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

[1] 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/kinetic reaction. An equilibrium reaction is modeled with an infinite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. Programmed kinetic reaction rates include multiple Monod kinetics, nth order empirical, and elementary formulations. In addition, user-specified rate formulations can be programmed into the model. No existing models to our knowledge offer these simultaneous features. Furthermore, most available reaction-based models assume chemical components a priori so that reactions can be written in basic (canonical) forms and implicitly assume that fast equilibrium reactions occur only for homogeneous reactions. The decoupling of fast reactions from slow reactions lessens the stiffness typical of these systems. The explicit enforcement of mass conservation overcomes the mass conservation error due to numerical integration errors. The removal of redundant fast reactions alleviates the problem of singularity. The exclusion of irrelevant slow reactions eliminates the issue of exporting their problematic rate formulations/parameter estimations to different environment conditions. Taking the advantage of the nonuniqueness of components, a dynamic basis-species switching strategy is employed to make the model numerically robust. Backward basis switching allows components to freely change in the simulation of the chemistry module, while being recovered for transport simulation. Three example problems were selected to demonstrate the versatility and robustness of the model

Application of a parallel 3-dimensional hydrogeochemistry HPF code to a proposed waste disposal site at the Oak Ridge National Laboratory

The objectives of this study are (1) to parallelize a 3-dimensional hydrogeochemistry code and (2) to apply the parallel code to a proposed waste disposal site at the Oak Ridge National Laboratory (ORNL). The 2-dimensional hydrogeochemistry code HYDROGEOCHEM, developed at the Pennsylvania State University for coupled subsurface solute transport and chemical equilibrium processes, was first modified to accommodate 3-dimensional problem domains. A bi-conjugate gradient stabilized linear matrix solver was then incorporated to solve the matrix equation. We chose to parallelize the 3-dimensional code on the Intel Paragons at ORNL by using an HPF (high performance FORTRAN) compiler developed at PGI. The data- and task-parallel algorithms available in the HPF compiler proved to be highly efficient for the geochemistry calculation. This calculation can be easily implemented in HPF formats and is perfectly parallel because the chemical speciation on one finite-element node is virtually independent of those on the others. The parallel code was applied to a subwatershed of the Melton Branch at ORNL. Chemical heterogeneity, in addition to physical heterogeneities of the geological formations, has been identified as one of the major factors that affect the fate and transport of contaminants at ORNL. This study demonstrated an application of the 3-dimensional hydrogeochemistry code on the Melton Branch site. A uranium tailing problem that involved in aqueous complexation and precipitation-dissolution was tested. Performance statistics was collected on the Intel Paragons at ORNL. Implications of these results on the further optimization of the code were discussed

Modeling Bay/Estuary Circulation with Method of Characteristics

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Reaction-Based Reactive Transport Modeling of Fe(III) and U(V) Reduction

Our new research project (started Fall 2004) was funded by a grant to The Pennsylvania State University, University of Central Florida, and The University of Alabama in the Integrative Studies Element of the NABIR Program (DE-FG04-ER63914/63915/63196). Our previous NABIR project (DE-FG02-01ER63180/63181/63182, funded within the Biotransformation Element) focused on (1) microbial reduction of Fe(III) and U(VI) individually, and concomitantly in natural sediments, (2) Fe(III) oxide surface chemistry, specifically with respect to reactions with Fe(II) and U(VI), (3) the influence of humic substances on Fe(III) and U(VI) bioreduction, and on U(VI) complexation, and (4) the development of reaction-based reactive transport biogeochemical models to numerically simulate our experimental results. The new project focuses on the development of a mechanistic understanding and quantitative models of coupled Fe(III)/U(VI) reduction in FRC Area 2 sediments. This work builds on our previous studies of microbial Fe(III) and U(VI) reduction, and is directly aligned with the Scheibe et al. NABIR FRC Field Project at Area 2

