NFYK14026U Biophysics of nonequilibrium processes and evolution

Volume 2014/2015
Content

This course goes beyond standard thermodynamics and introduces modern concepts of nonequilibrium process. This will be described the phenomena of life. Biological organisms are open thermodynamic systems with metabolism (food and breathing). Most processes are not in equilibrium. Thermodynamic forces and fluxes drive reaction 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. channel activities). Under certain conditions stable fluxes (stationary states) develop, or dissipative structures can form. Criteria for defining such states are formulated. Ultimately one arrives at the formation of chemical oscillations and biological clocks. In reproducing organisms, such oscillations can lead to reproductive cycles (hyper-cycles) that compete with other organisms. Fitness is a consequence of reproductive speed, error and death rate. Important key topics of this course are information, self reproduction, self organization and evolution.

Learning Outcome

Skills: Understanding of thermodynamics from the point of view of an entropy potential

Knowledge: In particular, thermodynamic forces and fluxes as well as theory of fluctuations and information theory.

Competences: After this course students should be able to:

- 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

- Understand the concept of 'information' and its relationship to entropy.

- Describe oscillatory reactions

- Derive the equation for evolution

- Understand the concepts of hypercycles, quasispecies, mutation

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".

No formal requirements. Previous knowledge in thermodynamics is of advantage
Physics bachelor, Chemists and Biologists with previous training in thermodynamics.
Lectures and excercises
The course is offered every second year.
  • Category
  • Hours
  • Exam
  • 0,5
  • Lectures
  • 35
  • Preparation
  • 156,5
  • Theory exercises
  • 14
  • Total
  • 206,0
Credit
7,5 ECTS
Type of assessment
Oral examination, 30 minutes
The course will be split in 6 major topic. The candidate gives a free 15 minute presentation of one of these subjects. The topic is chosen by roling 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
Presence in at least 50% of course lectures and one presentation in the excercises.
Aid
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 his presentations, but shall not contain detailed derivations.

Marking scale
7-point grading scale
Censorship form
No external censorship
several internal examiners
Criteria for exam assesment

12 is given for a presentation where the student displays an independent ability of deriving and working with the concepts described in the course goals. 2 is given for an insecure presentation where the student can only reproduce a minimum of what has been described under course goals.