreira; Kenton A. Rod; Jorge Hilbert; Marcelo V. Galdos; Michelle E. Cisz

    2015-01-01

    Rapid expansion in biomass production for biofuels and bioenergy in the Americas is increasing demand on the ecosystem resources required to sustain soil and site productivity. We review the current state of knowledge and highlight gaps in research on biogeochemical processes and ecosystem sustainability related to biomass production. Biomass production systems...

  16. Mechanical Systems, Classical Models

    CERN Document Server

    Teodorescu, Petre P

    2007-01-01

    All phenomena in nature are characterized by motion; this is an essential property of matter, having infinitely many aspects. Motion can be mechanical, physical, chemical or biological, leading to various sciences of nature, mechanics being one of them. Mechanics deals with the objective laws of mechanical motion of bodies, the simplest form of motion. In the study of a science of nature mathematics plays an important role. Mechanics is the first science of nature which was expressed in terms of mathematics by considering various mathematical models, associated to phenomena of the surrounding nature. Thus, its development was influenced by the use of a strong mathematical tool; on the other hand, we must observe that mechanics also influenced the introduction and the development of many mathematical notions. In this respect, the guideline of the present book is precisely the mathematical model of mechanics. A special accent is put on the solving methodology as well as on the mathematical tools used; vectors, ...

  17. Stochastic Modelling of Energy Systems

    DEFF Research Database (Denmark)

    Andersen, Klaus Kaae

    2001-01-01

    In this thesis dynamic models of typical components in Danish heating systems are considered. Emphasis is made on describing and evaluating mathematical methods for identification of such models, and on presentation of component models for practical applications. The thesis consists of seven...... of component models, such as e.g. heat exchanger and valve models, adequate for system simulations. Furthermore, the thesis demonstrates and discusses the advantages and disadvantages of using statistical methods in conjunction with physical knowledge in establishing adequate component models of heating...... research papers (case studies) together with a summary report. Each case study takes it's starting point in typical heating system components and both, the applied mathematical modelling methods and the application aspects, are considered. The summary report gives an introduction to the scope...

  18. Ecosystem services and biogeochemical cycles on a global scale: valuation of water, carbon and nitrogen processes

    International Nuclear Information System (INIS)

    Watanabe, Marcos D.B.; Ortega, Enrique

    2011-01-01

    Ecosystem services (ES) are provided by healthy ecosystems and are fundamental to support human life. However, natural systems have been degraded all over the world and the process of degradation is partially attributed to the lack of knowledge regarding the economic benefits associated with ES, which usually are not captured in the market. To valuate ES without using conventional approaches, such as the human's willingness-to-pay for ecosystem goods and services, this paper uses a different method based on Energy Systems Theory to estimate prices for biogeochemical flows that affect ecosystem services by considering their emergy content converted to equivalent monetary terms. Ecosystem services related to water, carbon and nitrogen biogeochemical flows were assessed since they are connected to a range of final ecosystem services including climate regulation, hydrological regulation, food production, soil formation and others. Results in this paper indicate that aquifer recharge, groundwater flow, carbon dioxide sequestration, methane emission, biological nitrogen fixation, nitrous oxide emission and nitrogen leaching/runoff are the most critical biogeochemical flows in terrestrial systems. Moreover, monetary values related to biogeochemical flows on a global scale could provide important information for policymakers concerned with payment mechanisms for ecosystem services and costs of greenhouse gas emissions.

  19. Model Reduction of Hybrid Systems

    DEFF Research Database (Denmark)

    Shaker, Hamid Reza

    for model reduction of switched systems is based on the switching generalized gramians. The reduced order switched system is guaranteed to be stable for all switching signal in this method. This framework uses stability conditions which are based on switching quadratic Lyapunov functions which are less...... conservative than the stability conditions based on common quadratic Lyapunov functions. The stability conditions which are used for this method are very useful in model reduction and design problems because they have slack variables in the conditions. Similar conditions for a class of switched nonlinear......High-Technological solutions of today are characterized by complex dynamical models. A lot of these models have inherent hybrid/switching structure. Hybrid/switched systems are powerful models for distributed embedded systems design where discrete controls are applied to continuous processes...

  20. Contrasting seasonality in optical-biogeochemical properties of the Baltic Sea.

    Directory of Open Access Journals (Sweden)

    Stefan G H Simis

    Full Text Available Optical-biogeochemical relationships of particulate and dissolved organic matter are presented in support of remote sensing of the Baltic Sea pelagic. This system exhibits strong seasonality in phytoplankton community composition and wide gradients of chromophoric dissolved organic matter (CDOM, properties which are poorly handled by existing remote sensing algorithms. Absorption and scattering properties of particulate matter reflected the seasonality in biological (phytoplankton succession and physical (thermal stratification processes. Inherent optical properties showed much wider variability when normalized to the chlorophyll-a concentration compared to normalization to either total suspended matter dry weight or particulate organic carbon. The particle population had the largest optical variability in summer and was dominated by organic matter in both seasons. The geographic variability of CDOM and relationships with dissolved organic carbon (DOC are also presented. CDOM dominated light absorption at blue wavelengths, contributing 81% (median of the absorption by all water constituents at 400 nm and 63% at 442 nm. Consequentially, 90% of water-leaving radiance at 412 nm originated from a layer (z90 no deeper than approximately 1.0 m. With water increasingly attenuating light at longer wavelengths, a green peak in light penetration and reflectance is always present in these waters, with z90 up to 3.0-3.5 m depth, whereas z90 only exceeds 5 m at biomass < 5 mg Chla m-3. High absorption combined with a weakly scattering particle population (despite median phytoplankton biomass of 14.1 and 4.3 mg Chla m-3 in spring and summer samples, respectively, characterize this sea as a dark water body for which dedicated or exceptionally robust remote sensing techniques are required. Seasonal and regional optical-biogeochemical models, data distributions, and an extensive set of simulated remote-sensing reflectance spectra for testing of remote sensing

  1. Linking soil and sediment properties for research on biogeochemical cycles

    Science.gov (United States)

    Kuhn, Nikolaus J.

    2013-04-01

    Conventional perspectives on soil erosion include the on-site damage to soil and reductions in crop yield, as well as the resulting off-site effects on water quality, runoff and sediment loads in rivers. Our evolving understanding of the Earth System has added a new dimension to the role of soil erosion within the global geochemical cycles. First, the relevance of soil as a nutrient and Carbon (C) pool was recognized. Initially, the role of soils in the global C cycle was largely considered to be limited to a vertical exchange of greenhouse house gases (GHG) between vegetation, soil and atmosphere and thus mostly studied by soil scientists, plant ecologists and climatologists. Even Critical Zone research focused mostly on weathering and regolith properties and ignored lateral fluxes of dissolved or particulate organic matter. Since the late 1990s, a wider role of soils in biogeochemical cycles has emerged. Recent estimates place the lateral movement of C between soil and sediment pools in terrestrial ecosystems (including rivers and lakes) at approximately 0.6 to 1.5 Gt per year. Some of the eroded C is replaced by photosynthesis from the atmosphere, but at a cost of additional emissions, for example due to fertilizer production. The long-term fate of the eroded and deposited soil organic matter is subject to an open debate and suffers from a lack of reliable spatial information on lateral C fluxes and its subsequent fate in terrestrial ecosystems. The connection between soil C pool, GHG emissions and erosion illustrates the relevance of surface processes for the C fluxes between Earth's spheres. Accordingly, soil is now considered as mobile system to make accurate predictions about the consequences of global change for terrestrial biogeochemical cycles and climate feedbacks. This expanded perspective on soils as dynamic pool of weathering regolith, sediment, nutrients and C at the interface between the geospheres requires the analysis of relevant soil properties

  2. The two-layer geochemical structure of modern biogeochemical provinces and its significance for spatially adequate ecological evaluations and decisions

    Science.gov (United States)

    Korobova, Elena; Romanov, Sergey

    2014-05-01

    regard to secondary redistribution of chemical elements; 3) selection of areas adequate for the short- and long-term ecogeochemical monitoring; 4) selection of areas as global and regional biogeochemical standards. The approach was used to evaluate contribution of stable iodine deficiency and radioactive iodine fallout to distribution of thyroid diseases among population of the Bryansk region [1], to evaluate natural transformation of the initially uniform spatial structure of N, P, K in agricultural fields [2] and radiocesium in forest and flood plain landscapes [3]. The work has been partly supported by the Russian Foundation for Basic Research (grants 07-05-00912; 10-05-01148; 13-05-00823). References Korobova E.M., S.L. Romanov, A.I. Kuvylin, E.I. Chesalova, V.Yu. Beriozkin, I.V. Kurnosova. Modern natural and technogenic iodine biogeochemical provinces: spatial structure and health effects. Goldschmidt 2011, Prague, August 14-19, 2011. Mineralogical Magazine, 75, 3, June 2011, Goldschmidt abstracts 2011, www.minersoc.org, 1224. Romanov S.L. Patterns of the structure of nitrogen, phosphorous and potassium fields in landscape systems of Belorussia. Thesis. Moscow, Moscow State University, 1991, 20 p. Korobova E.M., Romanov S.L., 2009. A Chernobyl 137Cs contamination study as an example for the spatial structure of geochemical fields and modeling of the geochemical field structure. Chemometrics and Intelligent Laboratory Systems 99, 1-8.

  3. Distribution system modeling and analysis

    CERN Document Server

    Kersting, William H

    2001-01-01

    For decades, distribution engineers did not have the sophisticated tools developed for analyzing transmission systems-often they had only their instincts. Things have changed, and we now have computer programs that allow engineers to simulate, analyze, and optimize distribution systems. Powerful as these programs are, however, without a real understanding of the operating characteristics of a distribution system, engineers using the programs can easily make serious errors in their designs and operating procedures. Distribution System Modeling and Analysis helps prevent those errors. It gives readers a basic understanding of the modeling and operating characteristics of the major components of a distribution system. One by one, the author develops and analyzes each component as a stand-alone element, then puts them all together to analyze a distribution system comprising the various shunt and series devices for power-flow and short-circuit studies. He includes the derivation of all models and includes many num...

  4. Biogeochemical controls on mercury methylation in the Allequash Creek wetland.

    Science.gov (United States)

    Creswell, Joel E; Shafer, Martin M; Babiarz, Christopher L; Tan, Sue-Zanne; Musinsky, Abbey L; Schott, Trevor H; Roden, Eric E; Armstrong, David E

    2017-06-01

    We measured mercury methylation potentials and a suite of related biogeochemical parameters in sediment cores and porewater from two geochemically distinct sites in the Allequash Creek wetland, northern Wisconsin, USA. We found a high degree of spatial variability in the methylation rate potentials but no significant differences between the two sites. We identified the primary geochemical factors controlling net methylmercury production at this site to be acid-volatile sulfide, dissolved organic carbon, total dissolved iron, and porewater iron(II). Season and demethylation rates also appear to regulate net methylmercury production. Our equilibrium speciation modeling demonstrated that sulfide likely regulated methylation rates by controlling the speciation of inorganic mercury and therefore its bioavailability to methylating bacteria. We found that no individual geochemical parameter could explain a significant amount of the observed variability in mercury methylation rates, but we found significant multivariate relationships, supporting the widely held understanding that net methylmercury production is balance of several simultaneously occurring processes.

  5. Hydronic distribution system computer model

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, J.W.; Strasser, J.J.

    1994-10-01

    A computer model of a hot-water boiler and its associated hydronic thermal distribution loop has been developed at Brookhaven National Laboratory (BNL). It is intended to be incorporated as a submodel in a comprehensive model of residential-scale thermal distribution systems developed at Lawrence Berkeley. This will give the combined model the capability of modeling forced-air and hydronic distribution systems in the same house using the same supporting software. This report describes the development of the BNL hydronics model, initial results and internal consistency checks, and its intended relationship to the LBL model. A method of interacting with the LBL model that does not require physical integration of the two codes is described. This will provide capability now, with reduced up-front cost, as long as the number of runs required is not large.

  6. Intrusion detection: systems and models

    Science.gov (United States)

    Sherif, J. S.; Dearmond, T. G.

    2002-01-01

    This paper puts forward a review of state of the art and state of the applicability of intrusion detection systems, and models. The paper also presents a classfication of literature pertaining to intrusion detection.

  7. Plant and safety system model

    International Nuclear Information System (INIS)

    Beltracchi, Leo

    1999-01-01

    The design and development of a digital computer-based safety system for a nuclear power plant is a complex process. The process of design and product development must result in a final product free of critical errors; operational safety of nuclear power plants must not be compromised. This paper focuses on the development of a safety system model to assist designers, developers, and regulators in establishing and evaluating requirements for a digital computer-based safety system. The model addresses hardware, software, and human elements for use in the requirements definition process. The purpose of the safety system model is to assist and serve as a guide to humans in the cognitive reasoning process of establishing requirements. The goals in the use of the model are to: (1) enhance the completeness of the requirements and (2) reduce the number of errors associated with the requirements definition phase of a project

  8. Biogeochemical cycling in the Strait of Georgia.

    Science.gov (United States)

    Johannessen, S C; Macdonald, R W; Burd, B; van Roodselaar, A

    2008-12-01

    The papers in this special issue present the results of a five-year project to study sedimentary biogeochemical processes in the Strait of Georgia, with special emphasis on the near-field of a large municipal outfall. Included in this special issue are overviews of the sedimentology, benthic biology, status of siliceous sponge reefs and distribution of organic carbon in the water column. Other papers address the cycling of contaminants (PCBs, PBDEs) and redox metals in the sediment, a method to map the extent of the influence of municipal effluent from staining on benthic bivalves, and the relationships among geochemical conditions and benthic abundance and diversity. The latter set of papers addresses the role of municipal effluent as a pathway of organic carbon and other contaminants into the Strait of Georgia and the effect of the effluent on benthic geochemistry and biology.

  9. Mathematical modeling of aeroelastic systems

    Science.gov (United States)

    Velmisov, Petr A.; Ankilov, Andrey V.; Semenova, Elizaveta P.

    2017-12-01

    In the paper, the stability of elastic elements of a class of designs that are in interaction with a gas or liquid flow is investigated. The definition of the stability of an elastic body corresponds to the concept of stability of dynamical systems by Lyapunov. As examples the mathematical models of flowing channels (models of vibration devices) at a subsonic flow and the mathematical models of protective surface at a supersonic flow are considered. Models are described by the related systems of the partial differential equations. An analytic investigation of stability is carried out on the basis of the construction of Lyapunov-type functionals, a numerical investigation is carried out on the basis of the Galerkin method. The various models of the gas-liquid environment (compressed, incompressible) and the various models of a deformable body (elastic linear and elastic nonlinear) are considered.

  10. ABSTRACT MODELS FOR SYSTEM VIRTUALIZATION

    Directory of Open Access Journals (Sweden)

    M. G. Koveshnikov

    2015-05-01

    Full Text Available The paper is dedicated to issues of system objects securing (system files and user system or application configuration files against unauthorized access including denial of service attacks. We have suggested the method and developed abstract system virtualization models, which are used toresearch attack scenarios for different virtualization modes. Estimation for system tools virtualization technology effectiveness is given. Suggested technology is based on redirection of access requests to system objects shared among access subjects. Whole and partial system virtualization modes have been modeled. The difference between them is the following: in the whole virtualization mode all copies of access system objects are created whereon subjects’ requests are redirected including corresponding application objects;in the partial virtualization mode corresponding copies are created only for part of a system, for example, only system objects for applications. Alternative solutions effectiveness is valued relating to different attack scenarios. We consider proprietary and approved technical solution which implements system virtualization method for Microsoft Windows OS family. Administrative simplicity and capabilities of correspondingly designed system objects security tools are illustrated on this example. Practical significance of the suggested security method has been confirmed.

  11. Aerodynamic and Mechanical System Modelling

    DEFF Research Database (Denmark)

    Jørgensen, Martin Felix

    This thesis deals with mechanical multibody-systems applied to the drivetrain of a 500 kW wind turbine. Particular focus has been on gearbox modelling of wind turbines. The main part of the present project involved programming multibody systems to investigate the connection between forces, moments...

  12. Preface: the hydra model system.

    Science.gov (United States)

    Galliot, Brigitte

    2012-01-01

    The freshwater Hydra polyp emerged as a model system in 1741 when Abraham Trembley not only discovered its amazing regenerative potential, but also demonstrated that experimental manipulations pave the way to research in biology. Since then, Hydra flourished as a potent and fruitful model system to help answer questions linked to cell and developmental biology, as such as the setting up of an organizer to regenerate a complex missing structure, the establishment and maintainance of polarity in a multicellular organism, the development of mathematical models to explain the robust developmental rules observed in this animal, the maintainance of stemness and multipotency in a highly dynamic environment, the plasticity of differentiated cells, to name but a few. However the Hydra model system is not restricted to cell and developmental biology; during the past 270 years it has also been heavily used to investigate the relationships between Hydra and its environment, opening new horizons concerning neurophysiology, innate immunity, ecosystems, ecotoxicology, symbiosis...

  13. Modeling Multi-Level Systems

    CERN Document Server

    Iordache, Octavian

    2011-01-01

    This book is devoted to modeling of multi-level complex systems, a challenging domain for engineers, researchers and entrepreneurs, confronted with the transition from learning and adaptability to evolvability and autonomy for technologies, devices and problem solving methods. Chapter 1 introduces the multi-scale and multi-level systems and highlights their presence in different domains of science and technology. Methodologies as, random systems, non-Archimedean analysis, category theory and specific techniques as model categorification and integrative closure, are presented in chapter 2. Chapters 3 and 4 describe polystochastic models, PSM, and their developments. Categorical formulation of integrative closure offers the general PSM framework which serves as a flexible guideline for a large variety of multi-level modeling problems. Focusing on chemical engineering, pharmaceutical and environmental case studies, the chapters 5 to 8 analyze mixing, turbulent dispersion and entropy production for multi-scale sy...

  14. EPIC Forest LAI Dataset: LAI estimates generated from the USDA Environmental Policy Impact Climate (EPIC) model (a widely used, field-scale, biogeochemical model) on four forest complexes spanning three physiographic provinces in VA and NC.

    Data.gov (United States)

    U.S. Environmental Protection Agency — This data depicts calculated and validated LAI estimates generated from the USDA Environmental Policy Impact Climate (EPIC) model (a widely used, field-scale,...

  15. System Convergence in Transport Modelling

    DEFF Research Database (Denmark)

    Rich, Jeppe; Nielsen, Otto Anker; Cantarella, Guilio E.

    2010-01-01

    A fundamental premise of most applied transport models is the existence and uniqueness of an equilibrium solution that balances demand x(t) and supply t(x). The demand consists of the people that travel in the transport system and on the defined network, whereas the supply consists of the resulting...... level-of-service attributes (e.g., travel time and cost) offered to travellers. An important source of complexity is the congestion, which causes increasing demand to affect travel time in a non-linear way. Transport models most often involve separate models for traffic assignment and demand modelling...

  16. Introducing a boreal wetland model within the Earth System model framework

    Science.gov (United States)

    Getzieh, R. J.; Brovkin, V.; Reick, C.; Kleinen, T.; Raddatz, T.; Raivonen, M.; Sevanto, S.

