Physics of Biological Systems I and II
Wintersemester 2002/2003 & Sommersemester 2003

Biological information is stored in sequences, processed in complex functional networks involving DNA, RNA, and proteins, and it evolves in a stochastic process at the level of a population. This course treats various quantitative aspects of biological information using concepts and methods of statistical physics. We start with the problem of retrieving information from sequences, expression arrays, or graphs of molecular interaction networks. Sequence information can be used to predict structural properties of biomolecules and to reconstruct evolutionary histories. Dynamical aspects of biological information are discussed first at the ``microscopic'' level of sequences, where evolution is an intricate stochastic process involving mutations, fitness, and population fluctuations. Fitness effects couple sequences a ``mesoscopic'' level of functional units, and a statistical theory is needed to link the two levels of description. In the last part of the course, we focus on the complex systems aspects of the genome, which is characterized by multiple interactions between genes. It is these interactions that translate information into biological function and shape the evolutionary dynamics.

1. Introduction
2. Molecular Information
   1. Sequence similarity
   2. Local motifs
   3. Gene expression
   4. Networks and topological similarity
3. Molecular Structures
   1. RNA secondary structure
   2. Structural properties of proteins
   3. Sequence and structure
4. Information and Evolution
   1. Reconstructing evolution: The tree of life
   2. Predicting evolution
5. Evolution of Genotypes
   1. Fitness and selection
   2. Error threshold and quasispecies
   3. Neutral evolution, population fluctuations
   4. Towards a comprehensive picture
6. Evolution of Phenotypes
   1. Strategies and games
   2. Evolutionary game theory
   3. Stochastic games
   4. Genetic constraints to phenotypic evolution
   5. Speciation
7. Evolution of complexity
   1. Early evolution and catalytic networks
   2. Gene networks I: evolution of regulatory DNA
   3. Gene networks II: evolution of topologies
   4. Species networks and large scale evolution