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Modeling crop growth, water, carbon and nitrogen dynamics in cropping systems (2018)

ECTS credits: 5 ECTS

Course parameters:

Language: English

Level of course: PhD course

Semester/quarter:  Q3 2018

Hours per week: Total workload app. 130 hours (including preparatory reading before and during the course, lectures and exercises during the course and report writing after the course)

Capacity limits: 22 participants


Objectives of the course:

Modeling the effects of climate, soil properties, soil organic matter and nitrogen fertilization on crop photosynthesis, growth and development is vital for evaluating the effects on yields and the risk of nitrogen losses of different cropping systems.

This course aims at giving the PhD student a thorough background in calibration, evaluation and use of existing models of crops, soil water, soil organic matter and mineral nitrogen in soil and their possible inter actions. The course will include a combination of lectures, hands-on model development, and hands-on evaluation and use of existing models. Lectures and exercises will cover all steps in the modeling process: qualitative and quantitative model formulation, parameter estimation, and model validation and analysis. Parts of the dynamic modeling process will be exemplified using the simulation model DAISY. Other parts will be based on use of the empirical nitrate leaching model NLES4. The practical and theoretical exercises will be conducted in groups. Each practical exercise will result in a short exercise report from each student. These reports will make up the student personal course portfolio.


Learning outcomes and competences:

At the end of the course the student should be able to:

  • Explain the relations between a model, empirical knowledge and the real system.
  • Explain the main classification of models (static/dynamic, empirical/mechanistic, deterministic/stochastic) and other central definitions.
  • Reflect on choice of model type for simulation of crop growth, soil water balance and soil organic transformation and on the level of detail.
  • Evaluate the possible effects of soil organic matter transformation in soil and its feedback on crop growth and nitrogen losses.
  • Use of empirical models predicting nitrate leaching and compare the results with deterministic mechanistic model predictions.
  • Evaluate the sensitivity of a model to uncertainty associated with parameters and input in crop models.
  • Reflect on the ability of the resulting model to describe a real cropping system and to predict change in nitrogen fertilization effects on crop growth and nitrogen losses.


Compulsory programme:

Report and exercises


Course contents:

Modeling the effects of climate, soil, nitrogen application and model formulation on crop photosynthesis, growth and development is vital for evaluating the effects on yields and to quantify the nitrogen losses of different cropping systems. Use of empirical nitrogen leaching model can be an attractive alternative to use of detailed simulations models due to less parameters to be calibrated and the uncertainty of models in general.  



PhD students within agronomy, environmental engineering or biology.


Name of lecturers:

Jørgen E. Olesen, Mathias Neumann Andersen, Christen Duus Børgesen and Finn Plauborg, Dept. of Agroecology, Science and Technology, Aarhus University

Claas Nendel Leibniz, Centre for Agricultural Landscape Research Müncheberg, Brandenburg, Germany


Type of course/teaching methods:

Lectures and exercises



Haefner, J.W. Modeling Biological Systems 1-213 (covers general modelling issues such as system analysis, model formulation, numerical methods, parameter estimation, model validation and model analysis)

Olesen, J.E., and M. Bindi, 2002. Consequences of climate change for European agricultural productivity, land use and policy. European Journal of Agronomy 16:239–262.

Hansen, S. Daisy, a flexible Soil-Plant-Atmosphere system Model. The Royal Veterinary- and Agricultural University, Department of Agricultural Sciences, Laboratory for Agrohydrology and Bioclimatology

Hay, R.K.M, Porter, J.R, 2006. The physiology of crop yield. Second Edition. Blackwell Publishing, Oxford, UK. ISBN-13: 978-14051-0859-1. Chapter2 Page 7-15 (Development and phenology) Chapter 9 Page 220-230.

Jones, H.G. 1992. Plants and Microclimate - A Quantitative Approach to Environmental Plant Physiology. 2nd Edition. Chapter. 5, 6, 7 and 10.

Kristensen, K., Waagepetersen, J., Børgesen, C.D., Vinther, F.P., Grant, R., Blicher-Mathiesen, G. (2008). Reestimation and further development in the N-LES – NLES3 to NLES4. DJF Plant Science no 139. 1-25.


Course homepage:


Course assessment:




Department of Agroecology


Special comments on this course:




24 September – 30 September 2018


Place: AU-Foulum, Blichers Allé 20, DK-8830 Tjele, meeting room 1



If you have any questions, please contact course organiser Christen Duus Børgesen, e-mail: christen.borgesen@agro.au.dk or course secretary Jytte Christensen, e-mail: jytte.christensen@agro.au.dk

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