    2009-04-01

    Wetlands of the northern high latitudes with their low temperatures and waterlogged conditions are prerequisite for peat accumulation. They store at least 25% of the global soil organic carbon and constitute currently the largest natural source of methane. These boreal and subarctic peat carbon pools are sensitive to climate change since the ratio of carbon sequestration and emission is closely dependent on hydrology and temperature. Global biogeochemistry models used for simulations of CO2 dynamics in the past and future climates usually ignore changes in the peat storages. Our approach aims at the evaluation of the boreal wetland feedback to climate through the CO2 and CH4 fluxes on decadal to millennial time scales. A generic model of organic matter accumulation and decay in boreal wetlands is under development in the MPI for Meteorology in cooperation with the University of Helsinki. Our approach is to develop a wetland model which is consistent with the physical and biogeochemical components of the land surface module JSBACH as a part of the Earth System model framework ECHAM5-MPIOM-JSBACH. As prototypes, we use modelling approach by Frolking et al. (2001) for the peat dynamics and the wetland model by Wania (2007) for vegetation cover and plant productivity. An initial distribution of wetlands follows the GLWD-3 map by Lehner and Döll (2004). First results of the modelling approach will be presented. References: Frolking, S. E., N. T. Roulet, T. R. Moore, P. J. H. Richard, M. Lavoie and S. D. Muller (2001): Modeling Northern Peatland Decomposition and Peat Accumulation, Ecosystems, 4, 479-498. Lehner, B., Döll P. (2004): Development and validation of a global database of lakes, reservoirs and wetlands. Journal of Hydrology 296 (1-4), 1-22. Wania, R. (2007): Modelling northern peatland land surface processes, vegetation dynamics and methane emissions. PhD thesis, University of Bristol, 122 pp.

  17. Role of zooplankton dynamics for Southern Ocean phytoplankton biomass and global biogeochemical cycles

    DEFF Research Database (Denmark)

    Le Quéré, Corinne; Buitenhuis, Erik T.; Moriarty, Róisín

    2016-01-01

    Global ocean biogeochemistry models currently employed in climate change projections use highly simplified representations of pelagic food webs. These food webs do not necessarily include critical pathways by which ecosystems interact with ocean biogeochemistry and climate. Here we present a global...... zooplankton community, despite iron limitation of phytoplankton community growth rates. This result has implications for the representation of global biogeochemical cycles in models as zooplankton faecal pellets sink rapidly and partly control the carbon export to the intermediate and deep ocean....

  18. Using eddy covariance of CO2, 13CO2 and CH4, continuous soil respiration measurements, and PhenoCams to constrain a process-based biogeochemical model for carbon market-funded wetland restoration

    Science.gov (United States)

    Oikawa, P. Y.; Baldocchi, D. D.; Knox, S. H.; Sturtevant, C. S.; Verfaillie, J. G.; Dronova, I.; Jenerette, D.; Poindexter, C.; Huang, Y. W.

    2015-12-01

    We use multiple data streams in a model-data fusion approach to reduce uncertainty in predicting CO2 and CH4 exchange in drained and flooded peatlands. Drained peatlands in the Sacramento-San Joaquin River Delta, California are a strong source of CO2 to the atmosphere and flooded peatlands or wetlands are a strong CO2 sink. However, wetlands are also large sources of CH4 that can offset the greenhouse gas mitigation potential of wetland restoration. Reducing uncertainty in model predictions of annual CO2 and CH4 budgets is critical for including wetland restoration in Cap-and-Trade programs. We have developed and parameterized the Peatland Ecosystem Photosynthesis, Respiration, and Methane Transport model (PEPRMT) in a drained agricultural peatland and a restored wetland. Both ecosystem respiration (Reco) and CH4 production are a function of 2 soil carbon (C) pools (i.e. recently-fixed C and soil organic C), temperature, and water table height. Photosynthesis is predicted using a light use efficiency model. To estimate parameters we use a Markov Chain Monte Carlo approach with an adaptive Metropolis-Hastings algorithm. Multiple data streams are used to constrain model parameters including eddy covariance of CO2, 13CO2 and CH4, continuous soil respiration measurements and digital photography. Digital photography is used to estimate leaf area index, an important input variable for the photosynthesis model. Soil respiration and 13CO2 fluxes allow partitioning of eddy covariance data between Reco and photosynthesis. Partitioned fluxes of CO2 with associated uncertainty are used to parametrize the Reco and photosynthesis models within PEPRMT. Overall, PEPRMT model performance is high. For example, we observe high data-model agreement between modeled and observed partitioned Reco (r2 = 0.68; slope = 1; RMSE = 0.59 g C-CO2 m-2 d-1). Model validation demonstrated the model's ability to accurately predict annual budgets of CO2 and CH4 in a wetland system (within 14% and 1

  19. Monitoring Biogeochemical Processes in Coral Reef Environments with Remote Sensing: A Cross-Disciplinary Approach.

    Science.gov (United States)

    Perez, D.; Phinn, S. R.; Roelfsema, C. M.; Shaw, E. C.; Johnston, L.; Iguel, J.; Camacho, R.

    2017-12-01

    Primary production and calcification are important to measure and monitor over time, because of their fundamental roles in the carbon cycling and accretion of habitat structure for reef ecosystems. However, monitoring biogeochemical processes in coastal environments has been difficult due to complications in resolving differences in water optical properties from biological productivity and other sources (sediment, dissolved organics, etc.). This complicates application of algorithms developed for satellite image data from open ocean conditions, and requires alternative approaches. This project applied a cross-disciplinary approach, using established methods for monitoring productivity in terrestrial environments to coral reef systems. Availability of regularly acquired high spatial (reefs. There is potential to further develop optical models for remote sensing applications to estimate and monitor reef system processes, such as primary productivity and calcification. This project collected field measurements of spectral absorptance and primary productivity and calcification rates for two reef systems: Heron Reef, southern Great Barrier Reef and Saipan Lagoon, Commonwealth of the Northern Mariana Islands. Field data were used to parameterize a light-use efficiency (LUE) model, estimating productivity from absorbed photosynthetically active radiation. The LUE model has been successfully applied in terrestrial environments for the past 40 years, and could potentially be used in shallow, marine environments. The model was used in combination with a map of benthic community composition produced from objective based image analysis of WorldView 2 imagery. Light-use efficiency was measured for functional groups: coral, algae, seagrass, and sediment. However, LUE was overestimated for sediment, which led to overestimation of productivity for the mapped area. This was due to differences in spatial and temporal resolution of field data used in the model. The limitations and

  20. Green Infrastructure Increases Biogeochemical Responsiveness, Vegetation Growth and Decreases Runoff in a Semi-Arid City, Tucson, AZ, USA

    Science.gov (United States)

    Meixner, T.; Papuga, S. A.; Luketich, A. M.; Rockhill, T.; Gallo, E. L.; Anderson, J.; Salgado, L.; Pope, K.; Gupta, N.; Korgaonkar, Y.; Guertin, D. P.

    2017-12-01

    Green Infrastructure (GI) is often viewed as a mechanism to minimize the effects of urbanization on hydrology, water quality, and other ecosystem services (including the urban heat island). Quantifying the effects of GI requires field measurements of the dimensions of biogeochemical, ecosystem, and hydrologic function that we expect GI to impact. Here we investigated the effect of GI features in Tucson, Arizona which has a low intensity winter precipitation regime and a high intensity summer regime. We focused on understanding the effect of GI on soil hydraulic and biogeochemical properties as well as the effect on vegetation and canopy temperature. Our results demonstrate profound changes in biogeochemical and hydrologic properties and vegetation growth between GI systems and nearby control sites. In terms of hydrologic properties GI soils had increased water holding capacity and hydraulic conductivity. GI soils also have higher total carbon, total nitrogen, and organic matter in general than control soils. Furthermore, we tested the sampled soils (control and GI) for differences in biogeochemical response upon wetting. GI soils had larger respiration responses indicating greater biogeochemical activity overall. Long-term Lidar surveys were used to investigate the differential canopy growth of GI systems versus control sites. The results of this analysis indicate that while a significant amount of time is needed to observe differences in canopy growth GI features due increase tree size and thus likely impact street scale ambient temperatures. Additionally monitoring of transpiration, soil moisture, and canopy temperature demonstrates that GI features increase vegetation growth and transpiration and reduce canopy temperatures. These biogeochemical and ecohydrologic results indicate that GI can increase the biogeochemical processing of soils and increase tree growth and thus reduce urban ambient temperatures.

  1. Executive Information Systems' Multidimensional Models

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Executive Information Systems are design to improve the quality of strategic level of management in organization through a new type of technology and several techniques for extracting, transforming, processing, integrating and presenting data in such a way that the organizational knowledge filters can easily associate with this data and turn it into information for the organization. These technologies are known as Business Intelligence Tools. But in order to build analytic reports for Executive Information Systems (EIS in an organization we need to design a multidimensional model based on the business model from the organization. This paper presents some multidimensional models that can be used in EIS development and propose a new model that is suitable for strategic business requests.

  2. Winners and losers: Ecological and biogeochemical changes in a warming ocean

    Science.gov (United States)

    Dutkiewicz, S.; Scott, J. R.; Follows, M. J.

    2013-04-01

    We employ a marine ecosystem model, with diverse and flexible phytoplankton communities, coupled to an Earth system model of intermediate complexity to explore mechanisms that will alter the biogeography and productivity of phytoplankton populations in a warming world. Simple theoretical frameworks and sensitivity experiments reveal that ecological and biogeochemical changes are driven by a balance between two impacts of a warming climate: higher metabolic rates (the "direct" effect), and changes in the supply of limiting nutrients and altered light environments (the "indirect" effect). On globally integrated productivity, the two effects compensate to a large degree. Regionally, the competition between effects is more complicated; patterns of productivity changes are different between high and low latitudes and are also regulated by how the supply of the limiting nutrient changes. These complex regional patterns are also found in the changes to broad phytoplankton functional groups. On the finer ecological scale of diversity within functional groups, we find that ranges of some phytoplankton types are reduced, while those of others (potentially minor players in the present ocean) expand. Combined change in areal extent of range and in regionally available nutrients leads to global "winners and losers." The model suggests that the strongest and most robust signal of the warming ocean is likely to be the large turnover in local phytoplankton community composition.

  3. Numerical Modeling of Microelectrochemical Systems

    DEFF Research Database (Denmark)

    Adesokan, Bolaji James

    for the reactants in the bulk electrolyte that are traveling waves. The first paper presents the mathematical model which describes an electrochemical system and simulates an electroanalytical technique called cyclic voltammetry. The model is governed by a system of advection–diffusion equations with a nonlinear...... reaction term at the boundary. We investigate the effect of flow rates, scan rates, and concentration on the cyclic voltammetry. We establish that high flow rates lead to the reduced hysteresis in the cyclic voltammetry curves and increasing scan rates lead to more pronounced current peaks. The final part...... of the paper shows that the response current in a cyclic voltammetry increases proportionally to the electrolyte concentration. In the second paper we present an experiment of an electrochemical system in a microfluidc system and compare the result to the numerical solutions. We investigate how the position...

  4. System Code Models and Capabilities

    International Nuclear Information System (INIS)

    Bestion, D.

    2008-01-01

    System thermalhydraulic codes such as RELAP, TRACE, CATHARE or ATHLET are now commonly used for reactor transient simulations. The whole methodology of code development is described including the derivation of the system of equations, the analysis of experimental data to obtain closure relation and the validation process. The characteristics of the models are briefly presented starting with the basic assumptions, the system of equations and the derivation of closure relationships. An extensive work was devoted during the last three decades to the improvement and validation of these models, which resulted in some homogenisation of the different codes although separately developed. The so called two-fluid model is the common basis of these codes and it is shown how it can describe both thermal and mechanical nonequilibrium. A review of some important physical models allows to illustrate the main capabilities and limitations of system codes. Attention is drawn on the role of flow regime maps, on the various methods for developing closure laws, on the role of interfacial area and turbulence on interfacial and wall transfers. More details are given for interfacial friction laws and their relation with drift flux models. Prediction of chocked flow and CFFL is also addressed. Based on some limitations of the present generation of codes, perspectives for future are drawn.

  5. Experimental Modeling of Dynamic Systems

    DEFF Research Database (Denmark)

    Knudsen, Morten Haack

    2006-01-01

    An engineering course, Simulation and Experimental Modeling, has been developed that is based on a method for direct estimation of physical parameters in dynamic systems. Compared with classical system identification, the method appears to be easier to understand, apply, and combine with physical...... insight. It is based on a sensitivity approach that is useful for choice of model structure, for experiment design, and for accuracy verification. The method is implemented in the Matlab toolkit Senstools. The method and the presentation have been developed with generally preferred learning styles in mind...

  6. Compositional Modeling of Biological Systems

    OpenAIRE

    Zámborszky, Judit

    2010-01-01

    Molecular interactions are wired in a fascinating way resulting in complex behavior of bio-logical systems. Theoretical modeling provides us a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological systems calls for conceptual tools that manage the combinatorial explosion of the set of possible interac-tions. A suitable conceptual tool to attack complexity is compositionality, already success-fully used in the process algebra field ...

  7. Parametric Modeling for Fluid Systems

    Science.gov (United States)

    Pizarro, Yaritzmar Rosario; Martinez, Jonathan

    2013-01-01

    Fluid Systems involves different projects that require parametric modeling, which is a model that maintains consistent relationships between elements as is manipulated. One of these projects is the Neo Liquid Propellant Testbed, which is part of Rocket U. As part of Rocket U (Rocket University), engineers at NASA's Kennedy Space Center in Florida have the opportunity to develop critical flight skills as they design, build and launch high-powered rockets. To build the Neo testbed; hardware from the Space Shuttle Program was repurposed. Modeling for Neo, included: fittings, valves, frames and tubing, between others. These models help in the review process, to make sure regulations are being followed. Another fluid systems project that required modeling is Plant Habitat's TCUI test project. Plant Habitat is a plan to develop a large growth chamber to learn the effects of long-duration microgravity exposure to plants in space. Work for this project included the design and modeling of a duct vent for flow test. Parametric Modeling for these projects was done using Creo Parametric 2.0.

  8. Understanding oceanic migrations with intrinsic biogeochemical markers.

    Directory of Open Access Journals (Sweden)

    Raül Ramos

    2009-07-01

    Full Text Available Migratory marine vertebrates move annually across remote oceanic water masses crossing international borders. Many anthropogenic threats such as overfishing, bycatch, pollution or global warming put millions of marine migrants at risk especially during their long-distance movements. Therefore, precise knowledge about these migratory movements to understand where and when these animals are more exposed to human impacts is vital for addressing marine conservation issues. Because electronic tracking devices suffer from several constraints, mainly logistical and financial, there is emerging interest in finding appropriate intrinsic markers, such as the chemical composition of inert tissues, to study long-distance migrations and identify wintering sites. Here, using tracked pelagic seabirds and some of their own feathers which were known to be grown at different places and times within the annual cycle, we proved the value of biogeochemical analyses of inert tissue as tracers of marine movements and habitat use. Analyses of feathers grown in summer showed that both stable isotope signatures and element concentrations can signal the origin of breeding birds feeding in distinct water masses. However, only stable isotopes signalled water masses used during winter because elements mainly accumulated during the long breeding period are incorporated into feathers grown in both summer and winter. Our findings shed new light on the simple and effective assignment of marine organisms to distinct oceanic areas, providing new opportunities to study unknown migration patterns of secretive species, including in relation to human-induced mortality on specific populations in the marine environment.

  9. Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates: BIOFILM DISTRIBUTION AND RATE SCALING

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Zhifeng [Institute of Surface-Earth System Science, Tianjin University, Tianjin China; Pacific Northwest National Laboratory, Richland WA USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland WA USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen China; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland WA USA; School of Earth Science and Engineering, Nanjing University, Nanjing China; Bailey, Vanessa L. [Pacific Northwest National Laboratory, Richland WA USA

    2017-11-01

    Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models, and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

  10. Model checking embedded system designs

    NARCIS (Netherlands)

    Brinksma, Hendrik; Mader, Angelika H.

    2002-01-01

    Model checking has established itself as a successful tool supported technique for the verification and debugging of various hardware and software systems [16]. Not only in academia, but also by industry this technique is increasingly being regarded as a promising and practical proposition,

  11. GENERIC model for multiphase systems

    NARCIS (Netherlands)

    Sagis, L.M.C.

    2010-01-01

    GENERIC is a nonequilibrium thermodynamic formalism in which the dynamic behavior of a system is described by a single compact equation involving two types of brackets: a Poisson bracket and a dissipative bracket. This formalism has proved to be a very powerful instrument to model the dynamic

  12. An extensible analysable system model

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, Rene Rydhof

    2008-01-01

    Analysing real-world systems for vulnerabilities with respect to security and safety threats is a difficult undertaking, not least due to a lack of availability of formalisations for those systems. While both formalisations and analyses can be found for artificial systems such as software......, this does not hold for real physical systems. Approaches such as threat modelling try to target the formalisation of the real-world domain, but still are far from the rigid techniques available in security research. Many currently available approaches to assurance of critical infrastructure security...... are based on (quite successful) ad-hoc techniques. We believe they can be significantly improved beyond the state-of-the-art by pairing them with static analyses techniques. In this paper we present an approach to both formalising those real-world systems, as well as providing an underlying semantics, which...

  13. Representing agriculture in Earth System Models: Approaches and priorities for development

    Science.gov (United States)

    McDermid, S. S.; Mearns, L. O.; Ruane, A. C.

    2017-09-01

    Earth System Model (ESM) advances now enable improved representations of spatially and temporally varying anthropogenic climate forcings. One critical forcing is global agriculture, which is now extensive in land-use and intensive in management, owing to 20th century development trends. Agriculture and food systems now contribute nearly 30% of global greenhouse gas emissions and require copious inputs and resources, such as fertilizer, water, and land. Much uncertainty remains in quantifying important agriculture-climate interactions, including surface moisture and energy balances and biogeochemical cycling. Despite these externalities and uncertainties, agriculture is increasingly being leveraged to function as a net sink of anthropogenic carbon, and there is much emphasis on future sustainable intensification. Given its significance as a major environmental and climate forcing, there now exist a variety of approaches to represent agriculture in ESMs. These approaches are reviewed herein, and range from idealized representations of agricultural extent to the development of coupled climate-crop models that capture dynamic feedbacks. We highlight the robust agriculture-climate interactions and responses identified by these modeling efforts, as well as existing uncertainties and model limitations. To this end, coordinated and benchmarking assessments of land-use-climate feedbacks can be leveraged for further improvements in ESM's agricultural representations. We suggest key areas for continued model development, including incorporating irrigation and biogeochemical cycling in particular. Last, we pose several critical research questions to guide future work. Our review focuses on ESM representations of climate-surface interactions over managed agricultural lands, rather than on ESMs as an estimation tool for crop yields and productivity.

  14. Systems modeling for laser IFE

    Science.gov (United States)

    Meier, W. R.; Raffray, A. R.; Sviatoslavsky, I. N.

    2006-06-01

    A systems model of a laser-driven IFE power plant is being developed to assist in design trade-offs and optimization. The focus to date has been on modeling the fusion chamber, blanket and power conversion system. A self-consistent model has been developed to determine key chamber and thermal cycle parameters (e.g., chamber radius, structure and coolant temperatures, cycle efficiency, etc.) as a function of the target yield and pulse repetition rate. Temperature constraints on the tungsten armor, ferritic steel wall, and structure/coolant interface are included in evaluating the potential design space. Results are presented for a lithium cooled first wall coupled with a Brayton power cycle. LLNL work performed under the auspices of the US Department of Energy by the University of California LLNL under Contract W-7405-Eng-48.

