Lyngby summer school 2013

Modeling plant uptake of chemicals:
Application in science and engineering

PhD-course and summer school, 17-21 June 2013
Technical University of Denmark, Lyngby, Denmark

Stefan Trapp, Charlotte Legind and invited teachers

In June 2013, the TIMBRE PhD summer school on "Plant Uptake Modeling" was taught at DTU in Lyngby, DK. Topics were plant uptake of pollutants and pesticides, risk assessment and phytoremediation. Participants came from all over the world, including China, USA, Germany, and members of the TIMBRE consortium. The course shall be developed to a blended learning course. More information on the background of the event can be found below and on the events special website, which also provides all teaching materials:

Background information

TIMBRE and the Danish Technical University organised the PhD course that aimed at giving a theoretical and practical introduction to uptake of chemicals in plants and its relevance for science and engineering. The focus was on mathematical modeling and its application. The course covered the plant physiological, physical, chemical and mathematical basics of plant uptake. Simple and advanced models were taught, and the source code with documentation was available for all participants. The models were applied to study plant uptake of pesticides, persistent organic pollutants, emerging pollutants (incl. pharmaceuticals), ionisable compounds and heavy metals. The participants worked with examples from risk assessment, pesticide design, dietary exposure, contaminated sites, urban gardening and phytoremediation. Students had hands-on exercises with all models and practice also the tree core phytoscreening method for delineation of subsurface contamination. Besides, the exchange between the participants by short presentations of their work was stimulated.

Credit Points


The course was given at the Technical University of Denmark by local and international teachers and is credited with 5 ECTS points. To finalize the course, participants are to prepare their own model simulation and a short report. The course material is electronically available from the course homepage.

Funding and Costs

The course was supported by the project TIMBRE and was free of charge for registered PhD students. The course fee for professionals was 800 €, but was reduced if interesting presentations from their work were provided.



For specific questions on this event, please contact Stefan Trapp

Course content

Week before: Reading (material will be provided in time)

The course will address the following topics:

Processes governing plant uptake of chemicals

  • Plant anatomy and physiological basis
  • Physico-chemical principles
  • Regressions and equations
  • Standard model for plant uptake

  • Exercises: Chemical risk assessment,  persistent organic pollutants

Crop-specific models

  • Introduction to root, potato, lettuce and fruit tree models
  • Dietary human exposure
  • Contaminated sites
  • Exercises: Pros and cons of urban gardening, dietary human exposure

Dynamic modeling

  • Mathematical principles of systems science
  • Multi-cascade model
  • Coupled model for solute transport in soil and plant
  • Heavy metals
  • Exercises: Pesticide optimization, field scale simulations, sensitive parameters

Ionisable compounds

  • Physico-chemical principles
  • Cell model
  • Standard model for ionisable compounds
  • Dynamic simulations on field scale
  • Exercises: Pesticide optimization, field scale simulations, sensitivity analysis

Experimental work

  • Tree coring
  • Phytoremediation
  • Uncertainty analysis

Download the programme outline here.

Download the announcement here. The course material are electronically available from the course homepage.