Course contents

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.

Intended learning outcomes

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
• explain models for synapes and their plasticity and of networks of neurons
• 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

Course Disposition

No information inserted

Specific prerequisites

Single course students: 90 university credits including 45 university credits in Mathematics or Information Technology. English B, or equivalent.

Recommended prerequisites

The mandatory courses for D, E, and F in mathematics, numerical analysis and computer science or the equivalent. Recommended the courses: DD2400 Cellular and Molecular Biology and DD2401 Neuroscience or the equivalent.

Equipment

No information inserted

Literature

To be announced at least 4 weeks before course start at course web page. Previous year: Fall et al., Computational Cell Biology, Springer Verlag.

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

A, B, C, D, E, FX, F

Examination

• LAB1 - Laboratory Work, 1,5 hp, betygsskala: P, F
• TEN2 - Examination, 4,5 hp, betygsskala: A, B, C, D, E, FX, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

In this course all the regulations of the code of honor at the School of Computer science and Communication apply, see: http://www.kth.se/csc/student/hederskodex/1.17237?l=en_UK.

Other requirements for final grade

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

Opportunity to complete the requirements via supplementary examination

No information inserted

Opportunity to raise an approved grade via renewed examination

No information inserted

Examiner

Erik Fransén

Ethical approach

• All members of a group are responsible for the group's work.
• In any assessment, every student shall honestly disclose any help received and sources used.
• In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Course web

Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.

Offered by

CSC/Computer Science

Main field of study

No information inserted

Education cycle

Second cycle

Add-on studies

Please discuss with the instructor.

Contact

Erik Fransén, e-post: erikf@kth.se

Supplementary information

This course is a part of DD2435 Mathematical Modelling of Biological Systems and can not be combined with that course.

The biggest part of the teaching in this course takes place at Campus Valhallavägen, but some teaching take place at Alba Nova.