  15. Cotangent Models for Integrable Systems

    Science.gov (United States)

    Kiesenhofer, Anna; Miranda, Eva

    2017-03-01

    We associate cotangent models to a neighbourhood of a Liouville torus in symplectic and Poisson manifolds focusing on b-Poisson/ b-symplectic manifolds. The semilocal equivalence with such models uses the corresponding action-angle theorems in these settings: the theorem of Liouville-Mineur-Arnold for symplectic manifolds and an action-angle theorem for regular Liouville tori in Poisson manifolds (Laurent- Gengoux et al., IntMath Res Notices IMRN 8: 1839-1869, 2011). Our models comprise regular Liouville tori of Poisson manifolds but also consider the Liouville tori on the singular locus of a b-Poisson manifold. For this latter class of Poisson structures we define a twisted cotangent model. The equivalence with this twisted cotangent model is given by an action-angle theorem recently proved by the authors and Scott (Math. Pures Appl. (9) 105(1):66-85, 2016). This viewpoint of cotangent models provides a new machinery to construct examples of integrable systems, which are especially valuable in the b-symplectic case where not many sources of examples are known. At the end of the paper we introduce non-degenerate singularities as lifted cotangent models on b-symplectic manifolds and discuss some generalizations of these models to general Poisson manifolds.

  16. Supercontinent tectonics and biogeochemical cycle: A matter of ‘life and death’

    Directory of Open Access Journals (Sweden)

    M. Santosh

    2010-10-01

    Full Text Available The formation and disruption of supercontinents have significantly impacted mantle dynamics, solid earth processes, surface environments and the biogeochemical cycle. In the early history of the Earth, the collision of parallel intra-oceanic arcs was an important process in building embryonic continents. Superdownwelling along Y-shaped triple junctions might have been one of the important processes that aided in the rapid assembly of continental fragments into closely packed supercontinents. Various models have been proposed for the fragmentation of supercontinents including thermal blanket and superplume hypotheses. The reassembly of supercontinents after breakup and the ocean closure occurs through “introversion”, “extroversion” or a combination of both, and is characterized by either Pacific-type or Atlantic-type ocean closure. The breakup of supercontinents and development of hydrothermal system in rifts with granitic basement create anomalous chemical environments enriched in nutrients, which serve as the primary building blocks of the skeleton and bone of early modern life forms. A typical example is the rifting of the Rodinia supercontinent, which opened up an N–S oriented sea way along which nutrient enriched upwelling brought about a habitable geochemical environment. The assembly of supercontinents also had significant impact on life evolution. The role played by the Cambrian Gondwana assembly has been emphasized in many models, including the formation of ‘Transgondwana Mountains’ that might have provided an effective source of rich nutrients to the equatorial waters, thus aiding the rapid increase in biodiversity. The planet has witnessed several mass extinction events during its history, mostly connected with major climatic fluctuations including global cooling and warming events, major glaciations, fluctuations in sea level, global anoxia, volcanic eruptions, asteroid impacts and gamma radiation. Some recent models

  17. Biogeochemical Processes Regulating the Mobility of Uranium in Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Belli, Keaton M.; Taillefert, Martial

    2016-07-01

    This book chapters reviews the latest knowledge on the biogeochemical processes regulating the mobility of uranium in sediments. It contains both data from the literature and new data from the authors.

  18. Climate, ecosystems, and planetary futures: The challenge to predict life in Earth system models.

    Science.gov (United States)

    Bonan, Gordon B; Doney, Scott C

    2018-02-02

    Many global change stresses on terrestrial and marine ecosystems affect not only ecosystem services that are essential to humankind, but also the trajectory of future climate by altering energy and mass exchanges with the atmosphere. Earth system models, which simulate terrestrial and marine ecosystems and biogeochemical cycles, offer a common framework for ecological research related to climate processes; analyses of vulnerability, impacts, and adaptation; and climate change mitigation. They provide an opportunity to move beyond physical descriptors of atmospheric and oceanic states to societally relevant quantities such as wildfire risk, habitat loss, water availability, and crop, fishery, and timber yields. To achieve this, the science of climate prediction must be extended to a more multifaceted Earth system prediction that includes the biosphere and its resources. Copyright © 2018, American Association for the Advancement of Science.

  19. Graph modeling systems and methods

    Science.gov (United States)

    Neergaard, Mike

    2015-10-13

    An apparatus and a method for vulnerability and reliability modeling are provided. The method generally includes constructing a graph model of a physical network using a computer, the graph model including a plurality of terminating vertices to represent nodes in the physical network, a plurality of edges to represent transmission paths in the physical network, and a non-terminating vertex to represent a non-nodal vulnerability along a transmission path in the physical network. The method additionally includes evaluating the vulnerability and reliability of the physical network using the constructed graph model, wherein the vulnerability and reliability evaluation includes a determination of whether each terminating and non-terminating vertex represents a critical point of failure. The method can be utilized to evaluate wide variety of networks, including power grid infrastructures, communication network topologies, and fluid distribution systems.

  20. Inferring Properties of Ancient Cyanobacteria from Biogeochemical Activity and Genomes of Siderophilic Cyanobacteria

    Science.gov (United States)

    McKay, David S.; Brown, I. I.; Tringe, S. G.; Thomas-Keprta, K. E.; Bryant, D. A.; Sarkisova, S. S.; Malley, K.; Sosa, O.; Klatt, C. G.; McKay, D. S.

    2010-01-01

    Interrelationships between life and the planetary system could have simultaneously left landmarks in genomes of microbes and physicochemical signatures in the lithosphere. Verifying the links between genomic features in living organisms and the mineralized signatures generated by these organisms will help to reveal traces of life on Earth and beyond. Among contemporary environments, iron-depositing hot springs (IDHS) may represent one of the most appropriate natural models [1] for insights into ancient life since organisms may have originated on Earth and probably Mars in association with hydrothermal activity [2,3]. IDHS also seem to be appropriate models for studying certain biogeochemical processes that could have taken place in the late Archean and,-or early Paleoproterozoic eras [4, 5]. It has been suggested that inorganic polyphosphate (PPi), in chains of tens to hundreds of phosphate residues linked by high-energy bonds, is environmentally ubiquitous and abundant [6]. Cyanobacteria (CB) react to increased heavy metal concentrations and UV by enhanced generation of PPi bodies (PPB) [7], which are believed to be signatures of life [8]. However, the role of PPi in oxygenic prokaryotes for the suppression of oxidative stress induced by high Fe is poorly studied. Here we present preliminary results of a new mechanism of Fe mineralization in oxygenic prokaryotes, the effect of Fe on the generation of PPi bodies in CB, as well as preliminary analysis of the diversity and phylogeny of proteins involved in the prevention of oxidative stress in phototrophs inhabiting IDHS.

  1. Decoupling biogeochemical records, extinction, and environmental change during the Cambrian SPICE event

    Science.gov (United States)

    Schiffbauer, James D.; Huntley, John Warren; Fike, David A.; Jeffrey, Matthew Jarrell; Gregg, Jay M.; Shelton, Kevin L.

    2017-01-01

    Several positive carbon isotope excursions in Lower Paleozoic rocks, including the prominent Upper Cambrian Steptoean Positive Carbon Isotope Excursion (SPICE), are thought to reflect intermittent perturbations in the hydrosphere-biosphere system. Models explaining these secular changes are abundant, but the synchronicity and regional variation of the isotope signals are not well understood. Examination of cores across a paleodepth gradient in the Upper Cambrian central Missouri intrashelf basin (United States) reveals a time-transgressive, facies-dependent nature of the SPICE. Although the SPICE event may be a global signal, the manner in which it is recorded in rocks should and does vary as a function of facies and carbonate platform geometry. We call for a paradigm shift to better constrain facies, stratigraphic, and biostratigraphic architecture and to apply these observations to the variability in magnitude, stratigraphic extent, and timing of the SPICE signal, as well as other biogeochemical perturbations, to elucidate the complex processes driving the ocean-carbonate system. PMID:28275734

  2. Web Strategy to Convey Marine Biogeochemical Feedback Concepts to the Policy Community: Aerosol and Sea Ice

    Directory of Open Access Journals (Sweden)

    Zachary M. Menzo

    2018-01-01

    Full Text Available Limited understanding of the climate system imposes upon policy makers an intimate reliance on results from Earth System Models (ESMs. However, climate simulations are necessarily incomplete since many strong channels through planetary scale biology and geochemistry remain too complex or poorly comprehended to include. This paper presents and describes an interactive, public domain website detailing the role of two marine biogeochemical (mBGC feedback loops currently excluded from many ESMs (www.marinefeedbacks.com. Every page on the website includes images or videos to foster engagement with its technically challenging content. Simultaneously, fundamentals of the natural science involved are reinforced. The site includes subsections of the following nature; background information, executive summaries for each feedback type, detailed descriptions of the chemical mechanisms, climate change impact, and recommendations for future research. The information provided is firmly grounded in the technical literature but is designed specifically for accessibility to non-scientists. Particular targets for the material are the next-generation of decision makers and those framing the international climate agenda. It is hoped that a site with tailored pedagogical value may contribute to well informed policy formulation and legislation.

  3. Probabilistic models for feedback systems.

    Energy Technology Data Exchange (ETDEWEB)

    Grace, Matthew D.; Boggs, Paul T.

    2011-02-01

    In previous work, we developed a Bayesian-based methodology to analyze the reliability of hierarchical systems. The output of the procedure is a statistical distribution of the reliability, thus allowing many questions to be answered. The principal advantage of the approach is that along with an estimate of the reliability, we also can provide statements of confidence in the results. The model is quite general in that it allows general representations of all of the distributions involved, it incorporates prior knowledge into the models, it allows errors in the 'engineered' nodes of a system to be determined by the data, and leads to the ability to determine optimal testing strategies. In this report, we provide the preliminary steps necessary to extend this approach to systems with feedback. Feedback is an essential component of 'complexity' and provides interesting challenges in modeling the time-dependent action of a feedback loop. We provide a mechanism for doing this and analyze a simple case. We then consider some extensions to more interesting examples with local control affecting the entire system. Finally, a discussion of the status of the research is also included.

  4. Stochastic Modelling of Hydrologic Systems

    DEFF Research Database (Denmark)

    Jonsdottir, Harpa

    2007-01-01

    In this PhD project several stochastic modelling methods are studied and applied on various subjects in hydrology. The research was prepared at Informatics and Mathematical Modelling at the Technical University of Denmark. The thesis is divided into two parts. The first part contains an introduct......In this PhD project several stochastic modelling methods are studied and applied on various subjects in hydrology. The research was prepared at Informatics and Mathematical Modelling at the Technical University of Denmark. The thesis is divided into two parts. The first part contains...... an introduction and an overview of the papers published. Then an introduction to basic concepts in hydrology along with a description of hydrological data is given. Finally an introduction to stochastic modelling is given. The second part contains the research papers. In the research papers the stochastic methods...... are described, as at the time of publication these methods represent new contribution to hydrology. The second part also contains additional description of software used and a brief introduction to stiff systems. The system in one of the papers is stiff....

  5. Restoration of biogeochemical function in mangrove forests

    Science.gov (United States)

    McKee, K.L.; Faulkner, P.L.

    2000-01-01

    Forest structure of mangrove restoration sites (6 and 14 years old) at two locations (Henderson Creek [HC] and Windstar [WS]) in southwest Florida differed from that of mixed-basin forests (>50 years old) with which they were once contiguous. However, the younger site (HC) was typical of natural, developing forests, whereas the older site (WS) was less well developed with low structural complexity. More stressful physicochemical conditions resulting from incomplete tidal flushing (elevated salinity) and variable topography (waterlogging) apparently affected plant survival and growth at the WS restoration site. Lower leaf fall and root production rates at the WS restoration site, compared with that at HC were partly attributable to differences in hydroedaphic conditions and structural development. However, leaf and root inputs at each restoration site were not significantly different from that in reference forests within the same physiographic setting. Macrofaunal consumption of tethered leaves also did not differ with site history, but was dramatically higher at HC compared with WS, reflecting local variation in leaf litter processing rates, primarily by snails (Melampus coffeus). Degradation of leaves and roots in mesh bags was slow overall at restoration sites, however, particularly at WS where aerobic decomposition may have been more limited. These findings indicate that local or regional factors such as salinity regime act together with site history to control primary production and turnover rates of organic matter in restoration sites. Species differences in senescent leaf nitrogen content and degradation rates further suggest that restoration sites dominated by Laguncularia racemosa and Rhizophora mangle should exhibit slower recycling of nutrients compared with natural basin forests where Avicennia germinans is more abundant. Structural development and biogeochemical functioning of restored mangrove forests thus depend on a number of factors, but site

  6. Discrete modelling of drapery systems

    Science.gov (United States)

    Thoeni, Klaus; Giacomini, Anna

    2016-04-01

    Drapery systems are an efficient and cost-effective measure in preventing and controlling rockfall hazards on rock slopes. The simplest form consists of a row of ground anchors along the top of the slope connected to a horizontal support cable from which a wire mesh is suspended down the face of the slope. Such systems are generally referred to as simple or unsecured draperies (Badger and Duffy 2012). Variations such as secured draperies, where a pattern of ground anchors is incorporated within the field of the mesh, and hybrid systems, where the upper part of an unsecured drapery is elevated to intercept rockfalls originating upslope of the installation, are becoming more and more popular. This work presents a discrete element framework for simulation of unsecured drapery systems and its variations. The numerical model is based on the classical discrete element method (DEM) and implemented into the open-source framework YADE (Šmilauer et al., 2010). The model takes all relevant interactions between block, drapery and slope into account (Thoeni et al., 2014) and was calibrated and validated based on full-scale experiments (Giacomini et al., 2012).The block is modelled as a rigid clump made of spherical particles which allows any shape to be approximated. The drapery is represented by a set of spherical particle with remote interactions. The behaviour of the remote interactions is governed by the constitutive behaviour of the wire and generally corresponds to a piecewise linear stress-strain relation (Thoeni et al., 2013). The same concept is used to model wire ropes. The rock slope is represented by rigid triangular elements where material properties (e.g., normal coefficient of restitution, friction angle) are assigned to each triangle. The capabilities of the developed model to simulate drapery systems and estimate the residual hazard involved with such systems is shown. References Badger, T.C., Duffy, J.D. (2012) Drapery systems. In: Turner, A.K., Schuster R

  7. Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon

    OpenAIRE

    Neubauer, S. C.; Franklin, R. B.; Berrier, D. J.

    2013-01-01

    Environmental perturbations in wetlands affect the integrated plant-microbial-soil system, causing biogeochemical responses that can manifest at local to global scales. The objective of this study was to determine how saltwater intrusion affects carbon mineralization and greenhouse gas production in coastal wetlands. Working with tidal freshwater marsh soils that had experienced ~ 3.5 yr of in situ saltwater additions, we quantified changes in soil properties, measured ex...

  8. Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon

    OpenAIRE

    S. C. Neubauer; R. B. Franklin; D. J. Berrier

    2013-01-01

    Environmental perturbations in wetlands affect the integrated plant-microbial-soil system, causing biogeochemical responses that can manifest at local to global scales. The objective of this study was to determine how saltwater intrusion affects carbon mineralization and greenhouse gas production in coastal wetlands. Working with tidal freshwater marsh soils that had experienced roughly 3.5 yr of in situ saltwater additions, we quantified changes in soil properties, measured extracellu...

  9. Modeling multi-component transport and enhanced anaerobic dechlorination processes in a single fracture-clay matrix system

    DEFF Research Database (Denmark)

    Chambon, Julie Claire Claudia; Broholm, Mette Martina; Binning, Philip John

    2010-01-01

    Clayey tills contaminated with chlorinated solvents are a threat to groundwater and are difficult to remediate. A numerical model is developed for assessing leaching processes and for simulating the remediation via enhanced anaerobic dechlorination. The model simulates the transport...... of a contaminant in a single fracture-clay matrix system coupled with a reactive model for anaerobic dechlorination. The model takes into account microbially driven anaerobic dechlorination, where sequential Monod kinetics with competitive inhibition is used to model the reaction rates, and degradation...... to the physical processes, mainly diffusion in the matrix, than to the biogeochemical processes, when dechlorination is assumed to take place in a limited reaction zone only. The inclusion of sequential dechlorination in clay fracture transport models is crucial, as the contaminant flux to the aquifer...

  10. Modelling Ecosystem Dynamics of the Oxygen Minimum Zones in the Angola Gyre and the Northern Benguela Upwelling System.

    Science.gov (United States)

    Schmidt, M.; Eggert, A.

    2016-02-01

    The Angola Gyre and the Northern Benguela Upwelling System are two major oxygen minimum zones (OMZ) of different kind connected by the system of African Eastern Boundary Currents. We discuss results from a 3-dimensional coupled biogeochemical model covering both oxygen-deficient systems. The biogeochemical model component comprises trophic levels up to zooplankton. Physiological properties of organisms are parameterized from field data gained mainly in the course of the project "Geochemistry and Ecology of the Namibian Upwelling System" (GENUS). The challenge of the modelling effort is the different nature of both systems. The Angola Gyre, located in a "shadow zone" of the tropical Atlantic, has a low productivity and little ventilation, hence a long residence time of water masses. In the northern Benguela Upwelling System, trade winds drive an intermittent, but permanent nutrient supply into the euphotic zone which fuels a high coastal productivity, large particle export and high oxygen consumption from dissimilatory processes. In addition to the local processes, oxygen-deficient water formed in the Angola Gyre is one of the source water masses of the poleward undercurrent, which feeds oxygen depleted water into the Benguela system. In order to simulate the oxygen distribution in the Benguela system, both physical transport as well as local biological processes need to be carefully adjusted in the model. The focus of the analysis is on the time scale and the relative contribution of the different oxygen related processes to the oxygen budgets in both the oxygen minimum zones. Although these are very different in both the OMZ, the model is found as suitable to produce oxygen minimum zones comparable with observations in the Benguela and the Angola Gyre as well. Variability of the oxygen concentration in the Angola Gyre depends strongly on organismic oxygen consumption, whereas the variability of the oxygen concentration on the Namibian shelf is governed mostly by

  11. Computational models of complex systems

    CERN Document Server

    Dabbaghian, Vahid

    2014-01-01

    Computational and mathematical models provide us with the opportunities to investigate the complexities of real world problems. They allow us to apply our best analytical methods to define problems in a clearly mathematical manner and exhaustively test our solutions before committing expensive resources. This is made possible by assuming parameter(s) in a bounded environment, allowing for controllable experimentation, not always possible in live scenarios. For example, simulation of computational models allows the testing of theories in a manner that is both fundamentally deductive and experimental in nature. The main ingredients for such research ideas come from multiple disciplines and the importance of interdisciplinary research is well recognized by the scientific community. This book provides a window to the novel endeavours of the research communities to present their works by highlighting the value of computational modelling as a research tool when investigating complex systems. We hope that the reader...

  12. Model reduction of parametrized systems

    CERN Document Server

    Ohlberger, Mario; Patera, Anthony; Rozza, Gianluigi; Urban, Karsten

    2017-01-01

    The special volume offers a global guide to new concepts and approaches concerning the following topics: reduced basis methods, proper orthogonal decomposition, proper generalized decomposition, approximation theory related to model reduction, learning theory and compressed sensing, stochastic and high-dimensional problems, system-theoretic methods, nonlinear model reduction, reduction of coupled problems/multiphysics, optimization and optimal control, state estimation and control, reduced order models and domain decomposition methods, Krylov-subspace and interpolatory methods, and applications to real industrial and complex problems. The book represents the state of the art in the development of reduced order methods. It contains contributions from internationally respected experts, guaranteeing a wide range of expertise and topics. Further, it reflects an important effor t, carried out over the last 12 years, to build a growing research community in this field. Though not a textbook, some of the chapters ca...

