WorldWideScience

Sample records for biogeochemical transport model

  1. Biogeochemical Transport and Reaction Model (BeTR) v1

    Energy Technology Data Exchange (ETDEWEB)

    2016-04-18

    The Biogeochemical Transport and Reaction Model (BeTR) is a F90 code that enables reactive transport modeling in land modules of earth system models (e.g. CESM, ACME). The code adopts the Objective-Oriented-Design, and allows users to plug in their own biogeochemical (BGC) formulations/codes, and compare them to other existing BGC codes in those ESMs. The code takes information of soil physics variables, such as variables, such as temperature, moisture, soil density profile; water flow, etc., from a land model to track the movement of different chemicals in presence of biogeochemical reactions.

  2. 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."

  3. 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.

  4. 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...

  5. A 3-D variational assimilation scheme in coupled transport-biogeochemical models: Forecast of Mediterranean biogeochemical properties.

    Science.gov (United States)

    Teruzzi, Anna; Dobricic, Srdjan; Solidoro, Cosimo; Cossarini, Gianpiero

    2014-01-01

    [1] Increasing attention is dedicated to the implementation of suitable marine forecast systems for the estimate of the state of the ocean. Within the framework of the European MyOcean infrastructure, the pre-existing short-term Mediterranean Sea biogeochemistry operational forecast system has been upgraded by assimilating remotely sensed ocean color data in the coupled transport-biogeochemical model OPATM-BFM using a 3-D variational data assimilation (3D-VAR) procedure. In the present work, the 3D-VAR scheme is used to correct the four phytoplankton functional groups included in the OPATM-BFM in the period July 2007 to September 2008. The 3D-VAR scheme decomposes the error covariance matrix using a sequence of different operators that account separately for vertical covariance, horizontal covariance, and covariance among biogeochemical variables. The assimilation solution is found in a reduced dimensional space, and the innovation for the biogeochemical variables is obtained by the sequential application of the covariance operators. Results show a general improvement in the forecast skill, providing a correction of the basin-scale bias of surface chlorophyll concentration and of the local-scale spatial and temporal dynamics of typical bloom events. Further, analysis of the assimilation skill provides insights into the functioning of the model. The computational costs of the assimilation scheme adopted are low compared to other assimilation techniques, and its modular structure facilitates further developments. The 3D-VAR scheme results especially suitable for implementation within a biogeochemistry operational forecast system.

  6. Technical Note: Simple formulations and solutions of the dual-phase diffusive transport for biogeochemical modeling

    Directory of Open Access Journals (Sweden)

    J. Y. Tang

    2014-01-01

    Full Text Available Representation of gaseous diffusion in variably saturated near-surface soils is becoming more common in land biogeochemical models, yet the formulations and numerical solution algorithms applied vary widely. We present three different but equivalent formulations of the dual-phase (gaseous and aqueous tracer diffusion transport problem that is relevant to a wide class of volatile tracers in land biogeochemical models. Of these three formulations (i.e., the gas-primary, aqueous-primary, and bulk tracer based formulations, we contend the gas-primary formulation is the most convenient for modeling tracer dynamics in biogeochemical models. We then provide finite volume approximation to the gas-primary equation and evaluate its accuracy against three analytical models: one for steady-state soil CO2 dynamics, one for steady-state soil CO2 dynamics, and one for transient tracer diffusion from a constant point source into two different sequentially aligned medias. All evaluations demonstrated good accuracy of the numerical approximation. We expect our result will standardize an efficient mechanistic numerical method for solving relatively simple, multi-phase, one-dimensional diffusion problems in land models.

  7. 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...

  8. In Situ Biostimulation at a Former Uranium Mill Tailings Site: Multicomponent Biogeochemical Reactive Transport Modeling

    Science.gov (United States)

    Yabusaki, S.; Fang, Y.; Long, P.

    2005-12-01

    In situ biostimulation at a Former Uranium Mill Tailings Site: Multicomponent Biogeochemical Reactive Transport Modeling Field experiments conducted at a former uranium mill tailings site in western Colorado are being used to investigate microbially mediated immobilization of uranium as a potential future remediation option for such sites. While the general principle of biostimulating microbial communities to reduce aqueous hexavalent uranium to immobile uraninite has been demonstrated in the laboratory and field, the ability to predictably engineer long lasting immobilization will require a more complete understanding of field-scale processes and properties. For this study, numerical simulation of the flow field, geochemical conditions, and micriobial communities is used to interpret field-scale biogeochemical reactive transport observed during experiments performed in 2002 to 2004. One key issue is identifying bioavailable Fe(III) oxide, which is the principal electron acceptor utilized by the acetate- oxidizing Geobacter sp. These organisms are responsible for uranium bioreduction that results in the removal of sufficient U(VI) to lower uranium groundwater concentrations to at or near applicable standards. The depletion of bioavailable Fe(III) leads to succession by sulfate reducers that are considerably less effective at uranium bioreduction. An important modeling consideration are the abiotic reactions (e.g., mineral precipitation and dissolution, aqueous and surface complexation) involving the Fe(II) and sulfide produced during biostimulation. These components, strongly associated with the solid phases, may play an important role in the evolving reactivity of the mineral surfaces that are likely to impact long-term uranium immobilization.

  9. Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment.

    Science.gov (United States)

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

    2011-11-01

    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 and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted

  10. 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

  11. Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume.

    Science.gov (United States)

    van Breukelen, Boris M; Griffioen, Jasper; Röling, Wilfred F M; van Verseveld, Henk W

    2004-06-01

    The biogeochemical processes governing leachate attenuation inside a landfill leachate plume (Banisveld, the Netherlands) were revealed and quantified using the 1D reactive transport model PHREEQC-2. Biodegradation of dissolved organic carbon (DOC) was simulated assuming first-order oxidation of two DOC fractions with different reactivity, and was coupled to reductive dissolution of iron oxide. The following secondary geochemical processes were required in the model to match observations: kinetic precipitation of calcite and siderite, cation exchange, proton buffering and degassing. Rate constants for DOC oxidation and carbonate mineral precipitation were determined, and other model parameters were optimized using the nonlinear optimization program PEST by means of matching hydrochemical observations closely (pH, DIC, DOC, Na, K, Ca, Mg, NH4, Fe(II), SO4, Cl, CH4, saturation index of calcite and siderite). The modelling demonstrated the relevance and impact of various secondary geochemical processes on leachate plume evolution. Concomitant precipitation of siderite masked the act of iron reduction. Cation exchange resulted in release of Fe(II) from the pristine anaerobic aquifer to the leachate. Degassing, triggered by elevated CO2 pressures caused by carbonate precipitation and proton buffering at the front of the plume, explained the observed downstream decrease in methane concentration. Simulation of the carbon isotope geochemistry independently supported the proposed reaction network.

  12. 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.

  13. Modeling Biogeochemical Reactive Transport in Fractured Granites: Implications for the Performance of a Deep Geological Repository

    Science.gov (United States)

    Molinero, J.; Samper, J.; Pedersen, K.; Puigdomenech, I.

    2003-12-01

    Several countries around the world are considering deep repositories in fractured granitic formations for the final disposal of high-level radioactive waste. Evaluating the long term safety of such repositories requires sound conceptual and numerical models which are being developed from data and knowledge gained from in situ experiments carried out at deep underground laboratories such as that of Žsp” in Sweden. One of the key aspects for performance assessment concerns to groundwater redox conditions because: (a) the presence of oxygen will affect to the corrosion of canisters, (b) possible production of hydrogen sulphide from sulphate reduction will also have a negative effect on these metallic containers, and (c) several long-lived radionuclides are much more soluble and mobile under oxidizing conditions. Several projects have been performed at Žsp” to investigate different aspects of the groundwater redox evolution. The vast amount of in situ-generated information has been used in this work to set up coupled hydrobiogeochemical models. Numerical models account for saturated groundwater flow, solute transport by advection, dispersion and molecular diffusion, geochemical reactions involving both the liquid and solid phases, and microbially-catallyzed processes. For the Žsp” site, modelling results provide quantitative support for the following conclusions. (A) At the operational phase of the repository, shallow fresh groundwater could reach the depth of the underground facility. Shallow groundwaters loose dissolved oxygen during the infiltration through soil layers and then, respiration of dissolved organic matter is induced along the flow paths through the reduction of Fe(III)-bearing minerals of the fracture zones. Microbial anaerobic respiration of DOC provides additional reducing capacity at the depth of the tunnel. (B) After repository closure, atmospheric oxygen will remain trapped within the tunnel. Abiotic consumption of this oxygen has been

  14. A biogeochemical model of contaminant fate and transport in river waters and sediments.

    Science.gov (United States)

    Massoudieh, Arash; Bombardelli, Fabián A; Ginn, Timothy R

    2010-03-01

    A quasi-two-dimensional model is presented for simulating transport and transformation of contaminant species in river waters and sediments, taking into account the effect of both biotic and abiotic geochemical reactions on the contaminant fate and mobility. The model considers the downstream transport of dissolved and sediment-associated species, and the mass transfer with bed sediments due to erosion and resuspension, using linked advection-dispersion-reaction equations. The model also couples both equations to the reactive transport within bed sediment phases. This is done by the use of a set of vertical one-dimensional columns representing sediment layers that take into account the reactive transport of chemicals, burial, sorption/desorption to/from the solid phase, and the diffusive transport of aqueous species. Kinetically-controlled reversible solid-water mass exchange models are adopted to simulate interactions between suspended sediments and bulk water, as well as the mass exchange between bed sediments and pore water. An innovative multi-time step approach is used to model the fully kinetic nonlinear reaction terms using a non-iterative explicit method. This approach enables the model to handle fast and near-equilibrium reactions without a significant increase in computational burden. At the end, two demonstration cases are simulated using the model, including transport of a sorbing, non-reactive trace metal and nitrogen cycling, both in the Colusa Basin Drain in the Central Valley of California.

  15. Modeling greenhouse gas emissions and nutrient transport in managed arable soils with a fully coupled hydrology-biogeochemical modeling system

    Science.gov (United States)

    Haas, Edwin; Klatt, Steffen; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in various virtual landscapes / catchment to demonstrate the capabilities of the modelling system. The modelling system was applied to simulate water and nutrient transport at the at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the

  16. CLM4-BeTR, a generic biogeochemical transport and reaction module for CLM4: model development, evaluation, and application

    Directory of Open Access Journals (Sweden)

    J. Tang

    2012-09-01

    Full Text Available To improve regional and global biogeochemistry modeling and climate predictability, we have developed a generic reactive transport module for the land model CLM4 (called CLM4-BeTR (Biogeochemical Transport and Reactions. CLM4-BeTR represents the transport, interactions, and biotic and abiotic transformations of an arbitrary number of tracers (aka chemical species in an arbitrary number of phases (e.g. dissolved, gaseous, sorbed, aggregate. An operator splitting approach was employed and consistent boundary conditions were derived for each modeled sub-process. Tracer fluxes, associated with hydrological processes such as surface run-on and run-off, belowground drainage, and ice to liquid conversion were also computed consistently with the bulk water fluxes calculated by the soil physics module in CLM4. The transport code was evaluated and found be in good agreement with several analytical test cases. The model was then applied at the Harvard Forest site with a representation of depth-dependent belowground biogeochemistry. The results indicated that, at this site, (1 CLM4-BeTR was able to simulate soil-surface CO2 effluxes and soil CO2 profiles accurately; (2 the transient surface CO2 effluxes calculated based on the tracer transport mechanism were in general not equal to the belowground CO2 production rates and that their differences varied according to the seasonal cycle of soil physics and biogeochemistry; (3 losses of CO2 through processes other than surface gas efflux were less than 1% of the overall soil respiration; and (4 the contributions of root respiration and heterotrophic respiration have distinct temporal signals in surface CO2 effluxes and soil CO2 concentrations. The development of CLM4-BeTR will allow detailed comparisons between ecosystem observations and predictions and insights to the modeling of terrestrial biogeochemistry.

  17. Modeling the nitrogen fluxes in the Black Sea using a 3D coupled hydrodynamical-biogeochemical model: transport versus biogeochemical processes, exchanges across the shelf break and comparison of the shelf and deep sea ecodynamics

    NARCIS (Netherlands)

    Grégoire, M.; Beckers, J.M.

    2004-01-01

    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 she

  18. CLM4-BeTR, a generic biogeochemical transport and reaction module for CLM4: model development, evaluation, and application

    Directory of Open Access Journals (Sweden)

    J. Y. Tang

    2013-01-01

    Full Text Available To improve regional and global biogeochemistry modeling and climate predictability, we have developed a generic reactive transport module for the land model CLM4 (called CLM4-BeTR (Biogeochemical Transport and Reactions. CLM4-BeTR represents the transport, interactions, and biotic and abiotic transformations of an arbitrary number of tracers (aka chemical species in an arbitrary number of phases (e.g., dissolved, gaseous, sorbed, aggregate. An operator splitting approach was employed and consistent boundary conditions were derived for each modeled sub-process. Aqueous tracer fluxes, associated with hydrological processes such as surface run-on and run-off, belowground drainage, and ice to liquid conversion were also computed consistently with the bulk water fluxes calculated by the soil physics module in CLM4. The transport code was evaluated and found in good agreement with several analytical test cases using a time step of 30 min. The model was then applied at the Harvard Forest site with a representation of depth-dependent belowground biogeochemistry. The results indicated that, at this site, (1 CLM4-BeTR was able to simulate soil–surface CO2 effluxes and soil CO2 profiles accurately; (2 the transient surface CO2 effluxes calculated based on the tracer transport mechanism were in general not equal to the belowground CO2 production rates with the magnitude of the difference being a function of averaging timescale and site conditions: differences were large (−20 ~ 20% on hourly, smaller (−5 ~ 5% at daily timescales, and persisted to the monthly timescales with a smaller magnitude (<4%; (3 losses of CO2 through processes other than surface gas efflux were less than 1% of the overall soil respiration; and (4 the contributions of root respiration and heterotrophic respiration have distinct temporal signals in surface CO2 effluxes and soil CO2 concentrations. The

  19. Modeling the nitrogen fluxes in the Black Sea using a 3D coupled hydrodynamical-biogeochemical model: transport versus biogeochemical processes, exchanges across the shelf break and comparison of the shelf and deep sea ecodynamics

    Directory of Open Access Journals (Sweden)

    J. M. Beckers

    2004-06-01

    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 130 g C m-2yr-1 for the whole basin, 220 g C m-2yr-1 for the shelf and 40 g C m-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 1010mol yr-1. This POC is definitely lost for the system and represents 2% of the annual primary production of the open sea.

  20. 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.

  1. A biogeochemical transport model to simulate the attenuation of chlorinated hydrocarbon contaminant fluxes across the groundwater-surface water interface

    DEFF Research Database (Denmark)

    Malaguerra, Flavio; Binning, Philip John; Albrechtsen, Hans-Jørgen

    2009-01-01

    Chlorinated hydrocarbons originating from point sources are amongst the most prevalent contaminants of ground water and surface water resources. Riparian zones may play an important role in the attenuation of contaminant concentrations when contaminant plumes flow from groundwater to surface water...... because of the occurrence of redox gradients, strongly reductive conditions and high biological activity. In order to meet the expectations of the EU Water Framework Directive, an evaluation of the impact of such plumes on surface water is needed. The aim of this work is to develop a groundwater transport...... number of geochemical processes, allows the simulation of soil geochemical transformations when microbial by-products are released to surface water, and the consideration of non-linear feedbacks on bacterial growth and pollutant transformations. Sensitivity analysis is performed through Monte Carlo...

  2. Mapping pan-Arctic methane emissions at high spatial resolution using an adjoint atmospheric transport and inversion method and process-based wetland and lake biogeochemical models

    Directory of Open Access Journals (Sweden)

    Z. Tan

    2015-11-01

    Full Text Available Understanding methane emissions from the Arctic, a fast warming carbon reservoir, is important for projecting changes in the global methane cycle under future climate scenarios. Here we optimize Arctic methane emissions with a nested-grid high-resolution inverse model by assimilating both high-precision surface measurements and column-average SCIAMACHY satellite retrievals of methane mole fraction. For the first time, methane emissions from lakes are integrated into an atmospheric transport and inversion estimate, together with prior wetland emissions estimated by six different biogeochemical models. We find that, the global methane emissions during July 2004–June 2005 ranged from 496.4 to 511.5 Tg yr−1, with wetland methane emissions ranging from 130.0 to 203.3 Tg yr−1. The Arctic methane emissions during July 2004–June 2005 were in the range of 14.6–30.4 Tg yr−1, with wetland and lake emissions ranging from 8.8 to 20.4 Tg yr−1 and from 5.4 to 7.9 Tg yr−1 respectively. Canadian and Siberian lakes contributed most of the estimated lake emissions. Due to insufficient measurements in the region, Arctic methane emissions are less constrained in northern Russia than in Alaska, northern Canada and Scandinavia. Comparison of different inversions indicates that the distribution of global and Arctic methane emissions is sensitive to prior wetland emissions. Evaluation with independent datasets shows that the global and Arctic inversions improve estimates of methane mixing ratios in boundary layer and free troposphere. The high-resolution inversions provide more details about the spatial distribution of methane emissions in the Arctic.

  3. 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.

  4. 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.

  5. Biogeochemical Filtering of Solute Signals Explored as a Function of Transport and Reaction Time Scales

    Science.gov (United States)

    Zanardo, S.; Basu, N. B.; Rao, P. C.

    2009-12-01

    Catchment biogeochemical responses are the result of superposition of diverse dynamic components, which can be related to climate forcing, water flow, and biogeochemical reactions. The interactions among these components are highly non-linear and contribute to the generation of emergent patterns at multiple spatial and temporal scales. The aim of this work is to explore the following biogeochemical signatures arising from such interactions: (1) the relationship between contaminant loads (L) and discharge (Q) at the annual timescale, leading to an apparent chemostatic relationship (i.e., linear L-Q plots) for different contaminants and at different spatial scales; (2) spatial patterns in the slope and the scatter of the L-Q relationships; and (3) correlation between the intra-annual flow duration curves (FDC) and the load duration curves (LDC). Exploring this relationship necessitates the use of a parsimonious model, with few spatially uniform time constants, that can generate synthetic time series of load and flow at the outlet of river basins. The Mass Response Functions (MRF) approach (Rinaldo et al., 2006), lends itself suitable for the purpose since it relies on the assumption that the evolution of solute concentration in the water pulses depends only on the residence time, and not on its trajectory - thus space is replaced by time. The model simulates the episodic delivery of water and contaminant pulses from the hillslopes to the stream network in response to temporally random but spatially uniform effective rainfall patterns. The domain is described by an immobile source zone in which first order biogeochemical reactions (degradation rate constant ke) alter the solute mass, while multiple mobile rainfall pulses exchange mass with the source zone following linear kinetics (mass transfer rate constant α). The biogeochemical module of MRF, that was originally written to simulate non-reactive tracer and nitrate transport, was modified to include the more

  6. Modeling greenhouse gas emissions (CO2, N2O, CH4) from managed arable soils with a fully coupled hydrology-biogeochemical modeling system simulating water and nutrient transport and associated carbon and nitrogen cycling at catchment scale

    Science.gov (United States)

    Klatt, Steffen; Haas, Edwin; Kraus, David; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Plesca, Ina; Breuer, Lutz; Zhu, Bo; Zhou, Minghua; Zhang, Wei; Zheng, Xunhua; Wlotzka, Martin; Heuveline, Vincent

    2014-05-01

    The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in a small catchment at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the evapotranspiration is based on Penman-Monteith. Biogeochemical processes are modelled by LandscapeDNDC, including soil microclimate, plant growth and biomass allocation

  7. A generic biogeochemical module for earth system models

    Directory of Open Access Journals (Sweden)

    Y. Fang

    2013-06-01

    Full Text Available Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from the atmosphere, influencing global climate changes. Integration of these processes into earth system models (e.g. community land models – CLM, however, currently faces three major challenges: (1 extensive efforts are required to modify modeling structures and to rewrite computer programs to incorporate new or updated processes as new knowledge is being generated, (2 computational cost is prohibitively expensive to simulate biogeochemical processes in land models due to large variations in the rates of biogeochemical processes, and (3 various mathematical representations of biogeochemical processes exist to incorporate different aspects of fundamental mechanisms, but systematic evaluation of the different mathematical representations is difficult, if not impossible. To address these challenges, we propose a new computational framework to easily incorporate physical and biogeochemical processes into land models. The new framework consists of a new biogeochemical module with a generic algorithm and reaction database so that new and updated processes can be incorporated into land models without the need to manually set up the ordinary differential equations to be solved numerically. The reaction database consists of processes of nutrient flow through the terrestrial ecosystems in plants, litter and soil. This framework facilitates effective comparison studies of biogeochemical cycles in an ecosystem using different conceptual models under the same land modeling framework. The approach was first implemented in CLM and benchmarked against simulations from the original CLM-CN code. A case study was then provided to demonstrate the advantages of using the new approach to incorporate a phosphorus cycle into the CLM model. To our knowledge, the phosphorus-incorporated CLM is a new model that can be used to simulate phosphorus limitation on the productivity of

  8. Numerical simulation of in-situ chemical oxidation (ISCO) and biodegradation of petroleum hydrocarbons using a coupled model for bio-geochemical reactive transport

    Science.gov (United States)

    Marin, I. S.; Molson, J. W.

    2013-05-01

    Petroleum hydrocarbons (PHCs) are a major source of groundwater contamination, being a worldwide and well-known problem. Formed by a complex mixture of hundreds of organic compounds (including BTEX - benzene, toluene, ethylbenzene and xylenes), many of which are toxic and persistent in the subsurface and are capable of creating a serious risk to human health. Several remediation technologies can be used to clean-up PHC contamination. In-situ chemical oxidation (ISCO) and intrinsic bioremediation (IBR) are two promising techniques that can be applied in this case. However, the interaction of these processes with the background aquifer geochemistry and the design of an efficient treatment presents a challenge. Here we show the development and application of BIONAPL/Phreeqc, a modeling tool capable of simulating groundwater flow, contaminant transport with coupled biological and geochemical processes in porous or fractured porous media. BIONAPL/Phreeqc is based on the well-tested BIONAPL/3D model, using a powerful finite element simulation engine, capable of simulating non-aqueous phase liquid (NAPL) dissolution, density-dependent advective-dispersive transport, and solving the geochemical and kinetic processes with the library Phreeqc. To validate the model, we compared BIONAPL/Phreeqc with results from the literature for different biodegradation processes and different geometries, with good agreement. We then used the model to simulate the behavior of sodium persulfate (NaS2O8) as an oxidant for BTEX degradation, coupled with sequential biodegradation in a 2D case and to evaluate the effect of inorganic geochemistry reactions. The results show the advantages of a treatment train remediation scheme based on ISCO and IBR. The numerical performance and stability of the integrated BIONAPL/Phreeqc model was also verified.

  9. Coupling a Terrestrial Biogeochemical Model to the Common Land Model

    Institute of Scientific and Technical Information of China (English)

    SHI Xiaoying; MAd Jiafu; WANG Yingping; DAI Yongjiu; TANG Xuli

    2011-01-01

    A terrestrial biogeochemical model (CASACNP) was coupled to a land surtace model (the Common Land Model,CoLM) to simulate the dynamics of carbon substrate in soil and its limitation on soil respiration.The combined model,CoLM_CASACNP,was able to predict long-term carbon sources and sinks that CoLM alone could not.The coupled model was tested using measurenents of belowground respiration and surface fluxes from two forest ecosystems.The combined model simulated reasonably well the diurnal and seasonal variations of net ecosystem carbon exchange,as well as seasonal variation in the soil respiration rate of both the forest sites chosen for this study.However,the agreement between model simulations and actual measurements was poorer under dry conditions.The model should be tested against more measurements before being applied globally to investigate the feedbacks between the carbon cycle and climate change.

  10. Calibrating a global three-dimensional biogeochemical ocean model (MOPS-1.0)

    Science.gov (United States)

    Kriest, Iris; Sauerland, Volkmar; Khatiwala, Samar; Srivastav, Anand; Oschlies, Andreas

    2017-01-01

    Global biogeochemical ocean models contain a variety of different biogeochemical components and often much simplified representations of complex dynamical interactions, which are described by many ( ≈ 10 to ≈ 100) parameters. The values of many of these parameters are empirically difficult to constrain, due to the fact that in the models they represent processes for a range of different groups of organisms at the same time, while even for single species parameter values are often difficult to determine in situ. Therefore, these models are subject to a high level of parametric uncertainty. This may be of consequence for their skill with respect to accurately describing the relevant features of the present ocean, as well as their sensitivity to possible environmental changes. We here present a framework for the calibration of global biogeochemical ocean models on short and long timescales. The framework combines an offline approach for transport of biogeochemical tracers with an estimation of distribution algorithm (Covariance Matrix Adaption Evolution Strategy, CMA-ES). We explore the performance and capability of this framework by five different optimizations of six biogeochemical parameters of a global biogeochemical model, simulated over 3000 years. First, a twin experiment explores the feasibility of this approach. Four optimizations against a climatology of observations of annual mean dissolved nutrients and oxygen determine the extent to which different setups of the optimization influence model fit and parameter estimates. Because the misfit function applied focuses on the large-scale distribution of inorganic biogeochemical tracers, parameters that act on large spatial and temporal scales are determined earliest, and with the least spread. Parameters more closely tied to surface biology, which act on shorter timescales, are more difficult to determine. In particular, the search for optimum zooplankton parameters can benefit from a sound knowledge of

  11. What sea-ice biogeochemical modellers need from observers

    Directory of Open Access Journals (Sweden)

    Nadja Steiner

    2016-02-01

    Full Text Available Abstract Numerical models can be a powerful tool helping to understand the role biogeochemical processes play in local and global systems and how this role may be altered in a changing climate. With respect to sea-ice biogeochemical models, our knowledge is severely limited by our poor confidence in numerical model parameterisations representing those processes. Improving model parameterisations requires communication between observers and modellers to guide model development and improve the acquisition and presentation of observations. In addition to more observations, modellers need conceptual and quantitative descriptions of the processes controlling, for example: primary production and diversity of algal functional types in sea ice, ice algal growth, release from sea ice, heterotrophic remineralisation, transfer and emission of gases (e.g., DMS, CH4, BrO, incorporation of seawater components in growing sea ice (including Fe, organic and inorganic carbon, and major salts and subsequent release; CO2 dynamics (including CaCO3 precipitation, flushing and supply of nutrients to sea-ice ecosystems; and radiative transfer through sea ice. These issues can be addressed by focused observations, as well as controlled laboratory and field experiments that target specific processes. The guidelines provided here should help modellers and observers improve the integration of measurements and modelling efforts and advance toward the common goal of understanding biogeochemical processes in sea ice and their current and future impacts on environmental systems.

  12. Diffuse hydrological mass transport through catchments: scenario analysis of coupled physical and biogeochemical uncertainty effects

    Directory of Open Access Journals (Sweden)

    K. Persson

    2011-10-01

    Full Text Available This paper quantifies and maps the effects of coupled physical and biogeochemical variability on diffuse hydrological mass transport through and from catchments. It further develops a scenario analysis approach and investigates its applicability for handling uncertainties about both physical and biogeochemical variability and their different possible cross-correlation. The approach enables identification of conservative assumptions, uncertainty ranges, as well as pollutant/nutrient release locations and situations for which further investigations are most needed in order to reduce the most important uncertainty effects. The present scenario results provide different statistical and geographic distributions of advective travel times for diffuse hydrological mass transport. The geographic mapping can be used to identify potential hotspot areas with large mass loading to downstream surface and coastal waters, as well as their opposite, potential lowest-impact areas within the catchment. Results for alternative travel time distributions show that neglect or underestimation of the physical advection variability, and in particular of those transport pathways with much shorter than average advective solute travel times, can lead to substantial underestimation of pollutant and nutrient loads to downstream surface and coastal waters. This is particularly true for relatively high catchment-characteristic product of average attenuation rate and average advective travel time, for which mass delivery would be near zero under assumed transport homogeneity but can be orders of magnitude higher for variable transport conditions. A scenario of high advection variability, with a significant fraction of relatively short travel times, combined with a relevant average biogeochemical mass attenuation rate, emerges consistently from the present results as a generally reasonable, conservative assumption for estimating maximum diffuse mass loading, when the prevailing

  13. Geomorphic and substrate controls on spatial variability in river solute transport and biogeochemical cycling

    Science.gov (United States)

    Blaen, Phillip; Kurz, Marie; Knapp, Julia; Mendoza-Lera, Clara; Lee-Cullin, Joe; Klaar, Megan; Drummond, Jen; Jaeger, Anna; Zarnetske, Jay; Lewandowski, Joerg; Marti, Eugenia; Ward, Adam; Fleckenstein, Jan; Datry, Thibault; Larned, Scott; Krause, Stefan

    2016-04-01

    Nutrient concentrations in surface waters and groundwaters are increasing in many agricultural catchments worldwide as a result of anthropogenic activities. Increasing geomorphological heterogeneity in river channels may help to attenuate nutrient pollution by facilitating water exchange fluxes with the hyporheic zone; a site of intense microbial activity where biogeochemical transformation rates (e.g. denitrification) can be high. However, the controls on spatial variability in biogeochemical cycling, particularly at scales relevant for river managers, are not well understood. Here, we aimed to assess: 1) how differences in geomorphological heterogeneity control river solute transport and rates of biogeochemical cycling at sub-reach scales (102 m); and 2) the relative magnitude of these differences versus those relating to reach scale substrate variability (103 m). We used the reactive 'smart' tracer resazurin (Raz), a weakly fluorescent dye that transforms to highly fluorescent resorufin (Rru) under mildly reducing conditions, as a proxy to assess rates of biogeochemical cycling in a lowland river in southern England. Solute tracer tests were conducted in two reaches with contrasting substrates: one sand-dominated and the other gravel-dominated. Each reach was divided into sub-reaches that varied in geomorphic complexity (e.g. by the presence of pool-riffle sequences or the abundance of large woody debris). Slug injections of Raz and the conservative tracer fluorescein were conducted in each reach during baseflow conditions (Q ≈ 80 L/s) and breakthrough curves monitored using in-situ fluorometers. Preliminary results indicate overall Raz:Rru transformation rates in the gravel-dominated reach were more than 50% higher than those in the sand-dominated reach. However, high sub-reach variability in Raz:Rru transformation rates and conservative solute transport parameters suggests small-scale targeted management interventions to alter geomorphic heterogeneity may be

  14. Modeling biogeochemical processes in subterranean estuaries : Effect of flow dynamics and redox conditions on submarine groundwater discharge of nutrients

    NARCIS (Netherlands)

    Spiteri, C.; Slomp, C.P.; Tuncay, K.; Meile, C.

    2008-01-01

    A two-dimensional density-dependent reactive transport model, which couples groundwater flow and biogeochemical reactions, is used to investigate the fate of nutrients (NO3 −, NH4 +, and PO4) in idealized subterranean estuaries representing four end-members of oxic/anoxic aquifer and seawater redox

  15. Biogeochemical Modeling of the Second Rise of Atmospheric Oxygen

    Science.gov (United States)

    Smith, M.; Catling, D. C.; Claire, M.

    2014-12-01

    The second rise of atmospheric oxygen (~600 Ma) marked an increase of atmospheric pO2 from a poorly constrained value of 0.1% atmospheric level (PAL) in the early and mid Proterozoic to >10%PAL1. The event is important because it ushered in the modern era of animal life. To understand the evolution of Earth's habitability, it is therefore key to understand the cause of this 2nd rise. Here, we quantitatively examine possible causes for the 2nd rise of oxygen. We use a biogeochemical box model2 originally developed to calculate the oxygen evolution before and after the 1st rise of oxygen (~2.4 Ga). The Claire et al. (2006) model calculates the evolution of atmospheric oxygen and methane given production and loss fluxes associated with the oxygen, carbon, and iron cycles. Because the model was unable to drive pO2 to end-Proterozoic levels, the authors suggested that another buffer, such as sulfur, is needed to explain the 2nd rise of oxygen. The sulfur and oxygen cycles are tied through various biogeochemical interactions; therefore, once sulfur (as sulfate) began to accumulate in Proterozoic oceans, it likely began to heavily influence the oxygen cycle. We have added a sulfur biogeochemical cycle to this model, enabling exploration of mechanisms that buffer pO2 at intermediate levels in the Proterozoic and fail to do so in the Phanerozoic. Preliminary results show evolution of oxygen and methane that are consistent with geologic proxies. However, the model-generated 2nd rise of oxygen is dependent upon sulfur fluxes that have uncertain magnitudes, so we will present the sensitivity of our results to model assumptions while constraining scenarios for the 2nd rise of atmospheric O2. In the future, we will also integrate isotopic fractionation effects, which will allow comparison with isotopic data from sedimentary sulfides, carbonates, and organic carbon. 1Canfield, C., 2014, Treatise on Geochemistry, 197 2Claire, M.W., et al., 2006, Geobiology, 4, 239

  16. Biogeochemical cycling in terrestrial ecosystems - Modeling, measurement, and remote sensing

    Science.gov (United States)

    Peterson, D. L.; Matson, P. A.; Lawless, J. G.; Aber, J. D.; Vitousek, P. M.

    1985-01-01

    The use of modeling, remote sensing, and measurements to characterize the pathways and to measure the rate of biogeochemical cycling in forest ecosystems is described. The application of the process-level model to predict processes in intact forests and ecosystems response to disturbance is examined. The selection of research areas from contrasting climate regimes and sites having a fertility gradient in that regime is discussed, and the sites studied are listed. The use of remote sensing in determining leaf area index and canopy biochemistry is analyzed. Nitrous oxide emission is investigated by using a gas measurement instrument. Future research projects, which include studying the influence of changes on nutrient cycling in ecosystems and the effect of pollutants on the ecosystems, are discussed.

  17. Vadose zone attenuation of organic compounds at a crude oil spill site - Interactions between biogeochemical reactions and multicomponent gas transport

    Science.gov (United States)

    Molins, S.; Mayer, K.U.; Amos, R.T.; Bekins, B.A.

    2010-01-01

    Contaminant attenuation processes in the vadose zone of a crude oil spill site near Bemidji, MN have been simulated with a reactive transport model that includes multicomponent gas transport, solute transport, and the most relevant biogeochemical reactions. Dissolution and volatilization of oil components, their aerobic and anaerobic degradation coupled with sequential electron acceptor consumption, ingress of atmospheric O2, and the release of CH4 and CO2 from the smear zone generated by the floating oil were considered. The focus of the simulations was to assess the dynamics between biodegradation and gas transport processes in the vadose zone, to evaluate the rates and contributions of different electron accepting processes towards vadose zone natural attenuation, and to provide an estimate of the historical mass loss. Concentration distributions of reactive (O2, CH4, and CO2) and non-reactive (Ar and N2) gases served as key constraints for the model calibration. Simulation results confirm that as of 2007, the main degradation pathway can be attributed to methanogenic degradation of organic compounds in the smear zone and the vadose zone resulting in a contaminant plume dominated by high CH4 concentrations. In accordance with field observations, zones of volatilization and CH4 generation are correlated to slightly elevated total gas pressures and low partial pressures of N2 and Ar, while zones of aerobic CH4 oxidation are characterized by slightly reduced gas pressures and elevated concentrations of N2 and Ar. Diffusion is the most significant transport mechanism for gases in the vadose zone; however, the simulations also indicate that, despite very small pressure gradients, advection contributes up to 15% towards the net flux of CH4, and to a more limited extent to O2 ingress. Model calibration strongly suggests that transfer of biogenically generated gases from the smear zone provides a major control on vadose zone gas distributions and vadose zone carbon

  18. [A biogeochemical model for the Gulf of Nicoya, Costa Rica].

    Science.gov (United States)

    Tabash Blanco, Farid A

    2007-03-01

    In agreement with the Broecker and Penn two-boxes model, I generated a biogeochemical balance model for the Gulf of Nicoya (Guanacaste, Costa Rica) using two nutrient reservoirs: surface water and deep water. The mixing zone was located at a depth of 20 m. There is a balance between surface waters descending to the bottom and upwelling waters that carry nutrients and other chemical elements to the surface. The main source of nitrogen (nitrate), was the outlet of the Tempisque and Tárcoles rivers. The Gulf of Nicoya is a net source of Dissolved Inorganic Nitrogen (DIN) with an availability rate of 87 x 10(3) mol day(-1) in the dry season and 3044 x 10(3) mol day(-1)in the rainy season. Dissolved Inorganic Phosphate (DIP) was estimated in 27 mol day(-1) in the dry season and 207 mol day(-1) in the rainy season. The dynamics of these biolimited nutrients, in relation to runoff seasonal variations, fits the biological processes reported for the gulf, for example, for variations in primary productivity levels, and maturity and reproduction seasons for species with short and long life cycles.

  19. 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.

  20. 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

    , location and tracer. The high computational effort of a model evaluation was encountered by using the transport matrix method with spatial parallelization, advanced derivative-based optimization algorithms and a cost saving approximation of the derivative. Globalization techniques were used to overcome local minima. Due to a special software interface, coupling of arbitrary water-column biogeochemical models is possible. In the talk, we present the used methods together with results for this exemplary model.

  1. New HYDRUS Modules for Simulating Preferential Flow, Colloid-Facilitated Contaminant Transport, and Various Biogeochemical Processes in Soils

    Science.gov (United States)

    Simunek, J.; Sejna, M.; Jacques, D.; Langergraber, G.; Bradford, S. A.; van Genuchten, M. Th.

    2012-04-01

    We have dramatically expanded the capabilities of the HYDRUS (2D/3D) software package by developing new modules to account for processes not available in the standard HYDRUS version. These new modules include the DualPerm, C-Hitch, HP2/3, Wetland, and Unsatchem modules. The dual-permeability modeling approach of Gerke and van Genuchten [1993] simulating preferential flow and transport is implemented into the DualPerm module. Colloid transport and colloid-facilitated solute transport, the latter often observed for many contaminants, such as heavy metals, radionuclides, pharmaceuticals, pesticides, and explosives [Šimůnek et al., 2006] are implemented into the C-Hitch module. HP2 and HP3 are the two and three-dimensional alternatives of the HP1 module, currently available with HYDRUS-1D [Jacques and Šimůnek, 2005], that couple HYDRUS flow and transport routines with the generic geochemical model PHREEQC of Parkhurst and Appelo [1999]. The Wetland module includes two alternative approaches (CW2D of Langergraber and Šimůnek [2005] and CWM1 of Langergraber et al. [2009]) for modeling aerobic, anaerobic, and anoxic biogeochemical processes in natural and constructed wetlands. Finally, the Unsatchem module simulates the transport and reactions of major ions in a soil profile. Brief descriptions and an application of each module will be presented. Except for HP3, all modules simulate flow and transport processes in two-dimensional transport domains. All modules are fully supported by the HYDRUS graphical user interface. Further development of these modules, as well as of several other new modules (such as Overland), is still envisioned. Continued feedback from the research community is encouraged.

  2. Transport modeling

    Institute of Scientific and Technical Information of China (English)

    R.E. Waltz

    2007-01-01

    @@ There has been remarkable progress during the past decade in understanding and modeling turbulent transport in tokamaks. With some exceptions the progress is derived from the huge increases in computational power and the ability to simulate tokamak turbulence with ever more fundamental and physically realistic dynamical equations, e.g.

  3. 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

  4. Modeling the Effects of Hydrological and Biogeochemical Processes on Denitrification and Stream Nitrogen Losses in River Networks

    Science.gov (United States)

    Alexander, R. B.; Bohlke, J. K.; Boyer, E. W.; David, M. B.; Harvey, J. W.; Mulholland, P. J.; Seitzinger, S. P.; Tobias, C. R.; Tonitto, C.; Wollheim, W. M.

    2008-12-01

    Nitrogen flux in streams is the cumulative result of biogeochemical and hydrological processes that control the supply and transport of nitrogen in terrestrial and aquatic ecosystems. These processes include the effects of denitrification on stream nitrogen removal, which influence the quantities of nitrogen delivered to downstream coastal waters, where increases in nitrogen flux have contributed to eutrophication and hypoxic conditions globally in recent decades. Despite progress in measuring and modeling stream denitrification, few studies have attempted to unravel the coupled effects of biogeochemical (nitrate loadings, concentration, temperature) and hydrological (streamflow, depth, velocity) factors on denitrification and stream nitrogen losses in river networks over space and time. We apply a dynamic nitrogen transport model to assess biogeochemical vs. hydrological effects on seasonal nitrate removal by denitrification in the river networks of two watersheds. The watershed streams have widely differing levels of nitrate concentrations, but similar flows. Unique to our model is the nonlinear dependence of stream denitrification on nitrate concentration, streamflow, and temperature, as determined by regression relations estimated from more than 300 published field measurements available for a variety of U.S. streams. We use these empirical relations to parameterize the nitrogen transport model, which was then applied to the first- through fourth-order stream reaches of the two watersheds. The model results indicate that in-stream nitrate removal by denitrification becomes less efficient as nitrate concentrations and flows increase. This is denoted by the appreciably low percentage of the in-stream nitrate flux (expressed per unit length of stream channel) that is removed in reaches during the highest nitrate concentration and flow months (Feb. to June). The importance of biogeochemical factors (which includes effects of anthropogenic nitrogen loadings, land

  5. 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.

  6. Inconsistent strategies to spin up models in CMIP5: implications for ocean biogeochemical model performance assessment

    Science.gov (United States)

    Séférian, Roland; Gehlen, Marion; Bopp, Laurent; Resplandy, Laure; Orr, James C.; Marti, Olivier; Dunne, John P.; Christian, James R.; Doney, Scott C.; Ilyina, Tatiana; Lindsay, Keith; Halloran, Paul R.; Heinze, Christoph; Segschneider, Joachim; Tjiputra, Jerry; Aumont, Olivier; Romanou, Anastasia

    2016-05-01

    During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were made to systematically assess the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. In routine assessments model historical hindcasts were compared with available modern biogeochemical observations. However, these assessments considered neither how close modeled biogeochemical reservoirs were to equilibrium nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESMs) contributes to model-to-model differences in the simulated fields. We take advantage of a 500-year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and holds when confronted with a larger ensemble of CMIP5 models. This shows that drift has implications for performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to-model uncertainty. This requires more attention in future model intercomparison exercises in order to provide quantitatively more correct ESM results on marine biogeochemistry and carbon cycle feedbacks.

  7. Simple parameter estimation for complex models — Testing evolutionary techniques on 3-dimensional biogeochemical ocean models

    Science.gov (United States)

    Mattern, Jann Paul; Edwards, Christopher A.

    2017-01-01

    Parameter estimation is an important part of numerical modeling and often required when a coupled physical-biogeochemical ocean model is first deployed. However, 3-dimensional ocean model simulations are computationally expensive and models typically contain upwards of 10 parameters suitable for estimation. Hence, manual parameter tuning can be lengthy and cumbersome. Here, we present four easy to implement and flexible parameter estimation techniques and apply them to two 3-dimensional biogeochemical models of different complexities. Based on a Monte Carlo experiment, we first develop a cost function measuring the model-observation misfit based on multiple data types. The parameter estimation techniques are then applied and yield a substantial cost reduction over ∼ 100 simulations. Based on the outcome of multiple replicate experiments, they perform on average better than random, uninformed parameter search but performance declines when more than 40 parameters are estimated together. Our results emphasize the complex cost function structure for biogeochemical parameters and highlight dependencies between different parameters as well as different cost function formulations.

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

    DEFF Research Database (Denmark)

    Legarth, Jens Jakob Fosselius; Bjerrum, Christian J.

    An understanding of the processes-dynamics governing the development of submarine fine grained clinoforms relies often on correlation of proxies (grain-size trends, spectral gamma, microfossils, TOC, d13C etc.) to more proximal settings where relative sea-level changes are more easily detected...... the dynamic biogeochemical-stratigraphic models to our global carbon-nutrient cycle model will permit investigation of how marine productivity indicators and d13C can be use to refine the interpretations of submarine clinoform development and as correlation tools....... 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...

  9. Mechanisms driving estuarine water quality: A 3D biogeochemical model for informed management

    Science.gov (United States)

    Wild-Allen, Karen; Skerratt, Jenny; Whitehead, Jason; Rizwi, Farhan; Parslow, John

    2013-12-01

    Estuaries are amongst the most productive marine ecosystems of the world but are also some of the most degraded due to coastal urban development. Sparse sampling of complex interactions between estuarine physics, sediment transport, chemistry, and biology limits understanding of the processes controlling estuarine water quality and confounds active management. We use a 3D coupled hydrodynamic, sediment and biogeochemical model to identify the key mechanisms driving fine-scale fluctuations in water quality in a temperate micro-tidal salt wedge estuary [Derwent Estuary, Tasmania]. Model results are dynamically consistent with relatively sparse monitoring data collected over a seasonal cycle and are considered to be a plausible hypothesis of sub-monitoring scale processes occurring in the estuary. The model shows enhanced mixing of nutrients across the pycnocline downstream of the salt wedge front that supports a persistent phytoplankton bloom. The length and flow regime of the estuary results in nutrient recycling and retention in the estuarine circulation driving a decline in bottom water dissolved oxygen in the mid- and upper-reaches. A budget analysis of modelled nitrogen suggests high levels of denitrification are critical to the maintenance of existing water quality. Active estuarine management focused on the improvement of bottom water dissolved oxygen for ecological health reasons must either concurrently reduce anthropogenic nitrogen loads or be sure to maintain high levels of microbial denitrification for net water quality improvement.

  10. Marine biogeochemical responses to the North Atlantic Oscillation in a coupled climate model

    Science.gov (United States)

    Patara, Lavinia; Visbeck, Martin; Masina, Simona; Krahmann, Gerd; Vichi, Marcello

    2011-07-01

    In this study a coupled ocean-atmosphere model containing interactive marine biogeochemistry is used to analyze interannual, lagged, and decadal marine biogeochemical responses to the North Atlantic Oscillation (NAO), the dominant mode of North Atlantic atmospheric variability. The coupled model adequately reproduces present-day climatologies and NAO atmospheric variability. It is shown that marine biogeochemical responses to the NAO are governed by different mechanisms according to the time scale considered. On interannual time scales, local changes in vertical mixing, caused by modifications in air-sea heat, freshwater, and momentum fluxes, are most relevant in influencing phytoplankton growth through light and nutrient limitation mechanisms. At subpolar latitudes, deeper mixing occurring during positive NAO winters causes a slight decrease in late winter chlorophyll concentration due to light limitation and a 10%-20% increase in spring chlorophyll concentration due to higher nutrient availability. The lagged response of physical and biogeochemical properties to a high NAO winter shows some memory in the following 2 years. In particular, subsurface nutrient anomalies generated by local changes in mixing near the American coast are advected along the North Atlantic Current, where they are suggested to affect downstream chlorophyll concentration with 1 year lag. On decadal time scales, local and remote mechanisms act contemporaneously in shaping the decadal biogeochemical response to the NAO. The slow circulation adjustment, in response to NAO wind stress curl anomalies, causes a basin redistribution of heat, freshwater, and biogeochemical properties which, in turn, modifies the spatial structure of the subpolar chlorophyll bloom.

  11. A general paradigm to model reaction-based biogeochemical processes in batch systems

    Science.gov (United States)

    Fang, Yilin; Yeh, Gour-Tsyh; Burgos, William D.

    2003-04-01

    This paper presents the development and illustration of a numerical model of reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions. The objective is to provide a general paradigm for modeling reactive chemicals in batch systems, with expectations that it is applicable to reactive chemical transport problems. The unique aspects of the paradigm are to simultaneously (1) facilitate the segregation (isolation) of linearly independent kinetic reactions and thus enable the formulation and parameterization of individual rates one reaction by one reaction when linearly dependent kinetic reactions are absent, (2) enable the inclusion of virtually any type of equilibrium expressions and kinetic rates users want to specify, (3) reduce problem stiffness by eliminating all fast reactions from the set of ordinary differential equations governing the evolution of kinetic variables, (4) perform systematic operations to remove redundant fast reactions and irrelevant kinetic reactions, (5) systematically define chemical components and explicitly enforce mass conservation, (6) accomplish automation in decoupling fast reactions from slow reactions, and (7) increase the robustness of numerical integration of the governing equations with species switching schemes. None of the existing models to our knowledge has included these scopes simultaneously. This model (BIOGEOCHEM) is a general computer code to simulate biogeochemical processes in batch systems from a reaction-based mechanistic standpoint, and is designed to be easily coupled with transport models. To make the model applicable to a wide range of problems, programmed reaction types include aqueous complexation, adsorption-desorption, ion-exchange, oxidation-reduction, precipitation-dissolution, acid-base reactions, and microbial mediated reactions. In addition, user-specified reaction types can be programmed into the model. Any reaction can be treated as fast/equilibrium or slow

  12. Assimilation of Sea Color Data Into A Three Dimensional Biogeochemical Model: Sensitivity Experiments

    Science.gov (United States)

    Echevin, V.; Levy, M.; Memery, L.

    The assimilation of two dimensional sea color data fields into a 3 dimensional coupled dynamical-biogeochemical model is performed using a 4DVAR algorithm. The biogeochemical model includes description of nitrates, ammonium, phytoplancton, zooplancton, detritus and dissolved organic matter. A subset of the biogeochemical model poorly known parameters (for example,phytoplancton growth, mortality,grazing) are optimized by minimizing a cost function measuring misfit between the observations and the model trajectory. Twin experiments are performed with an eddy resolving model of 5 km resolution in an academic configuration. Starting from oligotrophic conditions, an initially unstable baroclinic anticyclone splits into several eddies. Strong vertical velocities advect nitrates into the euphotic zone and generate a phytoplancton bloom. Biogeochemical parameters are perturbed to generate surface pseudo-observations of chlorophyll,which are assimilated in the model in order to retrieve the correct parameter perturbations. The impact of the type of measurement (quasi-instantaneous, daily mean, weekly mean) onto the retrieved set of parameters is analysed. Impacts of additional subsurface measurements and of errors in the circulation are also presented.

  13. 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

  14. Modeling the Impact of Biogeochemical Hotspots and Hot Moments on Subsurface Carbon Fluxes from a Flood Plain Site

    Science.gov (United States)

    Arora, B.; Spycher, N.; Steefel, C. I.; King, E.; Conrad, M. E.

