Tfy-3.462 Advanced Topics in Biological and Soft-Matter Systems

Autumn 2004

Topical matters

• Copies of the lecture notes are in Perttu Niemela's office (U103 in the Laboratory of Physics). If you should like to take copies, please ask Perttu for the file.
• Topics for an independent research project are listed below (see: Passing the course). Further suggestions by the students are welcome.
• First lectures will be given on Friday, September 10, 2004, at 10 am - 1 pm. Location: Y227 close to the Laboratory of Physics. The course material and general guidelines for the course will be announced during the first lecture.

General matters

• Lectures will be given on Friday at 10 am - 1 pm in the seminar room Y227 close to the Laboratory of Physics.
• To pass the course, the students are expected to carry out an independent research project under the supervision of the lecturers. Choice of a topic should be made together with one of the lecturers.

Lecture notes 2004

• Lecture notes will be given after each lecture. The location (folder) from which they can be found will be announced later.

Description and contents of the course

• 1. Polymer physics spiced by thermodynamics and statistical physics (T. Ala-Nissila)
  • Basics of thermodynamics and statistical physics
  • Random walks and self-avoiding walks with polymer chain statistics and scaling
  • Correlation functions and diffusion together with phase transitions
• 2. Nonequilibrium and elastic aspects of biomolecular systems (M. Alava)
  • Nonequilibrium phase transitions in biology
  • Elasticity of biomolecules
  • Elasticity of membranes and networks
• 3. Electrostatics (M. Karttunen)
  • Electrostatics in soft matter and biological systems
  • Applications to proteins, DNA and transport
• 4. Dynamics on the cellular level (I. Vattulainen)
  • Cell dynamics
  • Diffusion, walks, reactions
  • Motility

Target group and background requirements

While a wide background of any field is not necessary, basic knowledge of thermodynamics and statistical mechanics would be of use.

Passing the course

Examples of topics for an independent research project are as follows (the lecturer proposing the topic is given in brackets):

• Real polymer chain in a tube (reserved) (TAN)
• Flory-Huggins theory of polymer mixing (TAN)
• Rouse vs. Zimm dynamics of single polymer chains (TAN)
• Reptation of polymers in diffusive motion: chain length vs. concentration (TAN)
• Non-equilibrium phase transitions in self-propelled particle systems. (reserved) (MA)
• Protein-interaction networks (MA)
• Single-molecule elasticity of DNA and/or RNA: experiments (MA)
• Brownian ratchet devices (reserved) (IV)
• Motility models (IV)
• Structural models of cellular membranes (reserved) (IV)
• Fluctuations of cell membrane surfaces: theory and experiments (reserved) (IV)
• Overcharging in polyelectrolyte systems: Manning condensation (MK)
• Simple Coulomb systems in two dimensions: the One Component Plasma -model (MK)
• Numerical treatment of Coulomb interactions (MK)

Course material

• David Boal, Mechanics of the cell.
• Jonathon Howard, Mechanics of Motor Proteins and the Cytoskeleton
• Robert Zwanzig, Nonequilibrium statistical mechanics
• Dennis Bray, Cell Movements - From Molecules to Motility

Fysiikan laboratorion kotisivulle