  13. Modeling software systems by domains

    Science.gov (United States)

    Dippolito, Richard; Lee, Kenneth

    1992-01-01

    The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

  14. The role of forcing agents on biogeochemical variability along the southwestern Adriatic coast: The Gulf of Manfredonia case study

    Science.gov (United States)

    Specchiulli, Antonietta; Bignami, Francesco; Marini, Mauro; Fabbrocini, Adele; Scirocco, Tommaso; Campanelli, Alessandra; Penna, Pierluigi; Santucci, Angela; D'Adamo, Raffaele

    2016-12-01

    This study investigates how multiple forcing factors such as rivers, surface marine circulation and winds affect hydrology and biogeochemical processes in the Gulf of Manfredonia and the seas around the Gargano peninsula, in the south-western Adriatic Sea. The study adopted an integrated approach, using in situ and remote sensing data, as well as the output of current models. The data reveal variability in the area's hydrography induced by local freshwater sources, the Western Adriatic Current (WAC) flowing from the north along the Italian coast, and the current patterns under different wind regimes. Specifically, exchange with offshore waters in the gulf induces variability in salinity and biogeochemical content, even within the same season, i.e. winter, in our case. This strong dependence on physical and biogeochemical factors makes the Manfredonia-Gargano ecosystem vulnerable to climate change, which could compromise its important role as a nursery area for the Adriatic Sea.

  15. Biogeochemical sensor performance in the SOCCOM profiling float array

    Science.gov (United States)

    Johnson, Kenneth S.; Plant, Joshua N.; Coletti, Luke J.; Jannasch, Hans W.; Sakamoto, Carole M.; Riser, Stephen C.; Swift, Dana D.; Williams, Nancy L.; Boss, Emmanuel; Haëntjens, Nils; Talley, Lynne D.; Sarmiento, Jorge L.

    2017-08-01

    The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) program has begun deploying a large array of biogeochemical sensors on profiling floats in the Southern Ocean. As of February 2016, 86 floats have been deployed. Here the focus is on 56 floats with quality-controlled and adjusted data that have been in the water at least 6 months. The floats carry oxygen, nitrate, pH, chlorophyll fluorescence, and optical backscatter sensors. The raw data generated by these sensors can suffer from inaccurate initial calibrations and from sensor drift over time. Procedures to correct the data are defined. The initial accuracy of the adjusted concentrations is assessed by comparing the corrected data to laboratory measurements made on samples collected by a hydrographic cast with a rosette sampler at the float deployment station. The long-term accuracy of the corrected data is compared to the GLODAPv2 data set whenever a float made a profile within 20 km of a GLODAPv2 station. Based on these assessments, the fleet average oxygen data are accurate to 1 ± 1%, nitrate to within 0.5 ± 0.5 µmol kg-1, and pH to 0.005 ± 0.007, where the error limit is 1 standard deviation of the fleet data. The bio-optical measurements of chlorophyll fluorescence and optical backscatter are used to estimate chlorophyll a and particulate organic carbon concentration. The particulate organic carbon concentrations inferred from optical backscatter appear accurate to with 35 mg C m-3 or 20%, whichever is larger. Factors affecting the accuracy of the estimated chlorophyll a concentrations are evaluated.Plain Language SummaryThe ocean science community must move toward greater use of autonomous platforms and sensors if we are to extend our knowledge of the effects of climate driven change within the ocean. Essential to this shift in observing strategies is an understanding of the performance that can be obtained from biogeochemical sensors on platforms deployed for years and the

  16. Suspended Particles: Their Role in Estuarine Biogeochemical Cycles

    Science.gov (United States)

    Turner, A.; Millward, G. E.

    2002-12-01

    Suspended particles are instrumental in controlling the reactivity, transport and biological impacts of substances in aquatic environments, and provide a crucial link for chemical constituents between the water column, bed sediment and food chain. This article reviews the role of suspended particles in the chemical and biological cycling of trace constituents (trace metals, organo-metallic compounds and hydrophobic organic micropollutants; HOMs) in estuaries, with particular emphasis on the effects of and changes to particle reactivity and composition. The partitioning (or distribution coefficient, KD ) and bioavailability of chemical constituents, and assimilation efficiency (AE) of such by bivalve suspension feeders, are identified as key parameters requiring definition for accurate biogeochemical modelling, and the discussion centres around the determination of and controls on these parameters. Particle-water interactions encompass a variety of physical, biological, electrostatic and hydrophobic effects, and are largely dependent on the character and concentration of suspended particles and salinity. The salinity-dependence results from the competing and complexing effects of seawater ions for trace metals, and the compression of water in the presence of dissolved seawater ions and consequent salting out of neutral solute (HOMs, organo-metallic compounds and some trace metal complexes). The extent of biological solubilization of chemical constituents from suspended particles is dependent on the nature of chemical components of the gastro-intestinal environment and their interactions with ingested particles, and the physiological (e.g. gut passage time) and chemical (e.g. redox conditions and pH) constraints imposed on these interactions. Generally, chemicals that associate with fine, organic-rich particles (or, for some HOMs, fine inorganic particles), and desorb at pH 5-6 and/or complex with digestive enzymes or surfactants are most readily solubilized in the

  17. Depressional Wetlands Affect Watershed Hydrological, Biogeochemical, and Ecological Functions.

    Science.gov (United States)

    Evenson, Grey R; Golden, Heather E; Lane, Charles R; McLaughlin, Daniel L; D'Amico, Ellen

    2018-02-13

    Depressional wetlands of the extensive U.S. and Canadian Prairie Pothole Region afford numerous ecosystem processes that maintain healthy watershed functioning. However, these wetlands have been lost at a prodigious rate over past decades due to drainage for development, climate effects, and other causes. Options for management entities to protect the existing wetlands - and their functions - may focus on conserving wetlands based on spatial location vis-à-vis a floodplain or on size limitations (e.g., permitting smaller wetlands to be destroyed but not larger wetlands). Yet the effects of such management practices and the concomitant loss of depressional wetlands on watershed-scale hydrological, biogeochemical, and ecological functions are largely unknown. Using a hydrological model, we analyzed how different loss scenarios by wetland size and proximal location to the stream network affected watershed storage (i.e., inundation patterns and residence times), connectivity (i.e., streamflow contributing areas), and export (i.e., streamflow) in a large watershed in the Prairie Pothole Region of North Dakota, USA. Depressional wetlands store consequential amounts of precipitation and snowmelt. The loss of smaller depressional wetlands (watershed connectivity and storage characteristics of larger wetlands. The wetland management scenario based on stream proximity (i.e., protecting wetlands 30-m and ~450-m from the stream) alone resulted in considerable landscape heterogeneity loss and decreased inundated area and residence times. With more snowmelt and precipitation available for runoff with wetland losses, contributing area increased across all loss scenarios. We additionally found that depressional wetlands attenuated peak flows; the probability of increased downstream flooding from wetland loss was also consistent across all loss scenarios. It is evident from this study that optimizing wetland management for one end-goal (e.g., protection of large depressional

  18. The Baltic Inflow Event 2014 and its Biogeochemical Response in the Anoxic Central Baltic Basins

    Science.gov (United States)

    Schulz-Bull, D. E.; Naumann, M.; Mohrholz, V.; Nausch, G.; Prien, R. D.

    2016-02-01

    The brackish Baltic Sea and the deeper anoxic basins in the central parts are occasionally ventilated by the intrusion of high saline and oxygen rich water from the North Atlantic entering the Baltic Sea. With a volume of 198 km3 containing 4 Gt salt, the inflow event in 2014 was the third largest ever observed. As a result the redox conditions in the anoxic parts of the Baltic Sea changed. In the Bornholm Basin and the Gotland Deep area the biogeochemical conditions for many elements and redox sensitive substances changed crucial by the inflow water. Oxidation of the hydrogen sulfide and consequent changes in the pH and the carbonate system were observed. Other chemicals such as the nitrogen nutrients, phosphate, trace metals and the dissolved organic matter react with the fresh inflow water ingredients. The chronological sequence of the biogeochemical reactions following the inflow event where monitored by autonomous stations and several ship expeditions in high spatial and temporal resolution.

  19. Biogeochemical Cycling of Sulfur in Soil

    Science.gov (United States)

    Lehmann, J.; Solomon, D.; Janzen, H.; Amelung, W.; Lobe, I.; Martinez, C. E.; Dupreez, C.; Machado, S.

    2002-12-01

    Sulfur is an important element of the global biogeochemical cycle, since it is highly reactive and moves freely among the lithosphere, atmosphere and hydrosphere. Climatic and environmental changes affecting sulfur in the pedosphere will inevitably change the rate and forms of global sulfur cycling which are intertwined with that of carbon, nitrogen and phosphorus. In soil, inorganic sulfur derived from atmospheric deposition or fertilization is largely immobilized and incorporated into soil organic matter (>95%). During the last decades, however, these emissions have been significantly reduced in North America and Europe, and S deficiency can increasingly be observed in crops. This process was accelerated by a change to low-S-containing fertilizers. Therefore, we studied the long-term dynamics of S forms in relation to organic C to evaluate its impact on the soil cycle. Synchrotron-based sulfur K-edge X-ray Absorption Near-Edge Structure spectroscopy (XANES) was used to speciate and quantify the different oxidation states of soil sulfur (organic and inorganic forms of S). Direct measurement of S species in bulk soil indicated the presence of large background on the spectra, which could not easily be corrected without affecting the results. However, humic acid extractions using 0.1 M NaOH/0.4 M NaF mixtures produced better signals, which can even be improved by additional filtration using a 0.2mm membrane filter under pressure. Traditional wet chemical analyses of soil S using hydriodic acid (HI) reduction showed that the major proportion (98%) of total S was present in organic forms, out of which 77-84% were C-bonded S, whereas ester SO4 -S constituted merely 16-23% of the organic S pool in bulk soils. These values were constant regardless of major soil disturbances by landuse and did not change between different particle size fractions. S-XANES spectroscopy, however, showed clear differences of S oxidation states after environmental disturbance of soil and

  20. A state-space Bayesian framework for estimating biogeochemical transformations using time-lapse geophysical data

    Energy Technology Data Exchange (ETDEWEB)

    Chen, J.; Hubbard, S.; Williams, K.; Pride, S.; Li, L.; Steefel, C.; Slater, L.

    2009-04-15

    We develop a state-space Bayesian framework to combine time-lapse geophysical data with other types of information for quantitative estimation of biogeochemical parameters during bioremediation. We consider characteristics of end-products of biogeochemical transformations as state vectors, which evolve under constraints of local environments through evolution equations, and consider time-lapse geophysical data as available observations, which could be linked to the state vectors through petrophysical models. We estimate the state vectors and their associated unknown parameters over time using Markov chain Monte Carlo sampling methods. To demonstrate the use of the state-space approach, we apply it to complex resistivity data collected during laboratory column biostimulation experiments that were poised to precipitate iron and zinc sulfides during sulfate reduction. We develop a petrophysical model based on sphere-shaped cells to link the sulfide precipitate properties to the time-lapse geophysical attributes and estimate volume fraction of the sulfide precipitates, fraction of the dispersed, sulfide-encrusted cells, mean radius of the aggregated clusters, and permeability over the course of the experiments. Results of the case study suggest that the developed state-space approach permits the use of geophysical datasets for providing quantitative estimates of end-product characteristics and hydrological feedbacks associated with biogeochemical transformations. Although tested here on laboratory column experiment datasets, the developed framework provides the foundation needed for quantitative field-scale estimation of biogeochemical parameters over space and time using direct, but often sparse wellbore data with indirect, but more spatially extensive geophysical datasets.

  1. Relating hyporheic fluxes, residence times, and redox-sensitive biogeochemical processes upstream of beaver dams

    Science.gov (United States)

    Briggs, Martin A.; Lautz, Laura; Hare, Danielle K.

    2013-01-01

    Abstract. Small dams enhance the development of patchy microenvironments along stream corridors by trapping sediment and creating complex streambed morphologies. This patchiness drives intricate hyporheic flux patterns that govern the exchange of O2 and redox-sensitive solutes between the water column and the stream bed. We used multiple tracer techniques, naturally occurring and injected, to evaluate hyporheic flow dynamics and associated biogeochemical cycling and microbial reactivity around 2 beaver dams in Wyoming (USA). High-resolution fiber-optic distributed temperature sensing was used to collect temperature data over 9 vertical streambed profiles and to generate comprehensive vertical flux maps using 1-dimensional (1-D) heat-transport modeling. Coincident with these locations, vertical profiles of hyporheic water were collected every week and analyzed for dissolved O2, pH, dissolved organic C, and several conservative and redox-sensitive solutes. In addition, hyporheic and net stream aerobic microbial reactivity were analyzed with a constant-rate injection of the biologically sensitive resazurin (Raz) smart tracer. The combined results revealed a heterogeneous system with rates of downwelling hyporheic flow organized by morphologic unit and tightly coupled to the redox conditions of the subsurface. Principal component analysis was used to summarize the variability of all redox-sensitive species, and results indicated that hyporheic water varied from oxic-stream-like to anoxic-reduced in direct response to the hydrodynamic conditions and associated residence times. The anaerobic transition threshold predicted by the mean O2 Damko

  2. Pore-scale insights to the rate of organic carbon degradation and biofilm formation under variable hydro-biogeochemical conditions in soils and sediments

    Science.gov (United States)

    Liu, C.; Yan, Z.; Liu, Y.; Li, M.; Bailey, V. L.

    2015-12-01

    Biogeochemical processes that control microbial growth, organic carbon degradation, and CO2 production and migration are fundamentally occur at the pore scale. In this presentation, we will describe our recent results of a pore-scale simulation research to investigate: 1) how moisture content and distribution affects oxygen delivery, organic carbon availability, and microbial activities that regulate the rate of organic carbon degradation and CO2 production in aerobic systems; and 2) how pore-scale reactive transport processes affect local microbial growth, biofilm formation, and overall rate of microbial reactions in anoxic systems. The results revealed that there is an optimal moisture content for aerobic bacterial respiration and CO2 production. When moisture is below the optimal value, organic carbon availability limits its degradation due to diffusion and osmotic stress to bacterial reactivity; and when moisture is above the optimal value, oxygen delivery limits microbial respiration. The optimal moisture condition is, however, a function of soil texture and physical heterogeneity, bioavailable soil organic carbon, and microbial community function. In anoxic and saturated system, simulation results show that biofilm preferentially forms in concave areas around sand particles and macro aggregates where cross-directional fluxes of organic carbon and electron acceptors (e.g., nitrate) favor microbial growth and attachment. The results provide important insights to the establishment of constitutive relationships between the macroscopic rates of soil organic carbon degradation and moisture content, and to the development of biogeochemical reactive transport models that incorporate biofilm structures and physio-chemical heterogeneity in soils and sediments.

  3. Ocean Chlorophyll as a Precursor of ENSO: An Earth System Modeling Study

    Science.gov (United States)

    Park, Jong-Yeon; Dunne, John P.; Stock, Charles A.

    2018-02-01

    Ocean chlorophyll concentration, a proxy for phytoplankton, is strongly influenced by internal ocean dynamics such as those associated with El Niño-Southern Oscillation (ENSO). Observations show that ocean chlorophyll responses to ENSO generally lead sea surface temperature (SST) responses in the equatorial Pacific. A long-term global Earth system model simulation incorporating marine biogeochemical processes also exhibits a preceding chlorophyll response. In contrast to simulated SST anomalies, which significantly lag the wind-driven subsurface heat response to ENSO, chlorophyll anomalies respond rapidly. Iron was found to be the key factor connecting the simulated surface chlorophyll anomalies to the subsurface ocean response. Westerly wind bursts decrease central Pacific chlorophyll by reducing iron supply through wind-driven thermocline deepening but increase western Pacific chlorophyll by enhancing the influx of coastal iron from the maritime continent. Our results mechanistically support the potential for chlorophyll-based indices to inform seasonal ENSO forecasts beyond previously identified SST-based indices.

  4. Cognitive models embedded in system simulation models

    International Nuclear Information System (INIS)

    Siegel, A.I.; Wolf, J.J.

    1982-01-01

    If we are to discuss and consider cognitive models, we must first come to grips with two questions: (1) What is cognition; (2) What is a model. Presumably, the answers to these questions can provide a basis for defining a cognitive model. Accordingly, this paper first places these two questions into perspective. Then, cognitive models are set within the context of computer simulation models and a number of computer simulations of cognitive processes are described. Finally, pervasive issues are discussed vis-a-vis cognitive modeling in the computer simulation context

  5. Consequences of ecological, evolutionary and biogeochemical uncertainty for coral reef responses to climatic stress.

    Science.gov (United States)

    Mumby, Peter J; van Woesik, Robert

    2014-05-19

    Coral reefs are highly sensitive to the stress associated with greenhouse gas emissions, in particular ocean warming and acidification. While experiments show negative responses of most reef organisms to ocean warming, some autotrophs benefit from ocean acidification. Yet, we are uncertain of the response of coral reefs as systems. We begin by reviewing sources of uncertainty and complexity including the translation of physiological effects into demographic processes, indirect ecological interactions among species, the ability of coral reefs to modify their own chemistry, adaptation and trans-generational plasticity. We then incorporate these uncertainties into two simple qualitative models of a coral reef system under climate change. Some sources of uncertainty are far more problematic than others. Climate change is predicted to have an unambiguous negative effect on corals that is robust to several sources of uncertainty but sensitive to the degree of biogeochemical coupling between benthos and seawater. Macroalgal, zoanthid, and herbivorous fish populations are generally predicted to increase, but the ambiguity (confidence) of such predictions are sensitive to the source of uncertainty. For example, reversing the effect of climate-related stress on macroalgae from being positive to negative had no influence on system behaviour. By contrast, the system was highly sensitive to a change in the stress upon herbivorous fishes. Minor changes in competitive interactions had profound impacts on system behaviour, implying that the outcomes of mesocosm studies could be highly sensitive to the choice of taxa. We use our analysis to identify new hypotheses and suggest that the effects of climatic stress on coral reefs provide an exceptional opportunity to test emerging theories of ecological inheritance. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume.

    Science.gov (United States)

    Zielinski, Brian L; Allen, Andrew E; Carpenter, Edward J; Coles, Victoria J; Crump, Byron C; Doherty, Mary; Foster, Rachel A; Goes, Joaquim I; Gomes, Helga R; Hood, Raleigh R; McCrow, John P; Montoya, Joseph P; Moustafa, Ahmed; Satinsky, Brandon M; Sharma, Shalabh; Smith, Christa B; Yager, Patricia L; Paul, John H

    2016-01-01

    The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as

  7. Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume.

    Directory of Open Access Journals (Sweden)

    Brian L Zielinski

    Full Text Available The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon

  8. Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume

    Science.gov (United States)

    Allen, Andrew E.; Carpenter, Edward J.; Coles, Victoria J.; Crump, Byron C.; Doherty, Mary; Foster, Rachel A.; Goes, Joaquim I.; Gomes, Helga R.; Hood, Raleigh R.; McCrow, John P.; Montoya, Joseph P.; Moustafa, Ahmed; Satinsky, Brandon M.; Sharma, Shalabh; Smith, Christa B.; Yager, Patricia L.; Paul, John H.