    2015-12-01

    Biogeochemical hotspots and hot moments are known to account for a high percentage of carbon and nutrient cycling within flood plain environments. To quantify the impact of these hotspots and hot moments on the carbon cycle, a 2D reactive transport model was developed for the saturated-unsaturated zone of a flood plain site in Rifle, CO. Previous studies have identified naturally reduced zones (NRZs) in the saturated zone of the Rifle site to be hotspots and important regions for subsurface biogeochemical cycling. Wavelet analysis of geochemical concentrations at the site suggested that hydrologic and temperature variations are hot moments and exert an important control on biogeochemical conditions in the Rifle aquifer. Here, we describe the development of a reactive transport model that couples hydrologic and biogeochemical processes to microbial functional distributions inferred from site-specific 'omic' data. The model includes microbial contributions from heterotrophic and chemolithoautotrophic processes. We use Monod based formulations to represent biomass formation and consider energy partitioning between catabolic and anabolic processes. We use this model to explore community emergence at the Rifle site and further constrain the extent and rates of nutrient uptake as well as abiotic and biotic reactions using stable carbon isotopes. Results from 2D model simulations with only abiotic reactions predict lower CO2 partial pressures in the unsaturated zone and severely underpredict (~200%) carbon fluxes to the river compared to simulations with chemolithoautotrophic pathways. δ13C-CO2 profiles also point to biotic sources for the locally observed high CO2 concentrations above NRZs. Results further indicate that groundwater carbon fluxes from the Rifle site to the river are underestimated by almost 180% (to 3.3 g m-2 d-1) when temperature fluctuations are ignored in the simulations. Preliminary results demonstrate the emergence of denitrifiers at specific depths

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Alexander, R.B.; Böhlke, J.K.; Boyer, E.W.; David, M.B.; Harvey, J.W.; Mulholland, P.J.; Seitzinger, S.P.; Tobias, C.R.; Tonitto, C.; Wollheim, W.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

  18. High resolution modelling of the biogeochemical processes in the eutrophic Loire River (France)

    Science.gov (United States)

    Minaudo, Camille; Moatar, Florentina; Curie, Florence; Gassama, Nathalie; Billen, Gilles

    2016-04-01

    A biogeochemical model was developed, coupling a physically based water temperature model (T-NET) with a semi-mechanistic biogeochemical model (RIVE, used in ProSe and Riverstrahler models) in order to assess at a fine temporal and spatial resolution the biogeochemical processes in the eutrophic Middle Loire hydrosystem (≈10 000 km², 3361 river segments). The code itself allows parallelized computing, which decreased greatly the calculation time (5 hours for simulating 3 years hourly). We conducted a daily survey during the period 2012-2014 at 2 sampling stations located in the Middle Loire of nutrients, chlorophyll pigments, phytoplankton and physic-chemical variables. This database was used as both input data (upstream Loire boundary) and validation data of the model (basin outlet). Diffuse and non-point sources were assessed based on a land cover analysis and WWTP datasets. The results appeared very sensible to the coefficients governing the dynamic of suspended solids and of phosphorus (sorption/desorption processes) within the model and some parameters needed to be estimated numerically. Both the Lagrangian point of view and fluxes budgets at the seasonal and event-based scale evidenced the biogeochemical functioning of the Loire River. Low discharge levels set up favorable physical conditions for phytoplankton growth (long water travel time, limited water depth, suspended particles sedimentation). Conversely, higher discharge levels highly limited the phytoplankton biomass (dilution of the colony, washing-out, limited travel time, remobilization of suspended sediments increasing turbidity), and most biogeochemical species were basically transferred downstream. When hydrological conditions remained favorable for phytoplankton development, P-availability was the critical factor. However, the model evidenced that most of the P in summer was recycled within the water body: on one hand it was assimilated by the algae biomass, and on the other hand it was

  19. Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

    Science.gov (United States)

    Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

    2013-12-01

    Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

  20. Weathering Pathways and Limitations in Biogeochemical Models: Application to Earth System Evolution

    OpenAIRE

    Mills, Benjamin

    2012-01-01

    Current biogeochemical box models for Phanerozoic climate are reviewed and reduced to a robust, modular system, allowing application to the Precambrian. It is shown that stabilisation of climate following a Neoproterozoic snowball Earth should take more than 10(7) years, due to long-term geological limitation of global weathering rates. The timescale matches the observed gaps between extreme glaciations at this time, suggesting that the late Neoproterozoic system was oscillating around a s...

  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.

  2. Biogeochemical Processes Responsible for the Enhanced Transport of Plutonium Under transient Unsaturated Ground Water Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Fred J. Molz, III

    2010-05-28

    To better understand longer-term vadose zone transport in southeastern soils, field lysimeter experiments were conducted at the Savannah River Site (SRS) near Aiken, SC, in the 1980s. Each of the three lysimeters analyzed herein contained a filter paper spiked with different Pu solutions, and they were left exposed to natural environmental conditions (including the growth of annual weed grasses) for 11 years. The resulting Pu activity measurements from each lysimeter core showed anomalous activity distributions below the source, with significant migration of Pu above the source. Such results are not explainable by adsorption phenomena alone. A transient variably saturated flow model with root water uptake was developed and coupled to a soil reactive transport model. Somewhat surprisingly, the fully transient analysis showed results nearly identical to those of a much simpler steady flow analysis performed previously. However, all phenomena studied were unable to produce the upward Pu transport observed in the data. This result suggests another transport mechanism such as Pu uptake by roots and upward transport due to transpiration. Thus, the variably saturated flow and reactive transport model was extended to include uptake and transport of Pu within the root xylem, along with computational methodology and results. In the extended model, flow velocity in the soil was driven by precipitation input along with transpiration and drainage. Water uptake by the roots determined the flow velocity in the root xylem, and this along with uptake of Pu in the transpiration stream drove advection and dispersion of the two Pu species in the xylem. During wet periods with high potential evapotranspiration, maximum flow velocities through the xylem would approached 600 cm/hr, orders of magnitude larger that flow velocities in the soil. Values for parameters and the correct conceptual viewpoint for Pu transport in plant xylem was uncertain. This motivated further experiments devoted

  3. The distribution of soil phosphorus for global biogeochemical modeling

    Directory of Open Access Journals (Sweden)

    X. Yang

    2012-11-01

    Full Text Available Phosphorus (P is a major element required for biological activity in terrestrial ecosystems. Although the total P content in most soils can be large, only a small fraction is available or in an organic form for biological utilization because it is bound either in incompletely weathered mineral particles, adsorbed on mineral surfaces, or, over the time of soil formation, made unavailable by secondary mineral formation (occluded. In order to adequately represent phosphorus availability in global biogeochemistry-climate models, a representation of the amount and form of P in soils globally is required. We develop an approach that builds on existing knowledge of soil P processes and databases of parent material and soil P measurements to provide spatially explicit estimates of different forms of soil P on the global scale. We assembled data on the various forms of phosphorus in soils globally, chronosequence information, and several global spatial databases to develop a map of total soil P and the distribution among mineral bound, labile, organic, occluded, and secondary P forms in soils globally. The amount of P, to 50 cm soil depth, in soil labile, organic, occluded, and secondary pools is 3.5 ± 3, 8.7 ± 6, 13.2 ± 9, and 3.3 ± 2 Pg P respectively. The amount in soil mineral particles to the same depth is estimated at 12.5 ± 9 Pg P for a global soil total of 41.2 ± 20 Pg P. The large uncertainty in our estimates reflects our limited understanding of the processes controlling soil P transformations during pedogenesis and lack of measurements of soil P. In spite of the large uncertainty, the estimated global spatial variation and distribution of different soil P forms presented in this study will be useful for global biogeochemistry models that include P as a limiting element in biological production by providing initial estimates of the available soil P for plant uptake and microbial utilization.

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

    DEFF Research Database (Denmark)

    Muchamad, Al Azhar

    slope and deeper depths. The coupled model may potentially serve as a robust tool in investigation of the dynamics of oceanic biogeochemical cycle throughout Earth history as well as a practical method to quantified storage of carbon flux into the ocean across the continental margins under present day...... in eastern boundary upwelling systems is an example of the most productive ocean waters over continental margins where intense supply of nutrients occur from deeper ocean waters. Interesting questions arise related to the biogeochemical cycles in such upwelling systems; such as 1) how the recently observed...... active but cryptic sulfur cycle possibly is coupled to the nitrogen cycle in an oxygen-minimum-zone (OMZ), 2) what is the relation between the shelf–ocean exchange, continental shelf width and development of the observed bottom water anoxia/euxinia associated with different configurations of continental...

  5. Data assimilation of physical and chlorophyll a observations in the California Current System using two biogeochemical models

    Science.gov (United States)

    Mattern, Jann Paul; Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2017-01-01

    Biogeochemical numerical models coupled to physical ocean circulation models are commonly combined with data assimilation in order to improve the models' state or parameter estimates. Yet much still needs to be learned about important aspects of biogeochemical data assimilation, such as the effect of model complexity and the importance of more realistic model formulations on assimilation results. In this study, 4D-Var-based state estimation is applied to two biogeochemical ocean models: a simple NPZD model with 4 biogeochemical variables (including 1 phytoplankton, 1 zooplankton) and the more complex NEMURO model, containing 11 biogeochemical variables (including 2 phytoplankton, 3 zooplankton). Both models are coupled to a 3-dimensional physical ocean circulation model of the U.S. west coast based on the Regional Ocean Modelling System (ROMS). Chlorophyll satellite observations and physical observations are assimilated into the model, yielding substantial improvements in state estimates for the observed physical and biogeochemical variables in both model formulations. In comparison to the simpler NPZD model, NEMURO shows a better overall fit to the observations. The assimilation also results in small improvements for simulated nitrate concentrations in both models and no apparent degradation of the output for other unobserved variables. The forecasting skill of the biogeochemical models is strongly linked to model performance without data assimilation: for both models, the improved fit obtained through assimilation degrades at similar relative rates, but drops to different absolute levels. Despite the better performance of NEMURO in our experiments, the choice of model and desired level of complexity should depend on the model application and the data available for assimilation.

  6. The distribution of soil phosphorus for global biogeochemical modeling

    Directory of Open Access Journals (Sweden)

    X. Yang

    2013-04-01

    Full Text Available Phosphorus (P is a major element required for biological activity in terrestrial ecosystems. Although the total P content in most soils can be large, only a small fraction is available or in an organic form for biological utilization because it is bound either in incompletely weathered mineral particles, adsorbed on mineral surfaces, or, over the time of soil formation, made unavailable by secondary mineral formation (occluded. In order to adequately represent phosphorus availability in global biogeochemistry–climate models, a representation of the amount and form of P in soils globally is required. We develop an approach that builds on existing knowledge of soil P processes and databases of parent material and soil P measurements to provide spatially explicit estimates of different forms of naturally occurring soil P on the global scale. We assembled data on the various forms of phosphorus in soils globally, chronosequence information, and several global spatial databases to develop a map of total soil P and the distribution among mineral bound, labile, organic, occluded, and secondary P forms in soils globally. The amount of P, to 50cm soil depth, in soil labile, organic, occluded, and secondary pools is 3.6 ± 3, 8.6 ± 6, 12.2 ± 8, and 3.2 ± 2 Pg P (Petagrams of P, 1 Pg = 1 × 1015g respectively. The amount in soil mineral particles to the same depth is estimated at 13.0 ± 8 Pg P for a global soil total of 40.6 ± 18 Pg P. The large uncertainty in our estimates reflects our limited understanding of the processes controlling soil P transformations during pedogenesis and a deficiency in the number of soil P measurements. In spite of the large uncertainty, the estimated global spatial variation and distribution of different soil P forms presented in this study will be useful for global biogeochemistry models that include P as a limiting element in biological production by providing initial estimates of the available soil P for plant uptake

  7. Parameter sensitivity study of the biogeochemical model in the China coastal seas

    Institute of Scientific and Technical Information of China (English)

    JI Xuanliang; LIU Guimei; GAO Shan; WANG Hui

    2015-01-01

    In order to develop a coupled basin scale model of ocean circulation and biogeochemical cycling, we present a biogeochemical model including 12 components to study the ecosystem in the China coastal seas (CCS). The formulation of phytoplankton mortality and zooplankton growth are modified according to biological characteristics of CCS.The four sensitivity biological parameters, zooplankton assimilation efficiency rate (ZooAE_N), zooplankton basal metabolism rate (ZooBM), maximum specific growth rate of zooplankton (μ20) and maximum chlorophyll to carbon ratio (Chl2C_m) are obtained in sensitivity experiments for the phytoplankton, and experiments about the parameterμ20, half-saturation for phytoplankton NO3 uptake ( KNO3 ) and remineralization rate of small detritusN (SDeRRN) are conducted. The results demonstrate that the biogeochemical model is quite sensitive to the zooplankton grazing parameter when it ranges from 0.1 to 1.2 d–1. The KNO3 and SDeRRN also play an important role in determining the nitrogen cycle within certain ranges.The sensitive interval of KNO3 is from 0.1 to 1.5 (mmol/m3)–1, and interval of SEdRRN is from 0.01 and 0.1 d–1. The observational data from September 1998 to July 2000 obtained at SEATS station are used to validate the performance of biological model after parameters optimization. The results show that the modified model has a good capacity to reveal the biological process features, and the sensitivity analysis can save computational resources greatly during the model simulation.

  8. 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

  9. A coupled biogeochemical-Dynamic Energy Budget model as a tool for managing fish production ponds.

    Science.gov (United States)

    Serpa, Dalila; Pousão-Ferreira, Pedro; Caetano, Miguel; Cancela da Fonseca, Luís; Dinis, Maria Teresa; Duarte, Pedro

    2013-10-01

    The sustainability of semi-intensive aquaculture relies on management practices that simultaneously improve production efficiency and minimize the environmental impacts of this activity. The purpose of the present work was to develop a mathematical model that reproduced the dynamics of a semi-intensive fish earth pond, to simulate different management scenarios for optimizing fish production. The modeling approach consisted of coupling a biogeochemical model that simulated the dynamics of the elements that are more likely to affect fish production and cause undesirable environmental impacts (nitrogen, phosphorus and oxygen) to a fish growth model based on the Dynamic Energy Budget approach. The biogeochemical sub-model successfully simulated most water column and sediment variables. A good model fit was also found between predicted and observed white seabream (Diplodus sargus) growth data over a production cycle. In order to optimize fish production, different management scenarios were analysed with the model (e.g. increase stocking densities, decrease/increase water exchange rates, decrease/increase feeding rates, decrease phosphorus content in fish feeds, increase food assimilation efficiency and decrease pellets sinking velocity) to test their effects on the pond environment as well as on fish yields and effluent nutrient discharges. Scenarios were quantitatively evaluated and compared using the Analytical Hierarchical Process (AHP) methodology. The best management options that allow the maximization of fish production while maintaining a good pond environment and minimum impacts on the adjacent coastal system were to double standard stocking densities and to improve food assimilation efficiency.

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

    Directory of Open Access Journals (Sweden)

    Y. Wu

    2013-03-01

    Full Text Available 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.

  11. 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.

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

    NARCIS (Netherlands)

    Bouwman, A.F.; Bierkens, M.F.P.; Griffioen, J.; Hefting, M.M.; Middelburg, J.J.; Middelkoop, H.; Slomp, C.P.

    2013-01-01

    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

  13. Modeling ocean circulation and biogeochemical variability in the Gulf of Mexico

    Science.gov (United States)

    Xue, Z.; He, R.; Fennel, K.; Cai, W.-J.; Lohrenz, S.; Hopkinson, C.

    2013-11-01

    A three-dimensional coupled physical-biogeochemical model is applied to simulate and examine temporal and spatial variability of circulation and biogeochemical cycling in the Gulf of Mexico (GoM). The model is driven by realistic atmospheric forcing, open boundary conditions from a data assimilative global ocean circulation model, and observed freshwater and terrestrial nitrogen input from major rivers. A 7 yr model hindcast (2004-2010) was performed, and validated against satellite observed sea surface height, surface chlorophyll, and in situ observations including coastal sea level, ocean temperature, salinity, and dissolved inorganic nitrogen (DIN) concentration. The model hindcast revealed clear seasonality in DIN, phytoplankton and zooplankton distributions in the GoM. An empirical orthogonal function analysis indicated a phase-locked pattern among DIN, phytoplankton and zooplankton concentrations. The GoM shelf nitrogen budget was also quantified, revealing that on an annual basis the DIN input is largely balanced by the removal through denitrification (an equivalent of ~ 80% of DIN input) and offshore exports to the deep ocean (an equivalent of ~ 17% of DIN input).

  14. Modeling ocean circulation and biogeochemical variability in the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Z. Xue

    2013-05-01

    Full Text Available A three-dimensional coupled physical-biogeochemical model is applied to simulate and examine temporal and spatial variability of circulation and biogeochemical cycling in the Gulf of Mexico (GoM. The model is driven by realistic atmospheric forcing, open boundary conditions from a data assimilative global ocean circulation model, and observed freshwater and terrestrial nutrient input from major rivers. A 7 yr model hindcast (2004–2010 was performed, and validated against satellite observed sea surface height, surface chlorophyll, and in-situ observations including coastal sea-level, ocean temperature, salinity, and nutrient concentration. The model hindcast revealed clear seasonality in nutrient, phytoplankton and zooplankton distributions in the GoM. An Empirical Orthogonal Function analysis indicated a phase-locked pattern among nutrient, phytoplankton and zooplankton concentrations. The GoM shelf nutrient budget was also quantified, revealing that on an annual basis ~80% of nutrient input was denitrified on the shelf and ~17% was exported to the deep ocean.

  15. 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

    Glaciers and ice sheets in Polar and alpine regions are retreating in response to recent climate warming, exposing terrestrial ecosystems that have been locked under the ice for thousands of years. Exposed soils exhibit successional characteristics that can be characterised using a chronosequence approach. Decades of empirical research in glacier forefields has shown that soils are quickly colonised by microbes which drive biogeochemical cycling of elements and affect soil properties including nutrient concentrations, carbon fluxes and soil stability (Bradley et al, 2014). The characterisation of these soils is important for our understanding of the cycling of organic matter under extreme environmental and nutrient limiting conditions, and their potential contribution to global biogeochemical cycles. This is particularly important as these new areas will become more geographically expansive with continued ice retreat. SHIMMER (Soil biogeocHemIcal Model of Microbial Ecosystem Response) (Bradley et al, 2015) is a new mathematical model that simulates biogeochemical and microbial dynamics in glacier forefields. The model captures, explores and predicts the growth of different microbial groups (classified by function), and the associated cycling of carbon, nitrogen and phosphorus along a chronosequence. SHIMMER improves typical soil model formulations by including explicit representation of microbial dynamics, and those processes which are shown to be important for glacier forefields. For example, we categorise microbial groups by function to represent the diversity of soil microbial communities, and include the different metabolic needs and physiological pathways of microbial organisms commonly found in glacier forefields (e.g. microbes derived from underneath the glacier, typical soil bacteria, and microbes that can fix atmospheric nitrogen and assimilate soil nitrogen). Here, we present data from a study where we integrated modelling using SHIMMER with empirical

  16. A new biogeochemical model to simulate regional scale carbon emission from lakes, ponds and wetlands

    Science.gov (United States)

    Bayer, Tina; Brakebusch, Matthias; Gustafsson, Erik; Beer, Christian

    2016-04-01

    Small aquatic systems are receiving increasing attention for their role in global carbon cycling. For instance, lakes and ponds in permafrost are net emitters of carbon to the atmosphere, and their capacity to process and emit carbon is significant on a landscape scale, with a global flux of 8-103 Tg methane per year which amounts to 5%-30% of all natural methane emissions (Bastviken et al 2011). However, due to the spatial and temporal highly localised character of freshwater methane emissions, fluxes remain poorly qualified and are difficult to upscale based on field data alone. While many models exist to model carbon cycling in individual lakes and ponds, we perceived a lack of models that can work on a larger scale, over a range of latitudes, and simulate regional carbon emission from a large number of lakes, ponds and wetlands. Therefore our objective was to develop a model that can simulate carbon dioxide and methane emission from freshwaters on a regional scale. Our resulting model provides an additional tool to assess current aquatic carbon emissions as well as project future responses to changes in climatic drivers. To this effect, we have combined an existing large-scale hydrological model (the Variable Infiltration Capacity Macroscale Hydrologic Model (VIC), Liang & Lettenmaier 1994), an aquatic biogeochemical model (BALTSEM, Savchuk et al., 2012; Gustafsson et al., 2014) and developed a new methane module for lakes. The resulting new process-based biogeochemical model is designed to model aquatic carbon emission on a regional scale, and to perform well in high-latitude environments. Our model includes carbon, oxygen and nutrient cycling in lake water and sediments, primary production and methanogenesis. Results of calibration and validation of the model in two catchments (Torne-Kalix in Northern Sweden and of a large arctic river catchment) will be presented.

  17. A mercury transport and fate model (LM2-mercury) for mass budget assessment of mercury cycling in Lake Michigan

    Science.gov (United States)

    LM2-Mercury, a mercury mass balance model, was developed to simulate and evaluate the transport, fate, and biogeochemical transformations of mercury in Lake Michigan. The model simulates total suspended solids (TSS), disolved organic carbon (DOC), and total, elemental, divalent, ...

  18. How to `Elk-test' biogeochemical models in a data rich world? (Invited)

    Science.gov (United States)

    Reichstein, M.; Ciais, P.; Seneviratne, S. I.; Carvalhais, N.; Dalmonech, D.; Jung, M.; Luo, Y.; Mahecha, M. D.; Moffat, A. M.; Tomelleri, E.; Zaehle, S.

    2010-12-01

    Process-oriented biogeochemical models are a primary tool that has been used to project future states of climate and ecosystems in the earth system in response to anthropogenic and other forcing, and receive tremendous attention also in the context us the planned assessment report AR5 by the IPCC. However, model intercomparison and data-model comparison studies indicate large uncertainties regarding predictions of global interactions between atmosphere and biosphere. Rigorous scientific testing of these models is essential but very challenging, largely because neither it is technically and ethically possible to perform global earth-scale experiments, nor do we have replicate Earths for hypothesis testing. Hence, model evaluations have to rely on monitoring data such as ecological observation networks, global remote sensing or short-term and small-scale experiments. Here, we critically examine strategies of how model evaluations have been performed with a particular emphasis on terrestrial ecosystems. Often weak ‘validations’ are being presented which do not take advantage of all the relevant information in the observed data, but also apparent falsifications are made, that are hampered by a confusion of system processes with system behavior. We propose that a stronger integration of recent advances in pattern-oriented and system-oriented methodologies will lead to more satisfying earth system model evaluation and development, and show a few enlightening examples from terrestrial biogeochemical modeling and other disciplines. Moreover it is crucial to take advantage of the multidimensional nature of arising earth observation data sets which should be matched by models simultaneously, instead of relying on univariate simple comparisons. A new critical model evaluation is needed to improve future IPCC assessments in order to reduce uncertainties by distinguishing plausible simulation trajectories from fairy tales.

  19. UZ Colloid Transport Model

    Energy Technology Data Exchange (ETDEWEB)

    M. McGraw

    2000-04-13

    The UZ Colloid Transport model development plan states that the objective of this Analysis/Model Report (AMR) is to document the development of a model for simulating unsaturated colloid transport. This objective includes the following: (1) use of a process level model to evaluate the potential mechanisms for colloid transport at Yucca Mountain; (2) Provide ranges of parameters for significant colloid transport processes to Performance Assessment (PA) for the unsaturated zone (UZ); (3) Provide a basis for development of an abstracted model for use in PA calculations.

  20. 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.

  1. Empirical approaches to more accurately predict benthic-pelagic coupling in biogeochemical ocean models

    Science.gov (United States)

    Dale, Andy; Stolpovsky, Konstantin; Wallmann, Klaus

    2016-04-01

    The recycling and burial of biogenic material in the sea floor plays a key role in the regulation of ocean chemistry. Proper consideration of these processes in ocean biogeochemical models is becoming increasingly recognized as an important step in model validation and prediction. However, the rate of organic matter remineralization in sediments and the benthic flux of redox-sensitive elements are difficult to predict a priori. In this communication, examples of empirical benthic flux models that can be coupled to earth system models to predict sediment-water exchange in the open ocean are presented. Large uncertainties hindering further progress in this field include knowledge of the reactivity of organic carbon reaching the sediment, the importance of episodic variability in bottom water chemistry and particle rain rates (for both the deep-sea and margins) and the role of benthic fauna. How do we meet the challenge?

  2. 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

  3. Spatial modeling of coupled hydrologic-biogeochemical processes for the Southern Sierra Critical Zone Observatory

    Science.gov (United States)

    Tague, C.

    2007-12-01

    One of the primary roles of modeling in critical zone research studies is to provide a framework for integrating field measurements and theory and for generalizing results across space and time. In the Southern Sierra Critical Zone Observatory (SCZO), significant spatial heterogeneity associated with mountainous terrain combined with high inter-annual and seasonal variation in climate, necessitates the use of spatial-temporal models for generating landscape scale understanding and predictions. Science questions related to coupled hydrologic and biogeochemical fluxes within the critical zone require a framework that can account for multiple and interacting processes. One of the core tools for the SCZO will be RHESSYs (Regional hydro-ecologic simulation system). RHESSys is an existing GIS-based model of hydrology and biogeochemical cycling. For the SCZO, we use RHESSys as an open-source, objected oriented model that can be extended to incorporate findings from field-based monitoring and analysis. We use the model as a framework for data assimilation, spatial-temporal interpolation, prediction, and scenario and hypothesis generation. Here we demonstrate the use of RHESSys as a hypothesis generation tool. We show how initial RHESSys predictions can be used to estimate when and where connectivity within the critical zone will lead to significant spatial or temporal gradients in vegetation carbon and moisture fluxes. We use the model to explore the potential implications of heterogeneity in critical zone controls on hydrologic processes at two scales: micro and macro. At the micro scale, we examine the role of preferential flowpaths. At the macro scale we consider the importance of upland-riparian zone connectivity. We show how the model can be used to design efficient field experiments by, a-priori providing quantitative estimate of uncertainty and highlighting when and where measurements might most effectively reduce that uncertainty.

  4. 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 L

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    A. Ridgwell

    2006-08-01

    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 is based around a simple single nutrient (phosphate control on biological productivity. The addition of ocean-sediment interactions is presented elsewhere (Ridgwell and Hargreaves, 2006.

    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

  7. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.

    Science.gov (United States)

    Ho, Adrian; Angel, Roey; Veraart, Annelies J; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L E

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.

  8. Marine regime shifts in ocean biogeochemical models: a case study in the Gulf of Alaska

    Science.gov (United States)

    Beaulieu, Claudie; Cole, Harriet; Henson, Stephanie; Yool, Andrew; Anderson, Tom; de Mora, Lee; Buitenhuis, Erik T.; Butenschön, Momme; Totterdell, Ian J.; Icarus Allen, J.

    2016-08-01

    Regime shifts have been reported in many marine ecosystems, and are often expressed as an abrupt change occurring in multiple physical and biological components of the system. In the Gulf of Alaska, a regime shift in the late 1970s was observed, indicated by an abrupt increase in sea surface temperature and major shifts in the catch of many fish species. A thorough understanding of the extent and mechanisms leading to such regime shifts is challenged by data paucity in time and space. We investigate the ability of a suite of ocean biogeochemistry models of varying complexity to simulate regime shifts in the Gulf of Alaska by examining the presence of abrupt changes in time series of physical variables (sea surface temperature and mixed-layer depth), nutrients and biological variables (chlorophyll, primary productivity and plankton biomass) using change-point analysis. Our results show that some ocean biogeochemical models are capable of simulating the late 1970s shift, manifested as an abrupt increase in sea surface temperature followed by an abrupt decrease in nutrients and biological productivity. Models from low to intermediate complexity simulate an abrupt transition in the late 1970s (i.e. a significant shift from one year to the next) while the transition is smoother in higher complexity models. Our study demonstrates that ocean biogeochemical models can successfully simulate regime shifts in the Gulf of Alaska region. These models can therefore be considered useful tools to enhance our understanding of how changes in physical conditions are propagated from lower to upper trophic levels.

  9. Biogeochemical Cycling

    Science.gov (United States)

    Bebout, Brad; Fonda, Mark (Technical Monitor)

    2002-01-01

    This lecture will introduce the concept of biogeochemical cycling. The roles of microbes in the cycling of nutrients, production and consumption of trace gases, and mineralization will be briefly introduced.

  10. Modeling the fate of nitrogen on the catchment scale using a spatially explicit hydro-biogeochemical simulation system

    Science.gov (United States)

    Klatt, S.; Butterbach-Bahl, K.; Kiese, R.; Haas, E.; Kraus, D.; Molina-Herrera, S. W.; Kraft, P.

    2015-12-01

    The continuous growth of the human population demands an equally growing supply for fresh water and food. As a result, available land for efficient agriculture is constantly diminishing which forces farmers to cultivate inferior croplands and intensify agricultural practices, e.g., increase the use of synthetic fertilizers. This intensification of marginal areas in particular will cause a dangerous rise in nitrate discharge into open waters or even drinking water resources. In order to reduce the amount of nitrate lost by surface runoff or lateral subsurface transport, bufferstrips have proved to be a valuable means. Current laws, however, promote rather static designs (i.e., width and usage) even though a multitude of factors, e.g., soil type, slope, vegetation and the nearby agricultural management, determines its effectiveness. We propose a spatially explicit modeling approach enabling to assess the effects of those factors on nitrate discharge from arable lands using the fully distributed hydrology model CMF coupled to the complex biogeochemical model LandscapeDNDC. Such a modeling scheme allows to observe the displacement of dissolved nutrients in both vertical and horizontal directions and serves to estimate both their uptake by the vegetated bufferstrip and loss to the environment. First results indicate a significant reduction of nitrate loss in the presence of a bufferstrip (2.5 m). We show effects induced by various buffer strip widths and plant cover on the nitrate retention.

  11. 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.

    2015-02-01

    We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemical-ecosystem in a dynamic three-dimensional physical framework. The radiative transfer component resolves spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (the phytoplankton community, 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 north-south 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 conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, and the crucial feedbacks between the light field and the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at short wavelengths and in more productive waters, phytoplankton absorption is especially important at the deep chlorophyll a (Chl a) maximum, and absorption by water molecules is relatively most important in the highly oligotrophic gyres. Sensitivity experiments in which absorption by any of the optical constituents was increased led to a decrease in the size of the oligotrophic regions of the subtropical gyres: lateral nutrient supplies were enhanced as a result of decreasing high latitude productivity. Scattering does not as strongly affect the ecosystem and biogeochemistry fields within the water column but is important for setting the surface upwelling irradiance, and hence sea surface reflectance. Having a model capable of capturing bio-optical feedbacks will be important for

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

    Directory of Open Access Journals (Sweden)

    O. Aumont

    2015-02-01

    Full Text Available PISCES-v2 is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (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 twenty-four 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 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 silicium quotas are variable and 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 NEMO and 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.

  13. A quantitative assessment of methane cycling in Hikurangi Margin sediments (New Zealand) using geophysical imaging and biogeochemical modeling

    Science.gov (United States)

    Luo, Min; Dale, Andrew W.; Haffert, Laura; Haeckel, Matthias; Koch, Stephanie; Crutchley, Gareth; De Stigter, Henko; Chen, Duofu; Greinert, Jens

    2016-12-01

    Takahe seep, located on the Opouawe Bank, Hikurangi Margin, is characterized by a well-defined subsurface seismic chimney structure ˜80,500 m2 in area. Subseafloor geophysical data based on acoustic anomaly layers indicated the presence of gas hydrate and free gas layers within the chimney structure. Reaction-transport modeling was applied to porewater data from 11 gravity cores to constrain methane turnover rates and benthic methane fluxes in the upper 10 m. Model results show that methane dynamics were highly variable due to transport and dissolution of ascending gas. The dissolution of gas (up to 3761 mmol m-2 yr-1) dwarfed the rate of methanogenesis within the simulated sediment column (2.6 mmol m-2 yr-1). Dissolved methane is mainly consumed by anaerobic oxidation of methane (AOM) at the base of the sulfate reduction zone and trapped by methane hydrate formation below it, with maximum rates in the central part of the chimney (946 and 2420 mmol m-2 yr-1, respectively). A seep-wide methane budget was constrained by combining the biogeochemical model results with geophysical data and led to estimates of AOM rates, gas hydrate formation, and benthic dissolved methane fluxes of 3.68 × 104 mol yr-1, 73.85 × 104 mol yr-1, and 1.19 × 104 mol yr-1, respectively. A much larger flux of methane probably escapes in gaseous form through focused bubble vents. The approach of linking geochemical model results with spatial geophysical data put forward here can be applied elsewhere to improve benthic methane turnover rates from limited single spot measurements to larger spatial scales.

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

    Directory of Open Access Journals (Sweden)

    I. Epicoco

    2015-12-01

    Full Text Available 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.

  15. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    Energy Technology Data Exchange (ETDEWEB)

    Stegen, James C.; Konopka, Allan; McKinely, Jim; Murray, Christopher J.; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-07-29

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, diversity, and community composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial diversity—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  16. 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

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

    OpenAIRE

    Lee, Younjoo J.; Matrai, Patricia A.; Friedrichs, Marjorie A. M; Vincent S. Saba; Aumont, Olivier; Babin, Marcel; Buitenhuis, Erik T.; Chevallier, Matthieu; de Mora, Lee; Dessert, Morgane; Dunne, John P.; Ellingsen, Ingrid; Feldman, Doron; Frouin, Robert; Gehlen, Marion

    2016-01-01

    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 (i...

  18. 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.

  19. 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

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

    Directory of Open Access Journals (Sweden)

    T. Arsouze

    2009-06-01

    Full Text Available The decoupling of behaviour observed between Nd isotopic composition (Nd IC, also referred as εNd and Nd concentration 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, non-conservative behaviour typical of nutrients affected by scavenging in surface waters and remineralisation at depth. In addition, recent studies suggested that 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 did not simulates the real input/output fluxes of Nd to the ocean, and therefore did prevent from crucial information to apprehend the "Nd paradox". In this study, we investigate this paradox on a global scale using for the first time a fully prognostic coupled dynamical/biogeochemical model and an explicit representation of the sources and sinks to simulate the Nd oceanic cycle. Sources considered are dissolved river fluxes, atmospheric dusts and margin sediment re-dissolution. Sinks are scavenging by settling particles. This model satisfyingly simulate the global Nd oceanic cycle, and produces realistic distribution of Nd concentration and isotopic composition, though a slight overestimation of Nd concentrations in the deep Pacific Ocean, likely revealing an underestimation of the particle fields by the biogeochemical model. Our results underlines that 1 vertical cycling (scavenging/remineralisation is absolutely necessary to satisfyingly simulate both concentration and εNd, and 2 BE is the dominant Nd source

  1. LiDAR-derived spatial models of hydrological and biogeochemical source areas to improve estimates of terrestrial-aquatic mercury export in northern forested landscapes

    Science.gov (United States)

    Richardson, M. C.; Mitchell, C. P.; Branfireun, B. A.; Kolka, R. K.; Fortin, M.

    2010-12-01

    Recent research on watershed mercury (Hg) and dissolved organic carbon (DOC) cycling in headwater research catchments in south-central Ontario, northwestern Ontario and northern Minnesota points to the critical role of discrete landscape elements in dictating rainfall-runoff response and the mobilization of DOC, Hg and methyl-mercury (MeHg) to downstream surface-waters. An overview of this research will be presented, emphasising two newly developed techniques used to extract hydrological and biogeochemical sources areas from airborne Light Detection and Ranging (LiDAR) surveys. First, hydrogeomorphic edge-detection was used to partition the landscape into discrete functional units based on local drainage conditions. From this initial landscape segmentation, forested wetlands and non-wetland saturation prone depressional areas were classified and extracted using classification and regression tree models based on LiDAR-derived geomorphic indices aggregated to the scale of individual landscape elements. Following this procedure, a characteristic morphology analysis was conducted from LiDAR bare-earth returns to quantitatively define the upland-peatland interfaces within all peatlands greater than 0.2 ha. These two terrain analysis techniques produced a number of functionally different landscape element classes that were subsequently used in the south-central Ontario study sites to test statistical models of terrestrial-aquatic fluxes of DOC, total Hg and MeHg over different time-scales. The regression models indicate that functional differences exist among landscape element classes with respect to their solute source-strengths and runoff generating potentials, and showed marked improvements over previous landscape models of hydrological and biogeochemical source areas in northern forested regions. LiDAR remote sensing can therefore be used to refine estimates of biogeochemical transformations and solute transport at the landscape scale, thus improving our

  2. Reconciling surface ocean productivity, export fluxes and sediment composition in a global biogeochemical ocean model

    Directory of Open Access Journals (Sweden)

    M. Gehlen

    2006-01-01

    Full Text Available This study focuses on an improved representation of the biological soft tissue pump in the global three-dimensional biogeochemical ocean model PISCES. We compare three parameterizations of particle dynamics: (1 the model standard version including two particle size classes, aggregation-disaggregation and prescribed sinking speed; (2 an aggregation-disaggregation model with a particle size spectrum and prognostic sinking speed; (3 a mineral ballast parameterization with no size classes, but prognostic sinking speed. In addition, the model includes a description of surface sediments and organic carbon early diagenesis. Model output is compared to data or data based estimates of ocean productivity, pe-ratios, particle fluxes, surface sediment bulk composition and benthic O2 fluxes. Model results suggest that different processes control POC fluxes at different depths. In the wind mixed layer turbulent particle coagulation appears as key process in controlling pe-ratios. Parameterization (2 yields simulated pe-ratios that compare well to observations. Below the wind mixed layer, POC fluxes are most sensitive to the intensity of zooplankton flux feeding, indicating the importance of zooplankton community composition. All model parameters being kept constant, the capability of the model to reproduce yearly mean POC fluxes below 2000 m and benthic oxygen demand does at first order not dependent on the resolution of the particle size spectrum. Aggregate formation appears essential to initiate an intense biological pump. At great depth the reported close to constant particle fluxes are most likely the result of the combined effect of aggregate formation and mineral ballasting.

  3. STUDY OF CHLOROPHYLL-A DISTRIBUTIONS IN LOMBOK STRAIT USING BIOGEOCHEMICAL MODEL BASED ON REGIONAL OCEAN MODELLING SYSTEM (ROMS

    Directory of Open Access Journals (Sweden)

    KADEK ARY ANGGRAENI

    2015-06-01

    Full Text Available Regional Ocean Modelling System (ROMS has been intended to be a multi-purpose, multi-disciplinary oceanic modeling tool. The Biogeochemical model have coupled to ROMS consists of a system of seven coupled partial differential equations that include: nitrate, ammonium, small and large detritus, phytoplanJ..'ton, zooplankton, and a dynamic phytoplanJ..-ton carbon to chlorophyll ratio. The study of distribution patterns of chlorophyll-a in Lombok Strait (-7 °N - ·10 •sand 114 "E - 117 °E in 2006 was analyzed using the Biogeochemical model based on ROMS. The results show that low chlorophyll-a distributions (0.20 mgChl-a/m3 observed in Lombok Strait in ,January. Chlorophyll-a estimated around the southern part of Bali Strait and low chlorophyll-a distribution in upper layer of the Lomhok Strait. Chlorophyll-a of the booming (0.32 mgChl-a/m3 observed in August. The northeast current direction moves to the west and southern part of research area through Lombok Strait. The highest chlorophyll-a concentration estimated in the northern and southwestern part of Bali Tsland and also in the southern part of Lombok Island. During dry monsoon, southeasterly wind blow from Australia generates upwelling process (low temperature and nutrient-rich water near the surface also estimated from ROMS.

  4. 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

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

    Directory of Open Access Journals (Sweden)

    J. A. Bradley

    2015-08-01

    Full Text Available 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

  6. 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

  7. 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

  8. Community Sediment Transport Model

    Science.gov (United States)

    2007-01-01

    are used to determine that model results are consistent across compilers, platforms, and computer architectures , and to ensure that changes in code do...Mississippi State University: Bhate During the early months of this project, the focus was on understanding ROMS-CSTM model, architecture , and...Marchesiello, J.C. McWilliams, & K.D. Stolzenbach, 2007: Sediment transport modeling on Southern Californian shelves: A ROMS case study. Continental

  9. Nutrient biogeochemical cycles in the Gulf of Riga: scaling up field studies with a mathematical model

    Science.gov (United States)

    Savchuk, Oleg P.

    2002-05-01

    A box model has been implemented to understand the large-scale biogeochemical cycles of nitrogen, phosphorus, and silicon in the Gulf of Riga. The large data sets collected within the international Gulf of Riga Project in 1993/1995 were used to validate the model. The comparison to data was useful in scaling up to the gulf-wide level and scrutinizing the conclusions based on short-term field surveys and experimental studies. The simulations indicate that the limiting role was passing from silicon to phosphorus to nitrogen over the seasons of organic production. However, on an annual scale, nutrient limitation was close to the "Redfield equilibrium". Mass balance considerations, based on modeled coupled fluxes, disagree with the conclusions on low sediment denitrification and high phosphorus retention in the pelagic system, which were derived from isolated measurements. Nutrient budgets constructed with the model revealed the high buffer capacity of the Gulf of Riga. The nutrient residence times span a range from 6 years for N to 70 years for Si. The buffering arises from intensive internal recycling in the water body and by the bottom sediments. The budgets indicate that the Gulf retains about two-thirds of external nitrogen and silicon inputs, while phosphorus retention is only 10%. A slow response to external perturbations is demonstrated with numerical experiments run for 15 years under 50% reductions of terrestrial nutrient inputs. These experiments imply that the most effective is the N+P reduction scenario, which resulted in a 20% decrease of primary production after 12 years. A reduction of P resulted in only a 6% decrease of primary production; however, it yielded an 80% drop in the amount of nitrogen fixation.

  10. 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.

  11. 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

  12. Assessment of the GHG reduction potential from energy crops using a combined LCA and biogeochemical process models: a review.

    Science.gov (United States)

    Jiang, Dong; Hao, Mengmeng; Fu, Jingying; Wang, Qiao; Huang, Yaohuan; Fu, Xinyu

    2014-01-01

    The main purpose for developing biofuel is to reduce GHG (greenhouse gas) emissions, but the comprehensive environmental impact of such fuels is not clear. Life cycle analysis (LCA), as a complete comprehensive analysis method, has been widely used in bioenergy assessment studies. Great efforts have been directed toward establishing an efficient method for comprehensively estimating the greenhouse gas (GHG) emission reduction potential from the large-scale cultivation of energy plants by combining LCA with ecosystem/biogeochemical process models. LCA presents a general framework for evaluating the energy consumption and GHG emission from energy crop planting, yield acquisition, production, product use, and postprocessing. Meanwhile, ecosystem/biogeochemical process models are adopted to simulate the fluxes and storage of energy, water, carbon, and nitrogen in the soil-plant (energy crops) soil continuum. Although clear progress has been made in recent years, some problems still exist in current studies and should be addressed. This paper reviews the state-of-the-art method for estimating GHG emission reduction through developing energy crops and introduces in detail a new approach for assessing GHG emission reduction by combining LCA with biogeochemical process models. The main achievements of this study along with the problems in current studies are described and discussed.

  13. High-resolution mineralogical characterization and biogeochemical modeling of uranium reaction pathways at the FRC

    Energy Technology Data Exchange (ETDEWEB)

    Chen Zhu

    2006-06-15

    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

  14. 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.

  15. Groupage Cargo Transportation Model

    Directory of Open Access Journals (Sweden)

    Aleksejevs Ruslans

    2016-03-01

    Full Text Available In this work we consider a specific problem of optimal planning of maritime transportation of multiproduct cargo by ships of one (corporate strategy or several (partially corporate strategy companies: the core of the problem consists of the existence of the network of intermediate seaports (i.e. transitional seaports, where for every ship arrived the cargo handling is done, and which are situated between the starting and the finishing seaports. In this work, there are mathematical models built from scratch in the form of multicriteria optimization problem; then the goal attainment method of Gembicki is used for reducing the built models to a one-criterion problem of linear programming.

  16. 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.

  17. A Conceptual model of coupled biogeochemical and hydrogeological processes affected by in situ Cr(VI) bioreduction in groundwater at Hanford 100H Site

    OpenAIRE

    Faybishenko, B.; Long, P. E.; Hazen, T C; Hubbard, S.S.; Williams, K.H.; Peterson, J. E.; Chen, J.; E.V. Volkova; Newcomer, D.R.; Resch, C.T.; Cantrell, K.; Conrad, M.S.; Brodie, E. L.; Joyner, D.C.; Borglin, S.E.

    2006-01-01

    The overall objective of this presentation is to demonstrate a conceptual multiscale, multidomain model of coupling of biogeochemical and hydrogeological processes during bioremediation of Cr(VI) contaminated groundwater at Hanford 100H site. A slow release polylactate, Hydrogen Release Compound (HRCTM), was injected in Hanford sediments to stimulate immobilization of Cr(VI). The HRC injection induced a 2-order-of-magnitude increase in biomass and the onset of reducing biogeochemical con...

  18. Representing Microbial Processes in Environmental Reactive Transport Models

    Science.gov (United States)

    van Cappellen, P.

    2009-04-01

    Microorganisms play a key role in the biogeochemical functioning of the earth's surface and shallow subsurface. In the context of reactive transport modeling, a major challenge is to derive, parameterize, calibrate and verify mathematical expressions for microbially-mediated reactions in the environmental. This is best achieved by combining field observations, laboratory experiments, theoretical principles and modeling. Here, I will illustrate such an integrated approach for the case of microbial respiration processes in aquatic sediments. Important issues that will be covered include experimental design, model consistency and performance, as well as the bioenergetics and transient behavior of geomicrobial reaction systems.

  19. Transport hub flow modelling

    OpenAIRE

    Despagne, Wilfried; Frenod, Emmanuel

    2014-01-01

    Purpose: The purpose of this paper is to investigate the road freight haulage activity. Using the physical and data flow information from a freight forwarder, we intend to model the flow of inbound and outbound goods in a freight transport hub. Approach: This paper presents the operation of a road haulage group. To deliver goods within two days to any location in France, a haulage contractor needs to be part of a network. This network handles the processing of both physical goods and data. We...

  20. Stochastic modeling of nutrient losses in streams: Interactions of climatic, hydrologic, and biogeochemical controls

    Science.gov (United States)

    Botter, G.; Basu, N. B.; Zanardo, S.; Rao, P. S. C.; Rinaldo, A.

    2010-08-01

    We present an analytical, stochastic approach for quantifying intra-annual fluctuations of in-stream nutrient losses induced by naturally variable hydrologic conditions. The relevance of the problem we address lies in the growing concern for the major environmental impacts of increasing nutrient loads from watersheds to freshwater bodies and coastal waters. Here we express the first-order nutrient loss rate constant, ke, as a function of key biogeochemical and hydrologic controls, in particular the stream depth (h). The stage h modulates the impact of natural streamflow temporal fluctuations (induced by intermittent rainfall forcings) on the underlying biogeochemical processes and thus represents the major driver of at-a-site fluctuations of ke. Novel expressions for the probability distribution function (pdf) of h and ke are derived as a function of a few eco-hydrologic, morphologic and biogeochemical parameters. The shape of such pdf's chiefly depends on the following attributes: (1) the average frequency of streamflow-producing rainfall events, λ; (2) the inverse of mean catchment residence time, k; and (3) a stream channel shape factor, identified through the discharge rating curve exponent b. For λ/(kb) > 1, h and ke have lower intra-annual variability and lower sensitivity to climatic and morphologic controls, leading to improved predictability and ease of measurement of these attributes. Moment analyses suggest that the variability of ke, relative to that of h, is attenuated for λ/(kb) > 1. Thus, the interplay between climate-landscape parameters and the stream shape factor b controls the temporal variability induced by stochastic rainfall forcings on stream stages and nutrient removal rates.

  1. A skill assessment of the biogeochemical model REcoM2 coupled to the finite element sea-ice ocean model (FESOM 1.3)

    Science.gov (United States)

    Schourup-Kristensen, V.; Sidorenko, D.; Wolf-Gladrow, D. A.; Völker, C.

    2014-07-01

    In coupled ocean-biogeochemical models, the choice of numerical schemes in the ocean circulation component can have a large influence on the distribution of the biological tracers. Biogeochemical models are traditionally coupled to ocean general circulation models (OGCMs), which are based on dynamical cores employing quasi regular meshes, and therefore utilize limited spatial resolution in a global setting. An alternative approach is to use an unstructured-mesh ocean model, which allows variable mesh resolution. Here, we present initial results of a coupling between the Finite Element Sea-ice Ocean Model (FESOM) and the biogeochemical model REcoM2, with special focus on the Southern Ocean. Surface fields of nutrients, chlorophyll a and net primary production were compared to available data sets with focus on spatial distribution and seasonal cycle. The model produced realistic spatial distributions, especially regarding net primary production and chlorophyll a, whereas the iron concentration became too low in the Pacific Ocean. The modelled net primary production was 32.5 Pg C yr-1 and the export production 6.1 Pg C yr-1. This is lower than satellite-based estimates, mainly due to the excessive iron limitation in the Pacific along with too little coastal production. Overall, the model performed better in the Southern Ocean than on the global scale, though the assessment here is hindered by the lower availability of observations. The modelled net primary production was 3.1 Pg C yr-1 in the Southern Ocean and the export production 1.1 Pg C yr-1. All in all, the combination of a circulation model on an unstructured grid with an ocean biogeochemical model shows similar performance to other models at non-eddy-permitting resolution. It is well suited for studies of the Southern Ocean, but on the global scale deficiencies in the Pacific Ocean would have to be taken into account.

  2. Integration of the DAYCENT Biogeochemical Model within a Multi-Model Framework

    Energy Technology Data Exchange (ETDEWEB)

    David Muth

    2012-07-01

    Agricultural residues are the largest near term source of cellulosic 13 biomass for bioenergy production, but removing agricultural residues sustainably 14 requires considering the critical roles that residues play in the agronomic system. 15 Determining sustainable removal rates for agricultural residues has received 16 significant attention and integrated modeling strategies have been built to evaluate 17 sustainable removal rates considering soil erosion and organic matter constraints. 18 However the current integrated model does not quantitatively assess soil carbon 19 and long term crop yields impacts of residue removal. Furthermore the current 20 integrated model does not evaluate the greenhouse gas impacts of residue 21 removal, specifically N2O and CO2 gas fluxes from the soil surface. The DAYCENT 22 model simulates several important processes for determining agroecosystem 23 performance. These processes include daily Nitrogen-gas flux, daily carbon dioxide 24 flux from soil respiration, soil organic carbon and nitrogen, net primary productivity, 25 and daily water and nitrate leaching. Each of these processes is an indicator of 26 sustainability when evaluating emerging cellulosic biomass production systems for 27 bioenergy. A potentially vulnerable cellulosic biomass resource is agricultural 28 residues. This paper presents the integration of the DAYCENT model with the 29 existing integration framework modeling tool to investigate additional environment 30 impacts of agricultural residue removal. The integrated model is extended to 31 facilitate two-way coupling between DAYCENT and the existing framework. The 32 extended integrated model is applied to investigate additional environmental 33 impacts from a recent sustainable agricultural residue removal dataset. The 34 integrated model with DAYCENT finds some differences in sustainable removal 35 rates compared to previous results for a case study county in Iowa. The extended 36 integrated model with

  3. 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.

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

    Science.gov (United States)

    2009-09-01

    28 2.3 Delfin and Finel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.4 ELCIRC and...Designed for coastal oceans, shelves, estuaries, inlets, floodplains, rivers and beaches Delfin FV/FD ELCIRC Eularian-Lagrangian CIRCu- lation model FV/FD...NOAA’s National Ocean Services for storm surge/inundation applications. 2.3 Delfin and Finel Delfin was developed by D. Ham under the supervision of J

  5. Arctic Ocean shelf biogeochemical cycling under climate change

    Science.gov (United States)

    Bellerby, Richard; Silyakova, Anna; Slagstad, Dag

    2014-05-01

    Changes to Arctic Ocean biogeochemistry will result from a complex array of climate and chemical perturbations over the next decades. Changes to freshwater and nutrient supply through ice melt and continental runoff; warming of the ocean and an increasing ocean acidification through partial equilibrium with a rising anthropogenic CO2 load will change the nature of Arctic Ocean ecological and biogeochemical coupling. This is no more apparent on the shelf regions where there is strong influence from land sources of freshwater and total alkalinity. This presentation will document our combined approach of studying Arctic biogeochemical change through coupled observational, experimental and modelling campaigns. We have identified large changes in recent anthropogenic carbon transport to the Arctic and have characterised the associated regional and water mass ocean acidification. We have determined, through targeted Arctic pelagic ecosystem perturbations experiments, changes to ecosystem structure, succession and biogeochemical cycling under high CO2. Observations have been incorporated into regional, coupled physical-ecosystem-carbon biogeochemical models (informed at the boundaries by downscaled global earth system models) to develop scenarios of change in biogeochemical pathways. We have identified large regional variability in ocean acidification that is shown to impact on shelf biogeochemistry, ecosystems and climate feedbacks in the Arctic Ocean.

  6. Application of a SEEK filter to a 1D biogeochemical model of the Ligurian Sea: Twin experiments and real data assimilation

    NARCIS (Netherlands)

    Raick, C.; Alvera-Azcarate, A.; Barth, A.; Brankart, J.-M.; Soetaert, K.E.R.; Grégoire, M.

    2007-01-01

    The Singular Evolutive Extended Kalman (SEEK) filter has been implemented to assimilate in-situ data in a 1D coupled physical-ecosystem model of the Ligurian Sea. The biogeochemical model describes the partly decoupled nitrogen and carbon cycles of the pelagic food web. The GHER hydrodynamic model (

  7. A Conceptual Model of Coupled Biogeochemical and Hydrogeological Processes Affected by In Situ Cr(VI) Bioreduction in Groundwater at Hanford 100H Site

    Science.gov (United States)

    Faybishenko, B.; Long, P. E.; Hazen, T. C.; Hubbard, S. S.; Williams, K. H.; Peterson, J. E.; Chen, J.; Volkova, E. V.; Newcomer, D. R.; Resch, C. T.; Cantrell, K.; Conrad, M. S.; Brodie, E. L.; Joyner, D. C.; Borglin, S. E.; Chakraborty, R. C.

