DTULOGOSummer course 12906 Modeling of Plant Uptake timbre_logo_4c_name_rz


17-21 June in Lyngby, DK organized by Stefan Trapp stt@env.dtu.dk

last update June 26 by Stefan Trapp

We acknowledge the support by the TIMBRE project for our students (link below).

Find impressions from the summer school here: http://www.timbre-project.eu/en/lyngby-summer-school-2013.html


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Material - click on link and download

course program (new 10 June 2013)

flyer (distribute until end of May 2013)

Sign-up and housing issues (letter 1)

Letter two (course organization, travel description, reading)

How to come to DTU (descripion of way)

Travel to/from Hotel Fortunen (description of way, new June 10)

Letter III (June 10)


Participants - get to know each other


Reading before the course (important!)

Script (mandatory reading)

Trapp 2007 Fruit Tree Model (recommended reading)

additional material

Rein et al. 2011 (recommended reading for day 2)

Legind et al. (2011) (needed for exercise day 2)

Trapp & Eggen 2013 (needed for exercise day 3) and SI


Day 1 Monday: Basics, Standard Model and Risk Assessment

10Processes Lecture slides

11Partition coefficients Lecture slides

12Standard model and risk assessment Lecture slides

Standard model Program


Standard model empty for exercise 1

13Exercise_all hand exercises


TSCF lecture by Bill Doucette (slides)


Self-Introduction (movie)

Standard model and risk assessment (movie)

TSCF lecture by Bill Doucette (movie)

additional material

17_willowtree_test Manual

Book Trapp and Matthies (only chapters 3 and 4 needed)

Legind and Trapp 2009 (paper on crop-specific models)

Legind and Trapp 2009 SI (Supporting Information)

Crop-specific plant uptake models (program, not needed for course)


Day 2 Tuesday: Dynamic Modeling

21One hour math Lecture slides

22Exercise phytoextraction, hand exercise

22Exercise phytoextraction solution (do not cheat!)

23Dynamic modeling Lecture slides

24Exercise day 2 exercise using the dynamic model

24Exercise.xls Program needed for exercise 2

Legind et al 2011 paper needed for exercise day 2

1_Cascade prof CNL M no fit Fig 2 and 3.xls solution of exercise


Dynamic modeling (movie)


Sent by Peter Fantke (teacher):

lecture Analyzing pesticide dissipation in food crops by Peter Fantke

Reading = paper + SI


additional material

Rein et al. 2011 paper, challenging

Cascade Organic Aug-July.xls a one year cascade model programmed

Generic FLU US Corr April 2013 a ten-year cascade model

Chapter 9 of book with Frank Swartjes


Day 3 Wednesday: Soil & Plant

Presentation of Jens Streibig, ADME pesticides (slides)

31Buckets model Lecture slides

32exercise day 3

32exercise day 3.xls program for exercise day 3

Trapp&Eggen 2013 paper needed for exercise

Trapp&Eggen 2013 SI SI of paper needed for exercise

32Field TCPP with air mit Graphs.xls solution of exercise day 3 hej! do not cheat!

Cascade_Cell Cation Trim GUT.xlsx Cascade model for ionizable compounds

Lecture Arno Rein on water balance of soil and plants (slides)


Buckets model lecture (movie)


Sent by Peter Fantke (teacher):

Dynamic MultiCrop model lecture of Peter Fantke

Exercises Peter Fantke

Model Peter Fantke (needed for exercise)

Parameterization of model Peter Fantke (needed for exercise 2)

Paper 1 + SI 1 = documentation

Paper + SI = more documentation


additional material

Buckets model manual unfortunately for an older version

Legind et al. 2012 paper about Soil&plant model and field study in PLoS one

Legind et al. 2012 SI SI of paper about Soil&plant model

Day 4 Thursday: Ionics

41Cell model Lecture, updated thursday 13th

41Cell model Program


42 Standard model for Ionics

43TranslaminarLeaf Lecture

43TranslaminarLeaf Program


Cell model lecture (movie)

Cell model program (movie)

Standard model for Ionics (movie)


https://ilab.acdlabs.com/iLab2/index.php i-lab ACD login


additional material

Pest Manage Sci 2000 paper on pesticide root uptake

ESPR2004 first paper on new theory 2004

Trapp&Horobin2005 Cell model in medicin most cited!

Bioaccumulation of ... Ionizable Compounds in Plants Chapter in book J. Devillers

Franco&Trapp 2008 Koc of acids and bases

Koc.xls Koc regressions programmed

http://homepage.env.dtu.dk/stt/Homepage%20anf/Website.htm homepage Antonio

activity paper with Don Mackay 2010


Sent by John Byrne (PhD)

lecture on wetland modeling


Day 5 Friday: Phytoremediation

51TreeCoring Lecture slides

52Phytoremediation Lecture slides

Field TCE lecture by Bill Doucette (slides)


Progress in phytoscreening lecture (movie)

Field TCE lecture by Bill Doucette (movie)

Phytoremediation lecture (movie)


link guide to phytoscreening (German and English)

JSS 2001 Aspects of phytorem paper 2001, very optimistic

additional material

Trapp et al. 2008 paper about salt uptake and toxicity concerning our experiment

Willow tree test manual how its really done in the lab



The End

To the TIMBRE website http://www.timbre-project.eu/

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