    2016-01-01

    The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as

  9. Thermodynamic modeling of complex systems

    DEFF Research Database (Denmark)

    Liang, Xiaodong

    . Contrary to earlier theories, the oil is not only present on the surface, but also in great volumes both in the water column and on the seafloor, which indicates that we do not know enough about how oil behaves in water and interacts with it. Sonar detection is one of the most important and necessary...... after an oil spill. Engineering thermodynamics could be applied in the state-of-the-art sonar products through advanced artificial technology, if the speed of sound, solubility and density of oil-seawater systems could be satisfactorily modelled. The addition of methanol or glycols into unprocessed well...... streams during subsea pipelines is necessary to inhibit gas hydrate formation, and the offshore reservoirs often mean complicated temperature and pressure conditions. Accurate description of the phase behavior and thermalphysical properties of complex systems containing petroleum fluids and polar...

  10. Studies of Catalytic Model Systems

    DEFF Research Database (Denmark)

    Holse, Christian

    of the Cu/ZnO nanoparticles is highly relevant to industrial methanol synthesis for which the direct interaction of Cu and ZnO nanocrystals synergistically boost the catalytic activity. The dynamical behavior of the nanoparticles under reducing and oxidizing environments were studied by means of ex situ X...... as the nanoparticles are reduced. The Cu/ZnO nanoparticles are tested on a  µ-reactor platform and prove to be active towards methanol synthesis, making it an excellent model system for further investigations into activity depended morphology changes....

  11. Development and evaluation of an Earth-System model – HadGEM2

    Directory of Open Access Journals (Sweden)

    W. J. Collins

    2011-11-01

    Full Text Available We describe here the development and evaluation of an Earth system model suitable for centennial-scale climate prediction. The principal new components added to the physical climate model are the terrestrial and ocean ecosystems and gas-phase tropospheric chemistry, along with their coupled interactions.

    The individual Earth system components are described briefly and the relevant interactions between the components are explained. Because the multiple interactions could lead to unstable feedbacks, we go through a careful process of model spin up to ensure that all components are stable and the interactions balanced. This spun-up configuration is evaluated against observed data for the Earth system components and is generally found to perform very satisfactorily. The reason for the evaluation phase is that the model is to be used for the core climate simulations carried out by the Met Office Hadley Centre for the Coupled Model Intercomparison Project (CMIP5, so it is essential that addition of the extra complexity does not detract substantially from its climate performance. Localised changes in some specific meteorological variables can be identified, but the impacts on the overall simulation of present day climate are slight.

    This model is proving valuable both for climate predictions, and for investigating the strengths of biogeochemical feedbacks.

  12. Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

    NARCIS (Netherlands)

    Nazaries, L.; Pan, Y.; Bodrossy, L.; Baggs, E.M.; Millard, P.; Murrell, J.C.; Singh, B.K.

    2013-01-01

    Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack

  13. Ecotoxicological, ecophysiological and biogeochemical fundamentals of risk assessment

    International Nuclear Information System (INIS)

    Bashkin, V.; Evstafjeva, E.

    1995-01-01

    A quantitative risk assessment (RA) for complex influence of different factors in heavy polluted regions is possible to carry out only on a basis of determination of various links of biogeochemical trophical chains and analysis of the whole biogeochemical structure of the region under study. As an integrative assessment, the human adaptability should be chosen because the majority of trophical chains are closed by man. The given integrative criteria includes biogeochemical, ecophysiological and ecotoxicological assessment of risk factors. Consequently, ecological-biogeochemical regionalization, ecophysiological and ecotoxicological monitoring of human population health are the important approaches to RA. These criteria should be conjugated with LCA of various industrial and agricultural products. At the ultimate degree, the given approaches are needed for areas where traditional pollutants (heavy metals, POPS, pesticides, fertilizers) are enforced sharply by radioactive pollution. Due to the complex influence of pollutants, it is impossible to use individual guidelines. For RA of these complex pollutants, the methods of human adaptability assessment to a polluted environment have to be carried out. These methods include biogeochemical, ecotoxicological and ecophysiological analysis of risk factors as well as quantitative uncertainty analysis. Furthermore, the modern statistical methods such as correlative graphs etc., have to be used for quantitative assessment of human adaptability to complex influence of pollutants. The results obtained in the Chernobyl region have shown the acceptability of suggested methods

  14. Reservoir Model Information System: REMIS

    Science.gov (United States)

    Lee, Sang Yun; Lee, Kwang-Wu; Rhee, Taehyun; Neumann, Ulrich

    2009-01-01

    We describe a novel data visualization framework named Reservoir Model Information System (REMIS) for the display of complex and multi-dimensional data sets in oil reservoirs. It is aimed at facilitating visual exploration and analysis of data sets as well as user collaboration in an easier way. Our framework consists of two main modules: the data access point module and the data visualization module. For the data access point module, the Phrase-Driven Grammar System (PDGS) is adopted for helping users facilitate the visualization of data. It integrates data source applications and external visualization tools and allows users to formulate data query and visualization descriptions by selecting graphical icons in a menu or on a map with step-by-step visual guidance. For the data visualization module, we implemented our first prototype of an interactive volume viewer named REMVR to classify and to visualize geo-spatial specific data sets. By combining PDGS and REMVR, REMIS assists users better in describing visualizations and exploring data so that they can easily find desired data and explore interesting or meaningful relationships including trends and exceptions in oil reservoir model data.

  15. Caught in the flux net: disentangling error, uncertainty, heterogeneity, and spatial process in biogeochemical scaling

    Science.gov (United States)

    Dietze, M.

    2014-12-01

    Attempts to link observations across multiple scales, and in particular the problem of scaling up fine-scale observations to landscape and regional process, faces numerous theoretical, computational, and statistical challenges. This talk aims to link theoretical advances in the scaling of biotic heterogeneity, abiotic heterogeneity, and contagious disturbance with statistical advances for linking observations that integrate over different scales. Critical to this goal is the need to partition sources of uncertainty and variability. In particular, the variance you can calculate most readily is rarely the most important or relevant one to quantify. In community ecology, hierarchical Bayes (HB) latent-variable models that separate true variability in ecosystem processes from observation errors have challenged long-standing theory surrounding the maintenance of biodiversity, yet application of such approaches to regional-scale biogeochemical processes is just beginning. A special case of such models, focused on the change of support problem, deal specifically with linking observations that integrate over different spatial and temporal scales. Occurring in parallel with these statistical advances have been the development of new theories for the spatially-implicit scaling of biotic and abiotic heterogeneity, as well as contagious disturbances such as fire and pathogens, and the incorporation of such approaches into process-based ecosystem models. Such approaches upscale by integrating the probability distributions of system heterogeneity over the functional response of the ecosystem to such heterogeneity. We demonstrate that this approach can also be downscaled by conditioning on incomplete partial observation at a local scale, and can have lower uncertainty than brute-force spatially-explicit approaches. We also extend such approaches from integrating over observed heterogeneities to integrating the latent, high-dimensional variability in HB models. Finally, there is a

  16. Potential biogeochemical and biogeophysical consequences of afforestation in North America

    Science.gov (United States)

    O'Halloran, T. L.; Law, B. E.; Baldocchi, D. D.; Bonan, G. B.; Randerson, J. T.

    2009-12-01

    Sequestering atmospheric carbon dioxide via afforestation is an accepted method towards mitigating climate change under the Kyoto Protocol CDM (Clean Development Mechanism) and may see significant expansion in North America if motivated by new treaties or implementation of cap and trade in the United States. However, there are concomitant changes to biogeophysical processes/properties (e.g. evapotranspiration, albedo) that can enhance or dampen the climate benefits of increasing carbon uptake via changes in land use. These mechanisms have been examined previously, but mostly as modeling scenarios of deforestation. In light of increasing potential for implementation, afforestation scenarios have recently received more attention from the modeling community. Here we present a synthesis of flux tower measurements to define characteristics of carbon and energy processing in the four key biomes most likely involved in afforestation projects: croplands, grasslands, deciduous broadleaf forests, and evergreen needleleaf forests. We use nearly 100 site-years of flux data from ~25 AmeriFlux sites to develop biome-level statistics of surface turbulent fluxes. This includes mean annual cycles of carbon, sensible, and latent heat fluxes, normalized by energy inputs to allow for comparisons across space. Representative biome means are incorporated into a simple PBL model to evaluate potential perturbations to local air temperatures caused by changes in heat fluxes. A simple method for weighing the biogeochemical and biogeophysical benefits of terrestrial vegetation is also presented. Results suggest that, of the four scenarios investigated, afforesting grasslands to deciduous broadleaf would bring the largest climate benefits in terms of carbon sequestration and heat fluxes where water is not limiting.

  17. A framework to assess biogeochemical response to ecosystem disturbance using nutrient partitioning ratios

    Science.gov (United States)

    Kranabetter, J. Marty; McLauchlan, Kendra K.; Enders, Sara K.; Fraterrigo, Jennifer M.; Higuera, Philip E.; Morris, Jesse L.; Rastetter, Edward B.; Barnes, Rebecca; Buma, Brian; Gavin, Daniel G.; Gerhart, Laci M.; Gillson, Lindsey; Hietz, Peter; Mack, Michelle C.; McNeil, Brenden; Perakis, Steven

    2016-01-01

    Disturbances affect almost all terrestrial ecosystems, but it has been difficult to identify general principles regarding these influences. To improve our understanding of the long-term consequences of disturbance on terrestrial ecosystems, we present a conceptual framework that analyzes disturbances by their biogeochemical impacts. We posit that the ratio of soil and plant nutrient stocks in mature ecosystems represents a characteristic site property. Focusing on nitrogen (N), we hypothesize that this partitioning ratio (soil N: plant N) will undergo a predictable trajectory after disturbance. We investigate the nature of this partitioning ratio with three approaches: (1) nutrient stock data from forested ecosystems in North America, (2) a process-based ecosystem model, and (3) conceptual shifts in site nutrient availability with altered disturbance frequency. Partitioning ratios could be applied to a variety of ecosystems and successional states, allowing for improved temporal scaling of disturbance events. The generally short-term empirical evidence for recovery trajectories of nutrient stocks and partitioning ratios suggests two areas for future research. First, we need to recognize and quantify how disturbance effects can be accreting or depleting, depending on whether their net effect is to increase or decrease ecosystem nutrient stocks. Second, we need to test how altered disturbance frequencies from the present state may be constructive or destructive in their effects on biogeochemical cycling and nutrient availability. Long-term studies, with repeated sampling of soils and vegetation, will be essential in further developing this framework of biogeochemical response to disturbance.

  18. The biogeochemical iron cycle and astrobiology

    Energy Technology Data Exchange (ETDEWEB)

    Schröder, Christian, E-mail: christian.schroeder@stir.ac.uk [University of Stirling, Biological and Environmental Sciences, School of Natural Sciences (United Kingdom); Köhler, Inga [Eberhard Karls University of Tübingen, Geomicrobiology, Centre for Applied Geoscience (Germany); Muller, Francois L. L. [Qatar University, Department of Biological and Environmental Sciences (Qatar); Chumakov, Aleksandr I.; Kupenko, Ilya; Rüffer, Rudolf [ESRF-The European Synchrotron (France); Kappler, Andreas [Eberhard Karls University of Tübingen, Geomicrobiology, Centre for Applied Geoscience (Germany)

    2016-12-15

    Biogeochemistry investigates chemical cycles which influence or are influenced by biological activity. Astrobiology studies the origin, evolution and distribution of life in the universe. The biogeochemical Fe cycle has controlled major nutrient cycles such as the C cycle throughout geological time. Iron sulfide minerals may have provided energy and surfaces for the first pioneer organisms on Earth. Banded iron formations document the evolution of oxygenic photosynthesis. To assess the potential habitability of planets other than Earth one looks for water, an energy source and a C source. On Mars, for example, Fe minerals have provided evidence for the past presence of liquid water on its surface and would provide a viable energy source. Here we present Mössbauer spectroscopy investigations of Fe and C cycle interactions in both ancient and modern environments. Experiments to simulate the diagenesis of banded iron formations indicate that the formation of ferrous minerals depends on the amount of biomass buried with ferric precursors rather than on the atmospheric composition at the time of deposition. Mössbauer spectra further reveal the mutual stabilisation of Fe-organic matter complexes against mineral transformation and decay of organic matter into CO{sub 2}. This corresponds to observations of a ‘rusty carbon sink’ in modern sediments. The stabilisation of Fe-organic matter complexes may also aid transport of particulate Fe in the water column while having an adverse effect on the bioavailability of Fe. In the modern oxic ocean, Fe is insoluble and particulate Fe represents an important source. Collecting that particulate Fe yields small sample sizes that would pose a challenge for conventional Mössbauer experiments. We demonstrate that the unique properties of the beam used in synchrotron-based Mössbauer applications can be utilized for studying such samples effectively. Reactive Fe species often occur in amorphous or nanoparticulate form in the

  19. The biogeochemical iron cycle and astrobiology

    Science.gov (United States)

    Schröder, Christian; Köhler, Inga; Muller, Francois L. L.; Chumakov, Aleksandr I.; Kupenko, Ilya; Rüffer, Rudolf; Kappler, Andreas

    2016-12-01

    Biogeochemistry investigates chemical cycles which influence or are influenced by biological activity. Astrobiology studies the origin, evolution and distribution of life in the universe. The biogeochemical Fe cycle has controlled major nutrient cycles such as the C cycle throughout geological time. Iron sulfide minerals may have provided energy and surfaces for the first pioneer organisms on Earth. Banded iron formations document the evolution of oxygenic photosynthesis. To assess the potential habitability of planets other than Earth one looks for water, an energy source and a C source. On Mars, for example, Fe minerals have provided evidence for the past presence of liquid water on its surface and would provide a viable energy source. Here we present Mössbauer spectroscopy investigations of Fe and C cycle interactions in both ancient and modern environments. Experiments to simulate the diagenesis of banded iron formations indicate that the formation of ferrous minerals depends on the amount of biomass buried with ferric precursors rather than on the atmospheric composition at the time of deposition. Mössbauer spectra further reveal the mutual stabilisation of Fe-organic matter complexes against mineral transformation and decay of organic matter into CO2. This corresponds to observations of a `rusty carbon sink' in modern sediments. The stabilisation of Fe-organic matter complexes may also aid transport of particulate Fe in the water column while having an adverse effect on the bioavailability of Fe. In the modern oxic ocean, Fe is insoluble and particulate Fe represents an important source. Collecting that particulate Fe yields small sample sizes that would pose a challenge for conventional Mössbauer experiments. We demonstrate that the unique properties of the beam used in synchrotron-based Mössbauer applications can be utilized for studying such samples effectively. Reactive Fe species often occur in amorphous or nanoparticulate form in the environment and

  20. Modeling learning technology systems as business systems

    NARCIS (Netherlands)

    Avgeriou, Paris; Retalis, Symeon; Papaspyrou, Nikolaos

    2003-01-01

    The design of Learning Technology Systems, and the Software Systems that support them, is largely conducted on an intuitive, ad hoc basis, thus resulting in inefficient systems that defectively support the learning process. There is now justifiable, increasing effort in formalizing the engineering

  1. Bond graph modeling of centrifugal compression systems

    OpenAIRE

    Uddin, Nur; Gravdahl, Jan Tommy

    2015-01-01

    A novel approach to model unsteady fluid dynamics in a compressor network by using a bond graph is presented. The model is intended in particular for compressor control system development. First, we develop a bond graph model of a single compression system. Bond graph modeling offers a different perspective to previous work by modeling the compression system based on energy flow instead of fluid dynamics. Analyzing the bond graph model explains the energy flow during compressor surge. Two pri...

  2. Structuring Problem Analysis for Embedded Systems Modelling

    NARCIS (Netherlands)

    Marincic, J.; Mader, Angelika H.; Wieringa, Roelf J.; Lucas, Yan

    Our interest is embedded systems validation as part of the model-driven approach. To design a model, the modeller needs to obtain knowledge about the system and decide what is relevant to model and how. A part of the modelling activities is inherently informal - it cannot be formalised in such a way

  3. Microbial extracellular enzymes in biogeochemical cycling of ecosystems.

    Science.gov (United States)

    Luo, Ling; Meng, Han; Gu, Ji-Dong

    2017-07-15

    Extracellular enzymes, primarily produced by microorganisms, affect ecosystem processes because of their essential roles in degradation, transformation and mineralization of organic matter. Extracellular enzymes involved in the cycling of carbon (C), nitrogen (N) and phosphorus (P) have been widely investigated in many different ecosystems, and several enzymes have been recognized as key components in regulating C storage and nutrient cycling. In this review, it was the first time to summarize the specific extracellular enzymes related to C storage and nutrient cycling for better understanding the important role of microbial extracellular enzymes in biogeochemical cycling of ecosystems. Subsequently, ecoenzymatic stoichiometry - the relative ratio of extracellular enzyme, has been reviewed and further provided a new perspective for understanding biogeochemical cycling of ecosystems. Finally, the new insights of using microbial extracellular enzyme in indicating biogeochemical cycling and then protecting ecosystems have been suggested. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Co-Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Rick Colwell; Corey Radtke; Mark Delwiche; Deborah Newby; Lynn Petzke; Mark Conrad; Eoin Brodie; Hope Lee; Bob Starr; Dana Dettmers; Ron Crawford; Andrzej Paszczynski; Nick Bernardini; Ravi Paidisetti; Tonia Green

    2006-06-01

    Chlorinated solvent wastes (e.g., trichloroethene or TCE) often occur as diffuse subsurface plumes in complex geological environments where coupled processes must be understood in order to implement remediation strategies. Monitored natural attenuation (MNA) warrants study as a remediation technology because it minimizes worker and environment exposure to the wastes and because it costs less than other technologies. However, to be accepted MNA requires different ?lines of evidence? indicating that the wastes are effectively destroyed. We are studying the coupled biogeochemical processes that dictate the rate of TCE co-metabolism first in the medial zone (TCE concentration: 1,000 to 20,000 ?g/L) of a plume at the Idaho National Laboratory?s Test Area North (TAN) site and then at Paducah or the Savannah River Site. We will use flow-through in situ reactors (FTISR) to investigate the rate of methanotrophic co-metabolism of TCE and the coupling of the responsible biological processes with the dissolved methane flux and groundwater flow velocity. TCE co-metabolic rates at TAN are being assessed and interpreted in the context of enzyme activity, gene expression, and cellular inactivation related to intermediates of TCE co-metabolism. By determining the rate of TCE co-metabolism at different groundwater flow velocities, we will derive key modeling parameters for the computational simulations that describe the attenuation, and thereby refine such models while assessing the contribution of microbial co-metabolism relative to other natural attenuation processes. This research will strengthen our ability to forecast the viability of MNA at DOE and other sites contaminated with chlorinated hydrocarbons.