    2007-05-01

    The overall objective of this presentation is to demonstrate a conceptual multiscale, multidomain model of coupling of biogeochemical and hydrogeological processes during bioremediation of Cr(VI) contaminated groundwater at Hanford 100H site. A slow release polylactate, Hydrogen Release Compound (HRCTM), was injected in Hanford sediments to stimulate immobilization of Cr(VI). The HRC injection induced a 2-order-of- magnitude increase in biomass and the onset of reducing biogeochemical conditions [e.g., redox potential decreased from +240 to -130 mV and dissolved oxygen (DO) was completely removed]. A three-well system, comprised of an injection well and upgradient and downgradient monitoring wells, was used for conducting the in situ biostimulation, one regional flow (no-pumping) tracer test, and five pumping tests along with the Br-tracer injection. Field measurements were conducted using a Br ion-selective electrode and a multiparameter flow cell to collect hourly data on temperature, pH, redox potential, electrical conductivity, and DO. Groundwater sampling was conducted by pumping through specially designed borehole water samplers. Cross-borehole radar tomography and seismic measurements were carried out to assess the site background lithological heterogeneity and the migration pathways of HRC byproducts through groundwater after the HRC injection. Several alternative approaches, including conventional and fractional advective dispersion equations and geostatistical analysis, were used to characterize hydraulic and biogeochemical transport parameters. The results of a joint inversion of cross-borehole geophysical tomography and flow-rate measurements in boreholes indicate the presence of a bimodal distribution of hydraulic conductivity for Hanford sediments. The Br- concentration double-peak BTCs curves indicate that HRC injection caused an increase in the tracer travel time (mainly in the low-permeability zone) over the period of observations of about 2 years

  8. 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...

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

    CERN Document Server

    Große, Fabian; Pätsch, Johannes; Backhaus, Jan O

    2014-01-01

    In the recent past observational and modelling studies have shown that the vertical displacement of water parcels, and therefore, phytoplankton particles in regions of deep-reaching convection plays a key role in late winter/early spring primary production. The underlying mechanism describes how convection cells capture living phytoplankton cells and recurrently expose them to sunlight. This study presents a parameterisation called `phytoconvection' which focuses on the influence of convection on primary production. This parameterisation was implemented into a three-dimensional physical-biogeochemical model and applied to the Northwestern European Continental Shelf and areas of the adjacent Northeast Atlantic. The simulation was compared to a `conventional' parameterisation with respect to its influence on phytoplankton concentrations during the annual cycle and its effect on the carbon cycle. The simulation using the new parameterisation showed good agreement with observation data recorded during winter, whe...

  10. Stochastic models of intracellular transport

    KAUST Repository

    Bressloff, Paul C.

    2013-01-09

    The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures. © 2013 American Physical Society.

  11. Goods Transport Modelling, Vol 1

    DEFF Research Database (Denmark)

    Petersen, Morten Steen (red.); Kristiansen, Jørgen

    The report is a study of data requirements and methodologies for goods transport. The study is intended to provide the basis for general discussion about the application of goods transport models in Denmark. The report provides an overview of different types of models and data availability....

  12. Modelling Ballast Water Transport

    Digital Repository Service at National Institute of Oceanography (India)

    Jayakumar, S.; Babu, M.T.; Vethamony, P.

    Ballast water discharges in the coastal environs have caused a great concern over the recent periods as they account for transporting marine organisms from one part of the world to the other. The movement of discharged ballast water as well...

  13. Hawaii and Beyond: Volcanic Islands as Model Systems for Biogeochemical and Human Ecodynamic Research

    Science.gov (United States)

    Chadwick, O.

    2012-12-01

    The Hawaiian Islands provide an excellent natural lab for understanding geochemical and ecosystem processes. The most important features are: a) increasing volcano age with distance from the hotspot, b) asymmetric rainfall distribution imposed by the northeasterly trade winds and orographic processes, creating wet windward and dry leeward landscapes, c) an impoverished vegetation assemblage allowing the same species to grow in strongly varying climate and soil conditions, d) the ability to hold topography relatively constant over long time scales by sampling on volcanic shield remnants that are preserved even on the oldest high island, Kauai, and e) a long-term topographic evolution that carves the gently sloping shield surfaces into steep-sided, amphitheater headed, relatively flat floored valleys. Although deeply incised valleys are well represented in Kauai, the later stages of volcanic island evolution are not well expressed in the exposed Hawaiian Islands. Therefore, I also consider examples from the Society and Gambier Islands in French Polynesia to demonstrate the biogeochemical and human ecodynamic impacts of valley expansion and subsidence leading to drowning of all but the highest elevation interfluves. In Hawaii, I and many colleagues have characterized the details of biogeochemical processes such as: a) variations in oxygen isotopes in soil water and soil minerals, b) changing nutrient sources using Sr, Ca, and Mg isotopes, c) mineral - carbon sorption and its implications for carbon storage in soils and for mineral ripening, and d) the development of leaching and redox driven pedogenic thresholds. Here, I address how these biogeochemical features influence human land-use decisions in prehistoric Hawaii and elsewhere in the Pacific. Polynesian radiation into the eastern Pacific occurred rapidly after 1300 y bp. Although they carried with them a kitchen garden each new island presented a different environmental challenge. They were sensitive to

  14. 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

  15. Widespread euxinia in the aftermath of the Lomagundi event: insights from a modeling study of ocean biogeochemical dynamics

    Science.gov (United States)

    Ozaki, Kazumi; Tajika, Eiichi

    2015-04-01

    The emergence of strongly sulphidic oceanic waters (euxinia) during the Proterozoic may have affected biological turnover, extinction, and evolution, not only because of its toxicity to eukaryotes but also because of its fundamental role on bioessential trace metal availability. From this point of view, the evidence for euxinic environments in the Lomagundi-Jatuli event (LJE) aftermath (~2.08-2.05 billion years ago) in Gabon and Karelia are notable because their low δ98/95Mo values (less than 0.95o and 0.85o respectively) imply widespread euxinia at that time. The Francevillian Group in Gabon represents the oxic-anoxic/euxinic transitional sequence, implying a fluctuation in the atmospheric redox condition from oxic to relatively reducing, possibly due to the oxidation of substantial amount of organic matter deposited during the LJE. The large positive anomaly of sulphur isotopes and a substantial contraction of marine sulphate reservoir size through the latter part of the LJE also imply a fall in surface oxidation state. Variations of the oxygenation state of the Earth's surface would have caused substantial changes in oceanic chemical composition and, in turn, would surely have impacted the biosphere. However, the nature and dynamics of oceanic biogeochemical cycles for this interval are poorly understood. To unravel cause and effect of the variations of oceanic redox state in the Paleoproteorozoic, we improved the CANOPS model (a 1-D advection-diffusion-reaction marine biogeochemical cycle model), in which coupled C-N-O-P-S marine biogeochemical cycles and a series of redox reactions were adequately taken into account. Through systematic sensitivity experiments we show that a substantial drop in atmospheric oxygen level could cause a widespread euxinia for millions of years, which provides a theoretical explanation consistent with the geological records, such as large positive anomaly of δ34S, low δ98/95Mo, and a decrease in SO4 concentration, in the

  16. A skill assessment of the biogeochemical model REcoM2 coupled to the Finite Element Sea Ice-Ocean Model (FESOM 1.3)

    Science.gov (United States)

    Schourup-Kristensen, V.; Sidorenko, D.; Wolf-Gladrow, D. A.; Völker, C.

    2014-11-01

    In coupled biogeochmical-ocean models, the choice of numerical schemes in the ocean circulation component can have a large influence on the distribution of the biological tracers. Biogeochemical models are traditionally coupled to ocean general circulation models (OGCMs), which are based on dynamical cores employing quasi-regular meshes, and therefore utilize limited spatial resolution in a global setting. An alternative approach is to use an unstructured-mesh ocean model, which allows variable mesh resolution. Here, we present initial results of a coupling between the Finite Element Sea Ice-Ocean Model (FESOM) and the biogeochemical model REcoM2 (Regulated Ecosystem Model 2), with special focus on the Southern Ocean. Surface fields of nutrients, chlorophyll a and net primary production (NPP) were compared to available data sets with a focus on spatial distribution and seasonal cycle. The model produces realistic spatial distributions, especially regarding NPP and chlorophyll a, whereas the iron concentration becomes too low in the Pacific Ocean. The modelled NPP is 32.5 Pg C yr-1 and the export production 6.1 Pg C yr-1, which is lower than satellite-based estimates, mainly due to excessive iron limitation in the Pacific along with too little coastal production. The model performs well in the Southern Ocean, though the assessment here is hindered by the lower availability of observations. The modelled NPP is 3.1 Pg C yr-1 in the Southern Ocean and the export production 1.1 Pg C yr-1. All in all, the combination of a circulation model on an unstructured grid with a biogeochemical-ocean model shows similar performance to other models at non-eddy-permitting resolution. It is well suited for studies of the Southern Ocean, but on the global scale deficiencies in the Pacific Ocean would have to be taken into account.

  17. Container Logistic Transport Planning Model

    Directory of Open Access Journals (Sweden)

    Xin Zhang

    2013-05-01

    Full Text Available The study proposed a stochastic method of container logistic transport in order to solve the unreasonable transportation’s problem and overcome the traditional models’ two shortcomings. Container transport has rapidly developed into a modern means of transportation because of their significant advantages. With the development, it also exacerbated the flaws of transport in the original. One of the most important problems was that the invalid transport had not still reduced due to the congenital imbalances of transportation. Container transport exacerbated the invalid transport for the empty containers. To solve the problem, people made many efforts, but they did not make much progress. There had two theoretical flaws by analyzing the previous management methods in container transport. The first one was the default empty containers inevitability. The second one was that they did not overall consider how to solve the problem of empty containers allocation. In order to solve the unreasonable transportation’s problem and overcome the traditional models’ two shortcomings, the study re-built the container transport planning model-gravity model. It gave the general algorithm and has analyzed the final result of model.

  18. Stochastic parameterizations of biogeochemical uncertainties in a 1/4° NEMO/PISCES model for probabilistic comparisons with ocean color data

    Science.gov (United States)

    Garnier, F.; Brankart, J.-M.; Brasseur, P.; Cosme, E.

    2016-03-01

    In spite of recent advances, biogeochemical models are still unable to represent the full complexity of natural ecosystems. Their formulations are mainly based on empirical laws involving many parameters. Improving biogeochemical models therefore requires to properly characterize model uncertainties and their consequences. Subsequently, this paper investigates the potential of using random processes to simulate some uncertainties of the 1/4° coupled Physical-Biogeochemical NEMO/PISCES model of the North Atlantic ocean. Starting from a deterministic simulation performed with the original PISCES formulation, we propose a generic method based on AR(1) random processes to generate perturbations with temporal and spatial correlations. These perturbations are introduced into the model formulations to simulate 2 classes of uncertainties: the uncertainties on biogeochemical parameters and the uncertainties induced by unresolved scales in the presence of non-linear processes. Using these stochastic parameterizations, a probabilistic version of PISCES is designed and a 60-member ensemble simulation is performed. With respect to the simulation of chlorophyll, the relevance of the probabilistic configuration and the impacts of these stochastic parameterizations are assessed. In particular, it is shown that the ensemble simulation is in good agreement with the SeaWIFS ocean color data. Using these observations, the statistical consistency (reliability) of the ensemble is evaluated with rank histograms. Finally, the benefits expected from the probabilistic description of uncertainties (model error) are discussed in the context of future ocean color data assimilation.

  19. A high-resolution hydrodynamic-biogeochemical coupled model of the Gulf of Cadiz – Alboran Sea region.

    Directory of Open Access Journals (Sweden)

    D. M. MACIAS

    2015-01-01

    Full Text Available The southern Iberia regional seas comprise the Gulf of Cadiz and the Alboran Sea sub-basins connected by the narrow Strait of Gibraltar. Both basins are very different in their hydrological and biological characteristics but are, also, tightly connected to each other. Integrative studies of the whole regional oceanic system are scarce and difficult to perform due to the relative large area to cover and the different relevant time-scales of the main forcings in each sub-basin. Here we propose, for the first time, a fully coupled, 3D, hydrodynamic-biogeochemical model that covers, in a single domain (~2km resolution both marine basins for a 20 years simulation (1989-2008. Model performance is assessed against available data in terms of spatial and temporal distributions of biological variables. In general, the proposed model is able to represent the climatological distributions of primary and secondary producers and also the main seasonality of primary production in the different sub-regions of the analyzed basins. Potential causes of the observed mismatches between model and data are identified and some solutions are proposed for future model development. We conclude that most of these mismatches could be attributed to the missing tidal forcing in the actual model configuration. This model is a first step to obtain a meaningful tool to study past and future oceanographic conditions in this important marine region constituting the unique connection of the Mediterranean Sea with the open world’s ocean.

  20. Evaluating Southern Ocean biological production in two ocean biogeochemical models on daily to seasonal time-scales using satellite surface chlorophyll and O2/Ar observations

    Directory of Open Access Journals (Sweden)

    B. F. Jonsson

    2014-06-01

    Full Text Available We assess the ability of ocean biogeochemical models to represent seasonal structures in biomass and net community production (NCP in the Southern Ocean. Two models are compared to observations on daily to seasonal time scales in four different sections of the region. We use daily satellite fields of Chlorophyll (Chl as a proxy for biomass, and in-situ observations of O2 and Ar supersaturation (ΔO2Ar to estimate NCP. ΔO2Ar is converted to the flux of biologically generated O2 from sea to air ("O2 bioflux". All data are aggregated to a climatological year with a daily resolution. To account for potential regional differences within the Southern Ocean, we conduct separate analyses of sections south of South Africa, around the Drake Passage, south of Australia, and south of New Zealand. We find that the models simulate the upper range of Chl concentrations well, underestimate spring levels significantly, and show differences in skill between early and late parts of the growing season. While there is a great deal of scatter in the bioflux observations in general, the four sectors each have distinct patterns that the models pick up. Neither model exhibit a significant distinction between the Australian and New Zealand sectors, and between the Drake Passage and African sectors. South of 60° S, the models fail to predict the observed extent of biological O2 undersaturation. We suggest that this shortcoming may be due either to problems with the ecosystem dynamics or problems with the vertical transport of oxygen. Overall, the bioflux observations are in general agreement with the seasonal structures in satellite chlorophyll, suggesting that this seasonality represent changes in carbon biomass and not Chl : C ratios. This agreement is shared in the models and allows us to interpret the seasonal structure of satellite chlorophyll as qualitatively reflecting the integral of biological production over time for the purposes of model assessment.

  1. Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone?

    Science.gov (United States)

    Fraysse, Marion; Pinazo, Christel; Faure, Vincent Martin; Fuchs, Rosalie; Lazzari, Paolo; Raimbault, Patrick; Pairaud, Ivane

    2013-01-01

    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. PMID:24324589

  2. System Convergence in Transport Modelling

    DEFF Research Database (Denmark)

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

    2010-01-01

    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......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...... iterating between a route-choice (demand) model and a time-flow (supply) model. It is generally recognised that a simple iteration scheme where the level-of-service level is fed directly to the route-choice and vice versa may exhibit an unstable pattern and lead to cyclic unstable solutions. It can be shown...

  3. Pore-scale network modeling of microbially induced calcium carbonate precipitation: Insight into scale dependence of biogeochemical reaction rates

    Science.gov (United States)

    Qin, Chao-Zhong; Hassanizadeh, S. Majid; Ebigbo, Anozie

    2016-11-01

    The engineering of microbially induced calcium carbonate precipitation (MICP) has attracted much attention in a number of applications, such as sealing of CO2 leakage pathways, soil stabilization, and subsurface remediation of radionuclides and toxic metals. The goal of this work is to gain insight into pore-scale processes of MICP and scale dependence of biogeochemical reaction rates. This will help us develop efficient field-scale MICP models. In this work, we have developed a comprehensive pore-network model for MICP, with geochemical speciation calculated by the open-source PHREEQC module. A numerical pseudo-3-D micromodel as the computational domain was generated by a novel pore-network generation method. We modeled a three-stage process in the engineering of MICP including the growth of biofilm, the injection of calcium-rich medium, and the precipitation of calcium carbonate. A number of test cases were conducted to illustrate how calcite precipitation was influenced by different operating conditions. In addition, we studied the possibility of reducing the computational effort by simplifying geochemical calculations. Finally, the effect of mass transfer limitation of possible carbonate ions in a pore element on calcite precipitation was explored.

  4. Next Generation Transport Phenomenology Model

    Science.gov (United States)

    Strickland, Douglas J.; Knight, Harold; Evans, J. Scott

    2004-01-01

    This report describes the progress made in Quarter 3 of Contract Year 3 on the development of Aeronomy Phenomenology Modeling Tool (APMT), an open-source, component-based, client-server architecture for distributed modeling, analysis, and simulation activities focused on electron and photon transport for general atmospheres. In the past quarter, column emission rate computations were implemented in Java, preexisting Fortran programs for computing synthetic spectra were embedded into APMT through Java wrappers, and work began on a web-based user interface for setting input parameters and running the photoelectron and auroral electron transport models.

  5. Biogeochemical factors affecting the distribution, speciation, and transport of Hg species in the Deûle and Lys Rivers (Northern France).

    Science.gov (United States)

    Daye, Mirna; Kadlecova, Milada; Ouddane, Baghdad

    2015-02-01

    The Deûle River is a highly polluted River by heavy metals caused by the historical discharges of ore minerals from the former ore smelter "Metaleurop." The potential mercury (Hg) pollution in the Deûle River implicates the importance of Hg distribution study in the river. As well as to configure the different biogeochemical factors that control the distribution and the potential transport of Hg to distant places. Four different sites were studied as follows: D-A (Deûle River, a site located upstream the river), D-B (Deûle River, a site located near a Zn, Pb, Cu, and Ni smelter that closed in 2003), L-C (Lys River, a site located upstream the confluence of the Deûle River with Lys River), and L-D (downstream the rivers confluence). Different Hg analyses were performed including total mercury in sediment (HgTS), methylmercury (MeHg) in sediment, total mercury in pore water (HgTPW), total mercury in surface water (HgTD), and total suspended particulate Hg in water (HgTP). HgTS decreases downstream from the Deûle River sites with a mean value of 11 ± 0.34 mg/kg to Lys River site (L-D) with a mean value of 0.53 ± 0.02 mg/kg at the confluence. The unaffected side of the Lys River, localized before the confluence (L-C), is characterized by low HgTS of an average value of 0.042 ± 0.003 mg/kg and high % MeHg reaching 4.2 %. Whereas, the highly contaminated Deûle sites are designated by low % MeHg with an average value of 0.053 %. Low pristine environments like that found in L-C site with more favorable biogeochemical conditions of lower concentrations of HgTS, sulfides, and Corg host more active biotic methylation than that of the highly polluted Deûle sites with high concentrations of HgTS and sulfides concentrations. Methylation in D-B (the closet site to Metaleurop smelter) is an old and recent methylation activity that has contributed to MeHg accumulation in the sediments as opposed to the exclusive recent events of methylation in Lys sites. Me

  6. 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.

  7. A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 (KMBM2) for UVic 2.9

    Science.gov (United States)

    Nickelsen, L.; Keller, D. P.; Oschlies, A.

    2014-12-01

    Marine biological production and the associated biotic uptake of carbon in many ocean regions depend on the availability of nutrients in the euphotic zone. While large areas are limited by nitrogen and/or phosphorus, the micronutrient iron is considered the main limiting nutrient in the North Pacific, equatorial Pacific and Southern Ocean. Changes in iron availability via changes in atmospheric dust input are discussed to play an important role in glacial/interglacial cycles via climate feedbacks caused by changes in biological ocean carbon sequestration. Although many aspects of the iron cycle remain unknown, its incorporation into marine biogeochemical models is needed to test our current understanding and better constrain its role in the Earth system. In the University of Victoria Earth System Climate Model (UVic) iron limitation in the ocean was, until now, simulated pragmatically with an iron concentration masking scheme that did not allow a consistent interactive response to perturbations of ocean biogeochemistry or iron cycling sensitivity studies. Here, we replace the iron masking scheme with a dynamic iron cycle and compare the results to available observations and the previous marine biogeochemical model. Sensitivity studies are also conducted with the new model to test the importance of considering the variable solubility of iron in dust deposition, the importance of considering high resolution bathymetry for the sediment release of iron, the effect of scaling the sedimentary iron release with temperature and the sensitivity of the iron cycle to a climate change scenario.

  8. A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 (KMBM2 for UVic 2.9

    Directory of Open Access Journals (Sweden)

    L. Nickelsen

    2014-12-01

    Full Text Available Marine biological production and the associated biotic uptake of carbon in many ocean regions depend on the availability of nutrients in the euphotic zone. While large areas are limited by nitrogen and/or phosphorus, the micronutrient iron is considered the main limiting nutrient in the North Pacific, equatorial Pacific and Southern Ocean. Changes in iron availability via changes in atmospheric dust input are discussed to play an important role in glacial/interglacial cycles via climate feedbacks caused by changes in biological ocean carbon sequestration. Although many aspects of the iron cycle remain unknown, its incorporation into marine biogeochemical models is needed to test our current understanding and better constrain its role in the Earth system. In the University of Victoria Earth System Climate Model (UVic iron limitation in the ocean was, until now, simulated pragmatically with an iron concentration masking scheme that did not allow a consistent interactive response to perturbations of ocean biogeochemistry or iron cycling sensitivity studies. Here, we replace the iron masking scheme with a dynamic iron cycle and compare the results to available observations and the previous marine biogeochemical model. Sensitivity studies are also conducted with the new model to test the importance of considering the variable solubility of iron in dust deposition, the importance of considering high resolution bathymetry for the sediment release of iron, the effect of scaling the sedimentary iron release with temperature and the sensitivity of the iron cycle to a climate change scenario.

  9. Subsurface Biogeochemical Research FY11 Second Quarter Performance Measure

    Energy Technology Data Exchange (ETDEWEB)

    Scheibe, Timothy D.

    2011-03-31

    The Subsurface Biogeochemical Research (SBR) Long Term Measure for 2011 under the Performance Assessment Rating Tool (PART) measure is to "Refine subsurface transport models by developing computational methods to link important processes impacting contaminant transport at smaller scales to the field scale." The second quarter performance measure is to "Provide a report on computational methods linking genome-enabled understanding of microbial metabolism with reactive transport models to describe processes impacting contaminant transport in the subsurface." Microorganisms such as bacteria are by definition small (typically on the order of a micron in size), and their behavior is controlled by their local biogeochemical environment (typically within a single pore or a biofilm on a grain surface, on the order of tens of microns in size). However, their metabolic activity exerts strong influence on the transport and fate of groundwater contaminants of significant concern at DOE sites, in contaminant plumes with spatial extents of meters to kilometers. This report describes progress and key findings from research aimed at integrating models of microbial metabolism based on genomic information (small scale) with models of contaminant fate and transport in aquifers (field scale).

  10. Mathematical modeling of kidney transport.

    Science.gov (United States)

    Layton, Anita T

    2013-01-01

    In addition to metabolic waste and toxin excretion, the kidney also plays an indispensable role in regulating the balance of water, electrolytes, nitrogen, and acid-base. In this review, we describe representative mathematical models that have been developed to better understand kidney physiology and pathophysiology, including the regulation of glomerular filtration, the regulation of renal blood flow by means of the tubuloglomerular feedback mechanisms and of the myogenic mechanism, the urine concentrating mechanism, epithelial transport, and regulation of renal oxygen transport. We discuss the extent to which these modeling efforts have expanded our understanding of renal function in both health and disease.

  11. 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.

  12. A coupled hydrologic and biogeochemical model for assessing watershed responses to climate and land use

    Science.gov (United States)

    This seminar for Oregon State University’s Water Resources Graduate Program will describe the use of a spatially-distributed ecohydrological model, VELMA, for quantifying how alternative land use and climate scenarios affect tradeoffs among important ecosystem services. Sp...

  13. 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.

  14. Coupling AVHRR imagery with biogeochemical models of methane emission from rice crops

    Science.gov (United States)

    Paliouras, Eleni Joyce

    2000-10-01

    Rice is a staple food source for much of the world and most of it is grown in paddies which remain flooded for a large part of the growing season. This anaerobic environment is ideal for the activities of methanogenic bacteria, that are responsible for the production of methane gas, some of which is released into the atmosphere. In order to better understand the role that rice cropping plays in the levels of atmospheric methane, several models have been developed to predict the methane flux from the paddies. These models generally utilize some type of nominal plant growth curve based on one or two pieces of ground truth data. Ideally, satellite data could be used instead to provide these models with an estimate of biomass change over the growing season, eliminating the need for related ground truth. A technique proposed to accomplish this is presented here, and results that demonstrate its success when applied to rice cropping areas of Texas are discussed. Also presented is a method for utilizing satellite data to map rice cropping areas that could eventually aid in a scheme for populating a GIS-type database with information on exact rice cropping areas. Such a database could then be directly tied to the methane emission models to obtain flux estimates for extensive regional areas.

  15. 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

  16. Modelling of Transport Projects Uncertainties

    DEFF Research Database (Denmark)

    Salling, Kim Bang; Leleur, Steen

    2009-01-01

    This paper proposes a new way of handling the uncertainties present in transport decision making based on infrastructure appraisals. The paper suggests to combine the principle of Optimism Bias, which depicts the historical tendency of overestimating transport related benefits and underestimating...... investment costs, with a quantitative risk analysis based on Monte Carlo simulation and to make use of a set of exploratory scenarios. The analysis is carried out by using the CBA-DK model representing the Danish standard approach to socio-economic cost-benefit analysis. Specifically, the paper proposes...

  17. Modelling of Transport Projects Uncertainties

    DEFF Research Database (Denmark)

    Salling, Kim Bang; Leleur, Steen

    2012-01-01

    This paper proposes a new way of handling the uncertainties present in transport decision making based on infrastructure appraisals. The paper suggests to combine the principle of Optimism Bias, which depicts the historical tendency of overestimating transport related benefits and underestimating...... investment costs, with a quantitative risk analysis based on Monte Carlo simulation and to make use of a set of exploratory scenarios. The analysis is carried out by using the CBA-DK model representing the Danish standard approach to socio-economic cost-benefit analysis. Specifically, the paper proposes...

  18. Soil Biogeochemical Properties and Erosion Source Prediction Model Summary for the Buffalo Bayou Watershed, Houston, Texas

    Science.gov (United States)

    Ahmed, I.

    2015-12-01

    We draw conclusions on the research output and findings from a 4-year multidisciplinary USDA-CBG collaborative program in sustainable integrated monitoring of soil organic carbon (SOC) loss prediction via erosion. The underlying method uses the state-of-the-art stable isotope science of sediment tracing under uncertain hydrologic influences. The research finds are rooted in the (i) application of Bayesian Markov Chain Monte Carlo statistical models to assess the relationship between rainfall-runoff and soil erosion in space and time, (ii) capture of the episodic nature of rainfall events and its role in the spatial distribution of SOC loss from water erosion, (iii) stable isotope composition guided fingerprinting (source and quantity) of eroded soil, and (iv) the creation of an integrated watershed scale statistical soil loss monitoring model driven by spatial and temporal correlation of flow and stable isotope composition. The research theme was successfully applied on the urbanized Buffalo Bayou Watershed in Houston, Texas. The application brought to light novel future research conceptual outlines which will also be discussed in this deliverable to the AGU meeting. These include but not limited to: regional rainfall cluster research, physics of muddy river-bank soil and suspended sediment interaction, and friction & mobility that together make up the plasticity of soil aggregates that control erosion processes and landscape changes in a riparian corridor. References: Ahmed, I., Karim, A., Boutton, T.W., and Strom, K.B. (2013a). "Monitoring Soil Organic Carbon Loss from Erosion Using Stable Isotopes." Proc., Soil Carbon Sequestration, International Conference, May 26-29, Reykjavik, Iceland. Ahmed, I, Bouttom, T.W., Strom, K. B., Karim, A., and Irvin-Smith, N. (2013b). "Soil carbon distribution and loss monitoring in the urbanized Buffalo Bayou watershed, Houston, Texas." Proc., 4th Annual All Investigators Meeting of the North American Carbon Program, February 4

  19. PHT3D-UZF: A reactive transport model for variably-saturated porous media

    Science.gov (United States)

    Wu, Ming Zhi; Post, Vincent E. A.; Salmon, S. Ursula; Morway, Eric; Prommer, H.

    2016-01-01

    A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns.

  20. Ecological controls on biogeochemical lfuxes in the western Antarctic Peninsula studied with an inverse foodweb model

    Institute of Scientific and Technical Information of China (English)

    Hugh W Ducklow; S C Doney; S F Sailley

    2015-01-01

    Sea ice in the western Antarctic Peninsula (WAP) region is both highly variable and rapidly changing. In the Palmer Station region, the ice season duration has decreased by 92 d since 1978. The sea-ice changes affect ocean stratification and freshwater balance and in turn impact every component of the polar marine ecosystem. Long-term observations from the WAP nearshore and offshore regions show a pattern of chlorophyll (Chl) variability with three to ifve years of negative Chl anomalies interrupted by one or two years of positive anomalies (high and low Chl regimes). Both ifeld observations and results from an inverse food-web model show that these high and low Chl regimes differed significantly from each other, with high primary productivity and net community production (NCP) and other rates associated with the high Chl years and low rates with low Chl years. Gross primary production rates (GPP) averaged 30 mmolC.m-2.d-1 in the low Chl years and 100 mmolC.m-2.d-1 in the high Chl years. Both large and small phytoplankton were more abundant and more productive in high Chl years than in low Chl years. Similarly, krill were more important as grazers in high Chl years, but did not differ from microzooplankton in high or low Chl years. Microzooplankton did not differ between high and low Chl years. Net community production differed signiifcantly between high and low Chl years, but mobilized a similar proportion of GPP in both high and low Chl years. The composition of the NCP was uniform in high and low Chl years. These results emphasize the importance of microbial components in the WAP plankton system and suggest that food webs dominated by small phytoplankton can have pathways that funnel production into NCP, and likely, export.

  1. A Theoretic Model of Transport Logistics Demand

    Directory of Open Access Journals (Sweden)

    Natalija Jolić

    2006-01-01

    Full Text Available Concerning transport logistics as relation between transportand integrated approaches to logistics, some transport and logisticsspecialists consider the tenn tautological. However,transport is one of the components of logistics, along with inventories,resources, warehousing, infonnation and goods handling.Transport logistics considers wider commercial and operationalframeworks within which the flow of goods is plannedand managed. The demand for transport logistics services canbe valorised as highly qualitative, differentiated and derived.While researching transport phenomenon the implementationof models is inevitable and demand models highly desirable. Asa contribution to transport modelling this paper improves decisionmaking and planning in the transport logistics field.

  2. Development of advanced process-based model towards evaluation of boundless biogeochemical cycles in terrestrial-aquatic continuum

    Science.gov (United States)

    Nakayama, Tadanobu; Maksyutov, Shamil

    2014-05-01

    Recent research shows inland water may play some role in continental biogeochemical cycling though its contribution has remained uncertain due to a paucity of data (Battin et al. 2009). 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, regional and global scales, and can simulate iteratively nonlinear feedback between hydrologic, geomorphic, and ecological processes. In this study, NICE was extended to evaluate global hydrologic cycle by using various global datasets. The simulated result agreed reasonably with that in the previous research (Fan et al., 2013) and extended to clarify further eco-hydrological process in global scale. Then, NICE was further developed to incorporate the biogeochemical cycle including the reaction between inorganic and organic carbons (DOC, POC, DIC, pCO2, etc.) in the biosphere (terrestrial and aquatic ecosystems including surface water and groundwater). The model simulated the carbon cycle, for example, CO2 evasion from inland water in global scale, which is relatively in good agreement in that estimated by empirical relation using the previous pCO2 data (Aufdenkampe et al., 2011; Global River Chemistry Database, 2013). This simulation system would play important role in identification of full greenhouse gas balance of the biosphere and spatio-temporal hot spots in boundless biogeochemical cycle (Cole et al. 2007; Frei et al. 2012). References; Aufdenkampe, A.K., et al., Front. Ecol. Environ., doi:10.1890/100014, 2011. Battin, T.J., et al., Nat. Geosci., 2, 598-600, 2009. Cole, J.J. et al., Ecosystems, doi:10.1007/s10021-006-9013-8, 2007. Fan, Y. et al

  3. A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 for UVic 2.9

    Science.gov (United States)

    Nickelsen, L.; Keller, D. P.; Oschlies, A.

    2015-05-01

    Marine biological production as well as the associated biotic uptake of carbon in many ocean regions depends on the availability of nutrients in the euphotic zone. While large areas are limited by nitrogen and/or phosphorus, the micronutrient iron is considered the main limiting nutrient in the North Pacific, equatorial Pacific and Southern Ocean. Changes in iron availability via changes in atmospheric dust input are discussed to play an important role in glacial-interglacial cycles via climate feedbacks caused by changes in biological ocean carbon sequestration. Although many aspects of the iron cycle remain unknown, its incorporation into marine biogeochemical models is needed to test our current understanding and better constrain its role in the Earth system. In the University of Victoria Earth System Climate Model (UVic) iron limitation in the ocean was, until now, simulated pragmatically with an iron concentration masking scheme that did not allow a consistent interactive response to perturbations of ocean biogeochemistry or iron cycling sensitivity studies. Here, we replace the iron masking scheme with a dynamic iron cycle and compare the results to available observations and the previous marine biogeochemical model. Sensitivity studies are also conducted with the new model to test the sensitivity of the model to parameterized iron ligand concentrations, the importance of considering the variable solubility of iron in dust deposition, the importance of considering high-resolution bathymetry for the sediment release of iron, the effect of scaling the sedimentary iron release with temperature and the sensitivity of the iron cycle to a climate change scenario.

  4. 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

  5. Biogeochemical investigations on processes affecting the transport behaviour of trace elements in the tidal Elbe River; Biogeochemische Prozessuntersuchungen zum Transportverhalten von Spurenelementen in der Tide-Elbe

    Energy Technology Data Exchange (ETDEWEB)

    Hennies, K. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Gewaesserphysik

    1997-12-31

    This work concentrates on distribution and transport of micropollutants in anthropogenically affected estuary systems. Choosing the tidal Elbe River as an example, the influence of microlagae on two important partial processes of the transport regime, the remobilization (a) from undisturbed sediments and (b) from suspended particulate matter, was simulated and quantified in the laboratory. Benthic and planktonic release of Cd, Cu, Pb and Zn into the dissolved phase of the river pelagial were estimated and comparatively evaluated for summer/late summer situation. During that season natural decomposition of suspended particulate matter in the water column thus represents the quantitatively most significant mobilization pathway for particle bound heavy metals in the river section between Hamburg and Glueckstadt. Knowing the composition and heavy metal load of suspended particulate matter, rich in algae, mobilization rates can consequently be calculated for the water column with regard to conditions typical for estuaries. The prognosis of the differing transport behaviour of single heavy metals for greater sections of estuaries is also possible if these rates are implemented into transport-reaction models. (orig.) [Deutsch] Die vorliegende Arbeit befasst sich mit Verteilung und Transport von Spurenschadstoffen in anthropogen belasteten Aestuarsystemen. Am Beispiel der Tide-Elbe wurde der Einfluss von Mikroalgen auf zwei wichtige Teilprozesse des Transportregimes, die Remobilisierung (a) aus ungestoerten Sedimenten und (b) aus suspendierten Schwebstoffen, im Labor simuliert und quantifiziert. Benthische und planktische Freisetzung von Cd, Cu, Pb und Zn in die Loesungsphase des Flusspelagials der Tide-Elbe wurden fuer die Sommer-/Spaetsommer-Situation abgeschaetzt und vergleichend bewertet. Der natuerliche Schwebstoff-Abbau in der Wassersaeule stellt demnach in dieser Jahreszeit im Stromabschnitt zwischen Hamburg und Glueckstadt den quantitativ bedeutsamsten

  6. Modelling of radon transport in porous media

    NARCIS (Netherlands)

    van der Graaf, E.R.; de Meijer, R.J.; Katase, A; Shimo, M

    1998-01-01

    This paper aims to describe the state of the art of modelling radon transport in soil on basis of multiphase radon transport equations. Emphasis is given to methods to obtain a consistent set of input parameters needed For such models. Model-measurement comparisons with the KVI radon transport Facil

  7. Transport Properties for Combustion Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Brown, N.J.; Bastein, L.; Price, P.N.

    2010-02-19

    This review examines current approximations and approaches that underlie the evaluation of transport properties for combustion modeling applications. Discussed in the review are: the intermolecular potential and its descriptive molecular parameters; various approaches to evaluating collision integrals; supporting data required for the evaluation of transport properties; commonly used computer programs for predicting transport properties; the quality of experimental measurements and their importance for validating or rejecting approximations to property estimation; the interpretation of corresponding states; combination rules that yield pair molecular potential parameters for unlike species from like species parameters; and mixture approximations. The insensitivity of transport properties to intermolecular forces is noted, especially the non-uniqueness of the supporting potential parameters. Viscosity experiments of pure substances and binary mixtures measured post 1970 are used to evaluate a number of approximations; the intermediate temperature range 1 < T* < 10, where T* is kT/{var_epsilon}, is emphasized since this is where rich data sets are available. When suitable potential parameters are used, errors in transport property predictions for pure substances and binary mixtures are less than 5 %, when they are calculated using the approaches of Kee et al.; Mason, Kestin, and Uribe; Paul and Warnatz; or Ern and Giovangigli. Recommendations stemming from the review include (1) revisiting the supporting data required by the various computational approaches, and updating the data sets with accurate potential parameters, dipole moments, and polarizabilities; (2) characterizing the range of parameter space over which the fit to experimental data is good, rather than the current practice of reporting only the parameter set that best fits the data; (3) looking for improved combining rules, since existing rules were found to under-predict the viscosity in most cases; (4

  8. 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

    2013-02-01

    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. Since the beginning of the industrial era, the atmospheric concentration of carbon dioxide (CO2 has significantly increased above its natural, inter-glacial background concentration. 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, therefore requires that both organic and inorganic carbon be afforded a full 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 parameterisations of phytoplankton growth, calcification and detritus remineralisation. A full description of MEDUSA-2.0, including its additional functionality, is provided and a multi-decadal hindcast simulation described (1860–2005, to evaluate the biogeochemical performance of the model.

  9. Quantifying methane emissions from rice fields in Tai-Lake region, China by coupling detailed soil database with biogeochemical model

    Directory of Open Access Journals (Sweden)

    L. Zhang

    2008-12-01

    Full Text Available China's paddy rice accounts for about 22% of the world's rice fields, therefore it is crucial to accurately estimate the CH4 emissions at regional scale to gauge their contribution to global greenhouse gas effect. This paper reports an application of a biogeochemical model, DeNitrification and DeComposition or DNDC, for quantifying CH4 emissions from rice fields in Tai-Lake region of China by linking DNDC to a 1:50 000 soil database, which was derived from 1107 paddy soil profiles in the Second National Soil Survey of China in the 1980s–1990s. The modeled results estimate that the 2.34 M ha of paddy rice fields in Tai-Lake region emitted about CH4 of 5.67 Tg C for the period of 1982–2000, with the average CH4 flux ranged from 114 to 138 kg C ha−1y−1. The highest emission rate (659.24 kg C ha−1 y−1 occurred in the subgroup of "gleyed paddy soils", while the lowest (90.72 kg C ha−1y−1 were associated with the subgroup "degleyed paddy soils". The subgroup "hydromorphic paddy soils" accounted for about 52.82% of the total area of paddy soils, the largest of areas of all the soil subgroups, with the CH4 flux rate of 106.47 kg C ha−1y−1. On a sub-regional basis, the annual average CH4 flux in the Tai-Lake plain soil region and alluvial plain soil region was higher than that in low mountainous and hilly soil region and polder soil region. The model simulation was conducted with two databases using polygon or county as the basic unit. The county-based database contained soil information coarser than the polygon system built based on the 1:50 000 soil database. The modeled results with the two databases found similar spatial patterns CH4 emissions in Tai-Lake region. However, discrepancies exist between the results from the two methods, the relative deviation is

  10. Up-gradient transport in a probabilistic transport model

    DEFF Research Database (Denmark)

    Gavnholt, J.; Juul Rasmussen, J.; Garcia, O.E.

    2005-01-01

    The transport of particles or heat against the driving gradient is studied by employing a probabilistic transport model with a characteristic particle step length that depends on the local concentration or heat gradient. When this gradient is larger than a prescribed critical value, the standard....... These results supplement recent works by van Milligen [Phys. Plasmas 11, 3787 (2004)], which applied Levy distributed step sizes in the case of supercritical gradients to obtain the up-gradient transport. (c) 2005 American Institute of Physics....

  11. Multi-Fraction Bayesian Sediment Transport Model

    Directory of Open Access Journals (Sweden)

    Mark L. Schmelter

    2015-09-01

    Full Text Available A Bayesian approach to sediment transport modeling can provide a strong basis for evaluating and propagating model uncertainty, which can be useful in transport applications. Previous work in developing and applying Bayesian sediment transport models used a single grain size fraction or characterized the transport of mixed-size sediment with a single characteristic grain size. Although this approach is common in sediment transport modeling, it precludes the possibility of capturing processes that cause mixed-size sediments to sort and, thereby, alter the grain size available for transport and the transport rates themselves. This paper extends development of a Bayesian transport model from one to k fractional dimensions. The model uses an existing transport function as its deterministic core and is applied to the dataset used to originally develop the function. The Bayesian multi-fraction model is able to infer the posterior distributions for essential model parameters and replicates predictive distributions of both bulk and fractional transport. Further, the inferred posterior distributions are used to evaluate parametric and other sources of variability in relations representing mixed-size interactions in the original model. Successful OPEN ACCESS J. Mar. Sci. Eng. 2015, 3 1067 development of the model demonstrates that Bayesian methods can be used to provide a robust and rigorous basis for quantifying uncertainty in mixed-size sediment transport. Such a method has heretofore been unavailable and allows for the propagation of uncertainty in sediment transport applications.

  12. Biogeochemical fluxes and fate of diazotroph-derived nitrogen in the food web after a phosphate enrichment: modeling of the VAHINE mesocosms experiment

    Science.gov (United States)

    Gimenez, Audrey; Baklouti, Melika; Bonnet, Sophie; Moutin, Thierry

    2016-09-01

    The VAHINE mesocosm experiment in the oligotrophic waters of the Nouméa lagoon (New Caledonia), where high N2 fixation rates and abundant diazotroph organisms were observed, aimed to assess the role of the nitrogen input through N2 fixation in carbon production and export and to study the fate of diazotroph-derived nitrogen (DDN) throughout the planktonic food web. A 1-D vertical biogeochemical mechanistic model was used in addition to the in situ experiment to enrich our understanding of the dynamics of the planktonic ecosystem and the main biogeochemical carbon (C), nitrogen (N) and phosphate (P) fluxes. The mesocosms were intentionally enriched with ˜ 0.8 µmol L-1 of inorganic P to trigger the development of diazotrophs and amplify biogeochemical fluxes. Two simulations were run, one with and the other without the phosphate enrichment. In the P-enriched simulation, N2 fixation, primary production (PP) and C export increased by 201, 208 and 87 %, respectively, consistent with the trends observed in the mesocosms (+124, +141 and +261 % for N2 fixation, PP and C export, respectively). In total, 5-10 days were necessary to obtain an increase in primary and export productions after the dissolved inorganic phosphate (DIP) enrichment, thereby suggesting that classical methods (short-term microcosms experiments) used to quantify nutrient limitations of primary production may not be relevant. The model enabled us to monitor the fate of fixed N2 by providing the proportion of DDN in each compartment (inorganic and organic) of the model over time. At the end of the simulation (25 days), 43 % of the DDN was found in the non-diazotroph organisms, 33 % in diazotrophs, 16 % in the dissolved organic nitrogen pool, 3 % in the particulate detrital organic pool and 5 % in traps, indicating that N2 fixation was of benefit to non-diazotrophic organisms and contributed to C export.

  13. ParFlow.RT: Development and Verification of a New Reactive Transport Model

    Science.gov (United States)

    Beisman, J. J., III

    2015-12-01

    In natural subsurface systems, total elemental fluxes are often heavily influenced by areas of disproportionately high reaction rates. These pockets of high reaction rates tend to occur at interfaces, such as the hyporheic zone, where a hydrologic flowpath converges with either a chemically distinct hydrologic flowpath or a reactive substrate. Understanding the affects that these highly reactive zones have on the behavior of shallow subsurface systems is integral to the accurate quantification of nutrient fluxes and biogeochemical cycling. Numerical simulations of these systems may be able to offer some insight. To that end, we have developed a new reactive transport model, ParFlow.RT, by coupling the parallel flow and transport code ParFlow with the geochemical engines of both PFLOTRAN and CrunchFlow. The coupling was accomplished via the Alquimia biogeochemistry API, which provides a unified interface to several geochemical codes and allows a relatively simple implementation of advanced geochemical functionality in flow and transport codes. This model uses an operator-splitting approach, where the transport and reaction steps are solved separately. Here, we present the details of this new model, and the results of verification simulations and biogeochemical cycling simulations of the DOE's East River field site outside of Gothic, CO.

  14. Business Models For Transport eBusiness

    OpenAIRE

    Dragan Cisic; Ivan Franciskovic; Ana Peric

    2003-01-01

    In this paper authors are presenting expectations from electronic commerce and its connotations on transport logistics. Based on trends, the relations between the companies in the international transport have to be strengthened using Internet business models. In the paper authors are investigating e-business information models for usage in transport

  15. Modeling energy transport in nanostructures

    Science.gov (United States)

    Pattamatta, Arvind

    Heat transfer in nanostructures differ significantly from that in the bulk materials since the characteristic length scales associated with heat carriers, i.e., the mean free path and the wavelength, are comparable to the characteristic length of the nanostructures. Nanostructure materials hold the promise of novel phenomena, properties, and functions in the areas of thermal management and energy conversion. Example of thermal management in micro/nano electronic devices is the use of efficient nanostructured materials to alleviate 'hot spots' in integrated circuits. Examples in the manipulation of heat flow and energy conversion include nanostructures for thermoelectric energy conversion, thermophotovoltaic power generation, and data storage. One of the major challenges in Metal-Oxide Field Effect Transistor (MOSFET) devices is to study the 'hot spot' generation by accurately modeling the carrier-optical phonon-acoustic phonon interactions. Prediction of hotspot temperature and position in MOSFET devices is necessary for improving thermal design and reliability of micro/nano electronic devices. Thermoelectric properties are among the properties that may drastically change at nanoscale. The efficiency of thermoelectric energy conversion in a material is measured by a non-dimensional figure of merit (ZT) defined as, ZT = sigmaS2T/k where sigma is the electrical conductivity, S is the Seebeck coefficient, T is the temperature, and k is the thermal conductivity. During the last decade, advances have been made in increasing ZT using nanostructures. Three important topics are studied with respect to energy transport in nanostructure materials for micro/nano electronic and thermoelectric applications; (1) the role of nanocomposites in improving the thermal efficiency of thermoelectric devices, (2) the interfacial thermal resistance for the semiconductor/metal contacts in thermoelectric devices and for metallic interconnects in micro/nano electronic devices, (3) the

  16. Evaluating the ocean biogeochemical components of earth system models using atmospheric potential oxygen (APO and ocean color data

    Directory of Open Access Journals (Sweden)

    C. D. Nevison

    2014-06-01

    Full Text Available The observed seasonal cycles in atmospheric potential oxygen (APO at a range of mid to high latitude surface monitoring sites are compared to those inferred from the output of 6 Earth System Models participating in the fifth phase of the Coupled Model Intercomparison Project (CMIP5. The simulated air–sea O2 fluxes are translated into APO seasonal cycles using a matrix method that takes into account atmospheric transport model (ATM uncertainty among 13 different ATMs. Half of the ocean biogeochemistry models tested are able to reproduce the observed APO cycles at most sites, to within the current large ATM uncertainty, while the other half generally are not. Net Primary Production (NPP and net community production (NCP, as estimated from satellite ocean color data, provide additional constraints, albeit more with respect to the seasonal phasing of ocean model productivity than the overall magnitude. The present analysis suggests that, of the tested ocean biogeochemistry models, CESM and GFDL ESM2M are best able to capture the observed APO seasonal cycle at both Northern and Southern Hemisphere sites. In the northern oceans, the comparison to observed APO suggests that most models tend to underestimate NPP or deep ventilation or both.

  17. Improving the parameters of a global ocean biogeochemical model via variational assimilation of in situ data at five time series stations

    Science.gov (United States)

    Kane, A.; Moulin, C.; Thiria, S.; Bopp, L.; Berrada, M.; Tagliabue, A.; CréPon, M.; Aumont, O.; Badran, F.

    2011-06-01

    The global ocean biogeochemical models that are used in order to assess the ocean role in the global carbon cycle and estimate the impact of the climate change on marine ecosystems are getting more and more sophisticated. They now often account for several phytoplankton functional types that play particular roles in marine food webs and the ocean carbon cycle. These phytoplankton functional types have specific physiological characteristics, which are usually poorly known and therefore add uncertainties to model results. Indeed, this evolution in model complexity is not accompanied by a similar increase in the number and diversity of in situ data sets necessary for model calibration and evaluation. Thus, it is of primary importance to develop new methods to improve model performance using existing biogeochemical data sets, despite their current limitations. In this paper, we have optimized 45 physiological parameters of the PISCES global model, using a variational optimal control method. In order to bypass a global 3-D ocean variational assimilation, which would require enormous computation and memory storage, we have simplified the estimation procedure by assimilating monthly climatological in situ observations at five contrasted oceanographic stations of the JGOFS program in a 1-D version of the PISCES model. We began by estimating the weight matrix in the cost function by using heuristic considerations. Then we used this matrix to estimate the 45 parameters of the 1-D version of the PISCES model by assimilating the different monthly profiles (observed profiles at the five stations) in the same variational procedure on a time window of 1 year. This set of optimized parameters was then used in the standard 3-D global PISCES version to perform a 500 year global simulation. The results of both the standard and the optimized versions of the model were compared to satellite-derived chlorophyll-a images, which are an independent and global data set, showing that our

  18. Cholesterol transport in model membranes

    Science.gov (United States)

    Garg, Sumit; Porcar, Lionel; Butler, Paul; Perez-Salas, Ursula

    2010-03-01

    Physiological processes distribute cholesterol unevenly within the cell. The levels of cholesterol are maintained by intracellular transport and a disruption in the cell's ability to keep these normal levels will lead to disease. Exchange rates of cholesterol are generally studied in model systems using labeled lipid vesicles. Initially donor vesicles have all the cholesterol and acceptor vesicles are devoid of it. They are mixed and after some time the vesicles are separated and cholesterol is traced in each vesicle. The studies performed up to date have significant scatter indicating that the methodologies are not consistent. The present work shows in-situ Time-Resolved SANS studies of cholesterol exchange rates in unsaturated PC lipid vesicles. Molecular dynamics simulations were done to investigate the energetic and kinetic behavior of cholesterol in this system. This synergistic approach will provide insight into our efforts to understand cholesterol traffic.

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

    Science.gov (United States)

    Yool, A.; Popova, E. E.; Anderson, T. R.

    2013-10-01

    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).

  20. 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.

  1. SATURATED ZONE FLOW AND TRANSPORT MODEL ABSTRACTION

    Energy Technology Data Exchange (ETDEWEB)

    B.W. ARNOLD

    2004-10-27

    The purpose of the saturated zone (SZ) flow and transport model abstraction task is to provide radionuclide-transport simulation results for use in the total system performance assessment (TSPA) for license application (LA) calculations. This task includes assessment of uncertainty in parameters that pertain to both groundwater flow and radionuclide transport in the models used for this purpose. This model report documents the following: (1) The SZ transport abstraction model, which consists of a set of radionuclide breakthrough curves at the accessible environment for use in the TSPA-LA simulations of radionuclide releases into the biosphere. These radionuclide breakthrough curves contain information on radionuclide-transport times through the SZ. (2) The SZ one-dimensional (I-D) transport model, which is incorporated in the TSPA-LA model to simulate the transport, decay, and ingrowth of radionuclide decay chains in the SZ. (3) The analysis of uncertainty in groundwater-flow and radionuclide-transport input parameters for the SZ transport abstraction model and the SZ 1-D transport model. (4) The analysis of the background concentration of alpha-emitting species in the groundwater of the SZ.

