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MATSEDLAB is a module allowing biogeochemical reactive-transport modeling within MATLAB® for the purpose of modelling early diagenesis in bioturbated lake sediments. The model development followed the general approach outlined by Van Cappellen and Wang (1996) and Boudreau (1997). Mathematically, a set of partial differential equations (PDEs) defined a coupled transport-reaction system in which all the reactions were described by kinetic expressions. 

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 CappellenShafei wrote the code and Couture designed the reaction network. The rationale for MATSEDLAB development was twofold: on one hand, we were using 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, CanadaYou can read more on how MATSEDLAB compares to other diagenetic models in this review by Paraska et al. (2014). You can read the MATSEDLAB manual here to evaluate if it suits your modelling needs. MATSEDLAB is freely accessible via the GitHub MATSEDLAB repository

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*), maintained by the Norwegian Institute for Water ResearchBuilding 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  ( otherwise this link gives a 404 error.

Communications featuring MATSEDLAB

6- Torres  E, Couture RM, Shafei B, Nardi A, Ayora C and Van Cappellen P. (2015Reactive transport modeling of early diagenesis in a reservoir lake affected by acid mine drainage: Trace metals, lake overturn, benthic fluxes and remediation. Chemical Geology (419) 75-91. 10.1016/j.chemgeo.2015.10.023

5-  Couture R-M, Fischer R, Gobeil CCampisi D, Van Cappellen PReactive-transport modeling of the sulfur cycle in lake sediment : fixing the leaksASLO aquatic sciences meeting 2012 (Lake Biwa, Shiga, Japan).

4- Pastor LDeflandre B, Shafei B, Couture R-MCathalot CMetzger E, Van Cappellen PViollier E.Non-steady state modeling of early diagenetic processes following a major flood event in the Rhône prodelta (NW Mediterranean Sea, France).  Gordon Research Conference. Chemical Oceanography 2011

3-  Shafei B, Couture R-M, and Van Cappellen PArsenic sorption in aquatic sediments: Equilibrium, kinetic and mixed modeling approaches. GeochimCosmochimActa 2010 (74) A938-A938.

2- Couture R-MShafei B, Van Cappellen PTessier A, Gobeil CArsenic dynamics in lake sediments. GeochimCosmochimActa   2010 (74) A193-A193.

1-  Couture R-MShafei B, Van Cappellen PTessier A, Gobeil CNon-steady state modeling of arsenic diagenesis in lake sediments.  Environ. SciTechnol2010 (44) 197-203.


Raoul-Marie Couture, University of Waterloo & NIVA,

Babak Shafei, AMPHOS21,

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