dSED: a database tool for modeling sediment early diagenesis (2023)

Volume 30, Issues 9–10,

November–December 2004

, Pages 959-967

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Mathematical modeling of sediment early diagenesis always involves choosing and describing a set of chemical reactions and processes that is both self-consistent and sufficient for the problem at hand. This critical choice is always a compromise between describing the system's complexity in all details and using a manageable set of reactions with known or obtainable parameters such as equilibrium and rate constants. We present a database tool for modeling sediment early diagenesis (dSED) that is designed to help modelers and sediment geochemists in this difficult conceptual step. The database should facilitate the development of state-of-the-art spatially continuous reaction-transport models (RTM), as well as simpler interacting-compartment (box) models. It allows one to explore: available kinetic and thermodynamic information, alternative descriptions of the same major processes, different degrees of completeness in description, processes and reactions that could be added or modeled differently, published solutions used by previous workers, and other information. The database is searchable and allows viewing reactions by specific products or reactants, types of processes, or other customized criteria. It operates under Microsoft Access™ and can be added to, modified and programmed by the user. The latest version of dSED and its user manual can be downloaded at http://www.science.uottawa.ca/LSSE/dSED.


Sediment early diagenesis reaction-transport models (RTMs) are based on complex and interconnected sets of chemical reactions and transport processes that describe spatially continuous dynamics of both solid and dissolved species in the sediment (e.g., Berner, 1980; Boudreau, 1997). They have been employed to model a broad range of aquatic environments, including marine (Boudreau, 1996; Klump and Martens, 1989; Dhakar and Burdige, 1996; Wang and Van Cappellen, 1996; Tromp et al., 1995), lacustrine (Furrer and Wehrli, 1996), estuarine (Regnier et al., 1997), ground water (Mayer et al., 2002; Hunter et al., 1998), and potentially other environments such as rivers and wetlands.

Sediment early diagenesis is, to a large degree, controlled by the kinetics of the involved biogeochemical and physical transformations. Whereas thermodynamic equilibrium calculations have benefited from several good database/program combinations (e.g., Meeussen, 2003; Herberlin and Westall, 1999; Parkhurst and Appelo, 1999; Wolery, 1992a, Wolery, 1992b; Allison et al., 1991; Ball and Nordstrom, 1991), kinetic modeling of diagenesis is still in the early stages of a systematic integration of biogeochemical knowledge (Regnier et al., 2002a, Regnier et al., 2002b; Meysman et al., 2003a, Meysman et al., 2003b). At present, there exist no established database tools to classify and analyse the kinetic data that is essential to the development of sediment diagenesis RTMs.

An expandable web-distributed Knowledge Base (KB) (Regnier et al., 2002a, Regnier et al., 2002b, Regnier et al., 2003) has recently been introduced to amend this situation. It is an ambitious attempt to synthesize and organize conceptual and quantitative biogeochemical information relevant to diagenetic modeling. The KB is currently designed to be integrated with a reaction-transport modeling software that is being developed by the same group at Utrecht University. A user of such software will choose from a collection of reaction pathways, rate law formulations and parameter values for a particular site or problem, or will have an option of accepting the proposed default values. The MEDIA code (Meysman et al., 2003a, Meysman et al., 2003b) is another recently developed software tool that is based on object-oriented programming concepts. Its object database was designed to facilitate adding reactions, species, and parameters (objects) to the associated MEDIA modeling software. The database is a library of ASCII files that contain descriptions of reactions, species, and parameters in a pre-defined format and that can be selected by the user in constructing a model. Both MEDIA and the KB significantly facilitate integration of the required biogeochemical knowledge into diagenetic modeling and will increase the universality of RTMs. At the same time, we feel that there is a further need for a more general database tool (and at this stage more complete) that is free from restrictions imposed by integration with simulation software.

In this paper, we present our “database for reaction-transport modeling of sediment early diagenesis”, (dSED). It characterizes a diverse range of coupled biocatalytic, mineralogical, rheological, biological, photochemical, and other processes. Being complementary to KB and sharing much of its philosophy, our stand-alone tool offers flexibility provided by customizable search filters. Its main features, in comparison to those of KB and MEDIA, are presented in Table 1. dSED alleviates the historical bias in the data, as the database content is not selected based on subjective quality criteria or software formatting requirements. dSED can be used alone or in parallel with MEDIA or KB. Unlike KB, dSED does not provide in-depth reviews of current approaches, nor does it propose default parameter values and process formulations. dSED can also be used in parallel with equilibrium reaction databases, as we did not intend to include all available equilibrium data or all known aquatic speciation reactions. The database can also serve as a bibliographic tool.

As the field of diagenetic reaction-transport modeling is itself relatively new (Steefel and Van Cappellen, 1998), dSED is intended to be a work in progress that interested workers can contribute to. We feel that this searchable collection of experimental and conceptual data will facilitate the development of both spatially continuous RTMs and simpler (e.g., box-type or interacting compartment) models. It will also benefit sediment geochemists who are concerned with interpretations of molecular and larger scale processes without necessarily performing model simulations. The database and its user manual are freely available on the Web at http://www.science.uottawa.ca/LSSE/dSED

Note that, in this paper, we use the term ‘reaction’ to include all processes that can be represented by a chemical reaction equation (including precipitation, dissolution, sorption, and surface complexation).

Section snippets

dSED motivation and philosophy

The philosophy, goals and possible uses of dSED have been elaborated with the potential for future development in mind and can be summarized as follows.

The database should include as many reactions and processes as possible. In contrast to expert systems like KB, dSED strives to include not only a “most important set” of established reactions and processes but also all those that may be relevant in aquatic environments, including those that have not yet been formulated for modeling in the form

dSED description: content

dSED contains the following types of information:

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1. Reactions, including aqueous chemical reactions, solid phase precipitation and dissolution, and sorption. The reactions are characterized by their stoichiometries and by thermodynamic (Gibbs free energy change or equilibrium constant) and kinetic (rate law, rate constant) parameters. Sorption substrates are characterized by their surface properties. Parameters are given in the format and in the units of the original research articles and it is

dSED description: implementation

The database is implemented in Microsoft Access™, an easily available database software. The main entries in the database are individual reactions. For each reaction, the corresponding database record contains the reaction equation and, in many cases, its alternative forms (that is, reactions differing in the stoichiometries of their reactants, the ionic speciation, or the mineral species). The database also provides a short descriptive name of the reaction, values of thermodynamic parameters,


dSED is a valuable database tool for RTM, box-model, and interpretation development in sediment early diagenesis. We invite all interested researchers to contribute to it with experimental, theoretical, or bibliographic data. The dSED database is maintained by the Lake Sediment Structure and Evolution (LSSE) group at the University of Ottawa. Contributions to the database can be made by e-mail to the corresponding author.


The authors would like to thank Frederick Ghogomu, Darryl Roberts and Claar van der Zee for their helpful suggestions and Filip Meysman and an anonymous reviewer for constructive criticism. This work was funded by a Strategic Project Grant from the Natural Sciences and Engineering Research Council of Canada.

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