  2. An integrated water system model considering hydrological and biogeochemical processes at basin scale: model construction and application

    Directory of Open Access Journals (Sweden)

    Y. Y. Zhang

    2014-08-01

    Full Text Available Integrated water system modeling is a reasonable approach to provide scientific understanding and possible solutions to tackle the severe water crisis faced over the world and to promote the implementation of integrated river basin management. Such a modeling practice becomes more feasible nowadays due to better computing facilities and available data sources. In this study, the process-oriented water system model (HEXM is developed by integrating multiple water related processes including hydrology, biogeochemistry, environment and ecology, as well as the interference of human activities. The model was tested in the Shaying River Catchment, the largest, highly regulated and heavily polluted tributary of Huai River Basin in China. The results show that: HEXM is well integrated with good performance on the key water related components in the complex catchments. The simulated daily runoff series at all the regulated and less-regulated stations matches observations, especially for the high and low flow events. The average values of correlation coefficient and coefficient of efficiency are 0.81 and 0.63, respectively. The dynamics of observed daily ammonia-nitrogen (NH4N concentration, as an important index to assess water environmental quality in China, are well captured with average correlation coefficient of 0.66. Furthermore, the spatial patterns of nonpoint source pollutant load and grain yield are also simulated properly, and the outputs have good agreements with the statistics at city scale. Our model shows clear superior performance in both calibration and validation in comparison with the widely used SWAT model. This model is expected to give a strong reference for water system modeling in complex basins, and provide the scientific foundation for the implementation of integrated river basin management all over the world as well as the technical guide for the reasonable regulation of dams and sluices and environmental improvement in river

  3. Logistics and Transport - a conceptual model

    DEFF Research Database (Denmark)

    Jespersen, Per Homann; Drewes, Lise

    2004-01-01

    This paper describes how the freight transport sector is influenced by logistical principles of production and distribution. It introduces new ways of understanding freight transport as an integrated part of the changing trends of mobility. By introducing a conceptual model for understanding...... the interaction between logistics and transport, it points at ways to over-come inherent methodological difficulties when studying this relation...

  4. RADIONUCLIDE TRANSPORT MODELS UNDER AMBIENT CONDITIONS

    Energy Technology Data Exchange (ETDEWEB)

    S. Magnuson

    2004-11-01

    The purpose of this model report is to document the unsaturated zone (UZ) radionuclide transport model, which evaluates, by means of three-dimensional numerical models, the transport of radioactive solutes and colloids in the UZ, under ambient conditions, from the repository horizon to the water table at Yucca Mountain, Nevada.

  5. Discrepant estimates of primary and export production from satellite algorithms, a biogeochemical model, and geochemical tracer measurements in the North Pacific Ocean

    Science.gov (United States)

    Palevsky, Hilary I.; Quay, Paul D.; Nicholson, David P.

    2016-08-01

    Estimates of primary and export production (PP and EP) based on satellite remote sensing algorithms and global biogeochemical models are widely used to provide year-round global coverage not available from direct observations. However, observational data to validate these approaches are limited. We find that no single satellite algorithm or model can reproduce seasonal and annual geochemically determined PP, export efficiency (EP/PP), and EP rates throughout the North Pacific basin, based on comparisons throughout the full annual cycle at time series stations in the subarctic and subtropical gyres and basin-wide regions sampled by container ship transects. The high-latitude regions show large PP discrepancies in winter and spring and strong effects of deep winter mixed layers on annual EP that cannot be accounted for in current satellite-based approaches. These results underscore the need to evaluate satellite- and model-based estimates using multiple productivity parameters measured over broad ocean regions throughout the annual cycle.

  6. Biological transportation networks: Modeling and simulation

    KAUST Repository

    Albi, Giacomo

    2015-09-15

    We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation and angiogenesis) and ion transportation networks (e.g., neural networks) is explained in detail and basic analytical features like the gradient flow structure of the fluid transportation network model and the impact of the model parameters on the geometry and topology of network formation are analyzed. We also present a numerical finite-element based discretization scheme and discuss sample cases of network formation simulations.

  7. A Sediment Transport Model for Sewers

    DEFF Research Database (Denmark)

    Mark, Ole; Larsson, Johan; Larsen, Torben

    1993-01-01

    This paper describes a mathematical model for transport processes in sewers. The model consists of three sub models, a surface model for the description of the buildup and the washoff of sediment particles from the surface area, a morphological model and an advection-dispersion model. The model...

  8. 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

  9. Modeling potential hydrochemical responses to climate change and increasing CO2 at the Hubbard Brook Experimental Forest using a dynamic biogeochemical model (PnET-BGC)

    Science.gov (United States)

    Pourmokhtarian, Afshin; Driscoll, Charles T.; Campbell, John L.; Hayhoe, Katharine

    2012-07-01

    Dynamic hydrochemical models are useful tools for understanding and predicting the interactive effects of climate change, atmospheric CO2, and atmospheric deposition on the hydrology and water quality of forested watersheds. We used the biogeochemical model, PnET-BGC, to evaluate the effects of potential future changes in temperature, precipitation, solar radiation, and atmospheric CO2on pools, concentrations, and fluxes of major elements at the Hubbard Brook Experimental Forest in New Hampshire, United States. Future climate projections used to run PnET-BGC were generated specifically for the Hubbard Brook Experimental Forest with a statistical technique that downscales climate output (e.g., air temperature, precipitation, solar radiation) from atmosphere-ocean general circulation models (AOGCMs) to a finer temporal and spatial resolution. These climate projections indicate that over the twenty-first century, average air temperature will increase at the site by 1.7°C to 6.5°C with simultaneous increases in annual average precipitation ranging from 4 to 32 cm above the long-term mean (1970-2000). PnET-BGC simulations under future climate change show a shift in hydrology characterized by later snowpack development, earlier spring discharge (snowmelt), greater evapotranspiration, and a slight increase in annual water yield (associated with CO2 effects on vegetation). Model results indicate that under elevated temperature, net soil nitrogen mineralization and nitrification markedly increase, resulting in acidification of soil and stream water, thereby altering the quality of water draining from forested watersheds. Invoking a CO2 fertilization effect on vegetation under climate change substantially mitigates watershed nitrogen loss, highlighting the need for a more thorough understanding of CO2 effects on forest vegetation.

  10. STUDY OF CHLOROPHYLL-A DISTRIBUTIONS IN LOMBOK STRAIT USING BIOGEOCHEMICAL MODEL BASED ON REGIONAL OCEAN MODELLING SYSTEM (ROMS

    Directory of Open Access Journals (Sweden)

    KADEK ARY ANGGRENI

    2015-05-01

    Full Text Available Regional Ocean Modelling System atau Sistem Pemodelan Laut Regional (ROMS telah digunakan untuk bermacam keperluan, bermacam pemodelan kelautan. Model Biogeokimia yang dipasangkan dengan ROMS terdiri dari tujuh pasang bagian persamaan yang berbeda-beda mencakup: nitrat, amonium, detritus kecil dan besar, fitoplankton, zooplankton, dan karbon fitoplankton yang dinamis menjadi suatu rasio klorofi.1. Studi pola penyebaran klorofil-a di Selat Lombok (-7 °N - -10 °5 dan 114 °E - 117 °E pada tahun 2006 telah dianalisis menggunakan model Biogeokimia berdasar pada ROMS. Hasil penelitian menunjukkan bahwa sebaran klorofil-a teramati rendah (0,20 mgChl-a/m3 di Selat Lombok pada bulan Januari. Klorofil-a diperkirakan di bagian sebelah selatan Selat Bali dan penyebaran klorofil-a rendah pada lapisan atas dari Selat Lombok. Klorofil-a berlimpah (0,32 mgChl-a/m3 teramati di bulan Agustus. Arah arus timur laut bergerak kearah barat clan bagian selatan di daerah penelitian melalui Selat Lombok. Konsentrasi klorofil-a tertinggi diperkirakan di sebelah utara hingga bagian barat daya Pulau Bali clan juga di bagian selatan Pulau Lombok. Selama musim kering, angin arah tenggara berhembus dari Australia memicu terjadinya proses upwelling ( temperatur rendah clan air yang kaya nutrien di dekat permukaan juga diperkirakan berdasarkan ROMS.

  11. Eutrophication-induced acidification of coastal waters in the northern Gulf of Mexico: Insights into origin and processes from a coupled physical-biogeochemical model

    Science.gov (United States)

    Laurent, Arnaud; Fennel, Katja; Cai, Wei-Jun; Huang, Wei-Jen; Barbero, Leticia; Wanninkhof, Rik

    2017-01-01

    Nutrient inputs from the Mississippi/Atchafalaya River system into the northern Gulf of Mexico promote high phytoplankton production and lead to high respiration rates. Respiration coupled with water column stratification results in seasonal summer hypoxia in bottom waters on the shelf. In addition to consuming oxygen, respiration produces carbon dioxide (CO2), thus lowering the pH and acidifying bottom waters. Here we present a high-resolution biogeochemical model simulating this eutrophication-driven acidification and investigate the dominant underlying processes. The model shows the recurring development of an extended area of acidified bottom waters in summer on the northern Gulf of Mexico shelf that coincides with hypoxic waters. Not reported before, acidified waters are confined to a thin bottom boundary layer where the production of CO2 by benthic metabolic processes is dominant. Despite a reduced saturation state, acidified waters remain supersaturated with respect to aragonite.

  12. Data-driven approach to identify field-scale biogeochemical transitions using geochemical and geophysical data and hidden Markov models: Development and application at a uranium-contaminated aquifer

    Science.gov (United States)

    Chen, Jinsong; Hubbard, Susan S.; Williams, Kenneth H.

    2013-10-01

    Although mechanistic reaction networks have been developed to quantify the biogeochemical evolution of subsurface systems associated with bioremediation, it is difficult in practice to quantify the onset and distribution of these transitions at the field scale using commonly collected wellbore datasets. As an alternative approach to the mechanistic methods, we develop a data-driven, statistical model to identify biogeochemical transitions using various time-lapse aqueous geochemical data (e.g., Fe(II), sulfate, sulfide, acetate, and uranium concentrations) and induced polarization (IP) data. We assume that the biogeochemical transitions can be classified as several dominant states that correspond to redox transitions and test the method at a uranium-contaminated site. The relationships between the geophysical observations and geochemical time series vary depending upon the unknown underlying redox status, which is modeled as a hidden Markov random field. We estimate unknown parameters by maximizing the joint likelihood function using the maximization-expectation algorithm. The case study results show that when considered together aqueous geochemical data and IP imaginary conductivity provide a key diagnostic signature of biogeochemical stages. The developed method provides useful information for evaluating the effectiveness of bioremediation, such as the probability of being in specific redox stages following biostimulation where desirable pathways (e.g., uranium removal) are more highly favored. The use of geophysical data in the approach advances the possibility of using noninvasive methods to monitor critical biogeochemical system stages and transitions remotely and over field relevant scales (e.g., from square meters to several hectares).

  13. 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?

    Science.gov (United States)

    Tan, Zeli; Zhuang, Qianlai; Henze, Daven K.; Frankenberg, Christian; Dlugokencky, Ed; Sweeney, Colm; Turner, Alexander J.; Sasakawa, Motoki; Machida, Toshinobu

    2016-10-01

    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.

  14. Data assimilation in a coupled physical-biogeochemical model of the California Current System using an incremental lognormal 4-dimensional variational approach: Part 1-Model formulation and biological data assimilation twin experiments

    Science.gov (United States)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    A quadratic formulation for an incremental lognormal 4-dimensional variational assimilation method (incremental L4DVar) is introduced for assimilation of biogeochemical observations into a 3-dimensional ocean circulation model. L4DVar assumes that errors in the model state are lognormally rather than Gaussian distributed, and implicitly ensures that state estimates are positive definite, making this approach attractive for biogeochemical variables. The method is made practical for a realistic implementation having a large state vector through linear assumptions that render the cost function quadratic and allow application of existing minimization techniques. A simple nutrient-phytoplankton-zooplankton-detritus (NPZD) model is coupled to the Regional Ocean Modeling System (ROMS) and configured for the California Current System. Quadratic incremental L4DVar is evaluated in a twin model framework in which biological fields only are in error and compared to G4DVar which assumes Gaussian distributed errors. Five-day assimilation cycles are used and statistics from four years of model integration analyzed. The quadratic incremental L4DVar results in smaller root-mean-squared errors and better statistical agreement with reference states than G4DVar while maintaining a positive state vector. The additional computational cost and implementation effort are trivial compared to the G4DVar system, making quadratic incremental L4DVar a practical and beneficial option for realistic biogeochemical state estimation in the ocean.

  15. The european Trans-Tools transport model

    NARCIS (Netherlands)

    Rooijen, T. van; Burgess, A.

    2008-01-01

    The paper presents the use of ArcGIS in the Transtools Transport Model, TRANS-TOOLS, created by an international consortium for the European Commission. The model describe passenger as well as freight transport in Europe with all medium and long distance modes (cars, vans, trucks, train, inland wate

  16. Uncertainty calculation in transport models and forecasts

    DEFF Research Database (Denmark)

    Manzo, Stefano; Prato, Carlo Giacomo

    . & Prato, C. G. (2015). How uncertainty in input and parameters influences transport model output: a four-stage model case-study. Transport Policy, 38, 64-72. 3 Manzo, S., Nielsen, O. A. & Prato, C. G. (2015). How uncertainty in socio-economic variables affects large-scale transport model forecasts......Transport projects and policy evaluations are often based on transport model output, i.e. traffic flows and derived effects. However, literature has shown that there is often a considerable difference between forecasted and observed traffic flows. This difference causes misallocation of (public....... The results highlighted that both the choice of the variable distributions and the use of different assignment algorithms has a noticeable impact on model output. Besides, it showed that the higher the link congestion, the lower the level of final uncertainty. The third paper presented in this thesis deals...

  17. Optimal transportation networks models and theory

    CERN Document Server

    Bernot, Marc; Morel, Jean-Michel

    2009-01-01

    The transportation problem can be formalized as the problem of finding the optimal way to transport a given measure into another with the same mass. In contrast to the Monge-Kantorovitch problem, recent approaches model the branched structure of such supply networks as minima of an energy functional whose essential feature is to favour wide roads. Such a branched structure is observable in ground transportation networks, in draining and irrigation systems, in electrical power supply systems and in natural counterparts such as blood vessels or the branches of trees. These lectures provide mathematical proof of several existence, structure and regularity properties empirically observed in transportation networks. The link with previous discrete physical models of irrigation and erosion models in geomorphology and with discrete telecommunication and transportation models is discussed. It will be mathematically proven that the majority fit in the simple model sketched in this volume.

  18. Uncertainty in tsunami sediment transport modeling

    Science.gov (United States)

    Jaffe, Bruce E.; Goto, Kazuhisa; Sugawara, Daisuke; Gelfenbaum, Guy R.; La Selle, SeanPaul M.

    2016-01-01

    Erosion and deposition from tsunamis record information about tsunami hydrodynamics and size that can be interpreted to improve tsunami hazard assessment. We explore sources and methods for quantifying uncertainty in tsunami sediment transport modeling. Uncertainty varies with tsunami, study site, available input data, sediment grain size, and model. Although uncertainty has the potential to be large, published case studies indicate that both forward and inverse tsunami sediment transport models perform well enough to be useful for deciphering tsunami characteristics, including size, from deposits. New techniques for quantifying uncertainty, such as Ensemble Kalman Filtering inversion, and more rigorous reporting of uncertainties will advance the science of tsunami sediment transport modeling. Uncertainty may be decreased with additional laboratory studies that increase our understanding of the semi-empirical parameters and physics of tsunami sediment transport, standardized benchmark tests to assess model performance, and development of hybrid modeling approaches to exploit the strengths of forward and inverse models.

  19. Charge-transport model for conducting polymers

    Science.gov (United States)

    Dongmin Kang, Stephen; Jeffrey Snyder, G.

    2016-11-01

    The growing technological importance of conducting polymers makes the fundamental understanding of their charge transport extremely important for materials and process design. Various hopping and mobility edge transport mechanisms have been proposed, but their experimental verification is limited to poor conductors. Now that advanced organic and polymer semiconductors have shown high conductivity approaching that of metals, the transport mechanism should be discernible by modelling the transport like a semiconductor with a transport edge and a transport parameter s. Here we analyse the electrical conductivity and Seebeck coefficient together and determine that most polymers (except possibly PEDOT:tosylate) have s = 3 and thermally activated conductivity, whereas s = 1 and itinerant conductivity is typically found in crystalline semiconductors and metals. The different transport in polymers may result from the percolation of charge carriers from conducting ordered regions through poorly conducting disordered regions, consistent with what has been expected from structural studies.

  20. Polar auxin transport: models and mechanisms

    NARCIS (Netherlands)

    Berkel, van K.; Boer, de R.J.; Scheres, B.; Tusscher, ten K.

    2013-01-01

    Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Her

  1. Global changes in biogeochemical cycles in response to human activities

    Science.gov (United States)

    Moore, Berrien, III; Melillo, Jerry

    1994-01-01

    The main objective of our research was to characterize biogeochemical cycles at continental and global scales in both terrestrial and aquatic ecosystems. This characterization applied to both natural ecosystems and those disturbed by human activity. The primary elements of interest were carbon and nitrogen and the analysis sought to quantify standing stocks and dynamic cycling processes. The translocation of major nutrients from the terrestrial landscape to the atmosphere (via trace gases) and to fluvial systems (via leaching, erosional losses, and point source pollution) were of particular importance to this study. Our aim was to develop the first generation of Earth System Models. Our research was organized around the construction and testing of component biogeochemical models which treated terrestrial ecosystem processes, aquatic nutrient transport through drainage basins, and trace gas exchanges at the continental and global scale. A suite of three complementary models were defined within this construct. The models were organized to operate at a 1/2 degree latitude by longitude level of spatial resolution and to execute at a monthly time step. This discretization afforded us the opportunity to understand the dynamics of the biosphere down to subregional scales, while simultaneously placing these dynamics into a global context.

  2. Generic reactive transport codes as flexible tools to integrate soil organic matter degradation models with water, transport and geochemistry in soils

    Science.gov (United States)

    Jacques, Diederik; Gérard, Fréderic; Mayer, Uli; Simunek, Jirka; Leterme, Bertrand

    2016-04-01

    A large number of organic matter degradation, CO2 transport and dissolved organic matter models have been developed during the last decades. However, organic matter degradation models are in many cases strictly hard-coded in terms of organic pools, degradation kinetics and dependency on environmental variables. The scientific input of the model user is typically limited to the adjustment of input parameters. In addition, the coupling with geochemical soil processes including aqueous speciation, pH-dependent sorption and colloid-facilitated transport are not incorporated in many of these models, strongly limiting the scope of their application. Furthermore, the most comprehensive organic matter degradation models are combined with simplified representations of flow and transport processes in the soil system. We illustrate the capability of generic reactive transport codes to overcome these shortcomings. The formulations of reactive transport codes include a physics-based continuum representation of flow and transport processes, while biogeochemical reactions can be described as equilibrium processes constrained by thermodynamic principles and/or kinetic reaction networks. The flexibility of these type of codes allows for straight-forward extension of reaction networks, permits the inclusion of new model components (e.g.: organic matter pools, rate equations, parameter dependency on environmental conditions) and in such a way facilitates an application-tailored implementation of organic matter degradation models and related processes. A numerical benchmark involving two reactive transport codes (HPx and MIN3P) demonstrates how the process-based simulation of transient variably saturated water flow (Richards equation), solute transport (advection-dispersion equation), heat transfer and diffusion in the gas phase can be combined with a flexible implementation of a soil organic matter degradation model. The benchmark includes the production of leachable organic matter

  3. Data assimilation in a coupled physical-biogeochemical model of the California current system using an incremental lognormal 4-dimensional variational approach: Part 3-Assimilation in a realistic context using satellite and in situ observations

    Science.gov (United States)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    A fully coupled physical and biogeochemical ocean data assimilation system is tested in a realistic configuration of the California Current System using the Regional Ocean Modeling System. In situ measurements for sea surface temperature and salinity as well as satellite observations for temperature, sea level and chlorophyll are used for the year 2000. Initial conditions of the combined physical and biogeochemical state are adjusted at the start of each 3-day assimilation cycle. Data assimilation results in substantial reduction of root-mean-square error (RMSE) over unconstrained model output. RMSE for physical variables is slightly lower when assimilating only physical variables than when assimilating both physical variables and surface chlorophyll. Surface chlorophyll RMSE is lowest when assimilating both physical variables and surface chlorophyll. Estimates of subsurface, nitrate and chlorophyll show modest improvements over the unconstrained model run relative to independent, unassimilated in situ data. Assimilation adjustments to the biogeochemical initial conditions are investigated within different regions of the California Current System. The incremental, lognormal 4-dimensional data assimilation method tested here represents a viable approach to coupled physical biogeochemical state estimation at practical computational cost.

  4. A novel modeling tool with multi-stressor functionality for organic contaminant transport and fate in the Baltic Sea

    Energy Technology Data Exchange (ETDEWEB)

    Undeman, E., E-mail: emma.undeman@itm.su.se [Baltic Nest Institute, Baltic Sea Centre, Stockholm University, 10691 Stockholm (Sweden); Department of Applied Environmental Science, Stockholm University, 11418 Stockholm (Sweden); Gustafsson, E., E-mail: erik.gustafsson@su.se [Baltic Nest Institute, Baltic Sea Centre, Stockholm University, 10691 Stockholm (Sweden); Gustafsson, B.G., E-mail: bo.gustafsson@su.se [Baltic Nest Institute, Baltic Sea Centre, Stockholm University, 10691 Stockholm (Sweden)

    2014-11-01

    The coupled physical–biogeochemical model BALTSEM, previously used to assess nutrient/carbon cycles and eutrophication in the Baltic Sea, has been expanded to include algorithms for calculations of organic contaminant environmental transport and fate. This novel model version (BALTSEM-POP) is evaluated for polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) and hexachlorobenzene (HCB) in Baltic Sea surface water and sediment. Modeled dissolved concentrations are usually within a factor of 2–4 of observed concentrations, however with larger deviations for furans. Calculated concentrations in particulate organic matter are less accurate (within factors of 1–700), likely due to errors in estimated pelagic biomass, particulate matter–water partitioning, and large natural variability in field data. Concentrations in sediments are usually predicted within a factor of 6. The good performance of the model illustrates its usefulness for exploration of contaminant fate in response to variations in nutrient input and climatic conditions in the Baltic Sea marine environment. - Highlights: • A new model for organic chemical transport and fate in the Baltic Sea is presented. • Physical and biogeochemical processes are linked to organic contaminant transport. • The model is evaluated for PCBs, HCB and PCDD/Fs. • The model can predict dissolved concentrations within a factor of ca 2–4. • Predictions for concentrations in particulate matter and sediment are less accurate.

  5. Final Report Coupling in silico microbial models with reactive transport models to predict the fate of contaminants in the subsurface.

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R.

    2012-10-31

    This project successfully accomplished its goal of coupling genome-scale metabolic models with hydrological and geochemical models to predict the activity of subsurface microorganisms during uranium bioremediation. Furthermore, it was demonstrated how this modeling approach can be used to develop new strategies to optimize bioremediation. The approach of coupling genome-scale metabolic models with reactive transport modeling is now well enough established that it has been adopted by other DOE investigators studying uranium bioremediation. Furthermore, the basic principles developed during our studies will be applicable to much broader investigations of microbial activities, not only for other types of bioremediation, but microbial metabolism in diversity of environments. This approach has the potential to make an important contribution to predicting the impact of environmental perturbations on the cycling of carbon and other biogeochemical cycles.

  6. Computational modelling flow and transport

    NARCIS (Netherlands)

    Stelling, G.S.; Booij, N.

    1999-01-01

    Lecture notes CT wa4340. Derivation of equations using balance principles; numerical treatment of ordinary differential equations; time dependent partial differential equations; the strucure of a computer model:DUFLO; usage of numerical models.

  7. Full uncertainty quantification of a regional N2O, NO, NH3 emission and NO3 leaching inventory using the biogeochemical model LandscapeDNDC

    Science.gov (United States)

    Santabarbara, Ignacio; Haas, Edwin

    2016-04-01

    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 spatial scales. Regional inventories require 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 structure, initial condition data and parameter induced uncertainties). In this study we fully quantify uncertainty in regional simulation of the N cycle in arable, grassland and forest soils of Saxony (Germany) using the biogeochemical model LandscapeDNDC. We address model structural uncertainty (MU) by contrasting with Bayes factors two different soil biogeochemistry modules within LandscapeDNDC, the DNDC versus the MeTrx biogeochemistry process description. Initial conditions induced uncertainty (IU) was addressed with the parameter distribution obtained by a Bayesian calibration of soil properties, climate drivers and management practices. The parameter induced uncertainty (PU) was assessed by using a joint parameter distribution for key parameters describing microbial C and N turnover processes as obtained also by a Bayesian calibration study. Once the representative sample size from all parameters, initial conditions and model selection is set, we sampled the different configurations and used these to calculate individual realizations of the regional inventory. The ecosystems considered in this study (forest, arable and grasslands) are given spatially discretized into 8858 polygons (16058 km-2), each representing a unique land use and homogenous soil properties. For the overall uncertainty quantification we calculated

  8. Molecular model of the neural dopamine transporter

    Science.gov (United States)

    Ravna, Aina Westrheim; Sylte, Ingebrigt; Dahl, Svein G.

    2003-05-01

    The dopamine transporter (DAT) regulates the action of dopamine by reuptake of the neurotransmitter into presynaptic neurons, and is the main molecular target of amphetamines and cocaine. DAT and the Na+/H+ antiporter (NhaA) are secondary transporter proteins that carry small molecules across a cell membrane against a concentration gradient, using ion gradients as energy source. A 3-dimensional projection map of the E. coli NhaA has confirmed a topology of 12 membrane spanning domains, and was previously used to construct a 3-dimensional NhaA model with 12 trans-membrane α-helices (TMHs). The NhaA model, and site directed mutagenesis data on DAT, were used to construct a detailed 3-dimensional DAT model using interactive molecular graphics and empiric force field calculations. The model proposes a dopamine transport mechanism involving TMHs 1, 3, 4, 5, 7 and 11. Asp79, Tyr252 and Tyr274 were the primary cocaine binding residues. Binding of cocaine or its analogue, (-)-2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT), seemed to lock the transporter in an inactive state, and thus inhibit dopamine transport. The present model may be used to design further experimental studies of the molecular structure and mechanisms of DAT and other secondary transporter proteins.

  9. Budget of organic carbon in the North-Western Mediterranean open sea over the period 2004-2008 using 3-D coupled physical-biogeochemical modeling

    Science.gov (United States)

    Ulses, C.; Auger, P.-A.; Soetaert, K.; Marsaleix, P.; Diaz, F.; Coppola, L.; Herrmann, M. J.; Kessouri, F.; Estournel, C.

    2016-09-01

    A 3-D hydrodynamic-biogeochemical coupled model has been used to estimate a budget of organic carbon and its interannual variability over the 5 year period 2004-2008 in the North-Western Mediterranean Open Sea (NWMOS). The comparison of its results with in situ and satellite observations reveals that the timing and the magnitude of the convection and bloom processes during the study period, marked by contrasted atmospheric conditions, are reasonably well reproduced by the model. Model outputs show that the amount of nutrients annually injected into the surface layer is clearly linked to the intensity of the events of winter convection. During cold winters, primary production is reduced by intense mixing events but then spectacularly increases when the water column restratifies. In contrast, during mild winters, the primary production progressively and continuously increases, sustained by moderate new production followed by regenerated production. Overall, interannual variability in the annual primary production is low. The export in subsurface and at middepth is however affected by the intensity of the convection process, with annual values twice as high during cold winters than during mild winters. Finally, the estimation of a global budget of organic carbon reveals that the NWMOS acts as a sink for the shallower areas and as a source for the Algerian and Balearic subbasins.

  10. Real time model for public transportation management

    Directory of Open Access Journals (Sweden)

    Ireneusz Celiński

    2014-03-01

    Full Text Available Background: The article outlines managing a public transportation fleet in the dynamic aspect. There are currently many technical possibilities of identifying demand in the transportation network. It is also possible to indicate legitimate basis of estimating and steering demand. The article describes a general public transportation fleet management concept based on balancing demand and supply. Material and methods: The presented method utilizes a matrix description of demand for transportation based on telemetric and telecommunication data. Emphasis was placed mainly on a general concept and not the manner in which data was collected by other researchers.  Results: The above model gave results in the form of a system for managing a fleet in real-time. The objective of the system is also to optimally utilize means of transportation at the disposal of service providers. Conclusions: The presented concept enables a new perspective on managing public transportation fleets. In case of implementation, the project would facilitate, among others, designing dynamic timetables, updated based on observed demand, and even designing dynamic points of access to public transportation lines. Further research should encompass so-called rerouting based on dynamic measurements of the characteristics of the transportation system.

  11. Utilizing Hydrologic and Biogeochemical Observations to Model the Impact of Climate Change on Denitrification Rates Across an Agricultural Watershed in Central New York

    Science.gov (United States)

    Barclay, J. R.; Anderson, T. R.; Archibald, J. A.; Walter, T.

    2012-12-01

    An overabundance of nitrogen (N) in marine and freshwater ecosystems has been linked to diverse effects such as eutrophication and hypoxic dead zones in marine waters, human health issues, marine wildlife mortality, and annual economic losses in excess of $3 billion. One natural process that reduces N loads to downstream waters is denitrification, the microbial process of converting NO3- to N2, NO, or N2O gas. Denitrification rates tend to be highest under conditions of warm temperatures and saturated soil. The distribution of these conditions will be effected by altered precipitation and temperature in future climate scenarios. Our goal is to develop a model to predict how denitrification rates, as well as its spatial and temporal distribution on a watershed scale, will be altered by climate change. We developed a spatially distributed hydrologic and denitrification model of a small agricultural watershed utilizing field measurements of hydrologic and biogeochemical properties and isotopic measurements of denitrification. Looking forward, we used end-of-century climate scenarios to predict changes in denitrification patterns. Our analysis suggests an increase in denitrification due primarily to increased temperatures. Understanding the magnitude and distribution of denitrification rate changes will allow us to better protect this important ecosystem service.

  12. 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.

  13. Calibration and validation of a one-dimensional complex marine biogeochemical flux model in different areas of the northern Adriatic shelf

    Directory of Open Access Journals (Sweden)

    M. Vichi

    Full Text Available In this paper we show results from numerical simulations carried out with a complex biogeochemical fluxes model coupled with a one-dimensional high-resolution hydrodynamical model and implemented at three different locations of the northern Adriatic shelf. One location is directly affected by the Po River influence, one has more open-sea characteristics and one is located in the Gulf of Trieste with an intermediate behavior; emphasis is put on the comparison with observations and on the functioning of the northern Adriatic ecosystem in the three areas. The work has been performed in a climatological context and has to be considered as preliminary to the development of three-dimensional numerical simulations. Biogeochemical model parameterizations have been ameliorated with a detailed description of bacterial substrate utilization associated with the quality of the dissolved organic matter (DOM, in order to improve the models capability in capturing the observed DOM dynamics in the basin. The coupled model has been calibrated and validated at the three locations by means of climatological data sets. Results show satisfactory model behavior in simulating local seasonal dynamics in the limit of the available boundary conditions and the one-dimensional implementation. Comparisons with available measurements of primary and bacterial production and bacterial abundances have been performed in all locations. Model simulated rates and bacterial dynamics are in the same order of magnitude of observations and show a qualitatively correct time evolution. The importance of temperature as a factor controlling bacteria efficiency is investigated with sensitivity experiments on the model parameterizations.

    The different model behavior and pelagic ecosystem structure developed by the model at the three locations can be attributed to the local hydrodynamical features and interactions with external inputs of nutrients. The onset

  14. Radionuclide Transport Models Under Ambient Conditions

    Energy Technology Data Exchange (ETDEWEB)

    G. Moridis; Q. Hu

    2001-12-20

    The purpose of Revision 00 of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada.

  15. Radionuclide Transport Models Under Ambient Conditions

    Energy Technology Data Exchange (ETDEWEB)

    G. Moridis; Q. Hu

    2000-03-12

    The purpose of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada. This is in accordance with the ''AMR Development Plan U0060, Radionuclide Transport Models Under Ambient Conditions'' (CRWMS M and O 1999a). This AMR supports the UZ Flow and Transport Process Model Report (PMR). This AMR documents the UZ Radionuclide Transport Model (RTM). This model considers: the transport of radionuclides through fractured tuffs; the effects of changes in the intensity and configuration of fracturing from hydrogeologic unit to unit; colloid transport; physical and retardation processes and the effects of perched water. In this AMR they document the capabilities of the UZ RTM, which can describe flow (saturated and/or unsaturated) and transport, and accounts for (a) advection, (b) molecular diffusion, (c) hydrodynamic dispersion (with full 3-D tensorial representation), (d) kinetic or equilibrium physical and/or chemical sorption (linear, Langmuir, Freundlich or combined), (e) first-order linear chemical reaction, (f) radioactive decay and tracking of daughters, (g) colloid filtration (equilibrium, kinetic or combined), and (h) colloid-assisted solute transport. Simulations of transport of radioactive solutes and colloids (incorporating the processes described above) from the repository horizon to the water table are performed to support model development and support studies for Performance Assessment (PA). The input files for these simulations include transport parameters obtained from other AMRs (i.e., CRWMS M and O 1999d, e, f, g, h; 2000a, b, c, d). When not available, the parameter values used are obtained from the literature. The results of the simulations are used to evaluate the transport of radioactive

  16. Transport properties site descriptive model. Guidelines for evaluation and modelling

    Energy Technology Data Exchange (ETDEWEB)

    Berglund, Sten [WSP Environmental, Stockholm (Sweden); Selroos, Jan-Olof [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)

    2004-04-01

    This report describes a strategy for the development of Transport Properties Site Descriptive Models within the SKB Site Investigation programme. Similar reports have been produced for the other disciplines in the site descriptive modelling (Geology, Hydrogeology, Hydrogeochemistry, Rock mechanics, Thermal properties, and Surface ecosystems). These reports are intended to guide the site descriptive modelling, but also to provide the authorities with an overview of modelling work that will be performed. The site descriptive modelling of transport properties is presented in this report and in the associated 'Strategy for the use of laboratory methods in the site investigations programme for the transport properties of the rock', which describes laboratory measurements and data evaluations. Specifically, the objectives of the present report are to: Present a description that gives an overview of the strategy for developing Site Descriptive Models, and which sets the transport modelling into this general context. Provide a structure for developing Transport Properties Site Descriptive Models that facilitates efficient modelling and comparisons between different sites. Provide guidelines on specific modelling issues where methodological consistency is judged to be of special importance, or where there is no general consensus on the modelling approach. The objectives of the site descriptive modelling process and the resulting Transport Properties Site Descriptive Models are to: Provide transport parameters for Safety Assessment. Describe the geoscientific basis for the transport model, including the qualitative and quantitative data that are of importance for the assessment of uncertainties and confidence in the transport description, and for the understanding of the processes at the sites. Provide transport parameters for use within other discipline-specific programmes. Contribute to the integrated evaluation of the investigated sites. The site descriptive

  17. 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.

  18. Comparison of Turbulent Transport Models and Transport Simulation of Internal Transport Barrier Formation

    Science.gov (United States)

    Honda, Mitsuru

    2005-10-01

    In order to predict the performance of ITER plasma, it is important to validate the existing theory-based turbulent transport models by systematicallycomparing them with the experimental observations. Taking experimental data from the ITPA profile database, we have carried out transport simulations with the CDBM, GLF23 and Weiland models by the one-dimensional diffusive transport code TASK/TR. The results are evaluated by the six figures of merit as specified in ITER Physics Basis^1. From the simulation on 55 discharges, it is found that each model has unique dependence on devices and operation modes and the CDBM model gives the most satisfactory results. We have incorporated the dependence on the elongation on the CDBM model^2 and confirmed that the accuracy of the prediction is improved for H-mode discharges. Single-particle-species heat transport simulations have indicated that the CDBM model reproduces Ti profiles more accurately than Te profiles. We will also show the results of the predictive simulations coupling TASK/TR and TASK/EQ, two-dimensional equilibrium code, for high performance plasmas with internal transport barriers like the high βp and reversed shear plasmas. [1] ITER Physics Basis Expert Groups, Nucl. Fusion, 39, 2175 (1999) [2] M. Yagi et al., J. Phys. Soc. Japan, 66, 379 (1997)

  19. Comparison of Greenhouse Gas Emissions between Two Dairy Farm Systems (Conventional vs. Organic Management) in New Hampshire Using the Manure DNDC Biogeochemical Model

    Science.gov (United States)

    Dorich, C.; Contosta, A.; Li, C.; Brito, A.; Varner, R. K.

    2013-12-01

    Agriculture contributes 20 to 25 % of the total anthropogenic greenhouse gas (GHG) emissions globally. These agricultural emissions are primarily in the form of methane (CH4) and nitrous oxide (N2O) with these GHG accounting for roughly 40 and 80 % of the total anthropogenic emissions of CH4 and N2O, respectively. Due to varied management and the complexities of agricultural ecosystems, it is difficult to estimate these CH4 and N2O emissions. The IPCC emission factors can be used to yield rough estimates of CH4 and N2O emissions but they are often based on limited data. Accurate modeling validated by measurements is needed in order to identify potential mitigation areas, reduce GHG emissions from agriculture, and improve sustainability of farming practices. The biogeochemical model Manure DNDC was validated using measurements from two dairy farms in New Hampshire, USA in order to quantify GHG emissions under different management systems. One organic and one conventional dairy farm operated by the University of New Hampshire's Agriculture Experiment Station were utilized as the study sites for validation of Manure DNDC. Compilation of management records started in 2011 to provide model inputs. Model results were then compared to field collected samples of soil carbon and nitrogen, above-ground biomass, and GHG fluxes. Fluxes were measured in crop, animal, housing, and waste management sites on the farms in order to examine the entire farm ecosystem and test the validity of the model. Fluxes were measured by static flux chambers, with enteric fermentation measurements being conducted by the SF6 tracer test as well as a new method called Greenfeeder. Our preliminary GHG flux analysis suggests higher emissions than predicted by IPCC emission factors and equations. Results suggest that emissions from manure management is a key concern at the conventional dairy farm while bedded housing at the organic dairy produced large quantities of GHG.

  20. DAC 22 High Speed Civil Transport Model

    Science.gov (United States)

    1992-01-01

    Between tests, NASA research engineer Dave Hahne inspects a tenth-scale model of a supersonic transport model in the 30- by 60-Foot Tunnel at NASA Langley Research Center, Hampton, Virginia. The model is being used in support of NASA's High-Speed Research (HSR) program. Langley researchers are applying advance aerodynamic design methods to develop a wing leading-edge flap system which significantly improves low-speed fuel efficiency and reduces noise generated during takeoff operation. Langley is NASA's lead center for the agency's HSR program, aimed at developing technology to help U.S. industry compete in the rapidly expanding trans-oceanic transport market. A U.S. high-speed civil transport is expected to fly in about the year 2010. As envisioned, it would fly 300 passengers across the Pacific in about four hours at Mach 2.4 (approximately 1,600 mph/1950 kph) for a modest increase over business class fares.

  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. GEOS-5 Chemistry Transport Model User's Guide

    Science.gov (United States)

    Kouatchou, J.; Molod, A.; Nielsen, J. E.; Auer, B.; Putman, W.; Clune, T.

    2015-01-01

    The Goddard Earth Observing System version 5 (GEOS-5) General Circulation Model (GCM) makes use of the Earth System Modeling Framework (ESMF) to enable model configurations with many functions. One of the options of the GEOS-5 GCM is the GEOS-5 Chemistry Transport Model (GEOS-5 CTM), which is an offline simulation of chemistry and constituent transport driven by a specified meteorology and other model output fields. This document describes the basic components of the GEOS-5 CTM, and is a user's guide on to how to obtain and run simulations on the NCCS Discover platform. In addition, we provide information on how to change the model configuration input files to meet users' needs.

  3. Modelling Transition Towards Sustainable Transportation Sector

    DEFF Research Database (Denmark)

    Dominkovic, Dominik Franjo; Bačeković, I.; Mýrdal, Jón Steinar Garðarsson

    2016-01-01

    In a transition towards 100% renewable energy system, transportation sector is rarely dealt withusing the holistic approach and measuring its impact on the whole energy system. Furthermore, assolutions for power and heat sectors are clearer, it is a tendency of the researchers to focus on thelatter...... two energy sectors. In order to deal with the raised issue, authors of this paper developed amethodology for calculation of the transition towards sustainable transport sector, focusing on thesolutions that are already available. Furthermore, as a part of the model, a detailed mapping ofresources...... needed has been carried out for each of the alternatives. It was shown that theelectrification of the transportation sector is a crucial point in transition, while for the transportmodes that cannot be electrified, or shifted to different transportation modes, four alternatives weredefined: synthetic...

  4. Boltzmann Transport in Hybrid PIC HET Modeling

    Science.gov (United States)

    2015-07-01

    Symposium on Space Technology and Science, 34th International Electric Propulsion Conference and 6th Nano-satellite Symposium Hyogo-Kobe, Japan July 4–10...key source of uncertainty inhibiting first-principal simulation of Hall -effect thruster (HET) physics. Fluid electron models depend heavily on the...transport models are a key source of uncertainty inhibiting first- principal simulation of Hall -effect thruster (HET) physics. Fluid electron models

  5. The GiBUU transport model

    Directory of Open Access Journals (Sweden)

    Mosel Ulrich

    2013-06-01

    Full Text Available We give an overview over the hadronic transport model GiBUU as a simulation tool for hadronic and electroweak reactions on nuclei over a wide energy range [1]. The model is able to handle hadron-, photon- and lepton-induced reactions as well as nucleus nucleus collisions from sub-GeV energies up to hundreds of GeV. After a general introduction of the model, we discuss its possible application to cosmic ray air showers.

  6. 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.

  7. The chemical transport model Oslo CTM3

    Directory of Open Access Journals (Sweden)

    O. A. Søvde

    2012-06-01

    Full Text Available We present here the global chemical transport model Oslo CTM3, an update of the Oslo CTM2. The update comprises a faster transport scheme, an improved wet scavenging scheme for large scale rain, updated photolysis rates and a new lightning parameterization. Oslo CTM3 is better parallelized and allows for stable, large time steps for advection, enabling more complex or high resolution simulations. Thorough comparisons between the Oslo CTM3, Oslo CTM2 and measurements are performed, and in general the Oslo CTM3 is found to reproduce measurements well. Inclusion of tropospheric sulfur chemistry and nitrate aerosols in CTM3 is shown to be important to reproduce tropospheric O3, OH and the CH4 lifetime well. Using the same meteorology to drive the two models, shows that some features related to transport are better resolved by the CTM3, such as polar cap transport, while features like transport close to the vortex edge are resolved better in the Oslo CTM2 due to its required shorter transport time step. The longer transport time steps in CTM3 result in larger errors e.g. near the jets, and when necessary, this can be remedied by using a shorter time step. An additional, more accurate and time consuming, treatment of polar cap transport is presented, however, both perform acceptably. A new treatment of the horizontal distribution of lightning is presented and found to compare well with measurements. Vertical distributions of lighting are updated, and tested against the old vertical distribution. The new profiles are found to produce more NOx in the tropical middle troposphere, and less at the surface and at high altitudes.

  8. 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 ...

  9. Simulation of annual biogeochemical cycles of nutrient balance, phytoplankton bloom(s), and DO in Puget Sound using an unstructured grid model

    Energy Technology Data Exchange (ETDEWEB)

    Khangaonkar, Tarang; Sackmann, Brandon; Long, Wen; Mohamedali, Teizeen; Roberts, Mindy

    2012-08-14

    Nutrient pollution from rivers, nonpoint source runoff, and nearly 100 wastewater discharges is a potential threat to the ecological health of Puget Sound with evidence of hypoxia in some basins. However, the relative contributions of loads entering Puget Sound from natural and anthropogenic sources, and the effects of exchange flow from the Pacific Ocean are not well understood. Development of a quantitative model of Puget Sound is thus presented to help improve our understanding of the annual biogeochemical cycles in this system using the unstructured grid Finite-Volume Coastal Ocean Model framework and the Integrated Compartment Model (CE-QUAL-ICM) water quality kinetics. Results based on 2006 data show that phytoplankton growth and die-off, succession between two species of algae, nutrient dynamics, and dissolved oxygen in Puget Sound are strongly tied to seasonal variation of temperature, solar radiation, and the annual exchange and flushing induced by upwelled Pacific Ocean waters. Concentrations in the mixed outflow surface layer occupying approximately 5–20 m of the upper water column show strong effects of eutrophication from natural and anthropogenic sources, spring and summer algae blooms, accompanied by depleted nutrients but high dissolved oxygen levels. The bottom layer reflects dissolved oxygen and nutrient concentrations of upwelled Pacific Ocean water modulated by mixing with biologically active surface outflow in the Strait of Juan de Fuca prior to entering Puget Sound over the Admiralty Inlet. The effect of reflux mixing at the Admiralty Inlet sill resulting in lower nutrient and higher dissolved oxygen levels in bottom waters of Puget Sound than the incoming upwelled Pacific Ocean water is reproduced. Finally, by late winter, with the reduction in algal activity, water column constituents of interest, were renewed and the system appeared to reset with cooler temperature, higher nutrient, and higher dissolved oxygen waters from the Pacific

  10. Error estimation and adaptive chemical transport modeling

    Directory of Open Access Journals (Sweden)

    Malte Braack

    2014-09-01

    Full Text Available We present a numerical method to use several chemical transport models of increasing accuracy and complexity in an adaptive way. In largest parts of the domain, a simplified chemical model may be used, whereas in certain regions a more complex model is needed for accuracy reasons. A mathematically derived error estimator measures the modeling error and provides information where to use more accurate models. The error is measured in terms of output functionals. Therefore, one has to consider adjoint problems which carry sensitivity information. This concept is demonstrated by means of ozone formation and pollution emission.

  11. A mass-conserving advection scheme for offline simulation of scalar transport in coastal ocean models

    Science.gov (United States)

    Gillibrand, P. A.; Herzfeld, M.

    2016-05-01

    We present a flux-form semi-Lagrangian (FFSL) advection scheme designed for offline scalar transport simulation with coastal ocean models using curvilinear horizontal coordinates. The scheme conserves mass, overcoming problems of mass conservation typically experienced with offline transport models, and permits long time steps (relative to the Courant number) to be used by the offline model. These attributes make the method attractive for offline simulation of tracers in biogeochemical or sediment transport models using archived flow fields from hydrodynamic models. We describe the FFSL scheme, and test it on two idealised domains and one real domain, the Great Barrier Reef in Australia. For comparison, we also include simulations using a traditional semi-Lagrangian advection scheme for the offline simulations. We compare tracer distributions predicted by the offline FFSL transport scheme with those predicted by the original hydrodynamic model, assess the conservation of mass in all cases and contrast the computational efficiency of the schemes. We find that the FFSL scheme produced very good agreement with the distributions of tracer predicted by the hydrodynamic model, and conserved mass with an error of a fraction of one percent. In terms of computational speed, the FFSL scheme was comparable with the semi-Lagrangian method and an order of magnitude faster than the full hydrodynamic model, even when the latter ran in parallel on multiple cores. The FFSL scheme presented here therefore offers a viable mass-conserving and computationally-efficient alternative to traditional semi-Lagrangian schemes for offline scalar transport simulation in coastal models.

  12. FORWARD AND INVERSE BIO-GEOCHEMICAL MODELING OF MICROBIALLY INDUCED PRECIPITATION IN 0.5M COLUMNAR EXPERIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Tammer Barkouki; Brian Martinez; Brina Mortensen; Tess Weathers; Jason DeJong; Nic Spycher; Tim Ginn; Yoshiko Fujita; Robert Smith

    2009-09-01

    Microbial ureolysis-induced calcite precipitation may offer an in situ remediation for heavy metal and radionuclide contamination, as well as an alternative to traditional soil strengthening techniques. A microbially mediated calcite precipitation model was built in TOUGHREACT v2 and calibrated to batch and columnar experimental data. Kinetic ureolysis and calcite precipitation-rate expressions were parameterized by coupling TOUCHREACT with UCODE.

  13. Perspectives on the terrestrial organic matter transport and burial along the land-deep sea continuum: Caveats in our understanding of biogeochemical processes and future needs

    Digital Repository Service at National Institute of Oceanography (India)

    Kandasamy, S.; Nath, B.N.

    . Here, we review the export and burial rates of terrestrial organic carbon in the oceans to understand the issue of “missing terrigenous carbon” by comparing data- and model-based estimates of terrestrial carbon fluxes. Our review reveals large...

  14. 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

  15. A depth integrated model for suspended transport

    NARCIS (Netherlands)

    Galappatti, R.

    1983-01-01

    A new depth averaged model for suspended sediment transport in open channels has been developed based on an asymptotic solution to the two dimensional convection-diffusion equation in the vertical plane. The solution for the depth averaged concentration is derived from the bed boundary condition and

  16. Logistics Chains in Freight Transport Modelling

    NARCIS (Netherlands)

    Davydenko, I.Y.

    2015-01-01

    The flow of trade is not equal to transport flows, mainly due to the fact that warehouses and distribution facilities are used as intermediary stops on the way from production locations to the points of consumption or further rework of goods. This thesis proposes a logistics chain model, which estim

  17. Transport properties of fully screened Kondo models

    NARCIS (Netherlands)

    Hörig, Christoph B M; Mora, Christophe; Schuricht, Dirk

    2014-01-01

    We study the nonequilibrium transport properties of fully (exactly) screened Kondo quantum dots subject to a finite bias voltage or a finite temperature. First, we calculate the Fermi-liquid coefficients of the conductance for models with arbitrary spin, i.e., its leading behavior for small bias vol

  18. Equilibrium models in multimodal container transport systems

    NARCIS (Netherlands)

    Corman, F.; Viti, F.; Negenborn, R.R.

    2015-01-01

    Optimizing the performance of multimodal freight transport networks involves adequately balancing the interplay between costs, volumes, times of departure and arrival, and times of travel. In order to study this interplay, we propose an assignment model that is able to efficiently determine flows an

  19. Quantifying metabolic rates in submarine hydrothermal vent chimneys: A reaction transport model

    Science.gov (United States)

    LaRowe, D.; Dale, A.; Aguilera, D.; Amend, J. P.; Regnier, P.

    2012-12-01

    The fluids emanating from active submarine hydrothermal vent chimneys provide a window into subseafloor processes and, through mixing with seawater, are responsible for steep thermal and compositional gradients that provide the energetic basis for diverse biological communities. Although several models have been developed to better understand the dynamic interplay of seawater, hydrothermal fluid, minerals and microorganisms inside chimney walls, none provide a fully integrated approach to quantifying the biogeochemistry of these hydrothermal systems. In an effort to remedy this, a fully coupled biogeochemical reaction transport model of a hydrothermal vent chimney has been developed that explicitly quantifies the rate of microbial catalysis while taking into account geochemical processes such as fluid flow, solute transport and oxidation-reduction reactions associated with fluid mixing as a function of temperature. Methanogenesis, hydrogen oxidation by oxygen and sulfate, sulfide oxidation by oxygen and methane oxidation by oxygen and sulfate are the metabolisms included in the reaction network. Model results indicate that microbial catalysis is fastest in the hottest habitable portion of the vent chimney except for methane oxidation by oxygen, which peaks near the seawater-side of the chimney at 20 nmol /cm^3 yr. The dominant metabolisms in the chimney are hydrogen oxidation by sulfate and oxygen and sulfide oxidation at peak rates 3200 , 300 and 900 nmol /cm^3 yr, respectively. The maximum rate of hydrogenotrophic methanogensis is just under 0.07 nmol /cm^3 yr, the slowest of the metabolisms considered. Due to thermodynamic inhibition, there is no anaerobic oxidation of methane by sulfate (AOM). The model developed here provides a quantitative approach to understanding the rates of biogeochemical transformations in hydrothermal systems and can be used to better understand the role of microbial activity in the deep subsurface.

