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Welcome to the MATSEDLAB (version 2012-ZTU) wiki!

MATSEDLAB is a one-dimensional multi-component reactive transport model to simulate sediment diagenesis and sediment water interactions in lakes and reservoirs. It is developed within MATLAB® and thus provides access to the advanced computational and visualization capabilities of this interactive programming environment. The system of partial differential equations (PDEs) describing the coupled transport and reaction processes is solved with the MATLAB®function pdepe. The MATSEDLAB module allows for a flexible, non steady-state, definition of transport and reaction components, model parameters, and boundary conditions at the sediment-water interface. The flexibility of MATSEDLAB are illustrated by four applications: (1) sensitivity analysis, (2) an early diagenetic simulation describing the transformation of Fe oxide from ferrihydrite to goethite and magnetite, (3) a simulation of the effect of oscillating organic matter fluxes at the sediment-water interface and (4) a simulation of the seasonal dynamic of phosphate, calibrated against field dataset. The new tool MATSEDLAB represents a promising approach for students, managers and scientists alike to guide the interpretations of observed data and learn about diagenetic processes using the programming environment MATLAB®.

A bit of history: The development of MATSEDLAB started in 2008 at Utrecht University as a collaboration between Babak Shafei (then PhD student at Utrecht University) and Raoul-Marie Couture (then PhD student at the University of Quebec) under the supervision of Philippe Van Cappellen. Shafei wrote the code and Couture designed the reaction network. The rationale for MATSEDLAB development was twofold: on one hand, we were hooked on MATLAB since the early university years (thanks to academic licences) and could not find a suitable code in our preferred language, and on the other hand, as reviewed in Janssen et al, developing one's own code is a great way to learn about processes and have full control on the model's feature set.

Original code: The original MATSEDLAB publication features an application of the model the non-steady state diagenesis of arsenic in Lake Tantare, Canada. You can read more on how MATSEDLAB compares to other diagenetic models in this review by Paraska et al. (2014). In this WIKI, you can find out more about the model itself and its features.

New developments: MATSEDLAB is no longer developed. As of 2015, the code is forked into two distinct iterations : (1) a model called Medialab, maintained by the Schmidt research group at EAWAG, and (2) a module for the lake model MyLake (MyLake-Sediment*). Building on Matsedlab, Medialab allows to easily add processes to the model, and is thus also appropriate as a learning and teaching tool. MyLake-Sediment is more complex to use, but handles both kinetic and equilibrium processes (e.g., pH and carbonate equilibria) and is fully coupled to the 1D lake water-column model MyLake.

In summary: If you are interested in exploring diagenetic models in Matlab, you can (1) explore the MATSEDLAB repository, (2) learn more about Medialab or (3) use the stand-alone version of the MyLake-Sediment module.

*This repo is not public, you need to gain access (raoul.couture@chm.ulaval.ca) otherwise this link gives a 404 error.