Modeling of processes in celll biology, 6 credits

Current course: cellmod11.

To find previous courses, old material, etc, see the old web pages.

The course focuses on mathematical modeling and computer simulation of biochemical reactions in the cell, reaction networks, and genetic networks.

Aim
After the course, the student should be able to
* explain the useage of, and the assumptions behind biophysical and biochemical models and methods
* compute basic biophysical and biochemical entities in stochiometry, ion statics and ion dynamics, diffusion and cell compartments
* exemplify the usage of continious, stochastic or boolean models
* use and develop simulation programs for genetic, biochemical, and neural networks

so that the student
* is able to explain the useage of, and the assumptions behind biological models
* in the working life can perform biological modeling and simulation work

Syllabus
Methods for mathematical modeling and computer simulation of sub cellular processes and functions. The main focus is on biochemical networks, enzyme kinetics and cell signaling, genetic networks, and switches, are covered, as is also ion channel dynamics and biological morphogenesis. Both dynamical and diffusion aspects will be covered.

Prerequisites
The mandatory courses for D, E, and F in mathematics, numerical analysis and computer science or the equivalent. Recommended the courses: DD2400/HL1008/7E1200 Cellular and Molecular Biology.

Follow-up
Please discuss with the instructor.

Requirements
Examination (TEN2; 4,5 university credits).
Laboratory assignments (LAB1; 1,5 university credits).

Required reading
To be announced at course start. Previous year: Fall et al., Computational Cell Biology, Springer Verlag.

Other
Usual examiner is Erik Fransén. For the student who is also interested in neurons and the nervous system, we instead recommend DD2435 Mathematical modeling of biological systems. That course is to a large extent joint with this course, and can not be combined with this one.