  20. Biogeochemical Cycles in Degraded Lands

    Science.gov (United States)

    Davidson, Eric A.; Vieira, Ima Celia G.; ReisdeCarvalho, Claudio Jose; DeanedeAbreuSa, Tatiana; deSouzaMoutinho, Paulo R.; Figueiredo, Ricardo O.; Stone, Thomas A.

    2004-01-01

    The objectives of this project were to define and describe the types of landscapes that fall under the broad category of "degraded lands" and to study biogeochemical cycles across this range of degradation found in secondary forests. We define degraded land as that which has lost part of its capacity of renovation of a productive ecosystem, either in the context of agroecosystems or as native communities of vegetation. This definition of degradation permits evaluation of biogeochemical constraints to future land uses.

  1. 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

  2. Modeling nutrient transports and exchanges of nutrients between shallow regions and the open Baltic sea in present and future climate.

    Science.gov (United States)

    Eilola, Kari; Rosell, Elin Almroth; Dieterich, Christian; Fransner, Filippa; Höglund, Anders; Meier, H E Markus

    2012-09-01

    We quantified horizontal transport patterns and the net exchange of nutrients between shallow regions and the open sea in the Baltic proper. A coupled biogeochemical-physical circulation model was used for transient simulations 1961-2100. The model was driven by regional downscaling of the IPCC climate change scenario A1B from two global General Circulation Models in combination with two nutrient load scenarios. Modeled nutrient transports followed mainly the large-scale internal water circulation and showed only small circulation changes in the future projections. The internal nutrient cycling and exchanges between shallow and deeper waters became intensified, and the internal removal of phosphorus became weaker in the warmer future climate. These effects counteracted the impact from nutrient load reductions according to the Baltic Sea Action Plan. The net effect of climate change and nutrient reductions was an increased net import of dissolved inorganic phosphorus to shallow areas in the Baltic proper.

  3. Marine biogeochemical influence on primary sea spray aerosol composition in the Southern Ocean: predictions from a mechanistic model

    Science.gov (United States)

    McCoy, D.; Burrows, S. M.; Elliott, S.; Frossard, A. A.; Russell, L. M.; Liu, X.; Ogunro, O. O.; Easter, R. C.; Rasch, P. J.

    2014-12-01

    Remote marine clouds, such as those over the Southern Ocean, are particularly sensitive to variations in the concentration and chemical composition of aerosols that serve as cloud condensation nuclei (CCN). Observational evidence indicates that the organic content of fine marine aerosol is greatly increased during the biologically active season near strong phytoplankton blooms in certain locations, while being nearly constant in other locations. We have recently developed a novel modeling framework that mechanistically links the organic fraction of submicron sea spray to ocean biogeochemistry (Burrows et al., in discussion, ACPD, 2014; Elliott et al., ERL, 2014). Because of its combination of large phytoplankton blooms and high wind speeds, the Southern Ocean is an ideal location for testing our understanding of the processes driving the enrichment of organics in sea spray aerosol. Comparison of the simulated OM fraction with satellite observations shows that OM fraction is a statistically significant predictor of cloud droplet number concentration over the Southern Ocean. This presentation will focus on predictions from our modeling framework for the Southern Ocean, specifically, the predicted geographic gradients and seasonal cycles in the aerosol organic matter and its functional group composition. The timing and location of a Southern Ocean field campaign will determine its utility in observing the effects of highly localized and seasonal phytoplankton blooms on aerosol composition and clouds. Reference cited: Burrows, S. M., Ogunro, O., Frossard, A. A., Russell, L. M., Rasch, P. J., and Elliott, S.: A physically-based framework for modelling the organic fractionation of sea spray aerosol from bubble film Langmuir equilibria, Atmos. Chem. Phys. Discuss., 14, 5375-5443, doi:10.5194/acpd-14-5375-2014, 2014. Elliott, S., Burrows, S. M., Deal, C., Liu, X., Long, M., Ogunro, O., Russell, L. M., and Wingenter O.. "Prospects for simulating macromolecular surfactant

  4. 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

    . The simulation using the new parameterisation showed good agreement with observation data recorded during winter, whereas the reference simulation did not capture the observed phytoplankton concentrations. The new parameterisation had a strong influence on the carbon export through the sinking of particulate...... 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...

  5. 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.

  6. 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

    2010-01-01

    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.

  7. Modeling nitrogen transport and transformation in aquifers using a particle-tracking approach

    Science.gov (United States)

    Cui, Zhengtao; Welty, Claire; Maxwell, Reed M.

    2014-09-01

    We have integrated multispecies biodegradation and geochemical reactions into an existing particle-tracking code to simulate reactive transport in three-dimensional variably saturated media, with a focus on nitrification and denitrification processes. This new numerical model includes reactive air-phase transport so that gases such as N2 and CO2 can be tracked. Although nitrogen biodegradation is the primary problem addressed here, the method presented is also applicable to other reactive multispecies transport problems. We verified the model by comparison with (1) analytical solutions for saturated one- and two-dimensional cases; (2) a finite element model for a one-dimensional unsaturated case; and (3) laboratory observations for a one-dimensional saturated case. Good agreement between the new code and the verification problems is demonstrated. The new model can simulate nitrogen transport and transformation in a heterogeneous permeability field where sharp concentration gradients are present. An example application to nitrogen species biodegradation and transport of a plume emanating from a leaking sewer in a heterogeneous, variably saturated aquifer is presented to illustrate this capability. This example is a novel application of coupling unsaturated/saturated zone transport with nitrogen species biodegradation. The code has the computational advantages of particle-tracking algorithms, including local and global mass conservation and minimal numerical dispersion. We also present new methods for improving particle code efficiency by implementing the concept of tracking surplus/deficit particles and particle recycling in order to control the growth of particle numbers. The new model retains the advantages of the particle tracking approach such as allowing relatively low spatial and temporal resolutions to be used, while incorporating the robustness of grid-based Monod kinetics to simulate biogeochemical reactions.

  8. ACE-Asia Chemical Transport Modeling Overview

    Science.gov (United States)

    UNO, I.; Chin, M.; Collins, W.; Ginoux, P.; Rasch, P.; Carmichael, G. R.; Yienger, J. J.

    2001-12-01

    ACE-Asia (Asia Pacific Regional Aerosol Characterization Experiment) was designed to increase our understanding of how atmospheric aerosol particles affect the Earth?s climate system. The intensive observation period was carried out during March to May, 2001, and more than 100 researchers from several countries (United States, Japan, Korea, China, and many other Asian countries) participated using aircraft, a research vessel, surface stations and numerical models. Aerosol transport forecast activities played an important role during the ACE-Asia intensive observation period. Three independent modeling groups operated chemical transport models in forecast mode and participated in flight planning activities at the operations center. These models were: MATCH (Model of Atmospheric Transport and Chemistry; Rasch and Collins); GOCART (Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport model; Chin and Ginour) and CFORS (Research Institute for Applied Mechanics, Kyushu University + University of Iowa - Chemical weather FORecast System; Uno, Carmichael and Yienger). The MATCH model used in ACE-Asia was a transport model applied for the Asia region, driven by NCEP forecast meteorology. A unique feature of this model was that it assimilated satellite derived optical depths into its forecast algorithm. The GOCART model provided global aerosol forecast using forecast meteorological fields provided by the Goddard Earth Observing System Data Assimilation System (GEOS DAS). The CFORS model provided regional forecasts using a limited area transport model coupled with Regional Meteorological Modeling System (RAMS), initialized by NCEP and JMA forecasts. All models produced 3-d aerosol forecast products consisting of aerosol mass distributions and optical depths for sulfate, black carbon, organic carbon, sea salt, and dust. In the field these model products were made available to all participating scientists via the Web, and were also presented during the

  9. Numerical modelling of ion transport in flames

    KAUST Repository

    Han, Jie

    2015-10-20

    This paper presents a modelling framework to compute the diffusivity and mobility of ions in flames. The (n, 6, 4) interaction potential is adopted to model collisions between neutral and charged species. All required parameters in the potential are related to the polarizability of the species pair via semi-empirical formulas, which are derived using the most recently published data or best estimates. The resulting framework permits computation of the transport coefficients of any ion found in a hydrocarbon flame. The accuracy of the proposed method is evaluated by comparing its predictions with experimental data on the mobility of selected ions in single-component neutral gases. Based on this analysis, the value of a model constant available in the literature is modified in order to improve the model\\'s predictions. The newly determined ion transport coefficients are used as part of a previously developed numerical approach to compute the distribution of charged species in a freely propagating premixed lean CH4/O2 flame. Since a significant scatter of polarizability data exists in the literature, the effects of changes in polarizability on ion transport properties and the spatial distribution of ions in flames are explored. Our analysis shows that changes in polarizability propagate with decreasing effect from binary transport coefficients to species number densities. We conclude that the chosen polarizability value has a limited effect on the ion distribution in freely propagating flames. We expect that the modelling framework proposed here will benefit future efforts in modelling the effect of external voltages on flames. Supplemental data for this article can be accessed at http://dx.doi.org/10.1080/13647830.2015.1090018. © 2015 Taylor & Francis.

  10. Delft Mass Transport model DMT-2

    Science.gov (United States)

    Ditmar, Pavel; Hashemi Farahani, Hassan; Inacio, Pedro; Klees, Roland; Zhao, Qile; Guo, Jing; Liu, Xianglin; Sun, Yu; Riva, Ricardo; Ran, Jiangjun

    2013-04-01

    Gravity Recovery And Climate Experiment (GRACE) satellite mission has enormously extended our knowledge of the Earth's system by allowing natural mass transport of various origin to be quantified. This concerns, in particular, the depletion and replenishment of continental water stocks; shrinking of polar ice sheets; deformation of the Earth's crust triggered by large earthquakes, and isostatic adjustment processes. A number of research centers compute models of temporal gravity field variations and mass transport, using GRACE data as input. One of such models - Delft Mass Transport model - is being produced at the Delft University of Technology in collaboration with the GNSS Research Center of Wuhan University. A new release of this model, DMT-2, has been produced on the basis of a new (second) release of GRACE level-1b data. This model consists of a time-series of monthly solutions spanning a time interval of more than 8 years, starting from Feb. 2003. Each solution consists of spherical harmonic coefficients up to degree 120. Both unconstrained and optimally filtered solutions are obtained. The most essential improvements of the DMT-2 model, as compared to its predecessors (DMT-1 and DMT-1b), are as follows: (i) improved estimation and elimination of low-frequency noise in GRACE data, so that strong mass transport signals are not damped; (ii) computation of accurate stochastic models of data noise for each month individually with a subsequent application of frequency-dependent data weighting, which allows statistically optimal solutions to be compiled even if data noise is colored and gradually changes in time; (iii) optimized estimation of accelerometer calibration parameters; (iv) incorporation of degree 1 coefficients estimated with independent techniques; (v) usage of state-of-the-art background models to de-alias GRACE data from rapid mass transport signals (this includes the EOT11a model of ocean tides and the latest release of the AOD1B product describing

  11. Symposium on unsaturated flow and transport modeling

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, E.M.; Gee, G.W.; Nelson, R.W. (eds.)

    1982-09-01

    This document records the proceedings of a symposium on flow and transport processes in partially saturated groundwater systems, conducted at the Battelle Seattle Research Center on March 22-24, 1982. The symposium was sponsored by the US Nuclear Regulatory Commission for the purpose of assessing the state-of-the-art of flow and transport modeling for use in licensing low-level nuclear waste repositories in partially saturated zones. The first day of the symposium centered around research in flow through partially saturated systems. Papers were presented with the opportunity for questions following each presentation. In addition, after all the talks, a formal panel discussion was held during which written questions were addressed to the panel of the days speakers. The second day of the Symposium was devoted to solute and contaminant transport in partially saturated media in an identical format. Individual papers are abstracted.

  12. Modeling the growth and constraints of thermophiles and biogeochemical processes in deep-sea hydrothermal environments (Invited)

    Science.gov (United States)

    Holden, J. F.; Ver Eecke, H. C.; Lin, T. J.; Butterfield, D. A.; Olson, E. J.; Jamieson, J.; Knutson, J. K.; Dyar, M. D.

    2010-12-01

    and contain an abundance of Fe(III) oxide and sulfate minerals, especially on surfaces of pore spaces. Hyperthermophilic iron reducers attach to iron oxide particles via cell wall invaginations and pili and reduce the iron through direct contact. The iron is reduced to magnetite, possibly with a maghemite intermediate. Thus iron reducers could outcompete methanogens in low H2, mildly reducing habitats such as Endeavour. Unlike strain JH146, respiration rates per cell were highest near the optimal growth temperature for the iron reducer Hyperthermus strain Ro04 and decreased near the temperature limits for growth. This study highlights the need to model microbe-metal interactions and improve respiration estimates from pure cultures to refine our in situ bioenergetic and habitat models.

  13. Model prodrugs for the intestinal oligopeptide transporter

    DEFF Research Database (Denmark)

    Nielsen, C U; Andersen, R; Brodin, Birger

    2001-01-01

    (sigma*) may influence the acid, water or base catalyzed model drug release rates, when released from series of D-Glu-Ala and D-Asp-Ala pro-moieties. Release rates were investigated in both aqueous solutions with varying pH, ionic strength, and buffer concentrations as well as in in vitro biological...... as Taft (sigma*) values, has a significant influence on the release rate of the model drug.......The human intestinal di/tri-peptide carrier, hPepT1, has been suggested as a target for increasing intestinal transport of low permeability compounds by creating prodrugs designed for the transporter. Model ester prodrugs using the stabilized dipeptides D-Glu-Ala and D-Asp-Ala as pro...

  14. Redox regime shifts in microbially-mediated biogeochemical cycles

    Science.gov (United States)

    Bush, T.; Butler, I. B.; Free, A.; Allen, R. J.

    2015-02-01

    Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the sulfur and nitrogen cycles in the present-day natural environment, and may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

  15. Redox regime shifts in microbially mediated biogeochemical cycles

    Science.gov (United States)

    Bush, T.; Butler, I. B.; Free, A.; Allen, R. J.

    2015-06-01

    Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

  16. 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

    Chlorine is very soluble at a global scale with chloride (Cl-), the dominating form. Because of its high mobility, chlorine is usually perceived as a good conservative tracer in hydrological studies and by analogy as little reactive in biosphere. Since 36Cl can be considered to have the same behaviour than stable Cl, a good knowledge of chlorine distribution between compartments of terrestrial ecosystems is sufficient to calibrate a specific activity model which supposes rapid dilution of 36Cl within the large pool of stable Cl and isotopic equilibrium between compartments. By assuming 36Cl redistribution similar to that of stable Cl at steady-state, specific activity models are simplified interesting tools for regulatory purposes in environmental safety assessment, especially in case of potential long term chronic contamination of agricultural food chain (IAEA, 2010). In many other more complex scenarios (accidental acute release, intermediate time frame, and contrasted natural ecosystems), new information and tools are necessary for improving (radio-)ecological realism, which entails a non-conservative behavior of chlorine. Indeed observed dynamics of chlorine in terrestrial ecosystems is far from a simple equilibrium notably because of natural processes of organic matter (SOM) chlorination mainly occurring in surface soils (Öberg, 1998) and mediated by microbial activities on a large extent (Bastviken et al. 2007). Our recent studies have strengthened the view that an organic cycle for chlorine should now be recognized, in addition to its inorganic cycle. Major results showed that: organochlorine (Clorg) formation occurs in all type of soils and ecosystems (culture, pasture, forest), leading to an average fraction of the total Cl pool in soil of about 80 % (Redon et al., 2012), chlorination in more organic soils over time leads to a larger Clorg pool and in turn to a possible high internal supply of inorganic chlorine (Clin) upon dechlorination. (Gustafsson et

  17. A Radiative Transport Model for Blazars

    Science.gov (United States)

    Lewis, Tiffany; Justin, Finke; Becker, Peter A.

    2017-01-01

    Blazars are observed across the electromagnetic spectrum, often with strong variability throughout. The underlying electron distribution associated with the observed emission is typically not computed from first principles. We start from first-principles to build up a transport model, whose solution is the electron distribution, rather than assuming a convenient functional form. Our analytical transport model considers shock acceleration, adiabatic expansion, stochastic acceleration, Bohm diffusion, and synchrotron radiation. We use this solution to generate predictions for the X-ray spectrum and time lags, and compare the results with data products from BeppoSAX observations of X-ray flares from Mrk 421. This new self-consistent model provides an unprecedented view into the jet physics at play in this source, especially the strength of the shock and stochastic acceleration components and the size of the acceleration region.More recently, we augmented the transport model to incorporate Compton scattering, including Klein-Nishina effects. In this case, an analytical solution cannot be derived, and therefore we obtain the steady-state electron distribution computationally. We compare the resulting radiation spectrum with multi-wavelength data for 3C 279. We show that our new Compton + synchrotron blazar model is the first to successfully fit the FermiLAT gamma-ray data for this source based on a first-principles physical calculation.

  18. Simulating Carbon Sequestration and GHGs Emissions in Abies fabric Forest on the Gongga Mountains Using a Biogeochemical Process Model Forest-DNDC

    Institute of Scientific and Technical Information of China (English)

    LU Xuyang; CHENG Genwei; XIAO Feipeng; HUO Changfu

    2008-01-01

    The process-oriented model Forest-DNDC describing biogeochemical cycling of C and N and GHGs (greenhouse gases) fluxes (CO2, NO and N2O) in forest ecosystems was applied to simulate carbon sequestration and GHGs emissions in Abies fabric forest of the Gongga Mountains at southeastern edge of the Tibetan Plateau. The results indicated that the simulated gross primary production (GPP) of Abies fabric forest was strongly affected by temperature. The annual total GPP was 24,245.3 kg C ha-1 yr-1 for 2005 and 26,318.8 kg C ha-1 yr-1 for 2006, respectively. The annual total net primary production (NPP) was 5,935.5 and 4,882.2 kg C ha-1 yr-1 for 2005 and 2006, and the annual total net ecosystem production (NEP) was 4,815.4 and 3,512.8 kg C ha-1 yr-1 for 2005 and 2006, respectively. The simulated seasonal variation in CO2 emissions generally followed the seasonal variations in temperature and precipitation. The annual total CO2 emissions were 3,109.0 and 4,821.0 kg C ha-1 yr-1 for 2005 and 2006, the simulated annual total N2O emissions from forest soil were 1.47 and 1.36 kg N ha-1 yr-1 for 2005 and 2006, and the annual total NO emissions were 0.09 and 0.12 kg N ha-1 yr-1 for 2005 and 2006, respectively.

  19. Transperitoneal transport of creatinine. A comparison of kinetic models

    DEFF Research Database (Denmark)

    Fugleberg, S; Graff, J; Joffe, P;

    1994-01-01

    Six kinetic models of transperitoneal creatinine transport were formulated and validated on the basis of experimental results obtained from 23 non-diabetic patients undergoing peritoneal dialysis. The models were designed to elucidate the presence or absence of diffusive, non-lymphatic convective...... including all three forms of transport is superior to other models. We conclude that the best model of transperitoneal creatinine transport includes diffusion, non-lymphatic convective transport and lymphatic convective transport....

  20. 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.

  1. 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.

  2. Modelling an Ammonium Transporter with SCLS

    Directory of Open Access Journals (Sweden)

    Angelo Troina

    2009-10-01

    Full Text Available The Stochastic Calculus of Looping Sequences (SCLS is a recently proposed modelling language for the representation and simulation of biological systems behaviour. It has been designed with the aim of combining the simplicity of notation of rewrite systems with the advantage of compositionality. It also allows a rather simple and accurate description of biological membranes and their interactions with the environment.In this work we apply SCLS to model a newly discovered ammonium transporter. This transporter is believed to play a fundamental role for plant mineral acquisition, which takes place in the arbuscular mycorrhiza, the most wide-spread plant-fungus symbiosis on earth. Due to its potential application in agriculture this kind of symbiosis is one of the main focuses of the BioBITs project. In our experiments the passage of NH3 / NH4+ from the fungus to the plant has been dissected in known and hypothetical mechanisms; with the model so far we have been able to simulate the behaviour of the system under different conditions. Our simulations confirmed some of the latest experimental results about the LjAMT2;2 transporter. The initial simulation results of the modelling of the symbiosis process are promising and indicate new directions for biological investigations.

  3. Porting marine ecosystem model spin-up using transport matrices to GPUs

    Directory of Open Access Journals (Sweden)

    E. Siewertsen

    2012-07-01

    Full Text Available We have ported an implementation of the spin-up for marine ecosystem models based on the "Transport Matrix Method" to graphics processing units (GPUs. The original implementation was designed for distributed-memory architectures and uses the PETSc library that is based on the "Message Passing Interface (MPI" standard. The spin-up computes a steady seasonal cycle of the ecosystem tracers with climatological ocean circulation data as forcing. Since the transport is linear with respect to the tracers, the resulting operator is represented in so-called "transport matrices". Each iteration of the spin-up involves two matrix-vector multiplications and the evaluation of the used biogeochemical model. The original code was written in C and Fortran. On the GPU, we use the CUDA standard, a specialized version of the PETSc toolkit and a CUDA Fortran compiler. We describe the extensions to PETSc and the modifications of the original C and Fortran codes that had to be done. Here we make use of freely available libraries for the GPU. We analyze the computational effort of the main parts of the spin-up for two exemplary ecosystem models and compare the overall computational time to those necessary on different CPUs. The results show that a consumer GPU can beat a significant number of cluster CPUs without further code optimization.

  4. Variational multiscale models for charge transport.

    Science.gov (United States)

    Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

    2012-01-01

    This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle

  5. Assessment of the sea-ice carbon pump: Insights from a three-dimensional ocean-sea-ice-biogeochemical model (MPIOM/HAMOCC

    Directory of Open Access Journals (Sweden)

    R. Grimm

    2016-11-01

    Full Text Available Abstract It has been suggested that geochemical processes related to sea-ice growth and melt might be important for the polar carbon cycle via the so called sea-ice carbon pump (SICP. The SICP affects the air-sea CO2 exchange by influencing the composition of dissolved inorganic carbon (DIC and total alkalinity (TA in the surface ocean. Here we quantify the strength of the SICP-induced air-sea CO2 flux using the global three-dimensional ocean-sea-ice-biogeochemical model MPIOM/HAMOCC. Simulations prescribing the range of observed DIC and TA concentrations in the sea ice were performed under two idealized climate scenarios for the present-day and the future oceanic and sea-ice state, both forced with a fixed atmospheric CO2 concentration. Model results indicate that the SICP-induced air-sea CO2 uptake increases with higher ratios of TA:DIC prescribed in the sea ice relative to the basic oceanic TA:DIC ratios. Independent of the modeled scenario, the simulated strength of the SICP is larger in the Antarctic than in the Arctic, because of more efficient export of brine-associated DIC from the Antarctic mixed layer. On an annual basis, we generally find an enhanced SICP-induced oceanic CO2 uptake in regions with net sea-ice melt, and enhanced SICP-induced oceanic CO2 out-gassing in regions with net sea-ice growth. These general regional patterns are modified further by the blockage of air-sea gas exchange through sea-ice coverage. Integrated over the sea-ice zones of both hemispheres, the SICP-induced oceanic CO2 uptake ranges from 2 to 14 Tg C yr−1, which is up to 7% of the simulated net CO2 uptake in polar regions, but far less than 1% of the current global oceanic CO2 uptake. Hence, while we find that the SICP plays a minor role in the modern global carbon cycle, it is of importance for the regional carbon cycle at high latitudes.

  6. Extracellular Electron Transport Coupling Biogeochemical Processes Centimeters

    DEFF Research Database (Denmark)

    Risgaard-Petersen, Nils; Fossing, Henrik; Christensen, Peter Bondo;

    2010-01-01

    Recent observations in marine sediment have revealed  conductive networks transmitting electrons from oxidation processes in the anoxic zone to oxygen reduction in the oxiczone [1]. The electrochemical processes and conductors seem to be biologically controlled and may account for more than half...... confirmed the depth range of the electric communication and indicated donation of electrons directly from organotrophic bacteria. The separation of oxidation and reduction processes created steep pH gradients eventually causing carbonate precipitation at the surface. The results indicate that electron...... of the oxygen uptake in laboratory incubations of initially homogenized and stabilized sediment. Using microsensors and process rate measurements we further investigated the effect of the electric currents on sediment biogeochemistry. Dissolved sulfide readily donated electrons to the networks and could...

  7. Meeting in Turkey: WASP Transport Modeling and WASP Ecological Modeling

    Science.gov (United States)

    A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...

  8. Model for radionuclide transport in running waters

    Energy Technology Data Exchange (ETDEWEB)

    Jonsson, Karin; Elert, Mark [Kemakta Konsult AB, Stockholm (Sweden)

    2005-11-15

    Two sites in Sweden are currently under investigation by SKB for their suitability as places for deep repository of radioactive waste, the Forsmark and Simpevarp/Laxemar area. As a part of the safety assessment, SKB has formulated a biosphere model with different sub-models for different parts of the ecosystem in order to be able to predict the dose to humans following a possible radionuclide discharge from a future deep repository. In this report, a new model concept describing radionuclide transport in streams is presented. The main difference from the previous model for running water used by SKB, where only dilution of the inflow of radionuclides was considered, is that the new model includes parameterizations also of the exchange processes present along the stream. This is done in order to be able to investigate the effect of the retention on the transport and to be able to estimate the resulting concentrations in the different parts of the system. The concentrations determined with this new model could later be used for order of magnitude predictions of the dose to humans. The presented model concept is divided in two parts, one hydraulic and one radionuclide transport model. The hydraulic model is used to determine the flow conditions in the stream channel and is based on the assumption of uniform flow and quasi-stationary conditions. The results from the hydraulic model are used in the radionuclide transport model where the concentration is determined in the different parts of the stream ecosystem. The exchange processes considered are exchange with the sediments due to diffusion, advective transport and sedimentation/resuspension and uptake of radionuclides in biota. Transport of both dissolved radionuclides and sorbed onto particulates is considered. Sorption kinetics in the stream water phase is implemented as the time scale of the residence time in the stream water probably is short in comparison to the time scale of the kinetic sorption. In the sediment

  9. Regional CO2 flux estimates from estuarine environments: a reactive-transport modeling approach

    Science.gov (United States)

    Goossens, Nicolas; Laruelle, Goulven G.; Arndt, Sandra; Regnier, Pierre

    2013-04-01

    Estuaries are key components of the land-ocean continuum and play an important role in the global carbon cycle. Large amounts of terrestrial carbon are channelled through estuaries before reaching the ocean. During estuarine transit, numerous biogeochemical processes transform the carbon flux, resulting in a significant CO2 evasion flux to the atmosphere. The global estuarine CO2 outgassing is evaluated at 0.25±0.25 PgC yr-1. Yet, these estimates rely on the extrapolation of local measurements and the scarcity of such measurements conducts to large uncertainties. Furthermore, the global quantification is biased towards anthropogenically impacted estuarine systems located in industrialized countries. Here we provide a first assessment of the estuarine carbon budget and, in particular, CO2 evasion fluxes using a generic and effective reactive-transport model (RTM) approach that is applicable at the regional scale. The new approach is based on the mutual dependency between estuarine geometry and hydrodynamics and uses idealized estuarine geometries. Global river databases (GLORICH) and watershed model outputs (GlobalNEWS) are used to quantify input fluxes for the generic estuarine model. The new modeling approach provides not only a quantification of the estuarine carbon budget, but also allows disentangling the relative contributions of biogeochemical and physical processes to estuarine CO2 emissions. Preliminary results are presented for the North Eastern coast of the US. Model results are consistent with observations and indicate that the net heterotrophy of these systems is the major contributor to estuarine CO2 fluxes (>50%), followed by outgassing of supersaturated riverine waters and nitrification. Results also highlight the strong seasonality in the biogeochemical dynamics. In addition, significant heterogeneity is observed across different estuaries due to spatial heterogeneities in climate forcing, estuarine geometry or riverine input fluxes. The proposed

  10. Understanding transport in model water desalination membranes

    Science.gov (United States)

    Chan, Edwin

    Polyamide based thin film composites represent the the state-of-the-art nanofiltration and reverse osmosis membranes used in water desalination. The performance of these membranes is enabled by the ultrathin (~100 nm) crosslinked polyamide film in facilitating the selective transport of water over salt ions. While these materials have been refined over the last several decades, understanding the relationships between polyamide structure and membrane performance remains a challenge because of the complex and heterogeneous nature of the polyamide film. In this contribution, we present our approach to addressing this challenge by studying the transport properties of model polyamide membranes synthesized via molecular layer-by-layer (mLbL) assembly. First, we demonstrate that mLbL can successfully construct polyamide membranes with well-defined nanoscale thickness and roughness using a variety of monomer formulations. Next, we present measurement tools for characterizing the network structure and transport of these model polyamide membranes. Specifically, we used X-ray and neutron scattering techniques to characterize their structure as well as a recently-developed indentation based poromechanics approach to extrapolate their water diffusion coefficient. Finally, we illustrate how these measurements can provide insight into the original problem by linking the key polyamide network properties, i.e. water-polyamide interaction parameter and characteristic network mesh size, to the membrane performance.

  11. Transport model of underground sediment in soils.

    Science.gov (United States)

    Jichao, Sun; Guangqian, Wang

    2013-01-01

    Studies about sediment erosion were mainly concentrated on the river channel sediment, the terrestrial sediment, and the underground sediment. The transport process of underground sediment is studied in the paper. The concept of the flush potential sediment is founded. The transport equation with stable saturated seepage is set up, and the relations between the flush potential sediment and water sediment are discussed. Flushing of underground sediment begins with small particles, and large particles will be taken away later. The pore ratio of the soil increases gradually. The flow ultimately becomes direct water seepage, and the sediment concentration at the same position in the water decreases over time. The concentration of maximal flushing potential sediment decreases along the path. The underground sediment flushing model reflects the flushing mechanism of underground sediment.

  12. Io Volcanism: Modeling Vapor And Heat Transport

    Science.gov (United States)

    Allen, Daniel R.; Howell, R. R.

    2010-10-01

    Loki is a large, active volcanic source on Jupiter's moon, Io, whose overall temperatures are well explained by current cooling models, but there are unexplainable subtleties. Using the SO2 atmospheric models of Ingersoll (1989) as a starting point, we are investigating how volatiles, specifically sulfur, are transported on the surface and how they modify the temperatures at Loki and other volcanoes. Voyager images reveal light colored deposits, colloquially called "sulfur bergs,” on Loki's dark patera floor that may be sulfur fumaroles. Galileo images show the presence of red short-chain sulfur deposits around the patera. We are investigating the mechanisms that lead to these features. The light deposits are a few kilometers across. Calculations of the mean free paths for day time conditions on Io indicate lengths on the order of 0.1 km while poorly constrained night time conditions indicate mean free paths about 100 times greater, on the order of what is needed to produce the deposits under ballistic conditions. Preliminary calculations reveal horizontal transport length scales for diffuse transport in a collisional atmosphere of approximately 30 km for sublimating S8 sulfur at 300 K. These length scales would be sufficient to move the sulfur from the warm patera floor to the locations of the red sulfur deposits. At a typical Loki temperature of 300 K, the sublimation/evaporation rate of S8 is a few tens of microns/day. It then requires just a few days to deposit an optically thick 100 µm layer of material. Preliminary length scales and sublimation rates are thus of sufficient scale to produce the deposits. Investigations into the sulfur transport and its effect on temperature are ongoing.

  13. 3 Lectures: "Lagrangian Models", "Numerical Transport Schemes", and "Chemical and Transport Models"

    Science.gov (United States)

    Douglass, A.

    2005-01-01

    The topics for the three lectures for the Canadian Summer School are Lagrangian Models, numerical transport schemes, and chemical and transport models. In the first lecture I will explain the basic components of the Lagrangian model (a trajectory code and a photochemical code), the difficulties in using such a model (initialization) and show some applications in interpretation of aircraft and satellite data. If time permits I will show some results concerning inverse modeling which is being used to evaluate sources of tropospheric pollutants. In the second lecture I will discuss one of the core components of any grid point model, the numerical transport scheme. I will explain the basics of shock capturing schemes, and performance criteria. I will include an example of the importance of horizontal resolution to polar processes. We have learned from NASA's global modeling initiative that horizontal resolution matters for predictions of the future evolution of the ozone hole. The numerical scheme will be evaluated using performance metrics based on satellite observations of long-lived tracers. The final lecture will discuss the evolution of chemical transport models over the last decade. Some of the problems with assimilated winds will be demonstrated, using satellite data to evaluate the simulations.

  14. A disaggregate freight transport model of transport chain and shipment size choice

    NARCIS (Netherlands)

    Windisch, E.; De Jong, G.C.; Van Nes, R.; Hoogendoorn, S.P.

    2010-01-01

    The field of freight transport modelling is relatively young compared to passenger transport modelling. However, some key issues in freight policy, like growing freight shares on the road, advanced logistics concepts or emerging strict freight transport regulations, have been creating increasing dem

  15. Quantifying methane emissions from rice fields in the Taihu Lake region, China by coupling a detailed soil database with biogeochemical model

    Directory of Open Access Journals (Sweden)

    L. Zhang

    2009-05-01

    Full Text Available As China has approximately 22% of the world's rice paddies, the regional quantification of CH4 emissions from these paddies is important in determining their contribution to the global greenhouse gas effect. This paper reports the use of a biogeochemical model (DeNitrification and DeComposition or DNDC for quantifying CH4 emissions from rice fields in the Taihu Lake region of China. For this application, the DNDC model was linked to a 1:50 000 soil database derived from 1107 paddy soil profiles compiled during the Second National Soil Survey of China in the 1980s–1990s. The simulated results showed that the 2.3 Mha of paddy rice fields in the Taihu Lake region emitted the equivalent of 5.7 Tg C from 1982–2000, with the average CH4 flux ranging from 114 to 138 kg C ha−1 y−1. As for soil subgroups, the highest emission rate (660 kg C ha−1 y−1 was linked to gleyed paddy soils accounting for about 4.4% of the total area of paddy soils. The lowest emission rate (91 kg C ha−1 y−1 was associated with degleyed paddy soils accounting for about 18% of the total area of paddy soils. The most common soil in the area was hydromorphic paddy soils, which accounted for about 53% of the total area of paddy soils with a CH4 flux of 106 kg C ha−1 y−1. On a regional basis, the annual averaged CH4 flux in the Taihu Lake plain soil region and alluvial plain soil region were higher than that in the low mountainous and hilly soil region and the polder soil region. The model simulation was conducted with two databases using polygons or counties as the basic units. The county-based database contained soil information coarser than the polygon system built based on the 1:50 000 soil database. The modeled results with the two databases found similar spatial patterns of CH4 emissions in the Taihu

  16. Modeling charge transport in organic photovoltaic materials.

    Science.gov (United States)

    Nelson, Jenny; Kwiatkowski, Joe J; Kirkpatrick, James; Frost, Jarvist M

    2009-11-17

    The performance of an organic photovoltaic cell depends critically on the mobility of charge carriers within the constituent molecular semiconductor materials. However, a complex combination of phenomena that span a range of length and time scales control charge transport in disordered organic semiconductors. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. This Account describes a set of computational methods, specifically molecular modeling methods, to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport. Using case studies, we show how this combination of methods can reproduce experimental mobilities with few or no fitting parameters. Although currently applied to material systems of high symmetry or well-defined structure, further developments of this approach could address more complex systems such anisotropic or multicomponent solids and conjugated polymers. Even with an approximate treatment of packing disorder, these computational methods simulate experimental mobilities within an order of magnitude at high electric fields. We can both reproduce the relative values of electron and hole mobility in a conjugated small molecule and rationalize those values based on the symmetry of frontier orbitals. Using fully atomistic molecular dynamics simulations of molecular packing, we can quantitatively replicate vertical charge transport along stacks of discotic liquid crystals which vary only in the structure of their side chains. We can reproduce the trends in mobility with molecular weight for self-organizing polymers using a cheap, coarse

  17. Risk management model in road transport systems

    Science.gov (United States)

    Sakhapov, R. L.; Nikolaeva, R. V.; Gatiyatullin, M. H.; Makhmutov, M. M.

    2016-08-01

    The article presents the results of a study of road safety indicators that influence the development and operation of the transport system. Road safety is considered as a continuous process of risk management. Authors constructed a model that relates the social risks of a major road safety indicator - the level of motorization. The model gives a fairly accurate assessment of the level of social risk for any given level of motorization. Authors calculated the dependence of the level of socio-economic costs of accidents and injured people in them. The applicability of the concept of socio-economic damage is caused by the presence of a linear relationship between the natural and economic indicators damage from accidents. The optimization of social risk is reduced to finding the extremum of the objective function that characterizes the economic effect of the implementation of measures to improve safety. The calculations make it possible to maximize the net present value, depending on the costs of improving road safety, taking into account socio-economic damage caused by accidents. The proposed econometric models make it possible to quantify the efficiency of the transportation system, allow to simulate the change in road safety indicators.

  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. Modeling in transport phenomena a conceptual approach

    CERN Document Server

    Tosun, Ismail

    2007-01-01

    Modeling in Transport Phenomena, Second Edition presents and clearly explains with example problems the basic concepts and their applications to fluid flow, heat transfer, mass transfer, chemical reaction engineering and thermodynamics. A balanced approach is presented between analysis and synthesis, students will understand how to use the solution in engineering analysis. Systematic derivations of the equations and the physical significance of each term are given in detail, for students to easily understand and follow up the material. There is a strong incentive in science and engineering to

  20. Porting marine ecosystem model spin-up using transport matrices to GPUs

    Directory of Open Access Journals (Sweden)

    E. Siewertsen

    2013-01-01

    Full Text Available We have ported an implementation of the spin-up for marine ecosystem models based on transport matrices to graphics processing units (GPUs. The original implementation was designed for distributed-memory architectures and uses the Portable, Extensible Toolkit for Scientific Computation (PETSc library that is based on the Message Passing Interface (MPI standard. The spin-up computes a steady seasonal cycle of ecosystem tracers with climatological ocean circulation data as forcing. Since the transport is linear with respect to the tracers, the resulting operator is represented by matrices. Each iteration of the spin-up involves two matrix-vector multiplications and the evaluation of the used biogeochemical model. The original code was written in C and Fortran. On the GPU, we use the Compute Unified Device Architecture (CUDA standard, a customized version of PETSc and a commercial CUDA Fortran compiler. We describe the extensions to PETSc and the modifications of the original C and Fortran codes that had to be done. Here we make use of freely available libraries for the GPU. We analyze the computational effort of the main parts of the spin-up for two exemplar ecosystem models and compare the overall computational time to those necessary on different CPUs. The results show that a consumer GPU can compete with a significant number of cluster CPUs without further code optimization.

  1. Model of reversible vesicular transport with exclusion

    Science.gov (United States)

    Bressloff, Paul C.; Karamched, Bhargav R.

    2016-08-01

    A major question in neurobiology concerns the mechanics behind the motor-driven transport and delivery of vesicles to synaptic targets along the axon of a neuron. Experimental evidence suggests that the distribution of vesicles along the axon is relatively uniform and that vesicular delivery to synapses is reversible. A recent modeling study has made explicit the crucial role that reversibility in vesicular delivery to synapses plays in achieving uniformity in vesicle distribution, so called synaptic democracy (Bressloff et al 2015 Phys. Rev. Lett. 114 168101). In this paper we generalize the previous model by accounting for exclusion effects (hard-core repulsion) that may occur between molecular motor-cargo complexes (particles) moving along the same microtubule track. The resulting model takes the form of an exclusion process with four internal states, which distinguish between motile and stationary particles, and whether or not a particle is carrying vesicles. By applying a mean field approximation and an adiabatic approximation we reduce the system of ODEs describing the evolution of occupation numbers of the sites on a 1D lattice to a system of hydrodynamic equations in the continuum limit. We find that reversibility in vesicular delivery allows for synaptic democracy even in the presence of exclusion effects, although exclusion does exacerbate nonuniform distributions of vesicles in an axon when compared with a model without exclusion. We also uncover the relationship between our model and other models of exclusion processes with internal states.

  2. 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

    and the contaminant flux out of the clay system are assessed for different distributions of microbial degradation. Results from a set of scenarios show that time to remove 90% of the initial mass is halved when dechlorination occurs in a 5 cm reaction zone in the clay at the fracture-matrix interface (from 419 to 195...... 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...... 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...

  3. Experimental & Numerical Modeling of Non-combusting Model Firebrands' Transport

    Science.gov (United States)

    Tohidi, Ali; Kaye, Nigel

    2016-11-01

    Fire spotting is one of the major mechanisms of wildfire spread. Three phases of this phenomenon are firebrand formation and break-off from burning vegetation, lofting and downwind transport of firebrands through the velocity field of the wildfire, and spot fire ignition upon landing. The lofting and downwind transport phase is modeled by conducting large-scale wind tunnel experiments. Non-combusting rod-like model firebrands with different aspect ratios are released within the velocity field of a jet in a boundary layer cross-flow that approximates the wildfire velocity field. Characteristics of the firebrand dispersion are quantified by capturing the full trajectory of the model firebrands using the developed image processing algorithm. The results show that the lofting height has a direct impact on the maximum travel distance of the model firebrands. Also, the experimental results are utilized for validation of a highly scalable coupled stochastic & parametric firebrand flight model that, couples the LES-resolved velocity field of a jet-in-nonuniform-cross-flow (JINCF) with a 3D fully deterministic 6-degrees-of-freedom debris transport model. The validation results show that the developed numerical model is capable of estimating average statistics of the firebrands' flight. Authors would like to thank support of the National Science Foundation under Grant No. 1200560. Also, the presenter (Ali Tohid) would like to thank Dr. Michael Gollner from the University of Maryland College Park for the conference participation support.

  4. Benchmarking reactive transport models at a hillslope scale

    Science.gov (United States)

    Kalbacher, T.; He, W.; Nixdorf, E.; Jang, E.; Fleckenstein, J. H.; Kolditz, O.

    2015-12-01

    The hillslope scale is an important transition between the field scale and the catchment scale. The water flow in the unsaturated zone of a hillslope can be highly dynamic, which can lead to dynamic changes of groundwater flow or stream outflow. Additionally, interactions among host rock formation, soil properties and recharge water from precipitation or anthropogenic activities (mining, agriculture etc.) can influence the water quality of groundwater and stream in the long term. To simulate reactive transport processes at such a scale is a challenging task. On the one hand, simulation of water flow in a coupled soil-aquifer system often involves solving of highly non-linear PDEs such as Richards equation; on the other hand, one has to consider complicated biogeochemical reactions (e.g. water-rock interactions, biological degradation, redox reactions). Both aspects are computationally expensive and have high requirements on the numerical precision and stabilities of the employed code. The primary goals of this study are as follows: i) Identify the bottlenecks and quantitatively analyse their influence on simulation of biogeochemical reactions at a hillslope scale; ii) find or suggest practical strategies to deal with these bottlenecks, thus to provide detailed hints for future improvements of reactive transport simulators. To achieve these goals, the parallelized reactive transport simulator OGS#IPhreeqc has been applied to simulate two benchmark examples. The first example is about uranium leaching based on Šimůnek et al. (2012), which considers the leaching of uranium from a mill tailing and accompanied mineral dissolution/precipitation. The geochemical system is then extended to include redox reactions in the second example. Based on these examples, the numerical stability and parallel performance of the tool is analysed. ReferenceŠimůnek, J., Jacques, D., Šejna, M., van Genuchten, M. T.: The HP2 program for HYDRUS (2D/3D), A coupled code for simulating two

  5. Documentation of TRU biological transport model (BIOTRAN)

    Energy Technology Data Exchange (ETDEWEB)

    Gallegos, A.F.; Garcia, B.J.; Sutton, C.M.

    1980-01-01

    Inclusive of Appendices, this document describes the purpose, rationale, construction, and operation of a biological transport model (BIOTRAN). This model is used to predict the flow of transuranic elements (TRU) through specified plant and animal environments using biomass as a vector. The appendices are: (A) Flows of moisture, biomass, and TRU; (B) Intermediate variables affecting flows; (C) Mnemonic equivalents (code) for variables; (D) Variable library (code); (E) BIOTRAN code (Fortran); (F) Plants simulated; (G) BIOTRAN code documentation; (H) Operating instructions for BIOTRAN code. The main text is presented with a specific format which uses a minimum of space, yet is adequate for tracking most relationships from their first appearance to their formulation in the code. Because relationships are treated individually in this manner, and rely heavily on Appendix material for understanding, it is advised that the reader familiarize himself with these materials before proceeding with the main text.

  6. A Theoretic Model of Transport Logistics Demand

    OpenAIRE

    Natalija Jolić; Nikolina Brnjac; Ivica Oreb

    2006-01-01

    Concerning transport logistics as relation between transportand integrated approaches to logistics, some transport and logisticsspecialists consider the tenn tautological. However,transport is one of the components of logistics, along with inventories,resources, warehousing, infonnation and goods handling.Transport logistics considers wider commercial and operationalframeworks within which the flow of goods is plannedand managed. The demand for transport logistics services canbe valorised as ...

  7. Numerical Modelling Approaches for Sediment Transport in Sewer Systems

    DEFF Research Database (Denmark)

    Mark, Ole

    A study of the sediment transport processes in sewers has been carried out. Based on this study a mathematical modelling system has been developed to describe the transport processes of sediments and dissolved matter in sewer systems. The modelling system consists of three sub-models which...... constitute the basic modelling system necessary to give a discription of the most dominant physical transport processes concerning particles and dissolved matter in sewer systems: A surface model. An advection-dispersion model. A sediment transport model....

  8. Ecosystem element transport model for Lake Eckarfjaerden

    Energy Technology Data Exchange (ETDEWEB)

    Konovalenko, L.; Bradshaw, C. [The Department of Ecology, Environment and Plant Sciences, Stockholm University (Sweden); Andersson, E.; Kautsky, U. [Swedish Nuclear Fuel and Waste Management Co. - SKB (Sweden)

    2014-07-01

    The ecosystem transport model of elements was developed for Lake Eckarfjaerden located in the Forsmark area in Sweden. Forsmark has currently a low level repository (SFR) and a repository for spent fuel is planned. A large number of data collected during site-investigation program 2002-2009 for planning the repository were available for the creation of the compartment model based on carbon circulation, physical and biological processes (e.g. primary production, consumption, respiration). The model is site-specific in the sense that the food web model is adapted to the actual food web at the site, and most estimates of biomass and metabolic rates for the organisms and meteorological data originate from site data. The functional organism groups of Lake Eckarfjaerden were considered as separate compartments: bacterio-plankton, benthic bacteria, macro-algae, phytoplankton, zooplankton, fish, benthic fauna. Two functional groups of bacteria were taken into account for the reason that they have the highest biomass of all functional groups during the winter, comprising 36% of the total biomass. Effects of ecological parameters, such as bacteria and algae biomass, on redistribution of a hypothetical radionuclide release in the lake were examined. The ecosystem model was used to estimate the environmental transfer of several elements (U, Th, Ra) and their isotopes (U-238, U-234,Th-232, Ra-226) to various aquatic organisms in the lake, using element-specific distribution coefficients for suspended particle and sediment. Results of chemical analyses of the water, sediment and biota were used for model validation. The model gives estimates of concentration factors for fish based on modelling rather on in situ measurement, which reduces the uncertainties for many radionuclides with scarce of data. Document available in abstract form only. (authors)

  9. Measurement and modeling of oil slick transport

    Science.gov (United States)

    Jones, Cathleen E.; Dagestad, Knut-Frode; Breivik, Åyvind; Holt, Benjamin; Röhrs, Johannes; Christensen, Kai Hâkon; Espeseth, Martine; Brekke, Camilla; Skrunes, Stine

    2016-10-01

    Transport characteristics of oil slicks are reported from a controlled release experiment conducted in the North Sea in June 2015, during which mineral oil emulsions of different volumetric oil fractions and a look-alike biogenic oil were released and allowed to develop naturally. The experiment used the Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) to track slick location, size, and shape for ˜8 h following release. Wind conditions during the exercise were at the high end of the range considered suitable for radar-based slick detection, but the slicks were easily detectable in all images acquired by the low noise, L-band imaging radar. The measurements are used to constrain the entrainment length and representative droplet radii for oil elements in simulations generated using the OpenOil advanced oil drift model. Simultaneously released drifters provide near-surface current estimates for the single biogenic release and one emulsion release, and are used to test model sensitivity to upper ocean currents and mixing. Results of the modeling reveal a distinct difference between the transport of the biogenic oil and the mineral oil emulsion, in particular in the vertical direction, with faster and deeper entrainment of significantly smaller droplets of the biogenic oil. The difference in depth profiles for the two types of oils is substantial, with most of the biogenic oil residing below depths of 10 m, compared to the majority of the emulsion remaining above 10 m depth. This difference was key to fitting the observed evolution of the two different types of slicks.

  10. A depth-averaged two-dimensional sediment transport model for environmental studies in the Scheldt Estuary and tidal river network

    Science.gov (United States)

    Gourgue, O.; Baeyens, W.; Chen, M. S.; de Brauwere, A.; de Brye, B.; Deleersnijder, E.; Elskens, M.; Legat, V.

    2013-12-01

    This paper presents the sediment module designed for the two-dimensional depth-averaged and one-dimensional section-averaged components of the finite-element model SLIM (Second-generation Louvain-la-Neuve Ice-ocean Model) in the framework of its application to the tidal part of the Scheldt Basin. This sediment transport module focuses on fine-grained, cohesive sediments. It is a necessary tool to undertake environmental biogeochemical studies, in which fine sediment dynamics play a crucial role.

  11. Complexities in coastal sediment transport studies by numerical modelling

    Digital Repository Service at National Institute of Oceanography (India)

    Ilangovan, D.; ManiMurali, R.

    Marine environmental studies related to erosion, accretion, pollution transport, dredge disposal, location of seawater intake, effluent disposal, etc., involve sediment transport studies. Numerical models use set of well linked mathematical...

  12. Modeling Transport of Flushed Reservoir Sediment

    Science.gov (United States)

    Dubinski, I. M.

    2014-12-01

    Drawdown flushing of a reservoir is often part of a reservoir sediment management program. Flushing can deliver higher than normal sediment loads to the river channel located downstream of a reservoir. The flushed sediment may contain a higher proportion of finer sediment than what was delivered to a channel prior to the presence of the reservoir. The extent of long-term impacts caused by the flushed sediment on the channel morphology and habitat will in part depend on the residence time of the sediment within the channel. In this study we used MIKE 21C to model the fate of flushed sediment through a river channel where the bed material consists of an armoring layer of gravels overlying finer sediment. MIKE 21C is a two-dimensional curvilinear morphological model for rivers developed by DHI. Curvilinear means that the model grid may curve to better follow the channel and flow direction, for example in a meandering channel. Multiple bed material layers are included in the model to represent the armoring and underlying layers existing in the bed separately from the overlying flushed sediment. These layers may also mix. The nature of the interactions between these two layers helps regulate transport and deposition of the flushed sediment, thus are critical to assessing the fate of the flushed sediment and associated potential impacts.

  13. Modeling sediment transport in river networks

    Science.gov (United States)

    Wang, Xu-Ming; Hao, Rui; Huo, Jie; Zhang, Jin-Feng

    2008-11-01

    A dynamical model is proposed to study sediment transport in river networks. A river can be divided into segments by the injection of branch streams of higher rank. The model is based on the fact that in a real river, the sediment-carrying capability of the stream in the ith segment may be modulated by the undergone state, which may be erosion or sedimentation, of the i-1th and ith segments, and also influenced by that of the ith injecting branch of higher rank. We select a database about the upper-middle reach of the Yellow River in the lower-water season to test the model. The result shows that the data, produced by averaging the erosion or sedimentation over the preceding transient process, are in good agreement with the observed average in a month. With this model, the steady state after transience can be predicted, and it indicates a scaling law that the quantity of erosion or sedimentation exponentially depends on the number of the segments along the reach of the channel. Our investigation suggests that fluctuation of the stream flow due to random rainfall will prevent this steady state from occurring. This is owing to the phenomenon that the varying trend of the quantity of erosion or sedimentation is opposite to that of sediment-carrying capability of the stream.