  5. What controls biological production in coastal upwelling systems? Insights from a comparative modeling study

    Directory of Open Access Journals (Sweden)

    Z. Lachkar

    2011-10-01

    Full Text Available The magnitude of net primary production (NPP in Eastern Boundary Upwelling Systems (EBUS is traditionally viewed as directly reflecting the wind-driven upwelling intensity. Yet, different EBUS show different sensitivities of NPP to upwelling-favorable winds (Carr and Kearns, 2003. Here, using a comparative modeling study of the California Current System (California CS and Canary Current System (Canary CS, we show how physical and environmental factors, such as light, temperature and cross-shore circulation modulate the response of NPP to upwelling strength. To this end, we made a series of eddy-resolving simulations of the two upwelling systems using the Regional Oceanic Modeling System (ROMS, coupled to a nitrogen-based Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD ecosystem model. Using identical ecological/biogeochemical parameters, our coupled model simulates a level of NPP in the California CS that is 50 % smaller than that in the Canary CS, in agreement with observationally based estimates. We find this much lower NPP in the California CS despite phytoplankton in this system having nearly 20 % higher nutrient concentrations available to fuel their growth. This conundrum can be explained by: (1 phytoplankton having a faster nutrient-replete growth in the Canary CS relative to the California CS; a consequence of more favorable light and temperature conditions in the Canary CS, and (2 the longer nearshore water residence times in the Canary CS, which permit a larger buildup of biomass in the upwelling zone, thereby enhancing NPP. The longer residence times in the Canary CS appear to be a result of the wider continental shelves and the lower mesoscale activity characterizing this upwelling system. This results in a weaker offshore export of nutrients and organic matter, thereby increasing local nutrient recycling and reducing the spatial decoupling between new and export production in the Canary CS. Our results suggest that climate change

  6. Modeling Power Systems as Complex Adaptive Systems

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Malard, Joel M.; Posse, Christian; Gangopadhyaya, Asim; Lu, Ning; Katipamula, Srinivas; Mallow, J V.

    2004-12-30

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We review and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.

  7. Next Generation Framework for Aquatic Modeling of the Earth System (NextFrAMES)

    Science.gov (United States)

    Fekete, B. M.; Wollheim, W. M.; Lakhankar, T.; Vorosmarty, C. J.

    2008-12-01

    Earth System model development is becoming an increasingly complex task. As scientists attempt to represent the physical and bio-geochemical processes and various feedback mechanisms in unprecedented detail, the models themselves are becoming increasingly complex. At the same time, the surrounding IT infrastructure needed to carry out these detailed model computations is growing increasingly complex as well. To be accurate and useful, Earth System models must manage a vast amount of data in heterogenous computing environments ranging from single CPU systems to Beowulf type computer clusters. Scientists developing Earth System models increasingly confront obstacles associated with IT infrastructure. Numerous development efforts are on the way to ease that burden and offer model development platforms that reduce IT challenges and allow scientists to focus on their science. While these new modeling frameworks (e.g. FMS, ESMF, CCA, OpenMI) do provide solutions to many IT challenges (performing input/output, managing space and time, establishing model coupling, etc.), they are still considerably complex and often have steep learning curves. Over the course of the last fifteen years ,the University of New Hampshire developed several modeling frameworks independently from the above-mentioned efforts (Data Assembler, Frameworks for Aquatic Modeling of the Earth System and NextFrAMES which is continued at CCNY). While the UNH modeling frameworks have numerous similarities to those developed by other teams, these frameworks, in particular the latest NextFrAMES, represent a novel model development paradigm. While other modeling frameworks focus on providing services to modelers to perform various tasks, NextFrAMES strives to hide all of those services and provide a new approach for modelers to express their scientific thoughts. From a scientific perspective, most models have two core elements: the overall model structure (defining the linkages between the simulated processes

  8. Visual computing model for immune system and medical system.

    Science.gov (United States)

    Gong, Tao; Cao, Xinxue; Xiong, Qin

    2015-01-01

    Natural immune system is an intelligent self-organizing and adaptive system, which has a variety of immune cells with different types of immune mechanisms. The mutual cooperation between the immune cells shows the intelligence of this immune system, and modeling this immune system has an important significance in medical science and engineering. In order to build a comprehensible model of this immune system for better understanding with the visualization method than the traditional mathematic model, a visual computing model of this immune system was proposed and also used to design a medical system with the immune system, in this paper. Some visual simulations of the immune system were made to test the visual effect. The experimental results of the simulations show that the visual modeling approach can provide a more effective way for analyzing this immune system than only the traditional mathematic equations.

  9. Model Information Exchange System (MIXS).

    Science.gov (United States)

    2013-08-01

    Many travel demand forecast models operate at state, regional, and local levels. While they share the same physical network in overlapping geographic areas, they use different and uncoordinated modeling networks. This creates difficulties for models ...

  10. Two sustainable energy system analysis models

    DEFF Research Database (Denmark)

    Lund, Henrik; Goran Krajacic, Neven Duic; da Graca Carvalho, Maria

    2005-01-01

    This paper presents a comparative study of two energy system analysis models both designed with the purpose of analysing electricity systems with a substantial share of fluctuating renewable energy.......This paper presents a comparative study of two energy system analysis models both designed with the purpose of analysing electricity systems with a substantial share of fluctuating renewable energy....

  11. Models for multimegawatt space power systems

    Energy Technology Data Exchange (ETDEWEB)

    Edenburn, M.W.

    1990-06-01

    This report describes models for multimegawatt, space power systems which Sandia's Advanced Power Systems Division has constructed to help evaluate space power systems for SDI's Space Power Office. Five system models and models for associated components are presented for both open (power system waste products are exhausted into space) and closed (no waste products) systems: open, burst mode, hydrogen cooled nuclear reactor -- turboalternator system; open, hydrogen-oxygen combustion turboalternator system; closed, nuclear reactor powered Brayton cycle system; closed, liquid metal Rankine cycle system; and closed, in-core, reactor therminonic system. The models estimate performance and mass for the components in each of these systems. 17 refs., 8 figs., 15 tabs.

  12. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    KAUST Repository

    Roux, Simon

    2016-05-12

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface-and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting â global ocean virome\\' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where

  13. Biogeochemical response to widespread anoxia in the past ocean

    NARCIS (Netherlands)

    Ruvalcaba Baroni, I.

    2015-01-01

    Oxygen is a key element for life on earth. Oxygen concentrations in the ocean vary greatly in space and time. These changes are regulated by various physical and biogeochemical processes, such as primary productivity, sea surface temperatures and ocean circulation. In the geological past, several

  14. The Amazon region: tropical deforestation, biogeochemical cycles and the climate

    NARCIS (Netherlands)

    Kabat, P.; Andreae, M.O.; Silva-Dias, M.A.; Veraart, J.A.; Brink, N.J.

    2003-01-01

    The biogeochemical cycling of carbon, water, energy, aerosols, and trace gases in the Amazon Basin, and the interactions between deforestation, rainfall and climate were all investigated in this programme as a part of an integrated cluster of inter-linked and complementary research projects. These

  15. The effect of biogeochemical processes on pH

    NARCIS (Netherlands)

    Soetaert, K.E.R.; Hofmann, A.F.; Middelburg, J.J.; Meysman, F.J.R.; Greenwood, J.E.

    2007-01-01

    The impact of biogeochemical and physical processes on aquatic chemistry is usually expressed in terms of alkalinity. Here we show how to directly calculate the effect of single processes on pH. Under the assumptions of equilibrium and electroneutrality, the rate of change of pH can be calculated as

  16. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    NARCIS (Netherlands)

    Roux, S.; Brum, J.R.; Dutilh, B.E.; Sunagawa, S.; Duhaime, M.B.; Loy, A.; Poulos, B.T.; Solonenko, N.; Lara, E.; Poulain, J.; Pesant, S.; Kandels-Lewis, S.; Dimier, C.; Picheral, M.; Searson, S.; Cruaud, C.; Alberti, A.; Duarte, C.M.; Gasol, J.M.; Vaque, D.; Bork, P.; Acinas, S.G.; Wincker, P.; Sullivan, M.B.

    2016-01-01

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains

  17. Modeling traceability in system of systems

    NARCIS (Netherlands)

    Tekinerdogan, Bedir; Erata, Ferhat

    2017-01-01

    An important aspect in SoS is the realization of the concerns in different systems that work together. Identifying and locating these concerns is important to orchestrate the overall activities and hereby to achieve the overall goal of the SoS. Moreover, concerns in SoS are rarely stable and need

  18. Modeling of Nonlinear Systems using Genetic Algorithm

    Science.gov (United States)

    Hayashi, Kayoko; Yamamoto, Toru; Kawada, Kazuo

    In this paper, a newly modeling system by using Genetic Algorithm (GA) is proposed. The GA is an evolutionary computational method that simulates the mechanisms of heredity or evolution of living things, and it is utilized in optimization and in searching for optimized solutions. Most process systems have nonlinearities, so it is necessary to anticipate exactly such systems. However, it is difficult to make a suitable model for nonlinear systems, because most nonlinear systems have a complex structure. Therefore the newly proposed method of modeling for nonlinear systems uses GA. Then, according to the newly proposed scheme, the optimal structure and parameters of the nonlinear model are automatically generated.

  19. Hydrological and biogeochemical controls on watershed dissolved organic matter transport: pulse-shunt concept.

    Science.gov (United States)

    Raymond, Peter A; Saiers, James E; Sobczak, William V

    2016-01-01

    Hydrological precipitation and snowmelt events trigger large "pulse" releases of terrestrial dissolved organic matter (DOM) into drainage networks due to an increase in DOM concentration with discharge. Thus, low-frequency large events, which are predicted to increase with climate change, are responsible for a significant percentage of annual terrestrial DOM input to drainage networks. These same events are accompanied by marked and rapid increases in headwater stream velocity; thus they also "shunt" a large proportion of the pulsed DOM to downstream, higher-order rivers and aquatic ecosystems geographically removed from the DOM source of origin. Here we merge these ideas into the "pulse-shunt concept" (PSC) to explain and quantify how infrequent, yet major hydrologic events may drive the timing, flux, geographical dispersion, and regional metabolism of terrestrial DOM. The PSC also helps reconcile long-standing discrepancies in C cycling theory and provides a robust framework for better quantifying its highly dynamic role in the global C cycle. The PSC adds a critical temporal dimension to linear organic matter removal dynamics postulated by the river continuum concept. It also can be represented mathematically through a model that is based on stream scaling approaches suitable for quantifying the important role of streams and rivers in the global C cycle. Initial hypotheses generated by the PSC include: (1) Infrequent large storms and snowmelt events account for a large and underappreciated percentage of the terrestrial DOM flux to drainage networks at annual and decadal time scales and therefore event statistics are equally important to total discharge when determining terrestrial fluxes. (2) Episodic hydrologic events result in DOM bypassing headwater streams and being metabolized in large rivers and exported to coastal systems. We propose that the PSC provides a framework for watershed biogeochemical modeling and predictions and discuss implications to

  20. Model Driven Development of Data Sensitive Systems

    DEFF Research Database (Denmark)

    Olsen, Petur

    2014-01-01

    to the values of variables. This theses strives to improve model-driven development of such data-sensitive systems. This is done by addressing three research questions. In the first we combine state-based modeling and abstract interpretation, in order to ease modeling of data-sensitive systems, while allowing...... efficient model-checking and model-based testing. In the second we develop automatic abstraction learning used together with model learning, in order to allow fully automatic learning of data-sensitive systems to allow learning of larger systems. In the third we develop an approach for modeling and model-based...... detection and pushing error detection to earlier stages of development. The complexity of modeling and the size of systems which can be analyzed is severely limited when introducing data variables. The state space grows exponentially in the number of variable and the domain size of the variables...

  1. South Florida wetlands ecosystem; biogeochemical processes in peat

    Science.gov (United States)

    Orem, William; ,

    1996-01-01

    The South Florida wetlands ecosystem is an environment of great size and ecological diversity (figs. 1 and 2). The landscape diversity and subtropical setting of this ecosystem provide a habitat for an abundance of plants and wildlife, some of which are unique to South Florida. South Florida wetlands are currently in crisis, however, due to the combined effects of agriculture, urbanization, and nearly 100 years of water management. Serious problems facing this ecosystem include (1) phosphorus contamination producing nutrient enrichment, which is causing changes in the native vegetation, (2) methylmercury contamination of fish and other wildlife, which poses a potential threat to human health, (3) changes in the natural flow of water in the region, resulting in more frequent drying of wetlands, loss of organic soils, and a reduction in freshwater flow to Florida Bay, (4) hypersalinity, massive algal blooms, and seagrass loss in parts of Florida Bay, and (5) a decrease in wildlife populations, especially those of wading birds. This U.S. Geological Survey (USGS) project focuses on the role of organic-rich sediments (peat) of South Florida wetlands in regulating the concentrations and impact of important chemical species in the environment. The cycling of carbon, nitrogen, phosphorus, and sulfur in peat is an important factor in the regulation of water quality in the South Florida wetlands ecosystem. These elements are central to many of the contamination issues facing South Florida wetlands, such as nutrient enrichment, mercury toxicity, and loss of peat. Many important chemical and biological reactions occur in peat and control the fate of chemical species in wetlands. Wetland scientists often refer to these reactions as biogeochemical processes, because they are chemical reactions usually mediated by microorganisms in a geological environment. An understanding of the biogeochemical processes in peat of South Florida wetlands will provide a basis for evaluating the

  2. Modeling of a Hydraulic Braking System

    OpenAIRE

    Lundin, Christopher

    2015-01-01

    The objective of this thesis is to derive an analytical model representing a reduced form of a mine hoist hydraulic braking system. Based primarily on fluid mechanical and mechanical physical modeling, along with a number of simplifying assumptions, the analytical model will be derived and expressed in the form of a system of differential equations including a set of static functions. The obtained model will be suitable for basic simulation and analysis of system dynamics, with the aim to cap...

  3. Silicon biogeochemical processes in a large river (Cauvery, India)

    Science.gov (United States)

    Kameswari Rajasekaran, Mangalaa; Arnaud, Dapoigny; Jean, Riotte; Sarma Vedula, V. S. S.; Nittala, S. Sarma; Sankaran, Subramanian; Gundiga Puttojirao, Gurumurthy; Keshava, Balakrishna; Cardinal, Damien

    2016-04-01

    Silicon (Si), one of the key nutrients for diatom growth in ocean, is principally released during silicate weathering on continents and then exported by rivers. Phytoplankton composition is determined by the availability of Si relative to other nutrients, mainly N and P, which fluxes in estuarine and coastal systems are affected by eutrophication due to land use and industrialization. In order to understand the biogeochemical cycle of Si and its supply to the coastal ocean, we studied a tropical monsoonal river from Southern India (Cauvery) and compare it with other large and small rivers. Cauvery is the 7th largest river in India with a basin covering 85626 sq.km. The major part of the basin (˜66%) is covered by agriculture and inhabited by more than 30 million inhabitants. There are 96 dams built across the basin. As a consequence, 80% of the historical discharge is diverted, mainly for irrigation (Meunier et al. 2015). This makes the Cauvery River a good example of current anthropogenic pressure on silicon biogeochemical cycle. We measured amorphous silica contents (ASi) and isotopic composition of dissolved silicon (δ30Si-DSi) in the Cauvery estuary, including freshwater end-member and groundwater as well as along a 670 km transect along the river course. Other Indian rivers and estuaries have also been measured, including some less impacted by anthropogenic pressure. The average Cauvery δ30Si signature just upstream the estuary is 2.21±0.15 ‰ (n=3) which is almost 1‰ heavier than the groundwater isotopic composition (1.38±0.03). The δ30Si-DSi of Cauvery water is also almost 1‰ heavier than the world river supply to the ocean estimated so far and 0.4‰ heavier than other large Indian rivers like Ganges (Frings et al 2015) and Krishna. On the other hand, the smaller watersheds (Ponnaiyar, Vellar, and Penna) adjacent to Cauvery also display heavy δ30Si-DSi. Unlike the effect of silicate weathering, the heavy isotopic compositions in the river

  4. Graphical Model Debugger Framework for Embedded Systems

    DEFF Research Database (Denmark)

    Zeng, Kebin

    2010-01-01

    Model Driven Software Development has offered a faster way to design and implement embedded real-time software by moving the design to a model level, and by transforming models to code. However, the testing of embedded systems has remained at the code level. This paper presents a Graphical Model...... Debugger Framework, providing an auxiliary avenue of analysis of system models at runtime by executing generated code and updating models synchronously, which allows embedded developers to focus on the model level. With the model debugger, embedded developers can graphically test their design model...... and check the running status of the system, which offers a debugging capability on a higher level of abstraction. The framework intends to contribute a tool to the Eclipse society, especially suitable for model-driven development of embedded systems....

  5. The impacts of climate change and human activities on biogeochemical cycles on the Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Chen, Huai; Zhu, Qiuan; Peng, Changhui; Wu, Ning; Wang, Yanfen; Fang, Xiuqing; Gao, Yongheng; Zhu, Dan; Yang, Gang; Tian, Jianqing; Kang, Xiaoming; Piao, Shilong; Ouyang, Hua; Xiang, Wenhua; Luo, Zhibin; Jiang, Hong; Song, Xingzhang; Zhang, Yao; Yu, Guirui; Zhao, Xinquan; Gong, Peng; Yao, Tandong; Wu, Jianghua

    2013-10-01

    With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles. © 2013 John Wiley & Sons Ltd.

  6. Hydrological modelling in forested systems

    Science.gov (United States)

    This chapter provides a brief overview of forest hydrology modelling approaches for answering important global research and management questions. Many hundreds of hydrological models have been applied globally across multiple decades to represent and predict forest hydrological p...

  7. Towards Modelling of Hybrid Systems

    DEFF Research Database (Denmark)

    Wisniewski, Rafal

    2006-01-01

    The article is an attempt to use methods of category theory and topology for analysis of hybrid systems. We use the notion of a directed topological space; it is a topological space together with a set of privileged paths. Dynamical systems are examples of directed topological spaces. A hybrid...... system consists of a number of dynamical systems that are glued together according to information encoded in the discrete part of the system. We develop a definition of a hybrid system as a functor from the category generated by a transition system to the category of directed topological spaces. Its...... directed homotopy colimit (geometric realization) is a single directed topological space. The behavior of hybrid systems can be then understood in terms of the behavior of dynamical systems through the directed homotopy colimit....

  8. Service systems concepts, modeling, and programming

    CERN Document Server

    Cardoso, Jorge; Poels, Geert

    2014-01-01

    This SpringerBrief explores the internal workings of service systems. The authors propose a lightweight semantic model for an effective representation to capture the essence of service systems. Key topics include modeling frameworks, service descriptions and linked data, creating service instances, tool support, and applications in enterprises.Previous books on service system modeling and various streams of scientific developments used an external perspective to describe how systems can be integrated. This brief introduces the concept of white-box service system modeling as an approach to mo

  9. On Verification Modelling of Embedded Systems

    NARCIS (Netherlands)

    Brinksma, Hendrik; Mader, Angelika H.

    Computer-aided verification of embedded systems hinges on the availability of good verification models of the systems at hand. Such models must be much simpler than full design models or specifications to be of practical value, because of the unavoidable combinatorial complexities in the

  10. Balmorel open source energy system model

    DEFF Research Database (Denmark)

    Wiese, Frauke; Bramstoft, Rasmus; Koduvere, Hardi

    2018-01-01

    As the world progresses towards a cleaner energy future with more variable renewable energy sources, energy system models are required to deal with new challenges. This article describes design, development and applications of the open source energy system model Balmorel, which is a result of a l...... transport of local biomass as part of the optimisation and speeding up the model....