An Automatic Method for Complete Triangular Mesh Conversion into Quadrilateral Mesh for Multiple Domain Geometry

This research developed an automatic two-dimensional finite element meshing system to resolve practical engineering problems in the fields of geology, hydrology, and water resources. This system first used the Delaunay triangulation method to create reasonable-density triangular mesh and then converted it into quadrilateral mesh by combining proper pairs of adjacent triangles. A series of combination patterns aiming at three cases were established. The effect of the number of boundary edges on the subsequent meshing procedures were studied and summarized. For the geometry with multiple domains an adjustment method is proposed to completely eliminate the residual triangles during quadrilateral meshing through adjusting the number of boundary edges in each loop to be even. A special boundary loop identification method is proposed for priority treatment. Corresponding treatment methods aimed at three different situations are established for common boundary loops. For a certain boundary loop with an odd number of boundary edges, the appropriate edge for new point insertion is determined by the position properties and relative density errors. Practical applications confirm that the method proposed in this paper could successfully implement the full conversion from the triangular mesh to the quadrilateral mesh

I1. Green’s Function and Watershed Modelling

Once downloaded, these high definition QuickTime videos may be played using a computer video player with H.264 codec, 1280x720 pixels, millions of colors, AAC audio at 44100Hz and 29.97 frames per second. The data rate is 5Mbps. File sizes are on the order of 600-900 MB. (Other formats may be added later.) Free QuickTime players for Macintosh and Window computers may be located using a Google search on QuickTime. The DVD was produced by J. Robert Cooke.Watershed modelling deals with multiple processes occurring in multiple media. The processes include flow and thermal, salinity, sediment, and biogeochemical transport. The multiple media cover stream/river/canal/open channel networks, lakes/reservoirs, land surfaces, and subsurface media. Analytical and numerical models are commonly employed for simulations to understand sciences or to assess environmental consequences. Why analytical models offer the advantage of clearly and easily explaining the physics involved, the numerical models give practical applications of assessing the impact and interaction among processes and media. This presentation will discuss the issues and difficulties associated with the employment of Green functions to yield analytical models and troubles associated with the use of numeric to generate computational models. Various means of overcoming these difficulties and troubles will be outlined and addressed.1_5evrosd

Reaction-based Transport Modeling of Iron Reduction and Uranium Immobilization at Area 2 of the NABIR Field Research Center

This research sought to examine biogeochemical processes likely to take place in the less conductive materials above and below the gravel during the in situ ethanol biostimulation experiment conducted at Area 2 during 2005-2006. The in situ experiment in turn examined the hypothesis that injection of electron donor into this layer would induce formation of a redox barrier in the less conductive materials, resulting in decreased mass transfer of uranium out these materials and attendant declines in groundwater U(VI) concentration. Our project focuses on the development of a mechanistic understanding and quantitative models of coupled Fe(III)/U(VI) reduction in FRC Area 2 sediments. This report summarizes research activities conducted at The University of Central Florida (2004-2007), the development of biogeochemical and reactive transport models and the conduction of numerical simulations at laboratory, column, and field scales

Analysis Of Point-Source And Boundary-Source Solutions Of One-Dimensional Groundwater Transport Equation

The solute transport equation is commonly used to describe the migration and fate of solutes in a groundwater flow system. Depending on the problem nature, the source of the solute may be represented as a point source term in the equation or specified as the first-type or third-type boundary condition. The solutions derived under the condition that the solute introduced into the flow system is from the boundary is herein considered as the boundary-source solutions. The solution obtained when solving the transport equation with a point-source term is considered as the point-source solution. The Laplace transform technique is employed to derive the formulas for those solutions expressed in terms of the normalized mass release rate. The underlying nature of different source release modes and the differences among those boundary-source solutions and the constant point-source solution can be easily and clearly differentiated based on the derived formulas for one-dimensional transport. The methodology could, however, be easily extended to two- and three-dimensional problems. © 2007 ASCE