CBRG - Computational Biochemistry Research Group

Modelling and Simulation

Lecturer: Prof. Gaston Gonnet

Assistants: Nives Skunca, Vincent Kusters, Hemant Tyagi, and Stefan Zoller

Time and Place

The lecture takes place on Monday, 10 - 12, CAB G11 and Thursday 10 - 12, CAB G51.

Exercises take place on Monday, 15-18, LFW C11 and Thursday, 15-18, ML H43.

Both exercise lectures, Tuesday and Thursday, cover the same content.


Linear and nonlinear least squares, sensitivity analysis, constraint minimization (Lagrange multipliers) , conjugate gradient method SVD, Linear programming, support vector classification, variational calculus, linear filter theory (Wiener filter), nonlinear diffusion, dynamic programming, parsimony.

Recommended Reading

The lecture closely follows the book "Scientific Computation" by Gaston Gonnet and Ralf Scholl. You can get the book in the Polybuchhandlung or at Amazon, among other shops.

There is a small addendum for the book online.


The exercises will be published on this page before each session. There will be one exercise each week (except for the first week). Both new and repeating students are highly recommended (but not required) to do the exercises.

The exercises should take about 3 hours of work each week; during exercise sessions, TAs will present the new problems and discuss the solved ones. You will also have time to solve your exercises during these sessions and ask questions about the lecture.

If you have any questions concerning the exercise sessions or the questions in the exercises, please send an email to one of the assistants.

The book mentions some interactive exercises. Please have a look here.


Lots of the solutions to the exercises (plus some code examples in the lecture) are written for Maple. Programming fluently in Maple is not a prerequisite for this course, but you might want to make yourself comfortable with the syntax to be able to follow all examples. For Maple newbies, you could work through a document such as this Maple tutorial in german. There are also other tutorials out there, e.g. this one in english.

Exercise sessions

Week Handed out Due to Assignment Solution Add. material
1 Feb 16/19 Feb 23/26 ex1.pdf sol1.pdf  
2 Feb 23/26 Mar 2/5 ex2.pdf sol2.pdf  
3 Mar 2/5 Mar 9/12 ex3.pdf sol3.pdf  
4 Mar 9/12 Mar 16/19 ex4.pdf sol4.pdf  
5 Mar 16/19 Mar 23/25 ex5.pdf sol5.pdf
solution: Maple code
6 Mar 30/April 16 April 20/23 ex6.pdf sol6.pdf  
7 April 20/23 April 27/30 ex7.pdf sol7.pdf  
8 April 27/30 May 4/7 ex8.pdf sol8.pdf  
9 May 4/7 May 11/21 ex9.pdf sol9.pdf  
10 May 11/21 May 18/21 ex10.pdf sol10.pdf Evolutionary algorithms slides The slides are based on a book chapter you can find here


The final exam will be in the Pruefungssession. Eight handwritten A4 pages (four sheets) and a non-programmable calculator are allowed on the exam. No communication devices or music players are allowed. There will be no midterm exam.


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