  11. Modeling, Control and Coordination of Helicopter Systems

    CERN Document Server

    Ren, Beibei; Chen, Chang; Fua, Cheng-Heng; Lee, Tong Heng

    2012-01-01

    Modeling, Control and Coordination of Helicopter Systems provides a comprehensive treatment of helicopter systems, ranging from related nonlinear flight dynamic modeling and stability analysis to advanced control design for single helicopter systems, and also covers issues related to the coordination and formation control of multiple helicopter systems to achieve high performance tasks. Ensuring stability in helicopter flight is a challenging problem for nonlinear control design and development. This book is a valuable reference on modeling, control and coordination of helicopter systems,providing readers with practical solutions for the problems that still plague helicopter system design and implementation. Readers will gain a complete picture of helicopters at the systems level, as well as a better understanding of the technical intricacies involved. This book also: Presents a complete picture of modeling, control and coordination for helicopter systems Provides a modeling platform for a general class of ro...

  12. Systems Biology—Biomedical Modeling

    OpenAIRE

    Sobie, Eric A.; Lee, Young-Seon; Jenkins, Sherry L.; Iyengar, Ravi

    2011-01-01

    Because of the complexity inherent in biological systems, many researchers frequently rely on a combination of global analysis and computational approaches to gain insight into both (i) how interacting components can produce complex system behaviors, and (ii) how changes in conditions may alter these behaviors. Because the biological details of a particular system are generally not taught along with the quantitative approaches that enable hypothesis generation and analysis of the system, we d...

  13. Modeling and simulation of systems using Matlab and Simulink

    CERN Document Server

    Chaturvedi, Devendra K

    2009-01-01

    Introduction to SystemsSystemClassification of SystemsLinear SystemsTime-Varying vs. Time-Invariant Systems Lumped vs. Distributed Parameter SystemsContinuous- and Discrete-Time Systems Deterministic vs. Stochastic Systems Hard and Soft Systems Analysis of Systems Synthesis of Systems Introduction to System Philosophy System Thinking Large and Complex Applied System Engineering: A Generic ModelingSystems ModelingIntroduction Need of System Modeling Modeling Methods for Complex Systems Classification of ModelsCharacteristics of Models ModelingMathematical Modeling of Physical SystemsFormulation of State Space Model of SystemsPhysical Systems Theory System Components and Interconnections Computation of Parameters of a Component Single Port and Multiport Systems Techniques of System Analysis Basics of Linear Graph Theoretic ApproachFormulation of System Model for Conceptual SystemFormulation System Model for Physical SystemsTopological RestrictionsDevelopment of State Model of Degenerative SystemSolution of Stat...

  14. Modelling and Verification of Relay Interlocking Systems

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth; Bliguet, Marie Le; Kjær, Andreas

    2010-01-01

    This paper describes how relay interlocking systems as used by the Danish railways can be formally modelled and verified. Such systems are documented by circuit diagrams describing their static layout. It is explained how to derive a state transition system model for the dynamic behaviour of a re...

  15. Compositional Modelling of Stochastic Hybrid Systems

    NARCIS (Netherlands)

    Strubbe, S.N.

    2005-01-01

    In this thesis we present a modelling framework for compositional modelling of stochastic hybrid systems. Hybrid systems consist of a combination of continuous and discrete dynamics. The state space of a hybrid system is hybrid in the sense that it consists of a continuous component and a discrete

  16. Global biogeochemical provinces of the mesopelagic zone

    DEFF Research Database (Denmark)

    Reygondeau, Gabriel; Guidi, Lionel; Beaugrand, Gregory

    2018-01-01

    spatially and vertically resolved (seven environmental parameters), we applied a combination of clustering algorithms (c-means, k-means, partition around medoids and agglomerative with Ward's linkage) associated with a nonparametric environmental model to identify the vertical and spatial delineation...

  17. Models of complex attitude systems

    DEFF Research Database (Denmark)

    Sørensen, Bjarne Taulo

    Existing research on public attitudes towards agricultural production systems is largely descriptive, abstracting from the processes through which members of the general public generate their evaluations of such systems. The present paper adopts a systems perspective on such evaluations, understa......Existing research on public attitudes towards agricultural production systems is largely descriptive, abstracting from the processes through which members of the general public generate their evaluations of such systems. The present paper adopts a systems perspective on such evaluations......, understanding them as embedded into a wider attitude system that consists of attitudes towards objects of different abstraction levels, ranging from personal value orientations over general socio-political attitudes to evaluations of specific characteristics of agricultural production systems. It is assumed...... that evaluative affect propagates through the system in such a way that the system becomes evaluatively consistent and operates as a schema for the generation of evaluative judgments. In the empirical part of the paper, the causal structure of an attitude system from which people derive their evaluations of pork...

  18. Modeling Control Situations in Power System Operations

    DEFF Research Database (Denmark)

    Saleem, Arshad; Lind, Morten; Singh, Sri Niwas

    2010-01-01

    Increased interconnection and loading of the power system along with deregulation has brought new challenges for electric power system operation, control and automation. Traditional power system models used in intelligent operation and control are highly dependent on the task purpose. Thus, a model...... of explicit principles for model construction. This paper presents a work on using explicit means-ends model based reasoning about complex control situations which results in maintaining consistent perspectives and selecting appropriate control action for goal driven agents. An example of power system...... for intelligent operation and control must represent system features, so that information from measurements can be related to possible system states and to control actions. These general modeling requirements are well understood, but it is, in general, difficult to translate them into a model because of the lack...

  19. How does global biogeochemical cycle become complicated by terrestrial-aquatic interactions ?

    Science.gov (United States)

    Nakayama, Tadanobu; Maksyutov, Shamil

    2015-04-01

    Inland water such as river and lake are now known to be important and active components of global carbon cycle though its contribution has remained uncertain due to data scarcity (Battin et al., 2009; Aufdenkampe et al., 2011). The author has developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (Nakayama, 2008a-b, 2010, 2011a-b, 2012a-c, 2013; Nakayama and Fujita, 2010; Nakayama and Hashimoto, 2011; Nakayama and Shankman, 2013a-b; Nakayama and Watanabe, 2004, 2006, 2008a-b; Nakayama et al., 2006, 2007, 2010, 2012), which incorporates surface-groundwater interactions, includes up- and down-scaling processes between local-global scales, and can simulate iteratively nonlinear feedback between hydrologic, geomorphic, and ecological processes. In this study, NICE was coupled with various biogeochemical models to incorporate biogeochemical cycle including reaction between inorganic and organic carbons (DOC, POC, DIC, pCO2, etc.) in terrestrial and aquatic ecosystems including surface water and groundwater. The coupled model simulated CO2 evasion from inland water in global scale, was relatively in good agreement in that estimated by empirical regression model (Raymond et al., 2013). In particular, the simulated result implied importance of connectivity between terrestrial and aquatic ecosystems in addition to surface and groundwater, and hillslopes and stream channels, etc. The model further improved the accuracy of CH4 flux in wetland which is sensitive to fluctuations of shallow groundwater because the original NICE incorporates 3-D groundwater sub-model and simulates lateral subsurface flow more reasonably. This simulation system would play important role in integration of greenhouse gas budget of the biosphere, quantification of hot spots in boundless biogeochemical cycle, and bridging gap between top-down and bottom-up approaches (Cole et al., 2007; Frei et al., 2012; Kiel and Cardenas, 2014). References; Aufdenkampe, A.K., et al

  20. Holonic Models for Traffic Control Systems

    Science.gov (United States)

    Ciufudean, Calin; Filote, Constantin

    This paper proposes a new time-placed net model for traffic control systems, respectively railway control traffic systems. This model can be interpreted as a holonic one, and contains three modules: Transport Planning Module, Transport Control Module and Priority Control Module. For railway traffic systems we introduce a strategy in a timed-place Petri net model to solve collision and traffic jam problems.

  1. Potential impacts of climate change on biogeochemical functioning of Cerrado ecosystems.

    Science.gov (United States)

    Bustamante, M M C; Nardoto, G B; Pinto, A S; Resende, J C F; Takahashi, F S C; Vieira, L C G

    2012-08-01

    The Cerrado Domain comprises one of the most diverse savannas in the world and is undergoing a rapid loss of habitats due to changes in fire regimes and intense conversion of native areas to agriculture. We reviewed data on the biogeochemical functioning of Cerrado ecosystems and evaluated the potential impacts of regional climate changes. Variation in temperature extremes and in total amount of rainfall and altitude throughout the Cerrado determines marked differences in the composition of species. Cerrado ecosystems are controlled by interactions between water and nutrient availability. In general, nutrient cycles (N, P and base cations) are very conservative, while litter, microbial and plant biomass are important stocks. In terms of C cycling, root systems and especially the soil organic matter are the most important stocks. Typical cerrado ecosystems function as C sinks on an annual basis, although they work as source of C to the atmosphere close to the end of the dry season. Fire is an important factor altering stocks and fluxes of C and nutrients. Predicted changes in temperature, amount and distribution of precipitation vary according to Cerrado sub-regions with more marked changes in the northeastern part of the domain. Higher temperatures, decreases in rainfall with increase in length of the dry season could shift net ecosystem exchanges from C sink to source of C and might intensify burning, reducing nutrient stocks. Interactions between the heterogeneity in the composition and abundance of biological communities throughout the Cerrado Domain and current and future changes in land use make it difficult to project the impacts of future climate scenarios at different temporal and spatial scales and new modeling approaches are needed.

  2. Potential impacts of climate change on biogeochemical functioning of Cerrado ecosystems

    Directory of Open Access Journals (Sweden)

    MMC Bustamante

    Full Text Available The Cerrado Domain comprises one of the most diverse savannas in the world and is undergoing a rapid loss of habitats due to changes in fire regimes and intense conversion of native areas to agriculture. We reviewed data on the biogeochemical functioning of Cerrado ecosystems and evaluated the potential impacts of regional climate changes. Variation in temperature extremes and in total amount of rainfall and altitude throughout the Cerrado determines marked differences in the composition of species. Cerrado ecosystems are controlled by interactions between water and nutrient availability. In general, nutrient cycles (N, P and base cations are very conservative, while litter, microbial and plant biomass are important stocks. In terms of C cycling, root systems and especially the soil organic matter are the most important stocks. Typical cerrado ecosystems function as C sinks on an annual basis, although they work as source of C to the atmosphere close to the end of the dry season. Fire is an important factor altering stocks and fluxes of C and nutrients. Predicted changes in temperature, amount and distribution of precipitation vary according to Cerrado sub-regions with more marked changes in the northeastern part of the domain. Higher temperatures, decreases in rainfall with increase in length of the dry season could shift net ecosystem exchanges from C sink to source of C and might intensify burning, reducing nutrient stocks. Interactions between the heterogeneity in the composition and abundance of biological communities throughout the Cerrado Domain and current and future changes in land use make it difficult to project the impacts of future climate scenarios at different temporal and spatial scales and new modeling approaches are needed.

  3. Hydrological modeling in forested systems

    Science.gov (United States)

    H.E. Golden; G.R. Evenson; S. Tian; Devendra Amatya; Ge Sun

    2015-01-01

    Characterizing and quantifying interactions among components of the forest hydrological cycle is complex and usually requires a combination of field monitoring and modelling approaches (Weiler and McDonnell, 2004; National Research Council, 2008). Models are important tools for testing hypotheses, understanding hydrological processes and synthesizing experimental data...

  4. Life-Cycle Models for Survivable Systems

    National Research Council Canada - National Science Library

    Linger, Richard

    2002-01-01

    .... Current software development life-cycle models are not focused on creating survivable systems, and exhibit shortcomings when the goal is to develop systems with a high degree of assurance of survivability...

  5. Model Updating Nonlinear System Identification Toolbox Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology (ZONA) proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology that utilizes flight data with...

  6. Modelling Biogeochemistry Across Domains with The Modular System for Shelves and Coasts (MOSSCO)

    Science.gov (United States)

    Burchard, H.; Lemmen, C.; Hofmeister, R.; Knut, K.; Nasermoaddeli, M. H.; Kerimoglu, O.; Koesters, F.; Wirtz, K.

    2016-02-01

    Coastal biogeochemical processes extend from the atmosphere through the water column and the epibenthos into the ocean floor, laterally they are determined by freshwater inflows and open water exchange, and in situ they are mediated by physical, chemical and biological interactions. We use the new Modular System for Shelves and Coasts (MOSSCO, http://www.mossco.de) to obtain an integrated view of coastal biogeochemistry. MOSSCO is a coupling framework that builds on existing coupling technologies like the Earth System Modeling Framework (ESMF, for domain-coupling) and the Framework for Aquatic Biogeochemistry (FABM, for process coupling). MOSSCO facilitates the communication about and the integration of existing and of new process models into a threedimensional regional coastal modelling context. In the MOSSCO concept, the integrating framework imposes very few restrictions on contributed data or models; in fact, there is no distinction made between data and models. The few requirements are: (1) principle coupleability, i.e. access to I/O and timing information in submodels, which has recently been referred to as the Basic Model Interface (BMI) (2) open source/open data access and licencing and (3) communication of metadata, such as spatiotemporal information, naming conventions, and physical units. These requirements suffice to integrate different models and data sets into the MOSSCO infrastructure and subsequently built a modular integrated modeling tool that can span a diversity of processes and domains. Here, we demonstrate a MOSSCO application for the southern North Sea, where atmospheric deposition, biochemical processing in the water column and the ocean floor, lateral nutrient replenishment, and wave- and current-dependent remobilization from sediments are accounted for by modular components. A multi-annual simulation yields realistic succession of the spatial gradients of dissolved nutrients, of chlorophyll variability and gross primary production rates

  7. Transforming Ocean Observations of the Carbon Budget, Acidification, Hypoxia, Nutrients, and Biological Productivity: a Global Array of Biogeochemical Argo Floats

    Science.gov (United States)

    Talley, L. D.; Johnson, K. S.; Claustre, H.; Boss, E.; Emerson, S. R.; Westberry, T. K.; Sarmiento, J. L.; Mazloff, M. R.; Riser, S.; Russell, J. L.

    2017-12-01

    Our ability to detect changes in biogeochemical (BGC) processes in the ocean that may be driven by increasing atmospheric CO2, as well as by natural climate variability, is greatly hindered by undersampling in vast areas of the open ocean. Argo is a major international program that measures ocean heat content and salinity with about 4000 floats distributed throughout the ocean, profiling to 2000 m every 10 days. Extending this approach to a global BGC-Argo float array, using recent, proven sensor technology, and in close synergy with satellite systems, will drive a transformative shift in observing and predicting the effects of climate change on ocean metabolism, carbon uptake, acidification, deoxygenation, and living marine resource management. BGC-Argo will add sensors for pH, oxygen, nitrate, chlorophyll, suspended particles, and downwelling irradiance, with sufficient accuracy for climate studies. Observing System Simulation Experiments (OSSEs) using BGC models indicate that 1000 BGC floats would provide sufficient coverage, hence equipping 1/4 of the Argo array. BGC-Argo (http://biogeochemical-argo.org) will enhance current sustained observational programs such as Argo, GO-SHIP, and long-term ocean time series. BGC-Argo will benefit from deployments on GO-SHIP vessels, which provide sensor verification. Empirically derived algorithms that relate the observed BGC float parameters to the carbon system parameters will provide global information on seasonal ocean-atmosphere carbon exchange. BGC Argo measurements could be paired with other emerging technology, such as pCO2 measurements from ships of opportunity and wave gliders, to extend and validate exchange estimates. BGC-Argo prototype programs already show the potential of a global observing system that can measure seasonal to decadal variability. Various countries have developed regional BGC arrays: Southern Ocean (SOCCOM), North Atlantic Subpolar Gyre (remOcean), Mediterranean (NAOS), the Kuroshio (INBOX

  8. An expert system for dispersion model interpretation

    International Nuclear Information System (INIS)

    Skyllingstad, E.D.; Ramsdell, J.V.

    1988-10-01

    A prototype expert system designed to diagnose dispersion model uncertainty is described in this paper with application to a puff transport model. The system obtains qualitative information from the model user and through an expert-derived knowledge base, performs a rating of the current simulation. These results can then be used in combination with dispersion model output for deciding appropriate evacuation measures. Ultimately, the goal of this work is to develop an expert system that may be operated accurately by an individual uneducated in meteorology or dispersion modeling. 5 refs., 3 figs

  9. Semantic models for adaptive interactive systems

    CERN Document Server

    Hussein, Tim; Lukosch, Stephan; Ziegler, Jürgen; Calvary, Gaëlle

    2013-01-01

    Providing insights into methodologies for designing adaptive systems based on semantic data, and introducing semantic models that can be used for building interactive systems, this book showcases many of the applications made possible by the use of semantic models.Ontologies may enhance the functional coverage of an interactive system as well as its visualization and interaction capabilities in various ways. Semantic models can also contribute to bridging gaps; for example, between user models, context-aware interfaces, and model-driven UI generation. There is considerable potential for using

  10. Models of the venous system

    DEFF Research Database (Denmark)

    Mehlsen, J

    2000-01-01

    of the venous system require at least three elements: a resistor, a capacitor and an inductor, with the latter being of more importance in the venous than in the arterial system. Non-linearities must be considered in pressure/flow relations in the small venules, during venous collapse, or low flow conditions...

  11. Stochastic Models of Polymer Systems

    Science.gov (United States)

    2016-01-01

    published in non-peer-reviewed journals (N/A for none) The dynamics of stochastic gradient algorithms (submitted); Noisy Hegselmann- Krause Systems...algorithms for big data applications. (2) We studied stochastic dynamics of polymer systems in the mean field limit. (3) We studied noisy Hegselmann- Krause

  12. Soil carbon management in large-scale Earth system modelling

    DEFF Research Database (Denmark)

    Olin, S.; Lindeskog, M.; Pugh, T. A. M.

    2015-01-01

    Croplands are vital ecosystems for human well-being and provide important ecosystem services such as crop yields, retention of nitrogen and carbon storage. On large (regional to global)-scale levels, assessment of how these different services will vary in space and time, especially in response......, carbon sequestration and nitrogen leaching from croplands are evaluated and discussed. Compared to the version of LPJ-GUESS that does not include land-use dynamics, estimates of soil carbon stocks and nitrogen leaching from terrestrial to aquatic ecosystems were improved. Our model experiments allow us...... modelling C–N interactions in agricultural ecosystems under future environmental change and the effects these have on terrestrial biogeochemical cycles....

  13. Switching model photovoltaic pumping system

    Science.gov (United States)

    Anis, Wagdy R.; Abdul-Sadek Nour, M.

    Photovoltaic (PV) pumping systems are widely used due to their simplicity, high reliability and low cost. A directly-coupled PV pumping system is the most reliable and least-cost PV system. The d.c. motor-pump group is not, however, working at its optimum operating point. A battery buffered PV pumping system introduces a battery between the PV array and the d.c. motor-pump group to ensure that the motor-pump group is operating at its optimum point. The size of the battery storage depends on system economics. If the battery is fully charged while solar radiation is available, the battery will discharge through the load while the PV array is disconnected. Hence, a power loss takes place. To overcome the above mentioned difficulty, a switched mode PV pumping is proposed. When solar radiation is available and the battery is fully charged, the battery is disconnected and the d.c. motor-pump group is directly coupled to the PV array. To avoid excessive operating voltage for the motor, a part of the PV array is switched off to reduce the voltage. As a result, the energy loss is significantly eliminated. Detailed analysis of the proposed system shows that the discharged water increases by about 10% when compared with a conventional battery-buffered system. The system transient performance just after the switching moment shows that the system returns to a steady state in short period. The variations in the system parameters lie within 1% of the rated values.

