Syllabus for Physical Molecular Biology

Fysikalisk molekylärbiologi

Syllabus

  • 5 credits
  • Course code: 1MB449
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Technology A1N
  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2017-03-07
  • Established by:
  • Revised: 2018-08-30
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 30, 2019
  • 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.
  • Responsible department: Biology Education Centre

Learning outcomes

On completion of 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). 
 
If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.

Reading list

Reading list

Applies from: week 30, 2019

A compendium will be handed out to the students.