  14. Signal Processing Model for Radiation Transport

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, D H

    2008-07-28

    This note describes the design of a simplified gamma ray transport model for use in designing a sequential Bayesian signal processor for low-count detection and classification. It uses a simple one-dimensional geometry to describe the emitting source, shield effects, and detector (see Fig. 1). At present, only Compton scattering and photoelectric absorption are implemented for the shield and the detector. Other effects may be incorporated in the future by revising the expressions for the probabilities of escape and absorption. Pair production would require a redesign of the simulator to incorporate photon correlation effects. The initial design incorporates the physical effects that were present in the previous event mode sequence simulator created by Alan Meyer. The main difference is that this simulator transports the rate distributions instead of single photons. Event mode sequences and other time-dependent photon flux sequences are assumed to be marked Poisson processes that are entirely described by their rate distributions. Individual realizations can be constructed from the rate distribution using a random Poisson point sequence generator.

  15. Modeling reactive geochemical transport of concentrated aqueous solutions in variably saturated media

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guoxiang; Zheng, Zuoping; Wan, Jiamin

    2004-01-28

    Concentrated aqueous solutions (CAS) have unique thermodynamic and physical properties. Chemical components in CAS are incompletely dissociated, especially those containing divalent or polyvalent ions. The problem is further complicated by the interaction between CAS flow processes and the naturally heterogeneous sediments. As the CAS migrates through the porous media, the composition may be altered subject to fluid-rock interactions. To effectively model reactive transport of CAS, we must take into account ion-interaction. A combination of the Pitzer ion-interaction and the ion-association model would be an appropriate way to deal with multiple-component systems if the Pitzer' parameters and thermodynamic data of dissolved components and the related minerals are available. To quantify the complicated coupling of CAS flow and transport, as well as the involved chemical reactions in natural and engineered systems, we have substantially extended an existing reactive biogeochemical transport code, BIO-CORE{sup 2D}{copyright}, by incorporating a comprehensive Pitzer ion-interaction model. In the present paper, the model, and two test cases against measured data were briefly introduced. Finally we present an application to simulate a laboratory column experiment studying the leakage of the high alkaline waste fluid stored in Hanford (a site of the U.S. Department of Energy, located in Washington State, USA). With the Pitzer ion-interaction ionic activity model, our simulation captures measured pH evolution. The simulation indicates that all the reactions controlling the pH evolution, including cation exchanges, mineral precipitation and dissolution, are coupled.

  16. Numerical Modelling of Sediment Transport in Combined Sewer Systems

    DEFF Research Database (Denmark)

    Schlütter, Flemming

    A conceptual sediment transport model has been developed. Through a case study a comparison with other numerical models is performed.......A conceptual sediment transport model has been developed. Through a case study a comparison with other numerical models is performed....

  17. Modeling Oxygen Transport in the Human Placenta

    Science.gov (United States)

    Serov, Alexander; Filoche, Marcel; Salafia, Carolyn; Grebenkov, Denis

    Efficient functioning of the human placenta is crucial for the favorable pregnancy outcome. We construct a 3D model of oxygen transport in the placenta based on its histological cross-sections. The model accounts for both diffusion and convention of oxygen in the intervillous space and allows one to estimate oxygen uptake of a placentone. We demonstrate the existence of an optimal villi density maximizing the uptake and explain it as a trade-off between the incoming oxygen flow and the absorbing villous surface. Calculations performed for arbitrary shapes of fetal villi show that only two geometrical characteristics - villi density and the effective villi radius - are required to predict fetal oxygen uptake. Two combinations of physiological parameters that determine oxygen uptake are also identified: maximal oxygen inflow of a placentone and the Damköhler number. An automatic image analysis method is developed and applied to 22 healthy placental cross-sections demonstrating that villi density of a healthy human placenta lies within 10% of the optimal value, while overall geometry efficiency is rather low (around 30-40%). In a perspective, the model can constitute the base of a reliable tool of post partum oxygen exchange efficiency assessment in the human placenta. Also affiliated with Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA.

  18. Applying computationally efficient schemes for biogeochemical cycles (ACES4BGC)

    Energy Technology Data Exchange (ETDEWEB)

    Vertenstein, Mariana [Univ. Corporation For Atmospheric Research, Boulder, CO (United States)

    2016-01-11

    NCAR contributed to the ACES4BGC project through software engineering work on aerosol model implementation, build system and script changes, coupler enhancements for biogeochemical tracers, improvements to the Community Land Model (CLM) code and testing infrastructure, and coordinating and integrating code changes from the various project participants.

  19. Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Y; Glascoe, L

    2005-06-09

    The computational modeling of the biodegradation of contaminated groundwater systems accounting for biochemical reactions coupled to contaminant transport is a valuable tool for both the field engineer/planner with limited computational resources and the expert computational researcher less constrained by time and computer power. There exists several analytical and numerical computer models that have been and are being developed to cover the practical needs put forth by users to fulfill this spectrum of computational demands. Generally, analytical models provide rapid and convenient screening tools running on very limited computational power, while numerical models can provide more detailed information with consequent requirements of greater computational time and effort. While these analytical and numerical computer models can provide accurate and adequate information to produce defensible remediation strategies, decisions based on inadequate modeling output or on over-analysis can have costly and risky consequences. In this chapter we consider both analytical and numerical modeling approaches to biodegradation and reactive transport. Both approaches are discussed and analyzed in terms of achieving bioremediation goals, recognizing that there is always a tradeoff between computational cost and the resolution of simulated systems.

  20. Biogeochemical controls of uranium bioavailability from the dissolved phase

    Science.gov (United States)

    Croteau, Marie-Noele; Fuller, Christopher C.; Cain, Daniel J.; Campbell, Kate M.; Aiken, George R.

    2016-01-01

    To gain insights into the risks associated with uranium (U) mining and processing, we investigated the biogeochemical controls of U bioavailability in the model freshwater speciesLymnaea stagnalis (Gastropoda). Bioavailability of dissolved U(VI) was characterized in controlled laboratory experiments over a range of water hardness, pH, and in the presence of complexing ligands in the form of dissolved natural organic matter (DOM). Results show that dissolved U is bioavailable under all the geochemical conditions tested. Uranium uptake rates follow first order kinetics over a range encompassing most environmental concentrations. Uranium uptake rates in L. stagnalis ultimately demonstrate saturation uptake kinetics when exposure concentrations exceed 100 nM, suggesting uptake via a finite number of carriers or ion channels. The lack of a relationship between U uptake rate constants and Ca uptake rates suggest that U does not exclusively use Ca membrane transporters. In general, U bioavailability decreases with increasing pH, increasing Ca and Mg concentrations, and when DOM is present. Competing ions did not affect U uptake rates. Speciation modeling that includes formation constants for U ternary complexes reveals that the aqueous concentration of dicarbonato U species (UO2(CO3)2–2) best predicts U bioavailability to L. stagnalis, challenging the free-ion activity model postulate

  1. Spatiotemporal differences in nitrogen fate and transport with application of NCDC and WRF precipitation data in the SWAT watershed model

    Science.gov (United States)

    Gabriel, M. C.; Knightes, C. D.; Cooter, E. J.; Dennis, R. L.

    2011-12-01

    Watershed fate and transport models are widely used within the US Environmental Protection Agency's (USEPA) Office of Research and Development (ORD) as tools to forecast ecosystem services and evaluate future scenarios associated with land use, climate change and emissions regulation. A critical step in applying fate and transport models is understanding model sensitivity and function, particularly as new and innovative methods become available to apply forcing function data, e.g. precipitation data. Currently, multiple precipitation data sources are available for use in watershed modeling, two of which include National Climactic Data Center (NCDC) and Weather Research and Forecasting (WRF) data. As there are clear distinctions in how precipitation is determined for these precipitation sources (gauge vs. model simulated), there can also exist significant differences in precipitation frequency on a site-by-site basis. These differences may translate to large contrasts in nitrogen transport due to the sensitivity of surface biogeochemical processes to precipitation characteristics, namely those influenced by soil moisture content. The objective of this study is to investigate potential differences in the fate and transport of reactive nitrogen for two watersheds in the Neuse Basin, North Carolina, USA, after separately applying NCDC and WRF precipitation data sources into the Soil and Water Assessment Tool (SWAT) watershed model. The spatiotemporal variation of several nitrogen transport processes will be compared, e.g. reactive nitrogen fixation, plant uptake, overland delivery to streams, denitrification. Results from this research will advance exposure science by providing a greater understanding of the operation and function of watershed fate and transport models, which are primary tools used to assess ecosystem exposure.

  2. Modelling the transport system in China and evaluating the current strategies towards the sustainable transport development

    DEFF Research Database (Denmark)

    Liu, W.; Lund, H.; Mathiesen, B.V.

    2013-01-01

    in China. With this purpose in mind, a Chinese transport model has been created and three current transport strategies which are high speed railway (HSR), urban rail transit (URT) and electric vehicle (EV) were evaluated together with a reference transport system in 2020. As conservative results, 13......Transport is one of the most challenge sectors when addressing energy security and climate change due to its high reliance on oil products and lack of the alternative fuels. This paper explores the ability of three transport strategies to contribute to the development of a sustainable transport......% of the energy saving and 12% of the CO2 emission reduction can be attained by accomplishing three strategies compared with the reference transport system. However, the energy demand of transport in 2020 with the implementation of three strategies will be about 1.7 times as much as today. The three strategies...

  3. Modeling sheet-flow sand transport under progressive surface waves

    NARCIS (Netherlands)

    Kranenburg, W.M.

    2013-01-01

    In the near-shore zone, energetic sea waves generate sheet-flow sand transport. In present day coastal models, wave-induced sheet-flow sand transport rates are usually predicted with semi-empirical transport formulas, based on extensive research on this phenomenon in oscillatory flow tunnels. Howeve

  4. Contaminant transport at a waste residue deposit: 1. Inverse flow and non-reactive transport modelling

    DEFF Research Database (Denmark)

    Sonnenborg, Torben Obel; Engesgaard, Peter Knudegaard; Rosbjerg, Dan

    1996-01-01

    and transport simulation model is combined with nonlinear least squares multiple regression. The U.S. Geological Survey method of characteristics model is used to simulate flow and transport, and the optimization part is solved using a Levenberg-Marquardt algorithm. The sensitivity of the optimization approach...

  5. Comparison of global passenger transport models and available literature

    NARCIS (Netherlands)

    Breugem RMH; Vuuren DP van; Wee B van; MNV

    2002-01-01

    Over the last decade transport has been strongest growing sector in terms of worldwide energy demand. As a result, proper modelling of transport has become more important in models describing global climate change. RIVM has developed the energy model TIMER as part of the global integrated assessmen

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    F. W. Primeau

    2011-11-01

    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 ΔC* method, and two are based on reconstructions of the Green function for the surface-to-interior transport, the TTD method and the maximum entropy inversion method (KPH. The KPH 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 KPH 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 KPH method are generally valid on the global scale, but may introduce significant errors in Cant estimates on regional scales. The KPH method should also be used with caution when predicting future oceanic anthropogenic carbon uptake.

  8. Modelling global container freight transport demand

    NARCIS (Netherlands)

    Tavasszy, L.A.; Ivanova, O.; Halim, R.A.

    2015-01-01

    The objective of this chapter is to discuss methods and techniques for a quantitative and descriptive analysis of future container transport demand at a global level. Information on future container transport flows is useful for various purposes. It is instrumental for the assessment of returns of i

  9. Modelling multicomponent solute transport in structured soils

    NARCIS (Netherlands)

    Beinum, van G.W.

    2007-01-01

    The mobility of contaminants in soil is an important factor in determining their ability to spread into the wider environment. For non-volatile substances, transport within the soil is generally dominated by transport of dissolved fractions in the soil water phase, via either diffusion or convection

  10. European initiatives for modeling emissions from transport

    DEFF Research Database (Denmark)

    Joumard, Robert; Hickman, A. John; Samaras, Zissis

    1998-01-01

    In Europe there have been many cooperative studies into transport emission inventories since the late 80s. These cover the scope of CORINAIR program involving experts from seven European Community laboratories addressing only road transport emissions at national level. These also include the late...

  11. Biogeochemical cycling and remote sensing

    Science.gov (United States)

    Peterson, D. L.

    1985-01-01

    Research is underway at the NASA Ames Research Center that is concerned with aspects of the nitrogen cycle in terrestrial ecosystems. An interdisciplinary research group is attempting to correlate nitrogen transformations, processes, and productivity with variables that can be remotely sensed. Recent NASA and other publications concerning biogeochemical cycling at global scales identify attributes of vegetation that could be related or explain the spatial variation in biologically functional variables. These functional variables include net primary productivity, annual nitrogen mineralization, and possibly the emission rate of nitrous oxide from soils.

  12. Spatio-temporal evolution of biogeochemical processes at a landfill site

    Science.gov (United States)

    Arora, B.; Mohanty, B. P.; McGuire, J. T.

    2011-12-01

    Predictions of fate and transport of contaminants are strongly dependent on spatio-temporal variability of soil hydraulic and geochemical properties. This study focuses on time-series signatures of hydrological and geochemical properties at different locations within the Norman landfill site. Norman Landfill is a closed municipal landfill site with prevalent organic contamination. Monthly data at the site include specific conductance, δ18O, δ2H, dissolved organic carbon (DOC) and anions (chloride, sulfate, nitrate) from 1998-2006. Column scale data on chemical concentrations, redox gradients, and flow parameters are also available on daily and hydrological event (infiltration, drainage, etc.) scales. Since high-resolution datasets of contaminant concentrations are usually unavailable, Wavelet and Fourier analyses were used to infer the dominance of different biogeochemical processes at different spatio-temporal scales and to extract linkages between transport and reaction processes. Results indicate that time variability controls the progression of reactions affecting biodegradation of contaminants. Wavelet analysis suggests that iron-sulfide reduction reactions had high seasonal variability at the site, while fermentation processes dominated at the annual time scale. Findings also suggest the dominance of small spatial features such as layered interfaces and clay lenses in driving biogeochemical reactions at both column and landfill scales. A conceptual model that caters to increased understanding and remediating structurally heterogeneous variably-saturated media is developed from the study.

  13. Modelling Transportation of Efavirenz: Inference on possibility of mixed modes of transportation and kinetic solubility

    Directory of Open Access Journals (Sweden)

    Tafireyi eNemaura

    2015-06-01

    Full Text Available Understanding drug transportation mechanisms in the human body is of paramount importance in modelling Pharmacokinetic-Pharmacodynamic relationships. This work gives a novel general model of efavirenz transportation projections based on concentrations simulated from patients on a dose of 600mg. The work puts forward a proposition that transportation can wholly be modeled by concentration and time in a uniform volumetric space. Furthermore, movement entities are used to inform the state of kinetic solubility of a solution. There is use of Ricker’s model, and forms of the Hill’s equation in modelling transportation. Characterization on the movement rates of solution particle are suggested in relation to advection rate of solution particle. At turning points on the transportation rate of solution particle vs concentration curve, a suggestion of possibly change of dominance in the mode of transportation and saturation is made. There are four movement rates postulated at primary micro-level transportation, that are attributed to convection, diffusion (passive transportation ( EI and energy dependent system transportation ( ED in relation to advection. Furthermore, a new parameter is introduced which is defined as an advection rate constant of solution particle. It is postulated to be dependent on two rate constants of solution particle, that is a convection rate constant of solution particle and a saturable transportation rate constant of solution particle. At secondary micro-level transportation, the results show convection as sum of advection and saturable transportation. The kinetics of dissolution of efavirenz in the solution space is postulated. Relatively, a good level of kinetics of dissolution is projected in the concentration region 0−32.82μg/ml.

  14. Towards Biogeochemical Modeling of Anaerobic Oxidation of Methane: Characterization of Microbial Communities in Methane-bearing North American Continental Margin Sediments

    Science.gov (United States)

    Graw, M. F.; Solomon, E. A.; Chrisler, W.; Krause, S.; Treude, T.; Ruppel, C. D.; Pohlman, J.; Colwell, F. S.

    2015-12-01

    Methane advecting through continental margin sediments may enter the water column and potentially contribute to ocean acidification and increase atmospheric methane concentrations. Anaerobic oxidation of methane (AOM), mediated by syntrophic consortia of anaerobic methanotrophic archaea and sulfate-reducing bacteria (ANME-SRB), consumes nearly all dissolved methane in methane-bearing sediments before it reaches the sediment-water interface. Despite the significant role ANME-SRB play in carbon cycling, our knowledge of these organisms and their surrounding microbial communities is limited. Our objective is to develop a metabolic model of ANME-SRB within methane-bearing sediments and to couple this to a geochemical reaction-transport model for these margins. As a first step towards this goal, we undertook fluorescent microscopic imaging, 16S rRNA gene deep-sequencing, and shotgun metagenomic sequencing of sediments from the US Pacific (Washington) and northern Atlantic margins where ANME-SRB are present. A successful Illumina MiSeq sequencing run yielded 106,257 bacterial and 857,834 archaeal 16S rRNA gene sequences from 12 communities from the Washington Margin using both universal prokaryotic and archaeal-specific primer sets. Fluorescent microscopy confirmed the presence of cells of the ANME-2c lineage in the sequenced communities. Microbial community characterization was coupled with measurements of sediment physical and geochemical properties and, for samples from the US Atlantic margin, 14C-based measurements of AOM rates and 35S-based measurements of sulfate reduction rates. These findings have the potential to increase understanding of ANME-SRB, their surrounding microbial communities, and their role in carbon cycling within continental margins. In addition, they pave the way for future efforts at developing a metabolic model of ANME-SRB and coupling it to geochemical models of the US Washington and Atlantic margins.

  15. Combinatorial model of solute transport in porous media

    Institute of Scientific and Technical Information of China (English)

    张妙仙; 张丽萍

    2004-01-01

    Modeling of solute transport is a key issue in the area of soil physics and hydrogeology. The most common approach (the convection-dispersion equation) considers an average convection flow rate and Fickian-like dispersion. Here,we propose a solute transport model in porous media of continuously expanding scale, according to the combinatorics principle. The model supposed actual porous media as a combinative body of many basic segments. First, we studied the solute transport process in each basic segment body, and then deduced the distribution of pore velocity in each basic segment body by difference approximation, finally assembled the solute transport process of each basic segment body into one of the combinative body. The simulation result coincided with the solute transport process observed in test. The model provides useful insight into the solute transport process of the non-Fickian dispersion in continuously expanding scale.

  16. Modeling of Anomalous Transport in Tokamaks with FACETS code

    Science.gov (United States)

    Pankin, A. Y.; Batemann, G.; Kritz, A.; Rafiq, T.; Vadlamani, S.; Hakim, A.; Kruger, S.; Miah, M.; Rognlien, T.

    2009-05-01

    The FACETS code, a whole-device integrated modeling code that self-consistently computes plasma profiles for the plasma core and edge in tokamaks, has been recently developed as a part of the SciDAC project for core-edge simulations. A choice of transport models is available in FACETS through the FMCFM interface [1]. Transport models included in FMCFM have specific ranges of applicability, which can limit their use to parts of the plasma. In particular, the GLF23 transport model does not include the resistive ballooning effects that can be important in the tokamak pedestal region and GLF23 typically under-predicts the anomalous fluxes near the magnetic axis [2]. The TGLF and GYRO transport models have similar limitations [3]. A combination of transport models that covers the entire discharge domain is studied using FACETS in a realistic tokamak geometry. Effective diffusivities computed with the FMCFM transport models are extended to the region near the separatrix to be used in the UEDGE code within FACETS. 1. S. Vadlamani et al. (2009) %First time-dependent transport simulations using GYRO and NCLASS within FACETS (this meeting).2. T. Rafiq et al. (2009) %Simulation of electron thermal transport in H-mode discharges Submitted to Phys. Plasmas.3. C. Holland et al. (2008) %Validation of gyrokinetic transport simulations using %DIII-D core turbulence measurements Proc. of IAEA FEC (Switzerland, 2008)

  17. Scale dependent importance of spatial heterogeneity in biogeochemical cycling at aquifer-river interfaces

    Science.gov (United States)

    Krause, Stefan; Blaen, Phillip; Hannah, David; Romejn, Paul; Gomez, Jesus; Kurz, Marie; Fleckenstein, Jan; Schmidt, Christian; Zarnetske, Jay; Cullin, Joe; Ward, Adam; Marti, Eugenia; Drummond, Jennifer; Schmadel, Noah; Knapp, Julia; Klaar, Megan; Mendoza, Clara

    2016-04-01

    The transport and transformation of carbon and nitrogen across aquifer - river interfaces are significantly altered along the streambed passage. Recent investigations have substantially improved the understanding of controls on streambed biogeochemical cycling, outlining a critical impact of exchange fluxes, temporal and spatial coincidence of reaction partners and streambed residence time distributions. Still, there is little understanding of the drivers of the widely observed strong spatial and temporal variability of interlinked carbon and nitrogen turnover at aquifer-river interfaces, including hotspots (locations) and hot moments (time periods) of increased reactivity. Previous research, predominantly with a surface water perspective, has mainly focused on the impact of bedform controlled hyporheic exchange fluxes and the chemical transformation of surface solutes transported along a hyporheic flow path. While such studies may explain nutrient turnover in the hyporheic zones of low-order streams in rather pristine headwater catchments, they fail to explain observations of spatially and temporally more variable nutrient turnover in streambeds with higher structural heterogeneity and relevant concentrations of autochthonous carbon and nitrogen. Here we combine laboratory, field and numerical modeling experiments from plot to stream reach/subcatchment scales to quantify the impacts of variability in physical and biogeochemical streambed properties on hyporheic nutrient (C, N, O) cycling. At the plot scale, hotspots of biogeochemical cycling have been found to be associated with peat and clay layers within streambed sediments, representing areas of significantly increased residence times and oxygen consumption what results in enhanced microbial metabolic activity and nitrogen removal capacity. We present distributed sensor network based up-scaling methods that allow identification of such features at larger reach scale. Numerical modeling based generalization

  18. Mathematical model of transportation flow dynamics on a multilane highway

    NARCIS (Netherlands)

    Mazurin, D. S.

    2013-01-01

    We present a microscopic model for the dynamics of a transportation flow based on cellular automata with improved lane changing rules. With this model, we study the influence of crossing transportation flows on the throughput of a multilane highway. For a two-lane highway with an exit, we obtain spa

  19. 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

  20. Symmetrization of mathematical model of charge transport in semiconductors

    Directory of Open Access Journals (Sweden)

    Alexander M. Blokhin

    2002-11-01

    Full Text Available A mathematical model of charge transport in semiconductors is considered. The model is a quasilinear system of differential equations. A problem of finding an additional entropy conservation law and system symmetrization are solved.

  1. One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

    Science.gov (United States)

    Runkel, Robert L.

    2010-01-01

    OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

  2. Efficiency of a statistical transport model for turbulent particle dispersion

    Science.gov (United States)

    Litchford, Ron J.; Jeng, San-Mou

    1992-01-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains.

  3. A new model for the global biogeochemical cycle of carbonyl sulfide - Part 1: Assessment of direct marine emissions with an oceanic general circulation and biogeochemistry model

    Science.gov (United States)

    Launois, T.; Belviso, S.; Bopp, L.; Fichot, C. G.; Peylin, P.

    2014-08-01

    The global budget of tropospheric carbonyl sulfide (OCS) is believed to be at equilibrium because background air concentrations have remained roughly stable over at least the last decade. Since the uptakes of OCS by leaves (associated to photosynthesis) and soils have been revised significantly upwards recently, an equilibrated budget can only be obtained with a compensatory source of OCS. It has been assumed that the missing source of OCS comes from the low latitude ocean, following the incident solar flux. The present work uses parameterizations of major production and removal processes of organic compounds in the NEMO-PISCES Ocean General Circulation and Biogeochemistry Model to assess the marine source of OCS. In addition, the OCS photo-production rates computed with the NEMO-PISCES model were evaluated independently using UV absorption coefficient of chromophoric dissolved organic matter (derived from satellite ocean color) and apparent quantum yields available in the literature. Our simulations show global direct marine emissions of COS in the range of 573-3997 Gg S yr-1, depending mostly on the quantification of the absorption rate of chromophoric dissolved organic matter. The high estimates on that range are unlikely, as they correspond to a formulation that most likely overestimate photo-production process. Low and medium (813 Gg S yr-1) estimates derived from the NEMO-PISCES model are however consistent spatially and temporally with the suggested missing source of Berry et al. (2013), allowing thus to close the global budget of OCS given the recent estimates of leaf and soil OCS uptakes.

  4. A new model for the global biogeochemical cycle of carbonyl sulfide – Part 1: Assessment of direct marine emissions with an oceanic general circulation and biogeochemistry model

    Directory of Open Access Journals (Sweden)

    T. Launois

    2014-08-01

    Full Text Available The global budget of tropospheric carbonyl sulfide (OCS is believed to be at equilibrium because background air concentrations have remained roughly stable over at least the last decade. Since the uptakes of OCS by leaves (associated to photosynthesis and soils have been revised significantly upwards recently, an equilibrated budget can only be obtained with a compensatory source of OCS. It has been assumed that the missing source of OCS comes from the low latitude ocean, following the incident solar flux. The present work uses parameterizations of major production and removal processes of organic compounds in the NEMO-PISCES Ocean General Circulation and Biogeochemistry Model to assess the marine source of OCS. In addition, the OCS photo-production rates computed with the NEMO-PISCES model were evaluated independently using UV absorption coefficient of chromophoric dissolved organic matter (derived from satellite ocean color and apparent quantum yields available in the literature. Our simulations show global direct marine emissions of COS in the range of 573–3997 Gg S yr−1, depending mostly on the quantification of the absorption rate of chromophoric dissolved organic matter. The high estimates on that range are unlikely, as they correspond to a formulation that most likely overestimate photo-production process. Low and medium (813 Gg S yr−1 estimates derived from the NEMO-PISCES model are however consistent spatially and temporally with the suggested missing source of Berry et al. (2013, allowing thus to close the global budget of OCS given the recent estimates of leaf and soil OCS uptakes.

  5. A mesoscale chemical transport model (MEDIUM) nested in a global chemical transport model (MEDIANTE)

    Energy Technology Data Exchange (ETDEWEB)

    Claveau, J.; Ramaroson, R. [Office National d`Etudes et de Recherches Aerospatiales (ONERA), 92 - Chatillon (France)

    1997-12-31

    The lower stratosphere and upper troposphere (UT-LS) are frequently subject to mesoscale or local scale exchange of air masses occurring along discontinuities. This exchange (e.g. downward) can constitute one of the most important source of ozone from the stratosphere down to the middle troposphere where strong mixing dilutes the air mass and competing the non-linear chemistry. The distribution of the chemical species in the troposphere and the lower stratosphere depends upon various source emissions, e.g. from polluted boundary layer or from aircraft emissions. Global models, as well as chemical transport models describe the climatological state of the atmosphere and are not able to describe correctly the stratosphere and troposphere exchange. Mesoscale models go further in the description of smaller scales and can reasonably include a rather detailed chemistry. They can be used to assess the budget of NO{sub x} from aircraft emissions in a mesoscale domain. (author) 4 refs.

  6. Biogeochemical patchiness at the sea surface

    Science.gov (United States)

    Mahadevan, A.; Campbell, J. W.

    2002-10-01

    The surface distributions of many tracers in the ocean are highly correlated in time and space on meso (~100 km) and smaller scales (refid="fig01" type="media">Figure 1). However, their characteristic scales of variability differ. Some variables like sea surface chlorophyll (Chl) are very fine-scaled or patchy, while others like sea surface temperature (SST) are not. We characterize the patchiness of a distribution quantitatively by the dependence of the variance V on the length scale L as V ~ Lp; smaller p corresponds to greater patchiness. Using scaling and a numerical model we show that patchiness, p, varies with the characteristic response time τ of the tracer to processes that alter its concentration in the upper ocean as p ~ log τ. This suggests that sea surface Chl is more patchy (has smaller p) than SST at mesoscales because the characteristic time scale of phytoplankton growth in response to the availability of nutrients is less than that for the equilibration of temperature in response to heat fluxes. Similarly, sea surface dissolved oxygen (O2) exhibits more fine-scaled variability than total dissolved inorganic carbon (TCO2) because O2 equilibrates with the atmosphere much more rapidly than TCO2. Tracers that are more patchy require higher resolution to model and sample; the sampling or model grid spacing required scales as exp(-1/log τ). The quantitative relationship between p and τ can be used to relate various biogeochemical distributions, particularly to those that are remotely sensed, and to deduce biogeochemical response times of various tracers or plankton species from the characteristics of their distributions in space or time.

  7. Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

    Science.gov (United States)

    Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

    2010-12-01

    Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs

  8. Coupling ANIMO and MT3DMS for 3D regional-scale modeling of nutrient transport in soil and groundwater

    Science.gov (United States)

    Janssen, G.; Del Val Alonso, L.; Groenendijk, P.; Griffioen, J.

    2012-12-01

    We developed an on-line coupling between the 1D/quasi-2D nutrient transport model ANIMO and the 3D groundwater transport model code MT3DMS. ANIMO is a detailed, process-oriented model code for the simulation of nitrate leaching to groundwater, N- and P-loads on surface waters and emissions of greenhouse gasses. It is the leading nutrient fate and transport code in the Netherlands where it is used primarily for the evaluation of fertilization related legislation. In addition, the code is applied frequently in international research projects. MT3DMS is probably the most commonly used groundwater solute transport package worldwide. The on-line model coupling ANIMO-MT3DMS combines the state-of-the-art descriptions of the biogeochemical cycles in ANIMO with the advantages of using a 3D approach for the transport through the saturated domain. These advantages include accounting for regional lateral transport, considering groundwater-surface water interactions more explicitly, and the possibility of using MODFLOW to obtain the flow fields. An additional merit of the on-line coupling concept is that it preserves feedbacks between the saturated and unsaturated zone. We tested ANIMO-MT3DMS by simulating nutrient transport for the period 1970-2007 in a Dutch agricultural polder catchment covering an area of 118 km2. The transient groundwater flow field had a temporal resolution of one day and was calculated with MODFLOW-MetaSWAP. The horizontal resolution of the model grid was 100x100m and consisted of 25 layers of varying thickness. To keep computation times manageable, we prepared MT3DMS for parallel computing, which in itself is a relevant development for a large community of groundwater transport modelers. For the parameterization of the soil, we applied a standard classification approach, representing the area by 60 units with unique combinations of soil type, land use and geohydrological setting. For the geochemical parameterization of the deeper subsurface, however, we

  9. Implementation of Gravity Model to Estimation of Transportation Market Shares

    Science.gov (United States)

    Krata, Przemysław

    2010-03-01

    The theoretical consideration presented in the paper is inspired by market gravity models, as an interesting attitude towards operations research on a market. The transportation market issues are emphasized. The mathematical model of relations, taking place between transportation companies and their customers on the market, which is applied in the course of the research is based on continuous functions characteristics. This attitude enables the use of the field theory notions. The resultant vector-type utility function facilitates obtaining of competitive advantage areas for all transportation companies located on the considered transportation market.

  10. Mathematical Modelling of Cation Transport and Regulation in Yeast.

    Science.gov (United States)

    Kahm, Matthiasé; Kschischo, Maik

    2016-01-01

    Mathematical modelling of ion transport is a strategy to understand the complex interplay between various ionic species and their transporters. Such models should provide new insights and suggest new interesting experiments. Two essential variables in models for ion transport and control are the membrane potential and the intracellular pH, which generates an additional layer of complexity absent from many other models of biochemical reaction pathways. The aim of this text is to introduce the reader to the basic principles and assumptions of modelling in this field. A simplified model of potassium transport will be used as an example and will be derived in a step by step manner. This forms the basis for understanding the advantages and limitations of more complex models. These are briefly reviewed at the end of this chapter.

  11. Particle Tracking Model and Abstraction of Transport Processes

    Energy Technology Data Exchange (ETDEWEB)

    B. Robinson

    2000-04-07

    The purpose of the transport methodology and component analysis is to provide the numerical methods for simulating radionuclide transport and model setup for transport in the unsaturated zone (UZ) site-scale model. The particle-tracking method of simulating radionuclide transport is incorporated into the FEHM computer code and the resulting changes in the FEHM code are to be submitted to the software configuration management system. This Analysis and Model Report (AMR) outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the unsaturated zone at Yucca Mountain. In addition, methods for determining colloid-facilitated transport parameters are outlined for use in the Total System Performance Assessment (TSPA) analyses. Concurrently, process-level flow model calculations are being carrier out in a PMR for the unsaturated zone. The computer code TOUGH2 is being used to generate three-dimensional, dual-permeability flow fields, that are supplied to the Performance Assessment group for subsequent transport simulations. These flow fields are converted to input files compatible with the FEHM code, which for this application simulates radionuclide transport using the particle-tracking algorithm outlined in this AMR. Therefore, this AMR establishes the numerical method and demonstrates the use of the model, but the specific breakthrough curves presented do not necessarily represent the behavior of the Yucca Mountain unsaturated zone.

  12. A transport-rate model of wind-blown sand

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Sand transport by wind plays an important role in environmental problems.Formulating the sand-transport rate model has been of continuing significance,because the majority of the existing models relate sand-transport rate to the wind-shear velocity.However,the wind-shear velocity readapted to blown sand is difficult to determine from the measured wind profiles when sand movement occurs,especially at high wind velocity.Detailed wind tunnel tests were carried out to reformulate the sand-transport rate model,followed by attempts to relate sand-transport rate to parameters of wind velocity,threshold shear-velocity,and grain size.Finally,we validated the model based on the data from field observations.

  13. Advanced transport systems analysis, modeling, and evaluation of performances

    CERN Document Server

    Janić, Milan

    2014-01-01

    This book provides a systematic analysis, modeling and evaluation of the performance of advanced transport systems. It offers an innovative approach by presenting a multidimensional examination of the performance of advanced transport systems and transport modes, useful for both theoretical and practical purposes. Advanced transport systems for the twenty-first century are characterized by the superiority of one or several of their infrastructural, technical/technological, operational, economic, environmental, social, and policy performances as compared to their conventional counterparts. The advanced transport systems considered include: Bus Rapid Transit (BRT) and Personal Rapid Transit (PRT) systems in urban area(s), electric and fuel cell passenger cars, high speed tilting trains, High Speed Rail (HSR), Trans Rapid Maglev (TRM), Evacuated Tube Transport system (ETT), advanced commercial subsonic and Supersonic Transport Aircraft (STA), conventionally- and Liquid Hydrogen (LH2)-fuelled commercial air trans...

  14. Reduced Fast Ion Transport Model For The Tokamak Transport Code TRANSP

    Energy Technology Data Exchange (ETDEWEB)

    Podesta,, Mario; Gorelenkova, Marina; White, Roscoe

    2014-02-28

    Fast ion transport models presently implemented in the tokamak transport code TRANSP [R. J. Hawryluk, in Physics of Plasmas Close to Thermonuclear Conditions, CEC Brussels, 1 , 19 (1980)] are not capturing important aspects of the physics associated with resonant transport caused by instabilities such as Toroidal Alfv en Eigenmodes (TAEs). This work describes the implementation of a fast ion transport model consistent with the basic mechanisms of resonant mode-particle interaction. The model is formulated in terms of a probability distribution function for the particle's steps in phase space, which is consistent with the MonteCarlo approach used in TRANSP. The proposed model is based on the analysis of fast ion response to TAE modes through the ORBIT code [R. B. White et al., Phys. Fluids 27 , 2455 (1984)], but it can be generalized to higher frequency modes (e.g. Compressional and Global Alfv en Eigenmodes) and to other numerical codes or theories.

  15. Diel biogeochemical processes in terrestrial waters

    Science.gov (United States)

    Compiled and Edited by 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.

  16. Model for Estimation Urban Transportation Supply-Demand Ratio

    Directory of Open Access Journals (Sweden)

    Chaoqun Wu

    2015-01-01

    Full Text Available The paper establishes an estimation model of urban transportation supply-demand ratio (TSDR to quantitatively describe the conditions of an urban transport system and to support a theoretical basis for transport policy-making. This TSDR estimation model is supported by the system dynamic principle and the VENSIM (an application that simulates the real system. It was accomplished by long-term observation of eight cities’ transport conditions and by analyzing the estimated results of TSDR from fifteen sets of refined data. The estimated results indicate that an urban TSDR can be classified into four grades representing four transport conditions: “scarce supply,” “short supply,” “supply-demand balance,” and “excess supply.” These results imply that transport policies or measures can be quantified to facilitate the process of ordering and screening them.

  17. Particle Tracking Model and Abstraction of Transport Processes

    Energy Technology Data Exchange (ETDEWEB)

    B. Robinson

    2004-10-21

    The purpose of this report is to document the abstraction model being used in total system performance assessment (TSPA) model calculations for radionuclide transport in the unsaturated zone (UZ). The UZ transport abstraction model uses the particle-tracking method that is incorporated into the finite element heat and mass model (FEHM) computer code (Zyvoloski et al. 1997 [DIRS 100615]) to simulate radionuclide transport in the UZ. This report outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the UZ at Yucca Mountain. In addition, methods for determining and inputting transport parameters are outlined for use in the TSPA for license application (LA) analyses. Process-level transport model calculations are documented in another report for the UZ (BSC 2004 [DIRS 164500]). Three-dimensional, dual-permeability flow fields generated to characterize UZ flow (documented by BSC 2004 [DIRS 169861]; DTN: LB03023DSSCP9I.001 [DIRS 163044]) are converted to make them compatible with the FEHM code for use in this abstraction model. This report establishes the numerical method and demonstrates the use of the model that is intended to represent UZ transport in the TSPA-LA. Capability of the UZ barrier for retarding the transport is demonstrated in this report, and by the underlying process model (BSC 2004 [DIRS 164500]). The technical scope, content, and management of this report are described in the planning document ''Technical Work Plan for: Unsaturated Zone Transport Model Report Integration'' (BSC 2004 [DIRS 171282]). Deviations from the technical work plan (TWP) are noted within the text of this report, as appropriate. The latest version of this document is being prepared principally to correct parameter values found to be in error due to transcription errors, changes in source data that were not captured in the report, calculation errors, and errors in interpretation of source data.

  18. A consistent transported PDF model for treating differential molecular diffusion

    Science.gov (United States)

    Wang, Haifeng; Zhang, Pei

    2016-11-01

    Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.

  19. Integration of Genome-Scale Metabolic Nodels of Iron-Reducing Bacteria With Subsurface Flow and Geochemical Reactive Transport Models

    Science.gov (United States)

    Scheibe, T. D.; Mahadevan, R.; Fang, Y.; Garg, S.; Long, P. E.; Lovley, D. M.

    2008-12-01

    Several field and laboratory experiments have demonstrated that the growth and activity of iron-reducing bacteria can be stimulated in many subsurface environments by amendment of groundwater with a soluble electron donor. Under strong iron-reducing conditions, these organisms mediate reactions that can impact a wide range of subsurface contaminants including chlorinated hydrocarbons, metals, and radionuclides. Therefore there is strong interest in in-situ bioremediation as a potential technology for cleanup of contaminated aquifers. To evaluate and design bioremediation systems, as well as to evaluate the viability of monitored natural attenuation as an alternative, quantitative models of biogeochemically reactive transport are needed. To date, most such models represent microbial activity in terms of kinetic rate (e.g., Monod- type) formulations. Such models do not account for fundamental changes in microbial functionality (such as utilization of alternative respiratory pathways) that occur as the result of spatial and temporal variations in the geochemical environment experienced by microorganisms. Constraint-based genome-scale in silico models of microbial metabolism present an alternative to simplified rate formulations that provide flexibility to account for changes in microbial function in response to local geochemical conditions. We have developed and applied a methodology for coupling a constraint-based in silico model of Geobacter sulfurreducens with a conventional model of groundwater flow, transport, and geochemical reaction. Two uses of the in silico model are tested: 1) incorporation of modified microbial growth yield coefficients based on the in silico model, and 2) variation of reaction rates in a reactive transport model based on in silico modeling of a range of local geochemical conditions. Preliminary results from this integrated model will be presented.

  20. Mathematical modeling of sediment transport jn estuaries and coastal regions

    Institute of Scientific and Technical Information of China (English)

    窦国仁; 董凤舞; 窦希萍; 李禔来

    1995-01-01

    Based on the suspended sediment transport equation and transport capacity formula under the action of tidal currents and wind waves, a horizontal 2-D mathematical model of suspended sediment transport for estuaries and coastal regions is established. The verification of calculations shows that the sediment concentration distribution and sea bed deformation in the estuaries and coastal regions can be successfully simulated. Therefore, a new method for studying and solving the sediment problems in the estuarine and coastal engineering is presented.

  1. Paving the road from transport models to “new mobilities” models

    DEFF Research Database (Denmark)

    Wind, Simon; Jensen, Ole B.; Kaplan, Sigal;

    2012-01-01

    For half a century, tremendous efforts have been invested in developing transport models as a decision aid for policy makers in designing effective policy interventions and deciding among costly public projects for the benefit of the population. Transport and activity-based models are often...... the traditional transport modeling approach and “new mobilities” research by suggesting a model framework that considers non-instrumental transport rationales, personal latent traits and intra-household decision dynamics....

  2. Backcasting in freight transport demand modelling – chances and challenges

    OpenAIRE

    Lange, Peter; Huber, Stefan

    2015-01-01

    Freight transport demand models are important tools to support policy decision-making by enabling decision makers to evaluate transport policies and correlated effects. This significance puts high pressure on freight models regarding their accuracy. In order to ensure model accuracy there are different methods within the wide area of quality assurance that can be applied. Although backcasting is such a method it is, however, often neglected or implemented insufficiently. The paper presents ma...

  3. 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.

  4. Logistics chains in freight transport modelling

    NARCIS (Netherlands)

    Davydenko, I.

    2015-01-01

    The research presented in this PhD thesis has been motivated by the fact that the Netherlands, and the Randstad region in particular, are affected by the large transport flows and extensive operations of the logistics sector. These operations create welfare for those people who work in the sector, w

  5. Structural Design of Oligopeptides for Intestinal Transport Model.

    Science.gov (United States)

    Hong, Seong-Min; Tanaka, Mitsuru; Koyanagi, Riho; Shen, Weilin; Matsui, Toshiro

    2016-03-16

    Glycyl-sarcosine (Gly-Sar) is a well-known model substrate for the intestinal uptake of dipeptides through peptide transporter 1 (PepT1). However, there are no other model peptides larger than tripeptides to evaluate their intestinal transport ability. In this study, we designed new oligopeptides based on the Gly-Sar structure in terms of protease resistance. Gly-Sar-Sar was found to be an appropriate transport model for tripeptides because it does not degrade during the transport across the rat intestinal membrane, while Gly-Gly-Sar was degraded to Gly-Sar during the 60 min transport. Caco-2 cell transport experiments revealed that the designed oligopeptides based on Gly-Sar-Sar showed a significantly (p transport ability by factors of 1/10-, 1/25-, and 1/40-fold for Gly-Sar-Sar, Gly-Sar-Sar-Sar, and Gly-Sar-Sar-Sar-Sar, respectively, compared to Gly-Sar (apparent permeability coefficient: 38.6 ± 11.4 cm/s). Cell experiments also showed that the designed tripeptide and Gly-Sar were transported across Caco-2 cell via PepT1, whereas the tetra- and pentapeptides were transported through the paracellular tight-junction pathway.

  6. Expanding the role of reactive transport models in critical zone processes

    Science.gov (United States)

    Li, Li; Maher, Kate; Navarre-Sitchler, Alexis; Druhan, Jennifer; Meile, Christof; Lawrence, Corey; Moore, Joel; Perdrial, Julia; Sullivan, Pamela; Thompson, Aaron; Jin, Lixin; Bolton, Edward W.; Brantley, Susan L.; Dietrich, William E.; Mayer, K. Ulrich; Steefel, Carl; Valocchi, Albert J.; Zachara, John M.; Kocar, Benjamin D.; McIntosh, Jennifer; Tutolo, Benjamin M.; Kumar, Mukesh; Sonnenthal, Eric; Bao, Chen; Beisman, Joe

    2017-01-01

    Models test our understanding of processes and can reach beyond the spatial and temporal scales of measurements. Multi-component Reactive Transport Models (RTMs), initially developed more than three decades ago, have been used extensively to explore the interactions of geothermal, hydrologic, geochemical, and geobiological processes in subsurface systems. Driven by extensive data sets now available from intensive measurement efforts, there is a pressing need to couple RTMs with other community models to explore non-linear interactions among the atmosphere, hydrosphere, biosphere, and geosphere. Here we briefly review the history of RTM development, summarize the current state of RTM approaches, and identify new research directions, opportunities, and infrastructure needs to broaden the use of RTMs. In particular, we envision the expanded use of RTMs in advancing process understanding in the Critical Zone, the veneer of the Earth that extends from the top of vegetation to the bottom of groundwater. We argue that, although parsimonious models are essential at larger scales, process-based models offer tools to explore the highly nonlinear coupling that characterizes natural systems. We present seven testable hypotheses that emphasize the unique capabilities of process-based RTMs for (1) elucidating chemical weathering and its physical and biogeochemical drivers; (2) understanding the interactions among roots, micro-organisms, carbon, water, and minerals in the rhizosphere; (3) assessing the effects of heterogeneity across spatial and temporal scales; and (4) integrating the vast quantity of novel data, including “omics” data (genomics, transcriptomics, proteomics, metabolomics), elemental concentration and speciation data, and isotope data into our understanding of complex earth surface systems. With strong support from data-driven sciences, we are now in an exciting era where integration of RTM framework into other community models will facilitate process

  7. Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation.

    Science.gov (United States)

    Wu, Yuxin; Ajo-Franklin, Jonathan B; Spycher, Nicolas; Hubbard, Susan S; Zhang, Guoxiang; Williams, Kenneth H; Taylor, Joanna; Fujita, Yoshiko; Smith, Robert

    2011-09-23

    Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH4

  8. Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation

    Directory of Open Access Journals (Sweden)

    Taylor Joanna

    2011-09-01

    Full Text Available Abstract Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT, and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes

  9. Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Y.; Ajo-Franklin, J.B.; Spycher, N.; Hubbard, S.S.; Zhang, G.; Williams, K.H.; Taylor, J.; Fujita, Y.; Smith, R.

    2011-07-15

    Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH{sub 4}{sup

  10. IOT technology application model research of transportation industry in China

    Institute of Scientific and Technical Information of China (English)

    Lai Mingyong; Zhou Tang; Liu Zhengchi

    2013-01-01

    The paper studied the connection between intemet of things (IOT) technology and transportation industry.Meanwhile,the definition of IOT in transportation was given.Concerning that many problems occurred during the process of traditional intelligent transportation system,the paper proposed a promising model of IOT in transportation.The advantage of the information utilization model from information to function was confirmed through comparative study.Finally,the model presented that a real interconnection of transportation would be achieved based on the unified information collection.It can greatly save cost on technology transfer,exploit potential value of information,and promote the emergence of a sustainable information service market and the industrial upgrade.

  11. 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

  12. 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

  13. Finite difference methods for coupled flow interaction transport models

    Directory of Open Access Journals (Sweden)

    Shelly McGee

    2009-04-01

    Full Text Available Understanding chemical transport in blood flow involves coupling the chemical transport process with flow equations describing the blood and plasma in the membrane wall. In this work, we consider a coupled two-dimensional model with transient Navier-Stokes equation to model the blood flow in the vessel and Darcy's flow to model the plasma flow through the vessel wall. The advection-diffusion equation is coupled with the velocities from the flows in the vessel and wall, respectively to model the transport of the chemical. The coupled chemical transport equations are discretized by the finite difference method and the resulting system is solved using the additive Schwarz method. Development of the model and related analytical and numerical results are presented in this work.

  14. Modeling Quantum Transport in Nanoscale Vertical SOI nMOSFET

    Institute of Scientific and Technical Information of China (English)

    TONG Jian-nong; ZOU Xue-chang; SHEN Xu-bang

    2004-01-01

    The electron transports in micro-architecture semiconductor are simulated using vertical SOI nMOSFET with different models. Some details in transport can be presented by changing channel length, channel thickness and drain voltage. An interesting phenomenon similar to collimation effect in mesoscopic system is observed. This may suggest the quite intriguing possibility that scattering may open new channel in sufficiently narrow devices.

  15. Fast Cherenkov model of optical photons generation and transportation

    CERN Document Server

    The ATLAS collaboration

    2017-01-01

    This note describes the technical details of Fast Cherenkov model of optical photons generation and transportation: in particular, the mechanism of Cherenkov photons transportation through the straight bar geometry. As an example of usage, the implemetation of the method inside Quartic detector simulation in GEANT4 will be presented and compared to the nominal results.

  16. Using Transport Diagnostics to Understand Chemistry Climate Model Ozone Simulations

    Science.gov (United States)

    Strahan, S. E.; Douglass, A. R.; Stolarski, R. S.; Akiyoshi, H.; Bekki, S.; Braesicke, P.; Butchart, N.; Chipperfield, M. P.; Cugnet, D.; Dhomse, S.; Frith, S. M.; Gettleman, A.; Hardiman, S. C.; Kinnison, D. E.; Lamarque, J.-F.; Mancini, E.; Marchand, M.; Michou, M.; Morgenstern, O.; Nakamura, T.; Olivie, D.; Pawson, S.; Pitari, G.; Plummer, D. A.; Pyle, J. A.

    2010-01-01

    We demonstrate how observations of N2O and mean age in the tropical and midlatitude lower stratosphere (LS) can be used to identify realistic transport in models. The results are applied to 15 Chemistry Climate Models (CCMs) participating in the 2010 WMO assessment. Comparison of the observed and simulated N2O/mean age relationship identifies models with fast or slow circulations and reveals details of model ascent and tropical isolation. The use of this process-oriented N2O/mean age diagnostic identifies models with compensating transport deficiencies that produce fortuitous agreement with mean age. We compare the diagnosed model transport behavior with a model's ability to produce realistic LS O3 profiles in the tropics and midlatitudes. Models with the greatest tropical transport problems show the poorest agreement with observations. Models with the most realistic LS transport agree more closely with LS observations and each other. We incorporate the results of the chemistry evaluations in the SPARC CCMVal Report (2010) to explain the range of CCM predictions for the return-to-1980 dates for global (60 S-60 N) and Antarctic column ozone. Later (earlier) Antarctic return dates are generally correlated to higher (lower) vortex Cl(sub y) levels in the LS, and vortex Cl(sub y) is generally correlated with the model's circulation although model Cl(sub y) chemistry or Cl(sub y) conservation can have a significant effect. In both regions, models that have good LS transport produce a smaller range of predictions for the return-to-1980 ozone values. This study suggests that the current range of predicted return dates is unnecessarily large due to identifiable model transport deficiencies.

  17. Modeling of titration experiments by a reactive transport model

    Institute of Scientific and Technical Information of China (English)

    Ma Hongyun; Samper Javier; Xin Xin

    2011-01-01

    Acid mine drainage (AMD) is commonly treated by neutralization with alkaline substances. This treatment is supported by titration experiments that illustrate the buffering mechanisms and estimate the base neutralization capacity (BNC) of the AMD. Detailed explanation of titration curves requires modeling with a hydro-chemical model. In this study the titration curves of water samples from the drainage of the As Pontes mine and the corresponding dumps have been investigated and six buffers are selected by analyzing those curves. Titration curves have been simulated by a reactive transport model to discover the detailed buffering mechanisms. These simulations show seven regions involving different buffering mechanism. The BNC is primarily from buffers of dissolved Fe, Al and hydrogen sulfate. The BNC can be approximated by: BNC = 3(CFe + CAl) + 0.05Csulfate, where the units are mol/L. The BNC of the sample from the mine is 9.25 × 10-3 mol/L and that of the dumps sample is 1.28 × 10-2 mol/L.

  18. Modelling heat transport through completely positive maps

    CERN Document Server

    Wichterich, H; Gemmer, J; Henrich, M J; Michel, M; Breuer, Heinz-Peter; Gemmer, Jochen; Henrich, Markus J.; Michel, Mathias; Wichterich, Hannu

    2007-01-01

    We investigate heat transport in a spin-1/2 Heisenberg chain, coupled locally to independent thermal baths of different temperature. The analysis is carried out within the framework of the theory of open systems by means of appropriate quantum master equations. The standard microscopic derivation of the weak-coupling Lindblad equation in the secular approximation is considered, and shown to be inadequate for the description of stationary nonequilibrium properties like a non-vanishing energy current. Furthermore, we derive an alternative master equation that is capable to describe a stationary energy current and, at the same time, leads to a completely positive dynamical map. This paves the way for efficient numerical investigations of heat transport in larger systems based on Monte Carlo wave function techniques.

