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Cursus: GEO4-1421
Reactive transport in the hydrosphere
Cursus informatie
Studiepunten (ECTS)7,5
Categorie / NiveauM (Master)
CursustypeCursorisch onderwijs
Aangeboden doorFaculteit Geowetenschappen; Graduate School Geowetenschappen; M Earth Sciences;
Contactpersoondr. L. Polerecky
Contactpersoon van de cursus
dr. L. Polerecky
Overige cursussen docent
3  (04-02-2019 t/m 19-04-2019)
TimeslotD: WO-middag, WO-namiddag, Vrijdag
Cursusinschrijving geopendvanaf 29-10-2018 08:00 t/m 25-11-2018 23:59
Inschrijven via OSIRISJa
Inschrijven voor bijvakkersJa
Na-inschrijving geopendvanaf 21-01-2019 08:00 t/m 22-01-2019 23:59
PlaatsingsprocedureStudiepunt/Student desk
The course teaches students how to create and use mechanistic and spatially explicit models to study (bio)geochemical processes in the various compartments of the Earth’s hydrosphere including sediments, aquifers, rivers, lakes and oceans.

By the end of the course, students will
  • have a general understanding of concepts and methods needed to quantitatively describe (bio)geochemical reactions and transport processes in various compartments of the hydrosphere;
  • be able to formulate models (conceptually and with mathematical equations) to describe transport and reactions in Earth's surface environments;
  • be able to solve simple models analytically and more complex models numerically using appropriate modeling software (R, with relevant packages ReacTran & deSolve);
  • be able to fit data with a model;
  • be able to interpret the results of the models in the relevant context (e.g., geochemical processes in rivers, lakes, aquifers, sediments, oceans);
  • be able to report the results in written and oral form.
The course will also help develop the following transferable skills:
  • Ability to work in a team: Practical exercises and final projects will be done in teams of 3-4 students. Students will need to distribute the tasks, organize and execute the workflow, and share responsibility for presentation of the results.
  • Written communication skills: Assignments and final projects will be presented as reports. Feedback will be given after each report, allowing students to improve.
  • Verbal communication skills: Results of the final projects will also be presented orally, as a group effort. Students will receive feedback on the quality of their presentations.
  • Analytical/quantitative skills: Throughout the course students will solve quantitative tasks using analytical and numerical methods. They will also interpret their results in the wider environmental context.
  • Strong work ethic: Students will be required to follow fixed deadlines for delivering assignments and results of their final projects.
  • Computer skills: Students will write their own code to solve models. This will develop their programming skills in the programming language R. Preparation of written reports and oral presentation will help them develop skills in programs used for word processing and slide shows.
  • Model formulation (from conceptual diagrams to differential equations)
  • Introduction to R (focus on packages deSolve and ReacTran)
  • Spatial components and parameterization
  • Model solution (graphical vs. analytical vs. numerical methods)
  • Stability and feedback analysis (graphical vs. algebraic approach)
  • Regression analysis (fitting of data by a model)
  • Case studies and applications: Biogoechemistry of rivers, lakes, aquifers, sediments, oceans
It is anticipated that students attending the course will have highly diverse levels of prior knowledge and experience in maths, programming and biogeochemistry, as well as diverse expectations from the course. The course can therefore be conducted at two levels, one aimed at students who want to use modeling as a way to improve their analytical skills, the other aimed at students who want to be more challanged and think about modeling as a possible direction of their future career. To facilitate this, students will be required to develop and maintain a degree of mutual understanding and co-operation.
Je moet voldoen aan de volgende eisen
  • Toelatingsbeschikking voor de master toegekend
Basic knowledge of aquatic chemistry, linear algebra and differential calculus.
Voorkennis kan worden opgedaan met
Aquatic and environmental chemistry (GEO4-1439), Lineaire algebra en vector analyse (GEO2-1201), Kinetic Processes (GEO4-1426).
Verplicht materiaal
Soetaert, K. and P.M.J. Herman. A practical guide to ecological modeling. Using R as a simulation platform. Springer. 372p. ISBN: 978-1-4020-8623-6
Handouts provided during lectures and through Blackboard (
Computer practicals


Student presentations

Minimum cijfer-

Two hand-in assignments, final project report, final project presentation, and final exam account, respectively, for 2x10%, 20%, 20% and 40% of the final grade.
To pass the course, grades for each of these tests must be 5 or higher, and the final grade must be 5.5 or higher.

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