NFYK15016U Physics of Biological Nonequilibrium Systems
MSc Programme in Physics
Biological organisms are open thermodynamic systems with metabolism. Therefore, most processes are not in equilibrium. Thermodynamic forces and fluxes drive biological processes under consumption of energy and dissipation of entropy. Such processes are irreversible. The understanding of nonequilibrium processes is important to analyze molecular reactions, protein function and metabolism in biology. This course introduces into the thermodynamics of irreversible processes and into the application of these concepts to elementary biological reactions (e.g. ion channel activities and ion pumps). Under certain conditions stable fluxes (stationary states) develop, or dissipative structures can form. Criteria for defining such states are formulated.
As an important example, this course also introduces into the foundations of the physics of nerve pulses. This includes the treatment of the basic physical features of nerves, electrical conductance through cell membranes, cable theory, ion channels and the Hodgkin-Huxley model in particular, which forms the nonequilibrium basis of the accepted models for the action potential. We contrast this classical theory of nerves by an adiabatic thermodynamic treatment of nerves leading to the possibility of solitons in membranes, thus forming an alternative basis for the origin of the nervous pulse that is based on reversible physics. The difference between reversible and dissipative processes is discussed. This includes channel activities and their lifetimes.
Understanding of thermodynamics from the point of view of an entropy potential, and the important examples in the theory of nerves pulse transmission.
Thermodynamic forces and fluxes as well as theory of fluctuations and theory of nerves.
After this course students should be able to:
- Derive the Hodgkin-Huxley model
- Describe the hydrodynamics of the nerve pulse
- Handle the entropy as a potential
- Derive cycle kinetics and its application to ion pumps
- Work with thermodynamic forces and fluxes
- Work with Onsager's equations, and understand the concept of microscopic reversibility
See Absalon for final course material. The following is an example of expected course litterature.
There will be handouts that are sufficient to understand the course.
Recommended is the reading of: "Modern Thermodynamics: From Heat Engines to Dissipative Structures (Paperback) by D. Kondepudi and I. Prigogine".
Previous knowledge in thermodynamics is
Academic qualifications equivalent to a BSc degree is recommended.
- Theory exercises
Students have to give oral presentations about historical papers during the course, which are discussed with the class.
- 7,5 ECTS
- Type of assessment
- Oral examination, 30 minutesThe course will be split in 6 major topics. The candidate gives a free 15 minute presentation of one of these subjects. The topic is chosen by rolling a die.
During the remaining 15 minutes of the exam questions about the other five topics will be asked by the course leader or the censor.
- Exam registration requirements
During the exercises student will present short oral contributions about historical papers. The oral presentation is mandatory.
- Only certain aids allowed
Lecture notes are not allowed during the exam. One card with key words is allowed for each topic (six in total).
The cards shall help the student to recall the prepared structure of the presentations, but shall not contain detailed derivations.
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
several internal examiners
Same as the regular exam. If the exam prerequisite has not been fulfilled, the student must contact the course responsible well in advance in order to arrange to give a presentation no later than 2 weeks before the re-exam.
Criteria for exam assesment
see learning outcome