  19. Modelling aeolian sand transport using a dynamic mass balancing approach

    Science.gov (United States)

    Mayaud, Jerome R.; Bailey, Richard M.; Wiggs, Giles F. S.; Weaver, Corinne M.

    2017-03-01

    Knowledge of the changing rate of sediment flux in space and time is essential for quantifying surface erosion and deposition in desert landscapes. Whilst many aeolian studies have relied on time-averaged parameters such as wind velocity (U) and wind shear velocity (u*) to determine sediment flux, there is increasing field evidence that high-frequency turbulence is an important driving force behind the entrainment and transport of sand. At this scale of analysis, inertia in the saltation system causes changes in sediment transport to lag behind de/accelerations in flow. However, saltation inertia has yet to be incorporated into a functional sand transport model that can be used for predictive purposes. In this study, we present a new transport model that dynamically balances the sand mass being transported in the wind flow. The 'dynamic mass balance' (DMB) model we present accounts for high-frequency variations in the horizontal (u) component of wind flow, as saltation is most strongly associated with the positive u component of the wind. The performance of the DMB model is tested by fitting it to two field-derived (Namibia's Skeleton Coast) datasets of wind velocity and sediment transport: (i) a 10-min (10 Hz measurement resolution) dataset; (ii) a 2-h (1 Hz measurement resolution) dataset. The DMB model is shown to outperform two existing models that rely on time-averaged wind velocity data (e.g. Radok, 1977; Dong et al., 2003), when predicting sand transport over the two experiments. For all measurement averaging intervals presented in this study (10 Hz-10 min), the DMB model predicted total saltation count to within at least 0.48%, whereas the Radok and Dong models over- or underestimated total count by up to 5.50% and 20.53% respectively. The DMB model also produced more realistic (less 'peaky') time series of sand flux than the other two models, and a more accurate distribution of sand flux data. The best predictions of total sand transport are achieved using

  20. Fluid transport and ion fluxes in mammalian kidney proximal tubule: a model analysis of isotonic transport

    DEFF Research Database (Denmark)

    Larsen, Erik Hviid; Møbjerg, N.; Sørensen, J. N.

    2006-01-01

    Aim: By mathematical modelling, we analyse conditions for near-isotonic and isotonic transport by mammalian kidney proximal tubule. Methods: The model comprises compliant lateral intercellular space (lis) and cells, and infinitely large luminal and peritubular compartments with diffusible species......: Na+, K+, Cl- and an intracellular non-diffusible anion. Unknown model variables are solute concentrations, electrical potentials, volumes and hydrostatic pressures in cell and lis, and transepithelial potential. We used data mainly from rat proximal tubule to model epithelial cells and interspace...... transport similar to rat proximal tubule. Na+ recirculation is required for truly isotonic transport. The tonicity of the absorbate and the recirculation flux depend critically on ion permeabilities of interspace basement membrane. Conclusion: Our model based on solute-solvent coupling in lateral space...

  1. Feedback network models for quantum transport.

    Science.gov (United States)

    Gough, John

    2014-12-01

    Quantum feedback networks have been introduced in quantum optics as a framework for constructing arbitrary networks of quantum mechanical systems connected by unidirectional quantum optical fields, and has allowed for a system theoretic approach to open quantum optics systems. Our aim here is to establish a network theory for quantum transport systems where typically the mediating fields between systems are bidirectional. Mathematically, this leads us to study quantum feedback networks where fields arrive at ports in input-output pairs, making it a special case of the unidirectional theory where inputs and outputs are paired. However, it is conceptually important to develop this theory in the context of quantum transport theory-the resulting theory extends traditional approaches which tend to view the components in quantum transport as scatterers for the various fields, in the process allowing us to consider emission and absorption of field quanta by these components. The quantum feedback network theory is applicable to both Bose and Fermi fields, moreover, it applies to nonlinear dynamics for the component systems. We advance the general theory, but study the case of linear passive quantum components in some detail.

  2. Metal transport across biomembranes: emerging models for a distinct chemistry.

    Science.gov (United States)

    Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

    2012-04-20

    Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

  3. Modeling Reactive Transport in Coupled Groundwater-Conduit Systems

    Science.gov (United States)

    Spiessl, S. M.; Sauter, M.; Zheng, C.; Viswanathan, H. S.

    2002-05-01

    Modeling reactive transport in coupled groundwater-conduit systems requires consideration of two transport time scales in the flow and transport models. Consider for example a subsurface mine consisting of a network of highly conductive shafts, drifts or ventilation raises (i.e., conduits) within the considerably less permeable ore material (i.e., matrix). In the conduits, potential contaminants can travel much more rapidly than in the background aquifer (matrix). Since conduits cannot necessarily be regarded as a continuum, double continuum models are only of limited use for simulation of contaminant transport in such coupled groundwater-conduit systems. This study utilizes a "hybrid" flow and transport model in which contaminants can in essence be transported at a slower time scale in the matrix and at a faster time scale in the conduits. The hybrid flow model uses an approach developed by Clemens et al. (1996), which is based on the modelling of flow in a discrete pipe network, coupled to a continuum representing the low-permeability inter-conduit matrix blocks. Laminar or turbulent flow can be simulated in the different pipes depending on the flow conditions in the model domain. The three-dimensional finite-difference groundwater flow model MODFLOW (Harbaugh and McDonald, 1996) is used to simulate flow in the continuum. Contaminant transport within the matrix is simulated with a continuum approach using the three-dimensional multi-species solute transport model MT3DMS (Zheng and Wang, 1999), while that in the conduit system is simulated with a one-dimensional advective transport model. As a first step for reactive transport modeling in such systems, only equilibrium reactions among multiple species are considered by coupling the hybrid transport model to a geochemical speciation package. An idealized mine network developed by Viswanathan and Sauter (2001) is used as a test problem in this study. The numerical experiment is based on reference date collected from

  4. Modeling of pollutant emissions from road transport; Modelisation des emissions de polluants par le transport routier

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    COPERT III (computer programme to calculate emissions from road transport) is the third version of an MS Windows software programme aiming at the calculation of air pollutant emissions from road transport. COPERT estimates emissions of all regulated air pollutants (CO, NO{sub x}, VOC, PM) produced by different vehicle categories as well as CO{sub 2} emissions on the basis of fuel consumption. This research seminar was organized by the French agency of environment and energy mastery (Ademe) around the following topics: the uncertainties and sensitiveness analysis of the COPERT III model, the presentation of case studies that use COPERT III for the estimation of road transport emissions, and the future of the modeling of road transport emissions: from COPERT III to ARTEMIS (assessment and reliability of transport emission models and inventory systems). This document is a compilation of 8 contributions to this seminar and dealing with: the uncertainty and sensitiveness analysis of the COPERT III model; the road mode emissions of the ESCOMPTE program: sensitivity study; the sensitivity analysis of the spatialized traffic at the time-aggregation level: application in the framework of the INTERREG project (Alsace); the road transport aspect of the regional air quality plan of Bourgogne region: exhaustive consideration of the road network; intercomparison of tools and methods for the inventory of emissions of road transport origin; evolution of the French park of vehicles by 2025: new projections; application of COPERT III to the French context: a new version of IMPACT-ADEME; the European ARTEMIS project: new structural considerations for the modeling of road transport emissions. (J.S.)

  5. Electronic transport in VO{sub 2}—Experimentally calibrated Boltzmann transport modeling

    Energy Technology Data Exchange (ETDEWEB)

    Kinaci, Alper; Rosenmann, Daniel; Chan, Maria K. Y., E-mail: debasish.banerjee@toyota.com, E-mail: mchan@anl.gov [Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Kado, Motohisa [Higashifuji Technical Center, Toyota Motor Corporation, Susono, Shizuoka 410-1193 (Japan); Ling, Chen; Zhu, Gaohua; Banerjee, Debasish, E-mail: debasish.banerjee@toyota.com, E-mail: mchan@anl.gov [Materials Research Department, Toyota Motor Engineering and Manufacturing North America, Inc., Ann Arbor, Michigan 48105 (United States)

    2015-12-28

    Materials that undergo metal-insulator transitions (MITs) are under intense study, because the transition is scientifically fascinating and technologically promising for various applications. Among these materials, VO{sub 2} has served as a prototype due to its favorable transition temperature. While the physical underpinnings of the transition have been heavily investigated experimentally and computationally, quantitative modeling of electronic transport in the two phases has yet to be undertaken. In this work, we establish a density-functional-theory (DFT)-based approach with Hubbard U correction (DFT + U) to model electronic transport properties in VO{sub 2} in the semiconducting and metallic regimes, focusing on band transport using the Boltzmann transport equations. We synthesized high quality VO{sub 2} films and measured the transport quantities across the transition, in order to calibrate the free parameters in the model. We find that the experimental calibration of the Hubbard correction term can efficiently and adequately model the metallic and semiconducting phases, allowing for further computational design of MIT materials for desirable transport properties.

  6. Modelling sediment transport processes in macro-tidal estuary

    Institute of Scientific and Technical Information of China (English)

    Rauen; William; B.

    2009-01-01

    This paper outlines a numerical modeling study to predict the sediment transport processes in a macro-tidal estuary, namely the Mersey Estuary, UK. An integrated numerical model study is conducted to investigate the interaction between the hydrodynamic, morphological and sediment transport processes occurring in the estuary. The numerical model widely used in environmental sediment transport studies worldwide, namely ECOMSED is used to simulate flow and sediment transport in estuary. A wetting and drying scheme is proposed and applied to the model, which defines "dry" cells as regions with a thin film of fluid O (cm). The primitive equations are solved in the thin film as well as in other regular wet cells. A model for the bed load transport is included in the code to account for the dynamics of the mobile bed boundary. The bed evolution due to bed load transport which is calculated according to van Rijn (1984a) is obtained by solving the sediment mass-balance equation. An estuary-related laboratory flume experiment is used to verify the model. Six sets of field measured hydrodynamic data are used to verify the corresponding predictions of the model, with the model-predicted water elevations and salinity levels generally agreeing well with the field measurements. The numerical model results show that in the Mersey Estuary both the tidal level and river discharge affect significantly the sediment transport. Reasonable agreement between the model results and field data has been obtained, indicating that the model can be used as computer-based tool for the environment management of estuarine system.

  7. Enhanced biogeochemical cycling and subsequent reduction of hydraulic conductivity associated with soil-layer interfaces in the vadose zone.

    Science.gov (United States)

    Hansen, David J; McGuire, Jennifer T; Mohanty, Binayak P

    2011-01-01

    Biogeochemical dynamics in the vadose zone are poorly understood due to the transient nature of chemical and hydrologic conditions but are nonetheless critical to understanding chemical fate and transport. This study explored the effects of a soil layer on linked geochemical, hydrological, and microbiological processes. Three laboratory soil columns were constructed: a homogenized medium-grained sand, a homogenized organic-rich loam, and a sand-over-loam layered column. Upward and downward infiltration of water was evaluated during experiments to simulate rising water table and rainfall events, respectively. In situ collocated probes measured soil water content, matric potential, and Eh. Water samples collected from the same locations were analyzed for Br, Cl, NO, SO, NH, Fe, and total sulfide. Compared with homogeneous columns, the presence of a soil layer altered the biogeochemistry and water flow of the system considerably. Enhanced biogeochemical cycling was observed in the layered column over the texturally homogeneous soil columns. Enumerations of iron- and sulfate-reducing bacteria showed 1 to 2 orders of magnitude greater community numbers in the layered column. Mineral and soil aggregate composites were most abundant near the soil-layer interface, the presence of which likely contributed to an observed order-of-magnitude decrease in hydraulic conductivity. These findings show that quantifying coupled hydrologic-biogeochemical processes occurring at small-scale soil interfaces is critical to accurately describing and predicting chemical changes at the larger system scale. These findings also provide justification for considering soil layering in contaminant fate and transport models because of its potential to increase biodegradation or to slow the rate of transport of contaminants.

  8. Kinetic modelling of coupled transport across biological membranes.

    Science.gov (United States)

    Korla, Kalyani; Mitra, Chanchal K

    2014-04-01

    In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.

  9. Probabilistic transport models for plasma transport in the presence of critical thresholds: Beyond the diffusive paradigma)

    Science.gov (United States)

    Sánchez, R.; van Milligen, B. Ph.; Carreras, B. A.

    2005-05-01

    It is argued that the modeling of plasma transport in tokamaks may benefit greatly from extending the usual local paradigm to accommodate scale-free transport mechanisms. This can be done by combining Lévy distributions and a nonlinear threshold condition within the continuous time random walk concept. The advantages of this nonlocal, nonlinear extension are illustrated by constructing a simple particle density transport model that, as a result of these ideas, spontaneously exhibits much of nondiffusive phenomenology routinely observed in tokamaks. The fluid limit of the system shows that the kind of equations that are appropriate to capture these dynamics are based on fractional differential operators. In them, effective diffusivities and pinch velocities are found that are dynamically set by the system in response to the specific characteristics of the fueling source and external perturbations. This fact suggests some dramatic consequences for the extrapolation of these transport properties to larger size systems.

  10. The thermoballistic transport model a novel approach to charge carrier transport in semiconductors

    CERN Document Server

    Lipperheide, Reinhard

    2014-01-01

    The book presents a comprehensive survey of the thermoballistic approach to charge carrier transport in semiconductors. This semi-classical approach, which the authors have developed over the past decade, bridges the gap between the opposing drift-diffusion and ballistic  models of carrier transport. While incorporating basic features of the latter two models, the physical concept underlying the thermoballistic approach constitutes a novel, unifying scheme. It is based on the introduction of "ballistic configurations" arising from a random partitioning of the length of a semiconducting sample into ballistic transport intervals. Stochastic averaging of the ballistic carrier currents over the ballistic configurations results in a position-dependent thermoballistic current, which is the key element of the thermoballistic concept and forms  the point of departure for the calculation of all relevant transport properties. In the book, the thermoballistic concept and its implementation are developed in great detai...

  11. Quantum Model of Energy Transport in Collagen Molecules

    Institute of Scientific and Technical Information of China (English)

    XIAO Yi; LIN Xian-Zhe

    2001-01-01

    A semi-quantum model for energy transport in collagen molecules is presented. Soliton-like dynamics of this model is investigated numerically without and with the temperature effect taking into account. It is found that in both the cases energy can transport for a long distance along the collagen chain. This indicates that collagen molecules can be taken as a candidate for the acupuncture channel.

  12. Transport properties of stochastic Lorentz models

    NARCIS (Netherlands)

    Beijeren, H. van

    1982-01-01

    Diffusion processes are considered for one-dimensional stochastic Lorentz models, consisting of randomly distributed fixed scatterers and one moving light particle. In waiting time Lorentz models the light particle makes instantaneous jumps between scatterers after a stochastically distributed waiti

  13. Transport modelling in coastal waters using stochastic differential equations

    NARCIS (Netherlands)

    Charles, W.M.

    2007-01-01

    In this thesis, the particle model that takes into account the short term correlation behaviour of pollutants dispersion has been developed. An efficient particle model for sediment transport has been developed. We have modified the existing particle model by adding extra equations for the suspensio

  14. Setting up a freight transportation model for Java in Indonesia

    NARCIS (Netherlands)

    De Baat, M.J.; Den Hertog, V.; De Jong, S.; De Regt, K.; Wijgergangs, K.

    2015-01-01

    The project consisted of the development of a freight transportation model for the island Java in Indonesia. A literature study concerning freight modelling has been performed to formulate an appropriate framework of such a model for the given situation. Different data sources have been identified,

  15. Analysing Models as a Knowledge Technology in Transport Planning

    DEFF Research Database (Denmark)

    Gudmundsson, Henrik

    2011-01-01

    Models belong to a wider family of knowledge technologies, applied in the transport area. Models sometimes share with other such technologies the fate of not being used as intended, or not at all. The result may be ill-conceived plans as well as wasted resources. Frequently, the blame for such a ......Models belong to a wider family of knowledge technologies, applied in the transport area. Models sometimes share with other such technologies the fate of not being used as intended, or not at all. The result may be ill-conceived plans as well as wasted resources. Frequently, the blame...... critical analytic literature on knowledge utilization and policy influence. A simple scheme based in this literature is drawn up to provide a framework for discussing the interface between urban transport planning and model use. A successful example of model use in Stockholm, Sweden is used as a heuristic...

  16. Transport lattice models of heat transport in skin with spatially heterogeneous, temperature-dependent perfusion

    Directory of Open Access Journals (Sweden)

    Martin Gregory T

    2004-11-01

    Full Text Available Abstract Background Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport lattice approach. Methods We represent heat transport processes by using a lattice that represents the Pennes bioheat equation in perfused tissues, and diffusion in nonperfused regions. The three layer skin model has a nonperfused viable epidermis, and deeper regions of dermis and subcutaneous tissue with perfusion that is constant or temperature-dependent. Two cases are considered: (1 surface contact heating and (2 spatially distributed heating. The model is relevant to the prediction of the transient and steady state temperature rise for different methods of power deposition within the skin. Accumulated thermal damage is estimated by using an Arrhenius type rate equation at locations where viable tissue temperature exceeds 42°C. Prediction of spatial temperature distributions is also illustrated with a two-dimensional model of skin created from a histological image. Results The transport lattice approach was validated by comparison with an analytical solution for a slab with homogeneous thermal properties and spatially distributed uniform sink held at constant temperatures at the ends. For typical transcutaneous blood gas sensing conditions the estimated damage is small, even with prolonged skin contact to a 45°C surface. Spatial heterogeneity in skin thermal properties leads to a non-uniform temperature distribution during a 10 GHz electromagnetic field exposure. A realistic two-dimensional model of the skin shows that tissue heterogeneity does not lead to a significant local temperature increase when heated by a hot wire tip. Conclusions The heat transport system model of the

  17. ATTILA - Atmospheric Tracer Transport In a Langrangian Model

    Energy Technology Data Exchange (ETDEWEB)

    Reithmeier, C.; Sausen, R.

    2000-07-01

    The Lagrangian model ATTILA (atmospheric tracer transport in a Lagrangian model) has been developed to treat the global-scale transport of passive trace species in the atmosphere within the framework of a general circulation model (GCM). ATTILA runs online within the GCM ECHAM4 and uses the GCM produced wind field to advect the centrois of 80.000 to 180.000 constant mass air parcels into which the model atmosphere is divided. Each trace constituent is thereby represented by a mass mixing ratio in each parcel. ATTILA contains state-of-the-art parameterizations of convection, turbulent boundary layer mixing, and interparcel transport and provides an algorithm to map the tracer concentrations from the trajectories to the ECHAM model grid. We use two experiments to evaluate the transport characteristics of ATTILA against observations and the standard semiLagrangian transport scheme of ECHAM. In the first experiment we simulate the distribution of the short-lived tracer Radon ({sup 222}Rn) in order to examine fast vertical transport over continents, and long-range transport from the continents to remote areas. In the second experiment, we simulate the distribution of radiocarbon ({sup 14}C) that was injected into the northern stratosphere during the nuclear weapon tests in the early 60ties, in order to examine upper tropospheric and stratospheric transport characteristics. ATTILA compares well to the observations and in many respects to the semiLagrangian scheme. However, contrary to the semiLagrangian scheme, ATTILA shows a greatly reduced meridional transport in the upper troposphere and lower stratosphere, and a reduced downward flux from the stratosphere to the troposphere, especially in midlatitudes. Since both transport schemes use the same model meteorology, we conclude that the often cited enhanced meridional transport and overestimated downward flux in ECHAM as described above is rather due to the numerical properties of the semiLagrangian scheme than due to an

  18. Collisional broadening of angular correlations in a multiphase transport model

    CERN Document Server

    Edmonds, Terrence; Wang, Fuqiang

    2016-01-01

    Systematic comparisons of jetlike correlation data to radiative and collisional energy loss model calculations are essential to extract transport properties of the quark-gluon medium created in relativistic heavy ion collisions. This paper presents a transport study of collisional broadening of jetlike correlations, by following parton-parton collision history in a multiphase transport (AMPT) model. The correlation shape is studied as a function of the number of parton-parton collisions suffered by a high transverse momentum probe parton ($N_{\\rm coll}$) and the azimuth of the probe relative to the reaction plane ($\\phi_{\\rm fin.}^{\\rm probe}$). Correlation is found to broaden with increasing $N_{\\rm coll}$ and $\\phi_{\\rm fin.}^{\\rm probe}$ from in- to out-of-plane direction. This study provides a transport model benchmark for future jet-medium interaction studies.

  19. Economic model of pipeline transportation systems

    Energy Technology Data Exchange (ETDEWEB)

    Banks, W. F.

    1977-07-29

    The objective of the work reported here was to develop a model which could be used to assess the economic effects of energy-conservative technological innovations upon the pipeline industry. The model is a dynamic simulator which accepts inputs of two classes: the physical description (design parameters, fluid properties, and financial structures) of the system to be studied, and the postulated market (throughput and price) projection. The model consists of time-independent submodels: the fluidics model which simulates the physical behavior of the system, and the financial model which operates upon the output of the fluidics model to calculate the economics outputs. Any of a number of existing fluidics models can be used in addition to that developed as a part of this study. The financial model, known as the Systems, Science and Software (S/sup 3/) Financial Projection Model, contains user options whereby pipeline-peculiar characteristics can be removed and/or modified, so that the model can be applied to virtually any kind of business enterprise. The several dozen outputs are of two classes: the energetics and the economics. The energetics outputs of primary interest are the energy intensity, also called unit energy consumption, and the total energy consumed. The primary economics outputs are the long-run average cost, profit, cash flow, and return on investment.

  20. Interfacial and Wall Transport Models for SPACE-CAP Code

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Soon Joon; Choo, Yeon Joon; Han, Tae Young; Hwang, Su Hyun; Lee, Byung Chul [FNC Tech., Seoul (Korea, Republic of); Choi, Hoon; Ha, Sang Jun [Korea Electric Power Research Institute, Daejeon (Korea, Republic of)

    2009-10-15

    The development project for the domestic design code was launched to be used for the safety and performance analysis of pressurized light water reactors. And CAP (Containment Analysis Package) code has been also developed for the containment safety and performance analysis side by side with SPACE. The CAP code treats three fields (gas, continuous liquid, and dispersed drop) for the assessment of containment specific phenomena, and is featured by its multidimensional assessment capabilities. Thermal hydraulics solver was already developed and now under testing of its stability and soundness. As a next step, interfacial and wall transport models was setup. In order to develop the best model and correlation package for the CAP code, various models currently used in major containment analysis codes, which are GOTHIC, CONTAIN2.0, and CONTEMPT-LT, have been reviewed. The origins of the selected models used in these codes have also been examined to find out if the models have not conflict with a proprietary right. In addition, a literature survey of the recent studies has been performed in order to incorporate the better models for the CAP code. The models and correlations of SPACE were also reviewed. CAP models and correlations are composed of interfacial heat/mass, and momentum transport models, and wall heat/mass, and momentum transport models. This paper discusses on those transport models in the CAP code.

  1. A mathematical model of inter-terminal transportation

    DEFF Research Database (Denmark)

    Tierney, Kevin; Voß, Stefan; Stahlbock, Robert

    2014-01-01

    We present a novel integer programming model for analyzing inter-terminal transportation (ITT) in new and expanding sea ports. ITT is the movement of containers between terminals (sea, rail or otherwise) within a port. ITT represents a significant source of delay for containers being transshipped...... contains special structures to model the long term loading and unloading of vehicles, and our model is general enough to model a number of important real-world aspects of ITT, such as traffic congestion, penalized late container delivery, multiple ITT transportation modes, and port infrastructure...

  2. Chemical Kinetic Modeling of Advanced Transportation Fuels

    Energy Technology Data Exchange (ETDEWEB)

    PItz, W J; Westbrook, C K; Herbinet, O

    2009-01-20

    Development of detailed chemical kinetic models for advanced petroleum-based and nonpetroleum based fuels is a difficult challenge because of the hundreds to thousands of different components in these fuels and because some of these fuels contain components that have not been considered in the past. It is important to develop detailed chemical kinetic models for these fuels since the models can be put into engine simulation codes used for optimizing engine design for maximum efficiency and minimal pollutant emissions. For example, these chemistry-enabled engine codes can be used to optimize combustion chamber shape and fuel injection timing. They also allow insight into how the composition of advanced petroleum-based and non-petroleum based fuels affect engine performance characteristics. Additionally, chemical kinetic models can be used separately to interpret important in-cylinder experimental data and gain insight into advanced engine combustion processes such as HCCI and lean burn engines. The objectives are: (1) Develop detailed chemical kinetic reaction models for components of advanced petroleum-based and non-petroleum based fuels. These fuels models include components from vegetable-oil-derived biodiesel, oil-sand derived fuel, alcohol fuels and other advanced bio-based and alternative fuels. (2) Develop detailed chemical kinetic reaction models for mixtures of non-petroleum and petroleum-based components to represent real fuels and lead to efficient reduced combustion models needed for engine modeling codes. (3) Characterize the role of fuel composition on efficiency and pollutant emissions from practical automotive engines.

  3. UNCERTAINTY SUPPLY CHAIN MODEL AND TRANSPORT IN ITS DEPLOYMENTS

    Directory of Open Access Journals (Sweden)

    Fabiana Lucena Oliveira

    2014-05-01

    Full Text Available This article discusses the Model Uncertainty of Supply Chain, and proposes a matrix with their transportation modes best suited to their chains. From the detailed analysis of the matrix of uncertainty, it is suggested transportation modes best suited to the management of these chains, so that transport is the most appropriate optimization of the gains previously proposed by the original model, particularly when supply chains are distant from suppliers of raw materials and / or supplies.Here we analyze in detail Agile Supply Chains, which is a result of Uncertainty Supply Chain Model, with special attention to Manaus Industrial Center. This research was done at Manaus Industrial Pole, which is a model of industrial agglomerations, based in Manaus, State of Amazonas (Brazil, which contemplates different supply chains and strategies sharing same infrastructure of transport, handling and storage and clearance process and uses inbound for suppliers of raw material.  The state of art contemplates supply chain management, uncertainty supply chain model, agile supply chains, Manaus Industrial Center (MIC and Brazilian legislation, as a business case, and presents concepts and features, of each one. The main goal is to present and discuss how transport is able to support Uncertainty Supply Chain Model, in order to complete management model. The results obtained confirms the hypothesis of integrated logistics processes are able to guarantee attractivity for industrial agglomerations, and open discussions when the suppliers are far from the manufacturer center, in a logistics management.

  4. A quasi-linear gyrokinetic transport model for tokamak plasmas

    CERN Document Server

    Casati, Alessandro

    2012-01-01

    The development of a quasi-linear gyrokinetic transport model for tokamak plasmas, ultimately designed to provide physically comprehensive predictions of the time evolution of the thermodynamic relevant quantities, is a task that requires tight links among theoretical, experimental and numerical studies. The framework of the model here proposed, which operates a reduction of complexity on the nonlinear self-organizing plasma dynamics, allows in fact multiple validations of the current understanding of the tokamak micro-turbulence. The main outcomes of this work stem from the fundamental steps involved by the formulation of such a reduced transport model, namely: (1) the verification of the quasi-linear plasma response against the nonlinearly computed solution, (2) the improvement of the turbulent saturation model through an accurate validation of the nonlinear codes against the turbulence measurements, (3) the integration of the quasi-linear model within an integrated transport solver.

  5. Application of the New Weiland Model for Studying Transport Barriers

    Science.gov (United States)

    Kritz, Arnold; Fan, Xiang; Rafiq, Tariq; Tangri, Varun; Pankin, Alexei; Weiland, Jan

    2012-10-01

    Recent advances in the Weiland drift wave model include new correlation length and new kink (peeling) terms as well as collisions on free electrons. The new model also includes electromagnetic effects on toroidal and poloidal momentum transport. These advances make the model suitable for simulating anomalous effects in transport barriers. A description of the Weiland model content is included in the adjacent poster by T. Rafiq et al. In this study, particle, thermal, and momentum transport coefficients are computed in systematic scans over electron and ion temperature gradients, temperature ratio, density gradient, magnetic q, collision frequency, trapped particle fraction, magnetic shear, Larmor radius, plasma β and elongation. Special consideration is given to the plasma parameter scans that correspond to the plasma edge region such as large temperature and density gradients, large magnetic shear and large magnetic q. The transport results yielded by the new Weiland drift wave model are contrasted with the earlier version of the model. Combined with high fidelity models for neoclassical effects such as NEO and XGC0 models, it is anticipated that the new Weiland model can be used to model H-mode pedestal buildup and recovery between ELM crashes.

  6. Transportation Sector Model of the National Energy Modeling System. Volume 2 -- Appendices: Part 1

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-01-01

    This volume contains input data and parameters used in the model of the transportation sector of the National Energy Modeling System. The list of Transportation Sector Model variables includes parameters for the following: Light duty vehicle modules (fuel economy, regional sales, alternative fuel vehicles); Light duty vehicle stock modules; Light duty vehicle fleet module; Air travel module (demand model and fleet efficiency model); Freight transport module; Miscellaneous energy demand module; and Transportation emissions module. Also included in these appendices are: Light duty vehicle market classes; Maximum light duty vehicle market penetration parameters; Aircraft fleet efficiency model adjustment factors; and List of expected aircraft technology improvements.

  7. Cosmic-Ray Transport in Heliospheric Magnetic Structures. II. Modeling Particle Transport through Corotating Interaction Regions

    Science.gov (United States)

    Kopp, Andreas; Wiengarten, Tobias; Fichtner, Horst; Effenberger, Frederic; Kühl, Patrick; Heber, Bernd; Raath, Jan-Louis; Potgieter, Marius S.

    2017-03-01

    The transport of cosmic rays (CRs) in the heliosphere is determined by the properties of the solar wind plasma. The heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric CR transport are structures such as corotating interaction regions (CIRs), which, due to the enhancement of the magnetic field strength and magnetic fluctuations within and due to the associated shocks as well as stream interfaces, do influence the CR diffusion and drift. In a three-fold series of papers, we investigate these effects by modeling inner-heliospheric solar wind conditions with the numerical magnetohydrodynamic (MHD) framework Cronos (Wiengarten et al., referred as Paper I), and the results serve as input to a transport code employing a stochastic differential equation approach (this paper). While, in Paper I, we presented results from 3D simulations with Cronos, the MHD output is now taken as an input to the CR transport modeling. We discuss the diffusion and drift behavior of Galactic cosmic rays using the example of different theories, and study the effects of CIRs on these transport processes. In particular, we point out the wide range of possible particle fluxes at a given point in space resulting from these different theories. The restriction of this variety by fitting the numerical results to spacecraft data will be the subject of the third paper of this series.

  8. Computer modeling of electron and proton transport in chloroplasts.

    Science.gov (United States)

    Tikhonov, Alexander N; Vershubskii, Alexey V

    2014-07-01

    Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of

  9. Examining an important urban transportation management tool: subarea modeling

    Directory of Open Access Journals (Sweden)

    Xueming CHEN

    2009-12-01

    Full Text Available At present, customized subarea models have been widely used in local transportation planning throughout the United States. The biggest strengths of a subarea model lie in its more detailed and accurate modeling outputs which better meet local planning requirements. In addition, a subarea model can substantially reduce database size and model running time. In spite of these advantages, subarea models remain quite weak in maintaining consistency with a regional model, modeling transit projects, smart growth measures, air quality conformity, and other areas. Both opportunities and threats exist for subarea modeling. In addition to examining subarea models, this paper introduces the decision-making process in choosing a proper subarea modeling approach (windowing versus focusing and software package. This study concludes that subarea modeling will become more popular in the future. More GIS applications, travel surveys, transit modeling, microsimulation software utilization, and other modeling improvements are expected to be incorporated into the subarea modeling process.

  10. Aeolian Sediment Transport Integration in General Stratigraphic Forward Modeling

    Directory of Open Access Journals (Sweden)

    T. Salles

    2011-01-01

    Full Text Available A large number of numerical models have been developed to simulate the physical processes involved in saltation, and, recently to investigate the interaction between soil vegetation cover and aeolian transport. These models are generally constrained to saltation of monodisperse particles while natural saltation occurs over mixed soils. We present a three-dimensional numerical model of steady-state saltation that can simulate aeolian erosion, transport and deposition for unvegetated mixed soils. Our model simulates the motion of saltating particles using a cellular automata algorithm. A simple set of rules is used and takes into account an erosion formula, a transport model, a wind exposition function, and an avalanching process. The model is coupled to the stratigraphic forward model Sedsim that accounts for a larger number of geological processes. The numerical model predicts a wide range of typical dune shapes, which have qualitative correspondence to real systems. The model reproduces the internal structure and composition of the resulting aeolian deposits. It shows the complex formation of dune systems with cross-bedding strata development, bounding surfaces overlaid by fine sediment and inverse grading deposits. We aim to use it to simulate the complex interactions between different sediment transport processes and their resulting geological morphologies.

  11. Evaluation of cloud convection and tracer transport in a three-dimensional chemical transport model

    Directory of Open Access Journals (Sweden)

    W. Feng

    2011-06-01

    Full Text Available We investigate the performance of cloud convection and tracer transport in a global off-line 3-D chemical transport model. Various model simulations are performed using different meteorological (reanalyses (ERA-40, ECMWF operational and ECMWF Interim to diagnose the updraft mass flux, convective precipitation and cloud top height.

    The diagnosed upward mass flux distribution from TOMCAT agrees quite well with the ECMWF reanalysis data (ERA-40 and ERA-Interim below 200 hPa. Inclusion of midlevel convection improves the agreement at mid-high latitudes. However, the reanalyses show strong convective transport up to 100 hPa, well into the tropical tropopause layer (TTL, which is not captured by TOMCAT. Similarly, the model captures the spatial and seasonal variation of convective cloud top height although the mean modelled value is about 2 km lower than observed.

    The ERA-Interim reanalyses have smaller archived upward convective mass fluxes than ERA-40, and smaller convective precipitation, which is in better agreement with satellite-based data. TOMCAT captures these relative differences when diagnosing convection from the large-scale fields. The model also shows differences in diagnosed convection with the version of the operational analyses used, which cautions against using results of the model from one specific time period as a general evaluation.

    We have tested the effect of resolution on the diagnosed modelled convection with simulations ranging from 5.6° × 5.6° to 1° × 1°. Overall, in the off-line model, the higher model resolution gives stronger vertical tracer transport, however, it does not make a large change to the diagnosed convective updraft mass flux (i.e., the model results using the convection scheme fail to capture the strong convection transport up to 100 hPa as seen in the archived convective mass fluxes. Similarly, the resolution of the forcing winds in the higher resolution CTM does not make a

  12. Development of interfacial area transport equation - modeling and experimental benchmark

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, M. [Purdue Univ., West Lafayette, Indiana (United States)

    2011-07-01

    A dynamic treatment of interfacial area concentration has been studied over the last decade by employing the interfacial area transport equation. When coupled with the two-fluid model, the interfacial area transport equation replaces the flow regime dependent correlations for interfacial area concentration and eliminates potential artificial bifurcation or numerical oscillations stemming from these static correlations. An extensive database has been established to evaluate the model under various two-phase flow conditions. These include adiabatic and heated conditions, vertical and horizontal flow orientations, round, rectangular, annulus and 8×8 rod bundle channel geometries, and normal-gravity and simulated reduced-gravity conditions. This paper reviews the current state-of-the-art in the development of the interfacial area transport equation, available experimental databases and 1D and 3D benchmarking work of the interfacial area transport equation. (author)

  13. Modeling passenger flows in public transport stations

    Directory of Open Access Journals (Sweden)

    Cem Kırlangıçoğlu

    2015-06-01

    Full Text Available There are many architectural design parameters for public transport stations which include urban and station level studies. Each station must be designed in accordance with the basic passenger requirements such as accessibility, safety, comfort, satisfaction and etc. Circulation spaces must be formed and sized to meet the minimum movement needs of passengers. For an underground station; main entrance region, position of gates, location and number of turnstiles, escalators, stairs, ramps, passageways, intermediate concourses and platforms must be arranged to minimize walking distances and to prevent congestion. In this study, circulation of passengers is simulated in a quantitatively verifiable manner, taking into account how individuals interact with each other and with the physical obstacles in their environment in a metro station. Virtual experiments are performed to see the continuity and density of pedestrian flow at different levels of Haram Area East Metro Station of the first metro line of Madinah Al-Munawwarah, Saudi Arabia. According to the predictions, more than 40.000 passengers are expected to use this station in one hour after a Friday prayer during Ramadan period in the year of 2040. That means a critically high travel demand and it is really significant to design the most convenient underground station for these passengers to fulfil the necessary requirements.

  14. Generic Procedure for Coupling the PHREEQC Geochemical Modeling Framework with Flow and Solute Transport Simulators

    Science.gov (United States)

    Wissmeier, L. C.; Barry, D. A.

    2009-12-01

    Computer simulations of water availability and quality play an important role in state-of-the-art water resources management. However, many of the most utilized software programs focus either on physical flow and transport phenomena (e.g., MODFLOW, MT3DMS, FEFLOW, HYDRUS) or on geochemical reactions (e.g., MINTEQ, PHREEQC, CHESS, ORCHESTRA). In recent years, several couplings between both genres of programs evolved in order to consider interactions between flow and biogeochemical reactivity (e.g., HP1, PHWAT). Software coupling procedures can be categorized as ‘close couplings’, where programs pass information via the memory stack at runtime, and ‘remote couplings’, where the information is exchanged at each time step via input/output files. The former generally involves modifications of software codes and therefore expert programming skills are required. We present a generic recipe for remotely coupling the PHREEQC geochemical modeling framework and flow and solute transport (FST) simulators. The iterative scheme relies on operator splitting with continuous re-initialization of PHREEQC and the FST of choice at each time step. Since PHREEQC calculates the geochemistry of aqueous solutions in contact with soil minerals, the procedure is primarily designed for couplings to FST’s for liquid phase flow in natural environments. It requires the accessibility of initial conditions and numerical parameters such as time and space discretization in the input text file for the FST and control of the FST via commands to the operating system (batch on Windows; bash/shell on Unix/Linux). The coupling procedure is based on PHREEQC’s capability to save the state of a simulation with all solid, liquid and gaseous species as a PHREEQC input file by making use of the dump file option in the TRANSPORT keyword. The output from one reaction calculation step is therefore reused as input for the following reaction step where changes in element amounts due to advection

  15. Mathematical modeling/problem solving in global oxygen transport.

    Science.gov (United States)

    Farrell, Kevin; Hill, Andrew; Dent, Leon; Nguyen, Minh Ly

    2009-08-01

    A simplified approach to mathematical modeling/problem solving in global oxygen transport is presented. In addition to standard oxygen transport formulae, it uses the S-Factor and a mathematical relationship relating SvO(2) to the ratio DO(2)/VO(2). This method allows the determination or specification of SvO(2), PvO(2), P(50), and systemic shunting in the context of this simplified approach. Heretofore this has not been possible. With this approach, essentially all clinical problems in global oxygen transport can be dealt with. This is illustrated by the broad scope of the five problems presented.

  16. Lithium ion transport in a model of amorphous polyethylene oxide.

    Energy Technology Data Exchange (ETDEWEB)

    Boinske, P. T.; Curtiss, L.; Halley, J. W.; Lin, B.; Sutjianto, A.; Chemical Engineering; Univ. of Minnesota

    1996-01-01

    We have made a molecular dynamics study of transport of a single lithium ion in a previously reported model of amorphous polyethylene oxide. New ab initio calculations of the interaction of the lithium ion with 1,2-dimethoxyethane and with dimethyl ether are reported which are used to determine force fields for the simulation. We report preliminary calculations of solvation energies and hopping barriers and a calculation of the ionic conductivity which is independent of any assumptions about the mechanism of ion transport. We also report some details of a study of transport of the trapped lithium ion on intermediate time and length scales.

  17. Langevin model for reactive transport in porous media

    Science.gov (United States)

    Tartakovsky, Alexandre M.

    2010-08-01

    Existing continuum models for reactive transport in porous media tend to overestimate the extent of solute mixing and mixing-controlled reactions because the continuum models treat both the mechanical and diffusive mixings as an effective Fickian process. Recently, we have proposed a phenomenological Langevin model for flow and transport in porous media [A. M. Tartakovsky, D. M. Tartakovsky, and P. Meakin, Phys. Rev. Lett. 101, 044502 (2008)10.1103/PhysRevLett.101.044502]. In the Langevin model, the fluid flow in a porous continuum is governed by a combination of a Langevin equation and a continuity equation. Pore-scale velocity fluctuations, the source of mechanical dispersion, are represented by the white noise. The advective velocity (the solution of the Langevin flow equation) causes the mechanical dispersion of a solute. Molecular diffusion and sub-pore-scale Taylor-type dispersion are modeled by an effective stochastic advection-diffusion equation. Here, we propose a method for parameterization of the model for a synthetic porous medium, and we use the model to simulate multicomponent reactive transport in the porous medium. The detailed comparison of the results of the Langevin model with pore-scale and continuum (Darcy) simulations shows that: (1) for a wide range of Peclet numbers the Langevin model predicts the mass of reaction product more accurately than the Darcy model; (2) for small Peclet numbers predictions of both the Langevin and the Darcy models agree well with a prediction of the pore-scale model; and (3) the accuracy of the Langevin and Darcy model deteriorates with the increasing Peclet number but the accuracy of the Langevin model decreases more slowly than the accuracy of the Darcy model. These results show that the separate treatment of advective and diffusive mixing in the stochastic transport model is more accurate than the classical advection-dispersion theory, which uses a single effective diffusion coefficient (the dispersion

  18. A MILP-Model for the Optimization of Transports

    Science.gov (United States)

    Björk, Kaj-Mikael

    2010-09-01

    This paper presents a work in developing a mathematical model for the optimization of transports. The decisions to be made are routing decisions, truck assignment and the determination of the pickup order for a set of loads and available trucks. The model presented takes these aspects into account simultaneously. The MILP model is implemented in the Microsoft Excel environment, utilizing the LP-solve freeware as the optimization engine and Visual Basic for Applications as the modeling interface.

  19. Transport modeling of sorbing tracers in artificial fractures

    Energy Technology Data Exchange (ETDEWEB)

    Keum, Dong Kwon; Baik, Min Hoon; Park, Chung Kyun; Cho, Young Hwan; Hahn, Phil Soo

    1998-02-01

    This study was performed as part of a fifty-man year attachment program between AECL (Atomic Energy Canada Limited) and KAERI. Three kinds of computer code, HDD, POMKAP and VAMKAP, were developed to predict transport of contaminants in fractured rock. MDDM was to calculate the mass transport of contaminants in a single fracture using a simple hydrodynamic dispersion diffusion model. POMKAP was to predict the mass transport of contaminants by a two-dimensional variable aperture model. In parallel with modeling, the validation of models was also performed through the analysis of the migration experimental data obtained in acrylic plastic and granite artificial fracture system at the Whiteshell laboratories, AECL, Canada. (author). 34 refs., 11 tabs., 76 figs.

  20. Model inter-comparison on transport and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Bergamaschi, P. [European Commission, DG Joint Research Centre, Institute for Environment and Sustainability, Ispra (Italy); Meirink, J.F. [Royal Netherlands Meteorological Institute KNMI, De Bilt (Netherlands); Mueller, J.F. [Belgian Institute for Space Aeronomy, Brussels (Belgium); Koerner, S.; Heimann, M. [Max Planck Institute for Biogeochemie, Jena (Germany); Bousquet, P.; Ramonet, M. [Laboratoire des Sciences du Climat et de l' Environment LSCE, Gif sur Yvette (France); Dlugokencky, E.J. [NOAA Earth Science Research Laboratory, Global Monitoring Division, Boulder, CO (United States); Kaminski, U. [Deutscher Wetterdienst, Meteorologisches Observatorium Hohenpeissenberg (Germany); Vecchi, R.; Marcazzan, G. [Istituto di Fisica Generale Applicata, Universita' degli Studi di Milano, Milan (Italy); Meinhardt, F. [Umweltbundesamt, Messstelle Schauinsland, Kirchzarten (Germany); Sartorius, H. [Bundesamt fuer Strahlenschutz, Freiburg (Germany); Zahorowski, W. [Australian Nuclear Science and Technology Organisation, Menai (Australia)

    2006-07-01

    A comprehensive inter-comparison of 5 atmospheric chemistry transport models (TM5, TM4, TM3, IMAGES, and LMDZ) has been performed. The main objective was to analyze differences in model transport, in particular vertical mixing (boundary layer and convective transport), synoptic variations, and large scale global circulation (including inter-hemispheric exchange and stratospheric tropospheric exchange (STE)). For this purpose simulations of various tracers with very different atmospheric lifetimes {tau} have been carried out: 222Rn ({tau} = 3.8 days), SF6 ({tau} {approx}3000 years), and CH4 ({tau} = {approx}9 years), using prescribed boundary conditions for all models. Furthermore, OH fields from various model simulations with full chemistry have been compared.

  1. Water Transport Models of Moisture Absorption and Sweat Discharge Yarns

    Institute of Scientific and Technical Information of China (English)

    WANG Fa-ming; ZHOU Xiao-hong; WANG Shan-yuan

    2008-01-01

    An important property of moisture absorption and sweat discharge yams is their water transport property. In the paper, two water transport models of moisture absorption and sweat discharge yams were developed to investigate the influence factors on their wicking rate. In parallel Column Pores Model, wicking rate is determined by the equivalent capillary radius R and length of the capillary tube L. In Pellets Accumulation Model, wicking rate is decided by the capillary radius r and length of the fiber unit assemble L0.

  2. MODELS FOR THE COUNTER-GRADIENT TRANSPORT PHENOMENA

    Institute of Scientific and Technical Information of China (English)

    蒋剑波; 卢志明; 刘晓明; 刘宇陆

    2001-01-01

    The counter gradient transport phenomena on momentum, energy and passive scalar in turbulent flows were studied by use of the single response function for TSDIA. As a result, models that can describe qualitatively the phenomena are obtained. Then the results are simplified by use of the inertial range theory, and the results for lower degrees agree with results of predecessor. Finally the counter gradient-transport phenomena in channel flow and circular wake flow are analyzed.

  3. Modelling of electron transport and of sawtooth activity in tokamaks

    Energy Technology Data Exchange (ETDEWEB)

    Angioni, C

    2001-10-01

    Transport phenomena in tokamak plasmas strongly limit the particle and energy confinement and represent a crucial obstacle to controlled thermonuclear fusion. Within the vast framework of transport studies, three topics have been tackled in the present thesis: first, the computation of neoclassical transport coefficients for general axisymmetric equilibria and arbitrary collisionality regime; second, the analysis of the electron temperature behaviour and transport modelling of plasma discharges in the Tokamak a configuration Variable (TCV); third, the modelling and simulation of the sawtooth activity with different plasma heating conditions. The work dedicated to neoclassical theory has been undertaken in order to first analytically identify a set of equations suited for implementation in existing Fokker-Planck codes. Modifications of these codes enabled us to compute the neoclassical transport coefficients considering different realistic magnetic equilibrium configurations and covering a large range of variation of three key parameters: aspect ratio, collisionality, and effective charge number. A comparison of the numerical results with an analytical limit has permitted the identification of two expressions for the trapped particle fraction, capable of encapsulating the geometrical effects and thus enabling each transport coefficient to be fitted with a single analytical function. This has allowed us to provide simple analytical formulae for all the neoclassical transport coefficients valid for arbitrary aspect ratio and collisionality in general realistic geometry. This work is particularly useful for a correct evaluation of the neoclassical contribution in tokamak scenarios with large bootstrap cur- rent fraction, or improved confinement regimes with low anomalous transport and for the determination of the plasma current density profile, since the plasma conductivity is usually assumed neoclassical. These results have been included in the plasma transport code

  4. Modelling of human transplacental transport as performed in Copenhagen, Denmark

    DEFF Research Database (Denmark)

    Mathiesen, Line; Mørck, Thit A.; Zuri, G.;

    2014-01-01

    Placenta perfusion models are very effective when studying the placental mechanisms in order to extrapolate to real-life situations. The models are most often used to investigate the transport of substances between mother and foetus, including the potential metabolism of these. We have studied...

  5. On the Economic Order Quantity Model With Transportation Costs

    NARCIS (Netherlands)

    S.I. Birbil (Ilker); K. Bulbul; J.B.G. Frenk (Hans); H.M. Mulder (Henry)

    2009-01-01

    textabstractWe consider an economic order quantity type model with unit out-of-pocket holding costs, unit opportunity costs of holding, fixed ordering costs and general transportation costs. For these models, we analyze the associated optimization problem and derive an easy procedure for determining

  6. A transport model for prediction of wildfire behavior

    Energy Technology Data Exchange (ETDEWEB)

    Linn, R.R.

    1997-07-01

    Wildfires are a threat to human life and property, yet they are an unavoidable part of nature. In the past people have tried to predict wildfire behavior through the use of point functional models but have been unsuccessful at adequately predicting the gross behavior of the broad spectrum of fires that occur in nature. The majority of previous models do not have self-determining propagation rates. The author uses a transport approach to represent this complicated problem and produce a model that utilizes a self-determining propagation rate. The transport approach allows one to represent a large number of environments including transition regions such as those with nonhomogeneous vegetation and terrain. Some of the most difficult features to treat are the imperfectly known boundary conditions and the fine scale structure that is unresolvable, such as the specific location of the fuel or the precise incoming winds. The author accounts for the microscopic details of a fire with macroscopic resolution by dividing quantities into mean and fluctuating parts similar to what is done in traditional turbulence modelling. The author develops a complicated model that includes the transport of multiple gas species, such as oxygen and volatile hydrocarbons, and tracks the depletion of various fuels and other stationary solids and liquids. From this model the author also forms a simplified local burning model with which he performs a number of simulations for the purpose of demonstrating the properties of a self-determining transport-based wildfire model.

  7. Genetics of traffic assignment models for strategic transport planning

    NARCIS (Netherlands)

    Bliemer, M.C.J.; Raadsen, M.; Brederode, L.; Bell, M.; Wismans, L.J.J.; Smith, M.

    2016-01-01

    This paper presents a review and classification of traffic assignment models for strategic transport planning purposes by using concepts analogous to genetics in biology. Traffic assignment models share the same theoretical framework (DNA), but differ in capability (genes). We argue that all traffic

  8. Spatial Economics Model Predicting Transport Volume

    Directory of Open Access Journals (Sweden)

    Lu Bo

    2016-10-01

    Full Text Available It is extremely important to predict the logistics requirements in a scientific and rational way. However, in recent years, the improvement effect on the prediction method is not very significant and the traditional statistical prediction method has the defects of low precision and poor interpretation of the prediction model, which cannot only guarantee the generalization ability of the prediction model theoretically, but also cannot explain the models effectively. Therefore, in combination with the theories of the spatial economics, industrial economics, and neo-classical economics, taking city of Zhuanghe as the research object, the study identifies the leading industry that can produce a large number of cargoes, and further predicts the static logistics generation of the Zhuanghe and hinterlands. By integrating various factors that can affect the regional logistics requirements, this study established a logistics requirements potential model from the aspect of spatial economic principles, and expanded the way of logistics requirements prediction from the single statistical principles to an new area of special and regional economics.

  9. Modeling tracer transport in randomly heterogeneous porous media by nonlocal moment equations: Anomalous transport

    Science.gov (United States)

    Morales-Casique, E.; Lezama-Campos, J. L.; Guadagnini, A.; Neuman, S. P.

    2013-05-01

    Modeling tracer transport in geologic porous media suffers from the corrupt characterization of the spatial distribution of hydrogeologic properties of the system and the incomplete knowledge of processes governing transport at multiple scales. Representations of transport dynamics based on a Fickian model of the kind considered in the advection-dispersion equation (ADE) fail to capture (a) the temporal variation associated with the rate of spreading of a tracer, and (b) the distribution of early and late arrival times which are often observed in field and/or laboratory scenarios and are considered as the signature of anomalous transport. Elsewhere we have presented exact stochastic moment equations to model tracer transport in randomly heterogeneous aquifers. We have also developed a closure scheme which enables one to provide numerical solutions of such moment equations at different orders of approximations. The resulting (ensemble) average and variance of concentration fields were found to display a good agreement against Monte Carlo - based simulation results for mildly heterogeneous (or well-conditioned strongly heterogeneous) media. Here we explore the ability of the moment equations approach to describe the distribution of early arrival times and late time tailing effects which can be observed in Monte-Carlo based breakthrough curves (BTCs) of the (ensemble) mean concentration. We show that BTCs of mean resident concentration calculated at a fixed space location through higher-order approximations of moment equations display long tailing features of the kind which is typically associated with anomalous transport behavior and are not represented by an ADE model with constant dispersive parameter, such as the zero-order approximation.

