Entry requirements

120 credits in the engineering programme in molecular biotechnology, including the courses Transform Methods, Probability and statistics, Chemical thermodynamics and Microbiology. Completed the course Scientific computing II.

Learning outcomes

After passing the course the student should be able to

• formulate quantitative dynamics models of biochemical reaction schemes
• explain the physical principles underlying speed and accuracy in enzymatic processes
• simulate stochastic and deterministic reaction models.

Content

Reaction kinetics and enzyme kinetics: Reaction and diffusion control, enzyme catalysis, relaxation kinetics, separation of time scales. Irreversible thermodynamics: Energy dissipation, accuracy and proofreading in chemical reactions. Non-linear deterministic systems analysis: Phase space analysis, bifurcation theory. Stability and oscillations in biological regulatory systems. Mesoscopic kinetics: Stochastic chemical processes, description of stochastic biological systems with Master equations. Reaction-diffusion models: Description of spatial dependent kinetics with both partial differential equations and reaction-diffusion Master equations. The course contain programming assignments in MATLAB, describing some selected control system illustrating the difference between stochastic and deterministic analysis. Furthermore, a wet lab session is included, where some example from the course is studied using fluorescence microscopy.

Instruction

Lectures, classroom exercises, laboratory sessions and written assignments.

Assessment

Written examination (3 credits), laboratory sessions and written assignments (2 credits).