  14. Multiple system modelling of waste management

    International Nuclear Information System (INIS)

    Eriksson, Ola; Bisaillon, Mattias

    2011-01-01

    Highlights: → Linking of models will provide a more complete, correct and credible picture of the systems. → The linking procedure is easy to perform and also leads to activation of project partners. → The simulation procedure is a bit more complicated and calls for the ability to run both models. - Abstract: Due to increased environmental awareness, planning and performance of waste management has become more and more complex. Therefore waste management has early been subject to different types of modelling. Another field with long experience of modelling and systems perspective is energy systems. The two modelling traditions have developed side by side, but so far there are very few attempts to combine them. Waste management systems can be linked together with energy systems through incineration plants. The models for waste management can be modelled on a quite detailed level whereas surrounding systems are modelled in a more simplistic way. This is a problem, as previous studies have shown that assumptions on the surrounding system often tend to be important for the conclusions. In this paper it is shown how two models, one for the district heating system (MARTES) and another one for the waste management system (ORWARE), can be linked together. The strengths and weaknesses with model linking are discussed when compared to simplistic assumptions on effects in the energy and waste management systems. It is concluded that the linking of models will provide a more complete, correct and credible picture of the consequences of different simultaneous changes in the systems. The linking procedure is easy to perform and also leads to activation of project partners. However, the simulation procedure is a bit more complicated and calls for the ability to run both models.

  15. Modeling of power electronic systems with EMTP

    Science.gov (United States)

    Tam, Kwa-Sur; Dravid, Narayan V.

    1989-01-01

    In view of the potential impact of power electronics on power systems, there is need for a computer modeling/analysis tool to perform simulation studies on power systems with power electronic components as well as to educate engineering students about such systems. The modeling of the major power electronic components of the NASA Space Station Freedom Electric Power System is described along with ElectroMagnetic Transients Program (EMTP) and it is demonstrated that EMTP can serve as a very useful tool for teaching, design, analysis, and research in the area of power systems with power electronic components. EMTP modeling of power electronic circuits is described and simulation results are presented.

  16. System Level Modelling and Performance Estimation of Embedded Systems

    DEFF Research Database (Denmark)

    Tranberg-Hansen, Anders Sejer

    The advances seen in the semiconductor industry within the last decade have brought the possibility of integrating evermore functionality onto a single chip forming functionally highly advanced embedded systems. These integration possibilities also imply that as the design complexity increases, so...... an efficient system level design methodology, a modelling framework for performance estimation and design space exploration at the system level is required. This thesis presents a novel component based modelling framework for system level modelling and performance estimation of embedded systems. The framework...... is performed by having the framework produce detailed quantitative information about the system model under investigation. The project is part of the national Danish research project, Danish Network of Embedded Systems (DaNES), which is funded by the Danish National Advanced Technology Foundation. The project...

  17. Marine and estuarine natural microbial biofilms: ecological and biogeochemical dimensions

    Directory of Open Access Journals (Sweden)

    O. Roger Anderson

    2016-08-01

    Full Text Available Marine and estuarine microbial biofilms are ubiquitously distributed worldwide and are increasingly of interest in basic and applied sciences because of their unique structural and functional features that make them remarkably different from the biota in the plankton. This is a review of some current scientific knowledge of naturally occurring microbial marine and estuarine biofilms including prokaryotic and microeukaryotic biota, but excluding research specifically on engineering and applied aspects of biofilms such as biofouling. Because the microbial communities including bacteria and protists are integral to the fundamental ecological and biogeochemical processes that support biofilm communities, particular attention is given to the structural and ecological aspects of microbial biofilm formation, succession, and maturation, as well as the dynamics of the interactions of the microbiota in biofilms. The intent is to highlight current state of scientific knowledge and possible avenues of future productive research, especially focusing on the ecological and biogeochemical dimensions.

  18. The Microbial Engines That Drive Earth’s Biogeochemical Cycles

    Science.gov (United States)

    Falkowski, Paul G.; Fenchel, Tom; Delong, Edward F.

    2008-05-01

    Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet’s history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.

  19. Network model of security system

    Directory of Open Access Journals (Sweden)

    Adamczyk Piotr

    2016-01-01

    Full Text Available The article presents the concept of building a network security model and its application in the process of risk analysis. It indicates the possibility of a new definition of the role of the network models in the safety analysis. Special attention was paid to the development of the use of an algorithm describing the process of identifying the assets, vulnerability and threats in a given context. The aim of the article is to present how this algorithm reduced the complexity of the problem by eliminating from the base model these components that have no links with others component and as a result and it was possible to build a real network model corresponding to reality.

  20. Modeling Adaptive Behavior for Systems Design

    DEFF Research Database (Denmark)

    Rasmussen, Jens

    1994-01-01

    Field studies in modern work systems and analysis of recent major accidents have pointed to a need for better models of the adaptive behavior of individuals and organizations operating in a dynamic and highly competitive environment. The paper presents a discussion of some key characteristics...... of the predictive models required for the design of work supports systems, that is,information systems serving as the human-work interface. Three basic issues are in focus: 1.) Some fundamental problems in analysis and modeling modern dynamic work systems caused by the adaptive nature of human behavior; 2.......) The basic difference between the models of system functions used in engineering and design and those evolving from basic research within the various academic disciplines and finally 3.) The models and methods required for closed-loop, feedback system design....

  1. Model-based version management system framework

    International Nuclear Information System (INIS)

    Mehmood, W.

    2016-01-01

    In this paper we present a model-based version management system. Version Management System (VMS) a branch of software configuration management (SCM) aims to provide a controlling mechanism for evolution of software artifacts created during software development process. Controlling the evolution requires many activities to perform, such as, construction and creation of versions, identification of differences between versions, conflict detection and merging. Traditional VMS systems are file-based and consider software systems as a set of text files. File based VMS systems are not adequate for performing software configuration management activities such as, version control on software artifacts produced in earlier phases of the software life cycle. New challenges of model differencing, merge, and evolution control arise while using models as central artifact. The goal of this work is to present a generic framework model-based VMS which can be used to overcome the problem of tradition file-based VMS systems and provide model versioning services. (author)

  2. Very Large System Dynamics Models - Lessons Learned

    Energy Technology Data Exchange (ETDEWEB)

    Jacob J. Jacobson; Leonard Malczynski

    2008-10-01

    This paper provides lessons learned from developing several large system dynamics (SD) models. System dynamics modeling practice emphasize the need to keep models small so that they are manageable and understandable. This practice is generally reasonable and prudent; however, there are times that large SD models are necessary. This paper outlines two large SD projects that were done at two Department of Energy National Laboratories, the Idaho National Laboratory and Sandia National Laboratories. This paper summarizes the models and then discusses some of the valuable lessons learned during these two modeling efforts.

  3. Test-driven modeling of embedded systems

    DEFF Research Database (Denmark)

    Munck, Allan; Madsen, Jan

    2015-01-01

    To benefit maximally from model-based systems engineering (MBSE) trustworthy high quality models are required. From the software disciplines it is known that test-driven development (TDD) can significantly increase the quality of the products. Using a test-driven approach with MBSE may have...... a similar positive effect on the quality of the system models and the resulting products and may therefore be desirable. To define a test-driven model-based systems engineering (TD-MBSE) approach, we must define this approach for numerous sub disciplines such as modeling of requirements, use cases......, scenarios, behavior, architecture, etc. In this paper we present a method that utilizes the formalism of timed automatons with formal and statistical model checking techniques to apply TD-MBSE to the modeling of system architecture and behavior. The results obtained from applying it to an industrial case...

  4. Precipitation-runoff modeling system; user's manual

    Science.gov (United States)

    Leavesley, G.H.; Lichty, R.W.; Troutman, B.M.; Saindon, L.G.

    1983-01-01

    The concepts, structure, theoretical development, and data requirements of the precipitation-runoff modeling system (PRMS) are described. The precipitation-runoff modeling system is a modular-design, deterministic, distributed-parameter modeling system developed to evaluate the impacts of various combinations of precipitation, climate, and land use on streamflow, sediment yields, and general basin hydrology. Basin response to normal and extreme rainfall and snowmelt can be simulated to evaluate changes in water balance relationships, flow regimes, flood peaks and volumes, soil-water relationships, sediment yields, and groundwater recharge. Parameter-optimization and sensitivity analysis capabilites are provided to fit selected model parameters and evaluate their individual and joint effects on model output. The modular design provides a flexible framework for continued model system enhancement and hydrologic modeling research and development. (Author 's abstract)

  5. An Empirical Model for Energy Storage Systems

    Energy Technology Data Exchange (ETDEWEB)

    Rosewater, David Martin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Scott, Paul [TransPower, Poway, CA (United States)

    2016-03-17

    Improved models of energy storage systems are needed to enable the electric grid’s adaptation to increasing penetration of renewables. This paper develops a generic empirical model of energy storage system performance agnostic of type, chemistry, design or scale. Parameters for this model are calculated using test procedures adapted from the US DOE Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage. We then assess the accuracy of this model for predicting the performance of the TransPower GridSaver – a 1 MW rated lithium-ion battery system that underwent laboratory experimentation and analysis. The developed model predicts a range of energy storage system performance based on the uncertainty of estimated model parameters. Finally, this model can be used to better understand the integration and coordination of energy storage on the electric grid.

  6. Impact of chlorophyll bias on the tropical Pacific mean climate in an earth system model

    Science.gov (United States)

    Lim, Hyung-Gyu; Park, Jong-Yeon; Kug, Jong-Seong

    2017-12-01

    Climate modeling groups nowadays develop earth system models (ESMs) by incorporating biogeochemical processes in their climate models. The ESMs, however, often show substantial bias in simulated marine biogeochemistry which can potentially introduce an undesirable bias in physical ocean fields through biogeophysical interactions. This study examines how and how much the chlorophyll bias in a state-of-the-art ESM affects the mean and seasonal cycle of tropical Pacific sea-surface temperature (SST). The ESM used in the present study shows a sizeable positive bias in the simulated tropical chlorophyll. We found that the correction of the chlorophyll bias can reduce the ESM's intrinsic cold SST mean bias in the equatorial Pacific. The biologically-induced cold SST bias is strongly affected by seasonally-dependent air-sea coupling strength. In addition, the correction of chlorophyll bias can improve the annual cycle of SST by up to 25%. This result suggests a possible modeling approach in understanding the two-way interactions between physical and chlorophyll biases by biogeophysical effects.

  7. Modeling Nitrogen Cycling in Delaware Estuary

    Science.gov (United States)

    Tabatabai, A.; Wilkin, J.

    2016-02-01

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

  8. Brief History of Agricultural Systems Modeling

    Science.gov (United States)

    Jones, James W.; Antle, John M.; Basso, Bruno O.; Boote, Kenneth J.; Conant, Richard T.; Foster, Ian; Godfray, H. Charles J.; Herrrero, Mario; Howitt, Richard E.; Janssen, Sandor; hide

    2016-01-01

    Agricultural systems science generates knowledge that allows researchers to consider complex problems or take informed agricultural decisions. The rich history of this science exemplifies the diversity of systems and scales over which they operate and have been studied. Modeling, an essential tool in agricultural systems science, has been accomplished by scientists from a wide range of disciplines, who have contributed concepts and tools over more than six decades. As agricultural scientists now consider the next generation models, data, and knowledge products needed to meet the increasingly complex systems problems faced by society, it is important to take stock of this history and its lessons to ensure that we avoid re-invention and strive to consider all dimensions of associated challenges. To this end, we summarize here the history of agricultural systems modeling and identify lessons learned that can help guide the design and development of next generation of agricultural system tools and methods. A number of past events combined with overall technological progress in other fields have strongly contributed to the evolution of agricultural system modeling, including development of process-based bio-physical models of crops and livestock, statistical models based on historical observations, and economic optimization and simulation models at household and regional to global scales. Characteristics of agricultural systems models have varied widely depending on the systems involved, their scales, and the wide range of purposes that motivated their development and use by researchers in different disciplines. Recent trends in broader collaboration across institutions, across disciplines, and between the public and private sectors suggest that the stage is set for the major advances in agricultural systems science that are needed for the next generation of models, databases, knowledge products and decision support systems. The lessons from history should be considered

  9. Estimating impacts of lichens and bryophytes on global biogeochemical cycles

    Science.gov (United States)

    Porada, Philipp; Weber, Bettina; Elbert, Wolfgang; Pöschl, Ulrich; Kleidon, Axel

    2014-02-01

    Lichens and bryophytes may significantly affect global biogeochemical cycles by fixation of nitrogen and biotic enhancement of surface weathering rates. Most of the studies suggesting these effects, however, are either conceptual or rely on upscaling of regional estimates to obtain global numbers. Here we use a different method, based on estimates of net carbon uptake, to quantify the impacts of lichens and bryophytes on biogeochemical cycles at the global scale. We focus on three processes, namely, nitrogen fixation, phosphorus uptake, and chemical weathering. Our estimates have the form of potential rates, which means that we quantify the amount of nitrogen and phosphorus needed by the organisms to build up biomass, also accounting for resorption and leaching of nutrients. Subsequently, we use potential phosphorus uptake on bare ground to estimate chemical weathering by the organisms, assuming that they release weathering agents to obtain phosphorus. The predicted requirement for nitrogen ranges from 3.5 to 34 Tgyr-1 and for phosphorus it ranges from 0.46 to 4.6 Tgyr-1. Estimates of chemical weathering are between 0.058 and 1.1 km3 yr-1 of rock. These values seem to have a realistic order of magnitude, and they support the notion that lichens and bryophytes have the potential to play an important role for biogeochemical cycles.

  10. Morphological, hydrological, biogeochemical and ecological changes and challenges in river restoration - the Thur River case study

    Science.gov (United States)

    Schirmer, M.; Luster, J.; Linde, N.; Perona, P.; Mitchell, E. A. D.; Barry, D. A.; Hollender, J.; Cirpka, O. A.; Schneider, P.; Vogt, T.; Radny, D.; Durisch-Kaiser, E.

    2014-06-01

    River restoration can enhance river dynamics, environmental heterogeneity and biodiversity, but the underlying processes governing the dynamic changes need to be understood to ensure that restoration projects meet their goals, and adverse effects are prevented. In particular, we need to comprehend how hydromorphological variability quantitatively relates to ecosystem functioning and services, biodiversity as well as ground- and surface water quality in restored river corridors. This involves (i) physical processes and structural properties, determining erosion and sedimentation, as well as solute and heat transport behavior in surface water and within the subsurface; (ii) biogeochemical processes and characteristics, including the turnover of nutrients and natural water constituents; and (iii) ecological processes and indicators related to biodiversity and ecological functioning. All these aspects are interlinked, requiring an interdisciplinary investigation approach. Here, we present an overview of the recently completed RECORD (REstored CORridor Dynamics) project in which we combined physical, chemical, and biological observations with modeling at a restored river corridor of the perialpine Thur River in Switzerland. Our results show that river restoration, beyond inducing morphologic changes that reshape the river bed and banks, triggered complex spatial patterns of bank infiltration, and affected habitat type, biotic communities and biogeochemical processes. We adopted an interdisciplinary approach of monitoring the continuing changes due to restoration measures to address the following questions: How stable is the morphological variability established by restoration? Does morphological variability guarantee an improvement in biodiversity? How does morphological variability affect biogeochemical transformations in the river corridor? What are some potential adverse effects of river restoration? How is river restoration influenced by catchment-scale hydraulics

  11. Long-term ERT monitoring of biogeochemical changes of an aged hydrocarbon contamination

    Science.gov (United States)

    Caterina, David; Flores Orozco, Adrian; Nguyen, Frédéric

    2017-06-01

    Adequate management of contaminated sites requires information with improved spatio-temporal resolution, in particular to assess bio-geochemical processes, such as the transformation and degradation of contaminants, precipitation of minerals or changes in groundwater geochemistry occurring during and after remediation procedures. Electrical Resistivity Tomography (ERT), a geophysical method sensitive to pore-fluid and pore-geometry properties, permits to gain quasi-continuous information about subsurface properties in real-time and has been consequently widely used for the characterization of hydrocarbon-impacted sediments. However, its application for the long-term monitoring of processes accompanying natural or engineered bioremediation is still difficult due to the poor understanding of the role that biogeochemical processes play in the electrical signatures. For in-situ studies, the task is further complicated by the variable signal-to-noise ratio and the variations of environmental parameters leading to resolution changes in the electrical images. In this work, we present ERT imaging results for data collected over a period of two years on a site affected by a diesel fuel contamination and undergoing bioremediation. We report low electrical resistivity anomalies in areas associated to the highest contaminant concentrations likely due transformations of the contaminant due to microbial activity and accompanying release of metabolic products. We also report large seasonal variations of the bulk electrical resistivity in the contaminated areas in correlation with temperature and groundwater level fluctuations. However, the amplitude of bulk electrical resistivity variations largely exceeds the amplitude expected given existing petrophysical models. Our results suggest that the variations in electrical properties are mainly controlled by microbial activity which in turn depends on soil temperature and hydrogeological conditions. Therefore, ERT can be suggested as

  12. Formal Modeling and Analysis of Timed Systems

    DEFF Research Database (Denmark)

    Larsen, Kim Guldstrand; Niebert, Peter

    This book constitutes the thoroughly refereed post-proceedings of the First International Workshop on Formal Modeling and Analysis of Timed Systems, FORMATS 2003, held in Marseille, France in September 2003. The 19 revised full papers presented together with an invited paper and the abstracts...... of two invited talks were carefully selected from 36 submissions during two rounds of reviewing and improvement. All current aspects of formal method for modeling and analyzing timed systems are addressed; among the timed systems dealt with are timed automata, timed Petri nets, max-plus algebras, real......-time systems, discrete time systems, timed languages, and real-time operating systems....

  13. Nanostructural and biogeochemical features of the crinoid stereom

    Science.gov (United States)

    Gorzelak, P.; Stolarski, J.; Mazur, M.; Marrocchi, Y.; Meibom, A.; Chalmin, E.

    2009-04-01

    Representatives of all echinoderm clades (e.g., echinoids, holothuroids, ophiuroids, asteroids, and crinoids) form elaborate calcitic (polymorph of calcium carbonate) skeletons composed of numerous plates. Each plate consists of a three-dimensional meshwork of mineral trabeculae (stereom) that results from precisely orchestrated biomineralization processes. Individual skeletal plates behave as single calcite crystals as shown by X-ray diffraction and polarizing microscopy, however, their physico-chemical properties differ significantly from the properties of geologic or synthetic calcites. For example, echinoderm bio-calcite does not show cleavage planes typical of calcite but reveals conchoidal fracture surfaces that reduce the brittleness of the material. The unique properties of echinoderm bio-calcite result from intimate involvement of organic molecules in the biomineralization process and their incorporation into the crystal structure. Remnants of echinoderm skeleton are among the most frequently found fossils in the Mesozoic and Palaeozoic rocks thus, in order to use them as environmental proxies, it is necessary to understand the degree of biological ("vital effect") and inorganic control over their formation. Here, we show first nanoscale structural and biogeochemical properties of the stereom of extant and fossil crinoids. Using FESEM and AFM imaging techniques we show that the skeleton has nanocomposite structure: individual grains have ca. 100 nm in diameter and occasionally form larger aggregates. Fine scale geobiochemical mappings of crinoid plates (NanoSIMS microprobe) show that Mg is distributed heterogeneously in the stereom with higher concentration in the middle part of the trabecular bars. Although organic components constitute only ca. 0.10-0.26 wt% of modern echinoderm bio-calcite, in situ synchrotron sulphur K-edge x-ray absorption near edge structure (XANES) spectra show that the central parts of stereom bars contain higher levels of SO4 that

  14. Grey Box Modelling of Hydrological Systems