  10. Clouds, aerosols and biogeochemical cycles. Risks of non-linear climate change

    Energy Technology Data Exchange (ETDEWEB)

    Van Ham, J.; Van Beers, R.J.; Builtjes, P.J.H.; Roemer, M.G.M. [TNO Institute of Environmental Sciences, Delft (Netherlands); Koennen, G.P. [Royal Netherlands Meteorological Institute KNMI, De Bilt (Netherlands); Oerlemans, J. [Institute for Meteorological and Atmospheric Research, University of Utrecht, Utrecht (Netherlands)

    1995-12-31

    Part of the results of an investigation into risks for climate change, which are presently not adequately covered in General Circulation Models, is described. The investigation included the interaction with biogeochemical cycles, the effects of clouds and aerosols, ice flow instability, albedo instability and modified ocean circulation. In this paper our results for clouds and aerosols and for bio-geochemical cycles are reported. 1 tab., 21 refs.

  11. A comparison of Gridded Quantile Mapping vs. Station Based Downscaling Approaches on Potential Hydrochemical Responses of Forested Watersheds to Climate Change Using a Dynamic Biogeochemical Model (PnET-BGC)

    Science.gov (United States)

    Pourmokhtarian, A.; Driscoll, C. T.; Campbell, J. L.; Hayhoe, K.

    2012-12-01

    Dynamic hydrochemical models are useful tools to understand and predict the interactive effects of climate change, atmospheric CO2, and atmospheric deposition on the hydrology and water quality of forested watersheds. Although application of these models for climate projections necessitates the use of climatic variables simulated by atmosphere-ocean general circulation models (AOGCMs) to determine inputs to drive model projections. Due to the coarse resolution of AOGCMs, outputs need to be downscaled to bridge the gap between coarse spatial resolution and higher resolution required for hydrochemical models. This research compares two different statistical downscaling approaches; Gridded Quantile Mapping (BCSD) and Station-based Daily Asynchronous Regression, and their effects on potential biogeochemical responses of forested watershed. In this study, we used the biogeochemical model, PnET-BGC, to assess, compare and contrast the effects of these two downscaling approaches on potential future changes in temperature, precipitation, solar radiation and atmospheric CO2 and their effects in projections of pools, concentrations, and fluxes of major elements at Hubbard Brook Experimental Forest in New Hampshire, U.S. Future emissions scenarios were developed from monthly output from three AOGCMs (HadCM3, GFDL, PCM) in conjunction with potential lower and upper bounds of projected atmospheric CO2 (550 and 970 ppm by 2099, respectively). The climate projections from both downscaling approaches indicate that over the 21st century, average air temperature will increase with simultaneous increases in annual average precipitation. The modeling results from both downscaling approaches suggest that climate change is projected to cause substantial temporal shifts in hydrologic and hydrochemistry patterns. The choice of downscaling approach had a major impact on the streamflow simulations, which was directly related to the ability of the downscaling approach to mimic observed

  12. Assessment of parametric uncertainty for groundwater reactive transport modeling,

    Science.gov (United States)

    Shi, Xiaoqing; Ye, Ming; Curtis, Gary P.; Miller, Geoffery L.; Meyer, Philip D.; Kohler, Matthias; Yabusaki, Steve; Wu, Jichun

    2014-01-01

    The validity of using Gaussian assumptions for model residuals in uncertainty quantification of a groundwater reactive transport model was evaluated in this study. Least squares regression methods explicitly assume Gaussian residuals, and the assumption leads to Gaussian likelihood functions, model parameters, and model predictions. While the Bayesian methods do not explicitly require the Gaussian assumption, Gaussian residuals are widely used. This paper shows that the residuals of the reactive transport model are non-Gaussian, heteroscedastic, and correlated in time; characterizing them requires using a generalized likelihood function such as the formal generalized likelihood function developed by Schoups and Vrugt (2010). For the surface complexation model considered in this study for simulating uranium reactive transport in groundwater, parametric uncertainty is quantified using the least squares regression methods and Bayesian methods with both Gaussian and formal generalized likelihood functions. While the least squares methods and Bayesian methods with Gaussian likelihood function produce similar Gaussian parameter distributions, the parameter distributions of Bayesian uncertainty quantification using the formal generalized likelihood function are non-Gaussian. In addition, predictive performance of formal generalized likelihood function is superior to that of least squares regression and Bayesian methods with Gaussian likelihood function. The Bayesian uncertainty quantification is conducted using the differential evolution adaptive metropolis (DREAM(zs)) algorithm; as a Markov chain Monte Carlo (MCMC) method, it is a robust tool for quantifying uncertainty in groundwater reactive transport models. For the surface complexation model, the regression-based local sensitivity analysis and Morris- and DREAM(ZS)-based global sensitivity analysis yield almost identical ranking of parameter importance. The uncertainty analysis may help select appropriate likelihood

  13. Computer-Supported Modelling of Multi modal Transportation Networks Rationalization

    Directory of Open Access Journals (Sweden)

    Ratko Zelenika

    2007-09-01

    Full Text Available This paper deals with issues of shaping and functioning ofcomputer programs in the modelling and solving of multimoda Itransportation network problems. A methodology of an integrateduse of a programming language for mathematical modellingis defined, as well as spreadsheets for the solving of complexmultimodal transportation network problems. The papercontains a comparison of the partial and integral methods ofsolving multimodal transportation networks. The basic hypothesisset forth in this paper is that the integral method results inbetter multimodal transportation network rationalization effects,whereas a multimodal transportation network modelbased on the integral method, once built, can be used as the basisfor all kinds of transportation problems within multimodaltransport. As opposed to linear transport problems, multimodaltransport network can assume very complex shapes. This papercontains a comparison of the partial and integral approach totransp01tation network solving. In the partial approach, astraightforward model of a transp01tation network, which canbe solved through the use of the Solver computer tool within theExcel spreadsheet inteiface, is quite sufficient. In the solving ofa multimodal transportation problem through the integralmethod, it is necessmy to apply sophisticated mathematicalmodelling programming languages which supp01t the use ofcomplex matrix functions and the processing of a vast amountof variables and limitations. The LINGO programming languageis more abstract than the Excel spreadsheet, and it requiresa certain programming knowledge. The definition andpresentation of a problem logic within Excel, in a manner whichis acceptable to computer software, is an ideal basis for modellingin the LINGO programming language, as well as a fasterand more effective implementation of the mathematical model.This paper provides proof for the fact that it is more rational tosolve the problem of multimodal transportation networks by

  14. Modeling transport and aggregation of volcanic ash particles

    Science.gov (United States)

    Costa, Antonio; Folch, Arnau; Macedonio, Giovanni; Durant, Adam

    2010-05-01

    A complete description of ash aggregation processes in volcanic clouds is an very arduous task and the full coupling of ash transport and ash aggregation models is still computationally prohibitive. A large fraction of fine ash injected in the atmosphere during explosive eruptions aggregate because of complex interactions of surface liquid layers, electrostatic forces, and differences in settling velocities. The formation of aggregates of size and density different from those of the primary particles dramatically changes the sedimentation dynamics and results in lower atmospheric residence times of ash particles and in the formation of secondary maxima of tephra deposit. Volcanic ash transport models should include a full aggregation model accounting for all particle class interaction. However this approach would require prohibitive computational times. Here we present a simplified model for wet aggregation that accounts for both atmospheric and volcanic water transport. The aggregation model assumes a fractal relationship for the number of primary particles in aggregates, average efficiencies factors, and collision frequency functions accounting for Brownian motion, laminar and turbulent fluid shear, and differential settling velocity. We implemented the aggregation model in the WRF+FALL3D coupled modelling system and applied it to different eruptions where aggregation has been recognized to play an important role, such as the August and September 1992 Crater Peak eruptions and the 1980 Mt St Helens eruption. Moreover, understanding aggregation processes in volcanic clouds will contribute to mitigate the risks related with volcanic ash transport and sedimentation.

  15. Quantum transport in RTD and atomistic modeling of nanostructures

    Science.gov (United States)

    Jiang, Zhengping

    As devices are scaled down to nanometer scale, new materials and device structures are introduced to extend Moore's law beyond Si devices. In this length scale, carrier transport moves from classical transport to quantum transport; material granularity has more and more impacts on performance. Computer Aided Design (CAD) becomes essential for both industrial and educational purposes. First part focuses on physical models and numerical issues in nano-scale devices modeling. Resonance Tunneling Diode (RTD) is simulated and used to illustrate phenomena in carrier transport. Non-Equilibrium Green's Function (NEGF) formulism is employed in quantum transport simulation. Inhomogeneous energy grid is used in energy integration, which is critical to capture essential physics in RTD simulation. All simulation results could be reproduced by developed simulators RTDNEGF and NEMO5. In nanostructures, device length becomes comparable to material granularity; it is not proper to consider materials as continuous in many situations. Second part of this work resolves this problem by introducing atomistic modeling method. Valley degeneracy in Si (110) QW is investigated. Inconsistency of experimental observations is resolved by introducing miscut in surface. Impacts of strain and electric field on electronic bandstructure are studied. Research of SiGe barrier disorder effects on valley splitting in Si (100) QW is then conducted. Behaviors of valley splitting in different well widths under electric field are predicted by atomistic simulation. Nearest neighbor empirical tight-binding method is used in electronic calculation and VFF Keating model is used in strain relaxation.

  16. 3D contaminant migration model with consolidation dependent transport coefficients

    Institute of Scientific and Technical Information of China (English)

    Lu Huang; Cheng-Gang Zhao; Yan Liu; Guo-Qing Cai

    2012-01-01

    Soil consolidation would induce variations of its transport coefficients such as hydraulic conductivity and diffusion coefficient. This paper presents a study of the influence of barrier consolidation on transport coefficients,and a 3D transport model based on mixture theory is proposed for describing the liners that involve circular defects in the geomembrane.The elastoplastic ALPHA model is revised by using the spatially mobilized plane (SMP) criterion for simulating the deformation of the soils.Then,the 3D model coupling the nonlinear consolidation and contaminant advection-diffusion is solved using the finite element software ABAQUS.The results show that the importance of reducing the defect size in the geomembrane and the liner porosity to control the contaminant concentration increase.

  17. Catalog of selected heavy duty transport energy management models

    Science.gov (United States)

    Colello, R. G.; Boghani, A. B.; Gardella, N. C.; Gott, P. G.; Lee, W. D.; Pollak, E. C.; Teagan, W. P.; Thomas, R. G.; Snyder, C. M.; Wilson, R. P., Jr.

    1983-01-01

    A catalog of energy management models for heavy duty transport systems powered by diesel engines is presented. The catalog results from a literature survey, supplemented by telephone interviews and mailed questionnaires to discover the major computer models currently used in the transportation industry in the following categories: heavy duty transport systems, which consist of highway (vehicle simulation), marine (ship simulation), rail (locomotive simulation), and pipeline (pumping station simulation); and heavy duty diesel engines, which involve models that match the intake/exhaust system to the engine, fuel efficiency, emissions, combustion chamber shape, fuel injection system, heat transfer, intake/exhaust system, operating performance, and waste heat utilization devices, i.e., turbocharger, bottoming cycle.

  18. A novel adaptive biogeochemical model, and its 3-D application for a decadal hindcast simulation of the biogeochemistry of the southern North Sea

    Science.gov (United States)

    Kerimoglu, Onur; Hofmeister, Richard; Wirtz, Kai

    2016-04-01

    Adaptation and acclimation processes are often ignored in ecosystem-scale model implementations, despite the long-standing recognition of their importance. Here we present a novel adaptive phytoplankton growth model where acclimation of the community to the changes in external resource ratios is accounted for, using optimality principles and dynamic physiological traits. We show that the model can reproduce the internal stoichiometries obtained at marginal supply ratios in chemostat experiments. The model is applied in a decadal hindcast simulation of the southern North Sea, where it is coupled to a 2-D benthic model and a 3-D hydrodynamic model in an approximately 1.5km horizontal resolution at the German Bight coast. The model is shown to have good skill in capturing the steep, coastal gradients in the German Bight, suggested by the match between the estimated and observed dissolved nutrient and chlorophyll concentrations. We then analyze the differential sensitivity of the coastal and off-shore zones to major drivers of the system, such as riverine nutrient loads. We demonstrate that the relevance of phytoplankton acclimation varies across coastal gradients and can become particularly significant in terms of summer nutrient depletion.

  19. Modelling vapour transport in Surtseyan bombs

    Science.gov (United States)

    McGuinness, Mark J.; Greenbank, Emma; Schipper, C. Ian

    2016-05-01

    We address questions that arise if a slurry containing liquid water is enclosed in a ball of hot viscous vesicular magma ejected as a bomb in the context of a Surtseyan eruption. We derive a mathematical model for transient changes in temperature and pressure due to flashing of liquid water to vapour inside the bomb. The magnitude of the transient pressure changes that are typically generated are calculated together with their dependence on material properties. A single criterion to determine whether the bomb will fragment as a result of the pressure changes is derived. Timescales for ejection of water vapour from a bomb that remains intact are also revealed.

  20. Creating transport models that matter: A strategic view on governance of transport models and road maps for innovation

    NARCIS (Netherlands)

    Tavasszy, L.A.; Duijnisveld, M; Hofman, F.; Pronk van Hoogeveen, S.; Schmorak, N.; Van de Berg, M.; Francke, J.; Van de Riet, O.; Van der Waard, J.; Poot, H.; Reiding, E.

    2010-01-01

    The basic use of transport models is that they help to increase our understanding of the mobility system. In more operational terms, they can be a basis for developing quantitative insights in the past and current state of the system or scenarios about the future. Models are also useful as impact as

  1. Groundwater transport modeling with nonlinear sorption and intraparticle diffusion

    Science.gov (United States)

    Singh, Anshuman; Allen-King, Richelle M.; Rabideau, Alan J.

    2014-08-01

    Despite recent advances in the mechanistic understanding of sorption in groundwater systems, most contaminant transport models provide limited support for nonideal sorption processes such as nonlinear isotherms and/or diffusion-limited sorption. However, recent developments in the conceptualization of "dual mode" sorption for hydrophobic organic contaminants have provided more realistic and mechanistically sound alternatives to the commonly used Langmuir and Freundlich models. To support the inclusion of both nonlinear and diffusion-limited sorption processes in groundwater transport models, this paper presents two numerical algorithms based on the split operator approach. For the nonlinear equilibrium scenario, the commonly used two-step split operator algorithm has been modified to provide a more robust treatment of complex multi-parameter isotherms such as the Polanyi-partitioning model. For diffusion-limited sorption, a flexible three step split-operator procedure is presented to simulate intraparticle diffusion in multiple spherical particles with different sizes and nonlinear isotherms. Numerical experiments confirmed the accuracy of both algorithms for several candidate isotherms. However, the primary advantages of the algorithms are: (1) flexibility to accommodate any isotherm equation including "dual mode" and similar expressions, and (2) ease of adapting existing grid-based transport models of any dimensionality to include nonlinear sorption and/or intraparticle diffusion. Comparisons are developed for one-dimensional transport scenarios with different isotherms and particle configurations. Illustrative results highlight (1) the potential influence of isotherm model selection on solute transport predictions, and (2) the combined effects of intraparticle diffusion and nonlinear sorption on the plume transport and flushing for both single-particle and multi-particle scenarios.

  2. Multiscale modeling for fluid transport in nanosystems.

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jonathan W.; Jones, Reese E.; Mandadapu, Kranthi Kiran; Templeton, Jeremy Alan; Zimmerman, Jonathan A.

    2013-09-01

    Atomistic-scale behavior drives performance in many micro- and nano-fluidic systems, such as mircrofludic mixers and electrical energy storage devices. Bringing this information into the traditionally continuum models used for engineering analysis has proved challenging. This work describes one such approach to address this issue by developing atomistic-to-continuum multi scale and multi physics methods to enable molecular dynamics (MD) representations of atoms to incorporated into continuum simulations. Coupling is achieved by imposing constraints based on fluxes of conserved quantities between the two regions described by one of these models. The impact of electric fields and surface charges are also critical, hence, methodologies to extend finite-element (FE) MD electric field solvers have been derived to account for these effects. Finally, the continuum description can have inconsistencies with the coarse-grained MD dynamics, so FE equations based on MD statistics were derived to facilitate the multi scale coupling. Examples are shown relevant to nanofluidic systems, such as pore flow, Couette flow, and electric double layer.

  3. A transport model for computer simulation of wildfires

    Energy Technology Data Exchange (ETDEWEB)

    Linn, R. [Los Alamos National Lab., NM (United States)

    1997-12-31

    Realistic self-determining simulation of wildfires is a difficult task because of a large variety of important length scales (including scales on the size of twigs or grass and the size of large trees), imperfect data, complex fluid mechanics and heat transfer, and very complicated chemical reactions. The author uses a transport approach to produce a model that exhibits a self-determining propagation rate. The transport approach allows him to represent a large number of environments such as those with nonhomogeneous vegetation and terrain. He accounts for the microscopic details of a fire with macroscopic resolution by dividing quantities into mean and fluctuating parts similar to what is done in traditional turbulence modeling. These divided quantities include fuel, wind, gas concentrations, and temperature. Reaction rates are limited by the mixing process and not the chemical kinetics. The author has developed a model that includes the transport of multiple gas species, such as oxygen and volatile hydrocarbons, and tracks the depletion of various fuels and other stationary solids and liquids. From this model he develops a simplified local burning model with which he performs a number of simulations that demonstrate that he is able to capture the important physics with the transport approach. With this simplified model he is able to pick up the essence of wildfire propagation, including such features as acceleration when transitioning to upsloping terrain, deceleration of fire fronts when they reach downslopes, and crowning in the presence of high winds.

  4. A coupled energy transport and hydrological model for urban canopies

    Science.gov (United States)

    Wang, Z.; Bou-Zeid, E.; Smith, J. A.

    2011-12-01

    Urban land-atmosphere interaction has been attracting more research efforts in order to understand the complex physics of flow and mass and heat transport in urban surfaces and the lower urban atmosphere. In this work, we developed and implemented a new physically-based single-layer urban canopy model, coupling the surface exchange of energy and the subsurface transport of water/soil moisture. The new model incorporates sub-facet heterogeneity for each urban surface (roof, wall or ground). This better simulates the energy transport in urban canopy layers, especially over low-intensity built (suburban type) terrains that include a significant fraction of vegetated surfaces. We implemented detailed urban hydrological models for both natural terrains (bare soil and vegetation) and porous engineered materials with water-holding capacity (concrete, gravel, etc). The skill of the new scheme was tested against experimental data collected through a wireless sensor network deployed over the campus of Princeton University. The model performance was found to be robust and insensitive to changes in weather conditions or seasonal variability. Predictions of the volumetric soil water content were also in good agreement with field measurements, highlighting the model capability of capturing subsurface water transport for urban lawns. The new model was also applied to a case study assessing different strategies, i.e. white versus green roofs, in the mitigation of urban heat island effect.

  5. Radon transport in fractured soil. Laboratory experiments and modelling

    Energy Technology Data Exchange (ETDEWEB)

    Hoff, A.

    1997-10-01

    Radon (Rn-222) transport in fractured soil has been investigated by laboratory experiments and by modelling. Radon transport experiments have been performed with two sand columns (homogeneous and inhomogeneous) and one undisturbed clayey till column containing a net of preferential flow paths (root holes). A numerical model (the finite-element model FRACTRAN) and an analytic model (a pinhole model) have been applied in simulations if soil gas and radon transport in fractured soil. Experiments and model calculations are included in a discussion of radon entry rates into houses placed on fractured soil. The main conclusion is, that fractures does not in general alter transport of internally generated radon out of soil, when the pressure and flow conditions in the soil is comparable to the conditions prevailing under a house. This indicates the important result, that fractures in soil have no impact on radon entry into a house beyond that of an increased gas permeability, but a more thorough investigation of this subject is needed. Only in the case where the soil is exposed to large pressure gradients, relative to gradients induced by a house, may it be possible to observe effects of radon exchange between fractures and matrix. (au) 52 tabs., 60 ill., 5 refs.

  6. Computer-based modelling and optimization in transportation

    CERN Document Server

    Rossi, Riccardo

    2014-01-01

    This volume brings together works resulting from research carried out by members of the EURO Working Group on Transportation (EWGT) and presented during meetings and workshops organized by the Group under the patronage of the Association of European Operational Research Societies in 2012 and 2013. The main targets of the EWGT include providing a forum to share research information and experience, encouraging joint research and the development of both theoretical methods and applications, and promoting cooperation among the many institutions and organizations which are leaders at national level in the field of transportation and logistics. The primary fields of interest concern operational research methods, mathematical models and computation algorithms, to solve and sustain solutions to problems mainly faced by public administrations, city authorities, public transport companies, service providers and logistic operators. Related areas of interest are: land use and transportation planning, traffic control and ...

  7. Simulation model for the WIPP transportation and delivery system

    Energy Technology Data Exchange (ETDEWEB)

    Sharif, F. [Westinghouse Electric Corp., Carlsbad, NM (United States); Lippis, J. [USDOE Albuquerque Operations Office, Carlsbad, NM (United States). Waste Isolation Pilot Plant Project Office; Quinn, D. [Systems Modeling Corp., Sewickley, PA (United States)

    1992-12-31

    The United States Department of Energy`s (DOE`s) Waste Isolation Pilot Plant (WIPP) is a first of its kind repository designed to demonstrate safe disposal of transuranic (TRU) waste in bedded salt 2150 feet underground. Contact-handled (CH) TRU waste, waste with low beta or gamma emitting radionuclides that can be handled without protective clothing or additional shielding, will be transported to WIPP in Nuclear Regulatory Commission (NRC) certified containers known as TRUPACT-IIs. The TRUPACT-II is the cornerstone of a transportation system designed for extraordinarily safe transport of TRU waste from ten DOE production and research sites to WIPP. This paper describes the complexities of the transportation system and discusses how a simulation model can be utilized as a tool to develop economical operating parameters for the system.

  8. Vertical shear instability in accretion disc models with radiation transport

    CERN Document Server

    Stoll, Moritz H R

    2014-01-01

    The origin of turbulence in accretion discs is still not fully understood. While the magneto-rotational instability is considered to operate in sufficiently ionized discs, its role in the poorly ionized protoplanetary disc is questionable. Recently, the vertical shear instability (VSI) has been suggested as a possible alternative. Our goal is to study the characteristics of this instability and the efficiency of angular momentum transport, in extended discs, under the influence of radiative transport and irradiation from the central star. We use multi-dimensional hydrodynamic simulations to model a larger section of an accretion disc. First we study inviscid and weakly viscous discs using a fixed radial temperature profile in two and three spatial dimensions. The simulations are then extended to include radiative transport and irradiation from the central star. In agreement with previous studies we find for the isothermal disc a sustained unstable state with a weak positive angular momentum transport of the o...

  9. Cuttings Transport Models and Experimental Visualization of Underbalanced Horizontal Drilling

    Directory of Open Access Journals (Sweden)

    Na Wei

    2013-01-01

    Full Text Available Aerated underbalanced horizontal drilling technology has become the focus of the drilling industry at home and abroad, and one of the engineering core issues is the horizontal borehole cleaning. Therefore, calculating the minimum injection volume of gas and liquid accurately is essential for the construction in aerated underbalanced horizontal drilling. This paper establishes a physical model of carrying cuttings and borehole cleaning in wellbore of horizontal well and a critical transport mathematical model according to gas-liquid-solid flow mechanism and large plane dunes particle transport theory.

  10. Continuous Modeling of Calcium Transport Through Biological Membranes

    Science.gov (United States)

    Jasielec, J. J.; Filipek, R.; Szyszkiewicz, K.; Sokalski, T.; Lewenstam, A.

    2016-08-01

    In this work an approach to the modeling of the biological membranes where a membrane is treated as a continuous medium is presented. The Nernst-Planck-Poisson model including Poisson equation for electric potential is used to describe transport of ions in the mitochondrial membrane—the interface which joins mitochondrial matrix with cellular cytosis. The transport of calcium ions is considered. Concentration of calcium inside the mitochondrion is not known accurately because different analytical methods give dramatically different results. We explain mathematically these differences assuming the complexing reaction inside mitochondrion and the existence of the calcium set-point (concentration of calcium in cytosis below which calcium stops entering the mitochondrion).

  11. Introduction to stochastic models of transportation flows. Part I

    CERN Document Server

    Malyshev, V A

    2011-01-01

    We consider here probabilistic models of transportation flows. The main goal of this introduction is rather not to present various techniques for problem solving but to present some intuition to invent adequate and natural models having visual simplicity and simple (but rigorous) formulation, the main objects being cars not abstract flows. The papers consists of three parts. First part considers mainly linear flows on short time scale - dynamics of the flow due to changing driver behavior. Second part studies linear flow on longer time scales - individual car trajectory from entry to exit from the road. Part three considers collective car movement in complex transport networks.

  12. Molybdate transport in a chemically complex aquifer: Field measurements compared with solute-transport model predictions

    Science.gov (United States)

    Stollenwerk, K.G.

    1998-01-01

    A natural-gradient tracer test was conducted in an unconfined sand and gravel aquifer on Cape Cod, Massachusetts. Molybdate was included in the injectate to study the effects of variable groundwater chemistry on its aqueous distribution and to evaluate the reliability of laboratory experiments for identifying and quantifying reactions that control the transport of reactive solutes in groundwater. Transport of molybdate in this aquifer was controlled by adsorption. The amount adsorbed varied with aqueous chemistry that changed with depth as freshwater recharge mixed with a plume of sewage-contaminated groundwater. Molybdate adsorption was strongest near the water table where pH (5.7) and the concentration of the competing solutes phosphate (2.3 micromolar) and sulfate (86 micromolar) were low. Adsorption of molybdate decreased with depth as pH increased to 6.5, phosphate increased to 40 micromolar, and sulfate increased to 340 micromolar. A one-site diffuse-layer surface-complexation model and a two-site diffuse-layer surface-complexation model were used to simulate adsorption. Reactions and equilibrium constants for both models were determined in laboratory experiments and used in the reactive-transport model PHAST to simulate the two-dimensional transport of molybdate during the tracer test. No geochemical parameters were adjusted in the simulation to improve the fit between model and field data. Both models simulated the travel distance of the molybdate cloud to within 10% during the 2-year tracer test; however, the two-site diffuse-layer model more accurately simulated the molybdate concentration distribution within the cloud.

  13. The Global Modeling Initiative Assessment Model: Model Description, Integration and Testing of the Transport Shell

    Energy Technology Data Exchange (ETDEWEB)

    Rotman, D.A.; Tannahill, J.R.; Kinnison, D.E.; Connell, P.S.; Bergmann, D.; Proctor, D.; Rodriquez, J.M.; Lin, S.J.; Rood, R.B.; Prather, M.J.; Rasch, P.J.; Considine, D.B.; Ramaroson, R.; Kawa, S.R.

    2000-04-25

    We describe the three dimensional global stratospheric chemistry model developed under the NASA Global Modeling Initiative (GMI) to assess the possible environmental consequences from the emissions of a fleet of proposed high speed civil transport aircraft. This model was developed through a unique collaboration of the members of the GMI team. Team members provided computational modules representing various physical and chemical processes, and analysis of simulation results through extensive comparison to observation. The team members' modules were integrated within a computational framework that allowed transportability and simulations on massively parallel computers. A unique aspect of this model framework is the ability to interchange and intercompare different submodules to assess the sensitivity of numerical algorithms and model assumptions to simulation results. In this paper, we discuss the important attributes of the GMI effort, describe the GMI model computational framework and the numerical modules representing physical and chemical processes. As an application of the concept, we illustrate an analysis of the impact of advection algorithms on the dispersion of a NO{sub y}-like source in the stratosphere which mimics that of a fleet of commercial supersonic transports (High-Speed Civil Transport (HSCT)) flying between 17 and 20 kilometers.

  14. A novel modeling tool with multi-stressor functionality for organic contaminant transport and fate in the Baltic Sea.

    Science.gov (United States)

    Undeman, E; Gustafsson, E; Gustafsson, B G

    2014-11-01

    The coupled physical-biogeochemical model BALTSEM, previously used to assess nutrient/carbon cycles and eutrophication in the Baltic Sea, has been expanded to include algorithms for calculations of organic contaminant environmental transport and fate. This novel model version (BALTSEM-POP) is evaluated for polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) and hexachlorobenzene (HCB) in Baltic Sea surface water and sediment. Modeled dissolved concentrations are usually within a factor of 2-4 of observed concentrations, however with larger deviations for furans. Calculated concentrations in particulate organic matter are less accurate (within factors of 1-700), likely due to errors in estimated pelagic biomass, particulate matter-water partitioning, and large natural variability in field data. Concentrations in sediments are usually predicted within a factor of 6. The good performance of the model illustrates its usefulness for exploration of contaminant fate in response to variations in nutrient input and climatic conditions in the Baltic Sea marine environment.

  15. Cretaceous-Palaeogene experiments in Biogeochemical Resilience

    Science.gov (United States)

    Penman, D. E.; Henehan, M. J.; Hull, P. M.; Planavsky, N.; Schmidt, D. N.; Rae, J. W. B.; Thomas, E.; Huber, B. T.

    2015-12-01

    Human activity is altering biogeochemical cycles in the ocean. While ultimately anthropogenic forcings may be brought under control, it is still unclear whether tipping points may exist beyond which human-induced changes to biogeochemical cycles become irreversible. We use the Late Cretaceous and the Cretaceous-Palaeogene (K-Pg) boundary interval as an informative case study. Over this interval, two carbon cycle perturbations (gradual flood basalt volcanism and abrupt bolide impact) occurred within a short time window, allowing us to investigate the resilience of biogeochemical cycles to different pressures applied to the same initial boundary conditions on very different time scales. We demonstrate that relatively gradual emission of CO2 from the Deccan large igneous province was efficiently mitigated within the limits of existing biogeochemical processes. However, the rapid extinction of pelagic calcifying organisms at the K-Pg boundary due to the Chicxulub bolide impact had more profound effects, and caused lasting (> 1 million years) changes to biogeochemical cycles. By combining sedimentological observations with boron isotope-based pH reconstructions over these events, we document two potentially useful partial analogues for best and worst case scenarios for anthropogenic global change. We suggest that if current ocean acidification results in the mass extinction of marine pelagic calcifiers, we may cause profound changes to the Earth system that will persist for 100,000s to millions of years.

  16. Green Transport Balanced Scorecard Model with Analytic Network Process Support

    Directory of Open Access Journals (Sweden)

    David Staš

    2015-11-01

    Full Text Available In recent decades, the performance of economic and non-economic activities has required them to be friendly with the environment. Transport is one of the areas having considerable potential within the scope. The main assumption to achieve ambitious green goals is an effective green transport evaluation system. However, these systems are researched from the industrial company and supply chain perspective only sporadically. The aim of the paper is to design a conceptual framework for creating the Green Transport (GT Balanced Scorecard (BSC models from the viewpoint of industrial companies and supply chains using an appropriate multi-criteria decision making method. The models should allow green transport performance evaluation and support of an effective implementation of green transport strategies. Since performance measures used in Balanced Scorecard models are interdependent, the Analytic Network Process (ANP was used as the appropriate multi-criteria decision making method. The verification of the designed conceptual framework was performed on a real supply chain of the European automotive industry.

  17. Novel biogeochemical fingerprinting approaches to sediment source apportionment in catchments (Invited)

    Science.gov (United States)

    Dungait, J.; Puttock, A.; Beniston, J. W.; Brazier, R. E.; Lal, R.; Collins, A.

    2013-12-01

    Apportioning the source of organic carbon in eroding sediments is important to constrain the scale of transport processes and to assess the impact of anthropogenic activity on environmental quality. Established biogeochemical techniques are used to trace organic inputs typically derived directly or indirectly from plants into soils, sediments and water using lipid biomarkers. Recently, advances in bulk and compound specific stable 13C isotope analyses have provided novel ways of exploring the source and residence times of organic matter in soils using the natural abundance stable 13C isotope signature of C3 and C4 plant end member values. However, the application of biogeochemical source tracing technologies at the molecular level at field to catchment scales has been slow to develop because of perceived problems with dilution of molecular-scale signals. This paper describes the results of recent experiments in natural and agricultural environments in the UK (Collins et al., 2013; Dungait et al., 2013) and United States (Puttock et al., 2012; Beniston et al., submitted) that have successfully applied new biogeochemical fingerprinting techniques using stable 13C isotope approaches and complementary modelling approaches to explore the transport of particulate and sediment-bound organic carbon at a range of scales from the small plot (m2) to field (ha) and small catchment (10's ha). References Beniston et al (submitted) The effects of crop residue removal on soil erosion and macronutrient dynamics on soils under no till for 42 years. Biogeosciences Collins et al (2013) Catchment source contributions to the sediment-bound organic matter degrading salmonid spawning gravels in a lowland river, southern England. Science of the Total Environment 456-457, 181-195. Dungait et al (2013) Microbial responses to the erosional redistribution of soil organic carbon in arable fields. Soil Biology and Biochemistry 60, 195-201. Puttock et al (2012) Stable carbon isotope analysis of

  18. Intelligent Transportation and Evacuation Planning A Modeling-Based Approach

    CERN Document Server

    Naser, Arab

    2012-01-01

    Intelligent Transportation and Evacuation Planning: A Modeling-Based Approach provides a new paradigm for evacuation planning strategies and techniques. Recently, evacuation planning and modeling have increasingly attracted interest among researchers as well as government officials. This interest stems from the recent catastrophic hurricanes and weather-related events that occurred in the southeastern United States (Hurricane Katrina and Rita). The evacuation methods that were in place before and during the hurricanes did not work well and resulted in thousands of deaths. This book offers insights into the methods and techniques that allow for implementing mathematical-based, simulation-based, and integrated optimization and simulation-based engineering approaches for evacuation planning. This book also: Comprehensively discusses the application of mathematical models for evacuation and intelligent transportation modeling Covers advanced methodologies in evacuation modeling and planning Discusses principles a...

  19. Measurements and models of reactive transport in geological media

    Science.gov (United States)

    Berkowitz, Brian; Dror, Ishai; Hansen, Scott K.; Scher, Harvey

    2016-12-01

    Reactive chemical transport plays a key role in geological media across scales, from pore scale to aquifer scale. Systems can be altered by changes in solution chemistry and a wide variety of chemical transformations, including precipitation/dissolution reactions that cause feedbacks that directly affect the flow and transport regime. The combination of these processes with advective-dispersive-diffusive transport in heterogeneous media leads to a rich spectrum of complex dynamics. The principal challenge in modeling reactive transport is to account for the subtle effects of fluctuations in the flow field and species concentrations; spatial or temporal averaging generally suppresses these effects. Moreover, it is critical to ground model conceptualizations and test model outputs against laboratory experiments and field measurements. This review emphasizes the integration of these aspects, considering carefully designed and controlled experiments at both laboratory and field scales, in the context of development and solution of reactive transport models based on continuum-scale and particle tracking approaches. We first discuss laboratory experiments and field measurements that define the scope of the phenomena and provide data for model comparison. We continue by surveying models involving advection-dispersion-reaction equation and continuous time random walk formulations. The integration of measurements and models is then examined, considering a series of case studies in different frameworks. We delineate the underlying assumptions, and strengths and weaknesses, of these analyses, and the role of probabilistic effects. We also show the key importance of quantifying the spreading and mixing of reactive species, recognizing the role of small-scale physical and chemical fluctuations that control the initiation of reactions.

  20. Dissipative particle dynamics model for colloid transport in porous media

    Energy Technology Data Exchange (ETDEWEB)

    Pan, W.; Tartakovsky, A. M.

    2013-08-01

    We present that the transport of colloidal particles in porous media can be effectively modeled with a new formulation of dissipative particle dynamics, which augments standard DPD with non-central dissipative shear forces between particles while preserving angular momentum. Our previous studies have demonstrated that the new formulation is able to capture accurately the drag forces as well as the drag torques on colloidal particles that result from the hydrodynamic retardation effect. In the present work, we use the new formulation to study the contact efficiency in colloid filtration in saturated porous media. Note that the present model include all transport mechanisms simultaneously, including gravitational sedimentation, interception and Brownian diffusion. Our results of contact efficiency show a good agreement with the predictions of the correlation equation proposed by Tufenkji and EliMelech, which also incorporate all transport mechanisms simultaneously without the additivity assumption.

  1. Proterozoic ocean redox and biogeochemical stasis

    Science.gov (United States)

    Reinhard, Christopher T.; Planavsky, Noah J.; Robbins, Leslie J.; Partin, Camille A.; Gill, Benjamin C.; Lalonde, Stefan V.; Bekker, Andrey; Konhauser, Kurt O.; Lyons, Timothy W.

    2013-01-01

    The partial pressure of oxygen in Earth’s atmosphere has increased dramatically through time, and this increase is thought to have occurred in two rapid steps at both ends of the Proterozoic Eon (∼2.5–0.543 Ga). However, the trajectory and mechanisms of Earth’s oxygenation are still poorly constrained, and little is known regarding attendant changes in ocean ventilation and seafloor redox. We have a particularly poor understanding of ocean chemistry during the mid-Proterozoic (∼1.8–0.8 Ga). Given the coupling between redox-sensitive trace element cycles and planktonic productivity, various models for mid-Proterozoic ocean chemistry imply different effects on the biogeochemical cycling of major and trace nutrients, with potential ecological constraints on emerging eukaryotic life. Here, we exploit the differing redox behavior of molybdenum and chromium to provide constraints on seafloor redox evolution by coupling a large database of sedimentary metal enrichments to a mass balance model that includes spatially variant metal burial rates. We find that the metal enrichment record implies a Proterozoic deep ocean characterized by pervasive anoxia relative to the Phanerozoic (at least ∼30–40% of modern seafloor area) but a relatively small extent of euxinic (anoxic and sulfidic) seafloor (less than ∼1–10% of modern seafloor area). Our model suggests that the oceanic Mo reservoir is extremely sensitive to perturbations in the extent of sulfidic seafloor and that the record of Mo and chromium enrichments through time is consistent with the possibility of a Mo–N colimited marine biosphere during many periods of Earth’s history. PMID:23515332

  2. Proterozoic ocean redox and biogeochemical stasis.

    Science.gov (United States)

    Reinhard, Christopher T; Planavsky, Noah J; Robbins, Leslie J; Partin, Camille A; Gill, Benjamin C; Lalonde, Stefan V; Bekker, Andrey; Konhauser, Kurt O; Lyons, Timothy W

    2013-04-02

    The partial pressure of oxygen in Earth's atmosphere has increased dramatically through time, and this increase is thought to have occurred in two rapid steps at both ends of the Proterozoic Eon (∼2.5-0.543 Ga). However, the trajectory and mechanisms of Earth's oxygenation are still poorly constrained, and little is known regarding attendant changes in ocean ventilation and seafloor redox. We have a particularly poor understanding of ocean chemistry during the mid-Proterozoic (∼1.8-0.8 Ga). Given the coupling between redox-sensitive trace element cycles and planktonic productivity, various models for mid-Proterozoic ocean chemistry imply different effects on the biogeochemical cycling of major and trace nutrients, with potential ecological constraints on emerging eukaryotic life. Here, we exploit the differing redox behavior of molybdenum and chromium to provide constraints on seafloor redox evolution by coupling a large database of sedimentary metal enrichments to a mass balance model that includes spatially variant metal burial rates. We find that the metal enrichment record implies a Proterozoic deep ocean characterized by pervasive anoxia relative to the Phanerozoic (at least ∼30-40% of modern seafloor area) but a relatively small extent of euxinic (anoxic and sulfidic) seafloor (less than ∼1-10% of modern seafloor area). Our model suggests that the oceanic Mo reservoir is extremely sensitive to perturbations in the extent of sulfidic seafloor and that the record of Mo and chromium enrichments through time is consistent with the possibility of a Mo-N colimited marine biosphere during many periods of Earth's history.

  3. A new turbulence-based model for sand transport

    Science.gov (United States)

    Mayaud, Jerome; Wiggs, Giles; Bailey, Richard

    2016-04-01

    Knowledge of the changing rate of sediment flux in space and time is essential for quantifying surface erosion and deposition in desert landscapes. While many aeolian studies have relied on time-averaged parameters such as wind velocity (U) and wind shear velocity (u*) to determine sediment flux, there is increasing evidence that high-frequency turbulence is an important driving force behind the entrainment and transport of sand. However, turbulence has yet to be incorporated into a functional sand transport model that can be used for predictive purposes. In this study we present a new transport model (the 'turbulence model') that accounts for high-frequency variations in the horizontal (u) and vertical (w) components of wind flow. The turbulence model is fitted to wind velocity and sediment transport data from a field experiment undertaken in Namibia's Skeleton Coast National Park, and its performance at three temporal resolutions (10 Hz, 1 Hz, 1 min) is compared to two existing models that rely on time-averaged wind velocity data (Radok, 1977; Dong et al., 2003). The validity of the three models is analysed under a variety of saltation conditions, using a 2-hour (1 Hz measurement resolution) dataset from the Skeleton Coast and a 5-hour (1 min measurement resolution) dataset from the southwestern Kalahari Desert. The turbulence model is shown to outperform the Radok and Dong models when predicting total saltation count over the three experimental periods. For all temporal resolutions presented in this study (10 Hz-10 min), the turbulence model predicted total saltation count to within at least 0.34%, whereas the Radok and Dong models over- or underestimated total count by up to 5.50% and 20.53% respectively. The strong performance of the turbulence model can be attributed to a lag in mass flux response built into its formulation, which can be adapted depending on the temporal resolution of investigation. This accounts for the inherent lag within the physical

  4. A quasilinear model for solute transport under unsaturated flow

    Energy Technology Data Exchange (ETDEWEB)

    Houseworth, J.E.; Leem, J.

    2009-05-15

    We developed an analytical solution for solute transport under steady-state, two-dimensional, unsaturated flow and transport conditions for the investigation of high-level radioactive waste disposal. The two-dimensional, unsaturated flow problem is treated using the quasilinear flow method for a system with homogeneous material properties. Dispersion is modeled as isotropic and is proportional to the effective hydraulic conductivity. This leads to a quasilinear form for the transport problem in terms of a scalar potential that is analogous to the Kirchhoff potential for quasilinear flow. The solutions for both flow and transport scalar potentials take the form of Fourier series. The particular solution given here is for two sources of flow, with one source containing a dissolved solute. The solution method may easily be extended, however, for any combination of flow and solute sources under steady-state conditions. The analytical results for multidimensional solute transport problems, which previously could only be solved numerically, also offer an additional way to benchmark numerical solutions. An analytical solution for two-dimensional, steady-state solute transport under unsaturated flow conditions is presented. A specific case with two sources is solved but may be generalized to any combination of sources. The analytical results complement numerical solutions, which were previously required to solve this class of problems.

  5. Improving Intercomparability of Marine Biogeochemical Time Series

    Science.gov (United States)

    Benway, Heather M.; Telszewski, Maciej; Lorenzoni, Laura

    2013-04-01

    Shipboard biogeochemical time series represent one of the most valuable tools scientists have to quantify marine elemental fluxes and associated biogeochemical processes and to understand their links to changing climate. They provide the long, temporally resolved data sets needed to characterize ocean climate, biogeochemistry, and ecosystem variability and change. However, to monitor and differentiate natural cycles and human-driven changes in the global oceans, time series methodologies must be transparent and intercomparable when possible. To review current shipboard biogeochemical time series sampling and analytical methods, the International Ocean Carbon Coordination Project (IOCCP; http://www.ioccp.org/) and the Ocean Carbon and Biogeochemistry Program (http://www.us-ocb.org/) convened an international ocean time series workshop at the Bermuda Institute for Ocean Sciences.

  6. 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.; Herchenroder, B.; Green, R.; Eldridge, P.

    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.

  7. Transport of nutrients from land to sea: Global modeling approaches and uncertainty analyses (Utrecht Studies in Earth Sciences 058)

    NARCIS (Netherlands)

    Beusen, A.H.W.

    2014-01-01

    This thesis presents four examples of global models developed as part of the Integrated Model to Assess the Global Environment (IMAGE). They describe different components of global biogeochemical cycles of the nutrients nitrogen (N), phosphorus (P) and silicon (Si), with a focus on approaches to ana

  8. Response of export production and dissolved oxygen concentrations in oxygen minimum zones to pCO2 and temperature stabilization scenarios in the biogeochemical model HAMOCC 2.0

    Science.gov (United States)

    Beaty, Teresa; Heinze, Christoph; Hughlett, Taylor; Winguth, Arne M. E.

    2017-02-01

    Dissolved oxygen (DO) concentration in the ocean is an important component of marine biogeochemical cycles and will be greatly altered as climate change persists. In this study a global oceanic carbon cycle model (HAMOCC 2.0) is used to address how mechanisms of oxygen minimum zone (OMZ) expansion respond to changes in CO2 radiative forcing. Atmospheric pCO2 is increased at a rate of 1 % annually and the model is stabilized at 2 ×, 4 ×, 6 ×, and 8 × preindustrial pCO2 levels. With an increase in CO2 radiative forcing, the OMZ in the Pacific Ocean is controlled largely by changes in particulate organic carbon (POC) export, resulting in increased remineralization and thus expanding the OMZs within the tropical Pacific Ocean. A potential decline in primary producers in the future as a result of environmental stress due to ocean warming and acidification could lead to a substantial reduction in POC export production, vertical POC flux, and thus increased DO concentration particularly in the Pacific Ocean at a depth of 600-800 m. In contrast, the vertical expansion of the OMZs within the Atlantic is linked to increases POC flux as well as changes in oxygen solubility with increasing seawater temperature. Changes in total organic carbon and increase sea surface temperature (SST) also lead to the formation of a new OMZ in the western subtropical Pacific Ocean. The development of the new OMZ results in dissolved oxygen concentration of ≤ 50 µmol kg-1 throughout the equatorial Pacific Ocean at 4 times preindustrial pCO2. Total ocean volume with dissolved oxygen concentrations of ≤ 50 µmol kg-1 increases by 2.4, 5.0, and 10.5 % for the 2 ×, 4 ×, and 8 × CO2 simulations, respectively.

  9. Kinetic models for nucleocytoplasmic transport of messenger RNA.

    Science.gov (United States)

    Schröder, H C; Müller, W E; Agutter, P S

    1995-05-21

    Much is known about the mechanism by which mRNAs cross the nuclear envelope (the translocation stage of nucleocytoplasmic transport), but far less is known about the preceding (intranuclear migration/release) and succeeding (cytoplasmic binding) stages. Therefore, existing information suffices for articulating detailed kinetic models of translocation, but not models for the overall mRNA transport process. In this paper, we show that simple kinetic models of translocation can (i) accommodate data about nucleocytoplasmic distributions of endogenous transcripts; (ii) predict the overall effects on these distributions of effectors such as insulin and epidermal growth factor; (iii) throw some light on the mechanism(s) of action of the HIV-1 protein Rev and produce experimentally testable predictions about this mechanism; and (iv) account for the action of influenza virus NS1 protein. However, the simplest forms of translocation models apparently fail to account for some properties of viral regulators such as HIV Rev and adenovirus E1B-E4 complex. To elucidate these topics, less narrowly focused models of mRNA transport are required, describing intranuclear binding/release as well as translocation. On the basis of our examination of translocation models, we suggest some criteria that the requisite broadly based models must satisfy.

  10. Modelling two-phase transport of 3H/3He

    NARCIS (Netherlands)

    Visser, A.; Schaap, J.D.; Leijnse, T.; Broers, H.P.; Bierkens, M.F.P.

    2008-01-01

    Degassing of groundwater by excess denitrification of agricultural pollution complicates the interpretation of 3H/3He data and hinders the estimation of travel times in nitrate pollution studies. In this study we used a two-phase flow and transport model (STOMP) to evaluate the method presented by V

  11. Development of numerical Grids for UZ Flow and Transport Modeling

    Energy Technology Data Exchange (ETDEWEB)

    P. Dobson

    2004-08-31

    This report describes the methods used to develop numerical grids of the unsaturated hydrogeologic system beneath Yucca Mountain, Nevada. Numerical grid generation is an integral part of the development of the unsaturated zone (UZ) flow and transport model, a complex, three-dimensional (3-D) model of Yucca Mountain. This revision contains changes made to improve the clarity of the description of grid generation. The numerical grids, developed using current geologic, hydrogeologic, and mineralogic data, provide the necessary framework to: (1) develop calibrated hydrogeologic property sets and flow fields, (2) test conceptual hypotheses of flow and transport, and (3) predict flow and transport behavior under a variety of climatic and thermal-loading conditions. The technical scope, content, and management for the current revision of this report are described in the planning document ''Technical Work Plan for: Unsaturated Zone Flow Analysis and Model Report Integration'' (BSC 2004 [DIRS 169654], Section 2). Grids generated and documented in this report supersede those documented in Revision 00 of this report, ''Development of Numerical Grids for UZ Flow and Transport Modeling'' (BSC 2001 [DIRS 159356]). The grids presented in this report are the same as those developed in Revision 01 (BSC 2003 [DIRS 160109]); however, the documentation of the development of the grids in Revision 02 has been updated to address technical inconsistencies and achieve greater transparency, readability, and traceability. The constraints, assumptions, and limitations associated with this report are discussed in the appropriate sections that follow.

  12. Analytical model for flux saturation in sediment transport.

    Science.gov (United States)

    Pähtz, Thomas; Parteli, Eric J R; Kok, Jasper F; Herrmann, Hans J

    2014-05-01

    The transport of sediment by a fluid along the surface is responsible for dune formation, dust entrainment, and a rich diversity of patterns on the bottom of oceans, rivers, and planetary surfaces. Most previous models of sediment transport have focused on the equilibrium (or saturated) particle flux. However, the morphodynamics of sediment landscapes emerging due to surface transport of sediment is controlled by situations out of equilibrium. In particular, it is controlled by the saturation length characterizing the distance it takes for the particle flux to reach a new equilibrium after a change in flow conditions. The saturation of mass density of particles entrained into transport and the relaxation of particle and fluid velocities constitute the main relevant relaxation mechanisms leading to saturation of the sediment flux. Here we present a theoretical model for sediment transport which, for the first time, accounts for both these relaxation mechanisms and for the different types of sediment entrainment prevailing under different environmental conditions. Our analytical treatment allows us to derive a closed expression for the saturation length of sediment flux, which is general and thus can be applied under different physical conditions.

  13. Modeling subsurface contaminant reactions and transport at the watershed scale

    Energy Technology Data Exchange (ETDEWEB)

    Gwo, J.P.; Jardine, P.M.; D`Azevedo, E.F. [Oak Ridge National Lab., TN (United States); Wilson, G.V. [Desert Research Inst., Las Vegas, NV (United States). Water Resources Center

    1997-12-01

    The objectives of this research are: (1) to numerically examine the multiscale effects of physical and chemical mass transfer processes on watershed scale, variably saturated subsurface contaminant transport, and (2) to conduct numerical simulations on watershed scale reactive solute transport and evaluate their implications to uncertainty characterization and cost benefit analysis. Concurrent physical and chemical nonequilibrium caused by inter aggregate gradients of pressure head and solute concentration and intra-aggregate geochemical and microbiological processes, respectively, may arise at various scales and flowpaths. To this date, experimental investigations of these complex processes at watershed scale remain a challenge and numerical studies are often needed for guidance of water resources management and decision making. This research integrates the knowledge bases developed during previous experimental and numerical investigations at a proposed waste disposal site at the Oak Ridge National Laboratory to study the concurrent effects of physical and chemical nonequilibrium. Comparison of numerical results with field data indicates that: (1) multiregion, preferential flow and solute transport exist under partially saturated condition and can be confirmed theoretically, and that (2) mass transfer between pore regions is an important process influencing contaminant movement in the subsurface. Simulations of watershed scale, multi species reactive solute transport suggest that dominance of geochemistry and hydrodynamics may occur simultaneously at different locales and influence the movement of one species relative to another. Execution times on the simulations of the reactive solute transport model also indicate that the model is ready to assist the selection of important parameters for site characterization.

  14. 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,