Theoretical Biophysics

Venue:

Lecture theatre: INF 227 / HS 2

Prerequisits:

Basic knowledge in Classical Mechanics, Electrodynamics and Statistical Mechanics

Abstract:

The emergence of new cross-disciplinary fields is one of the major driving forces in science and technology. Among the most important of these emerging fields are those which connect the life sciences with physics. Due to the vast amount of data that is now available there is the possibility to understand living organisms as complex dynamic systems. Biological processes occur on a wide range of spatial and temporal scales. The time scales of biological function range from very fast femtosecond molecular motions, to multi second protein folding pathways, to cell cycle and development processes that take place over the order of minutes, hours and days. Similarly, the dimensions of biological interest range from small organic molecules to multi-protein complexes, to cellular processes, to tissues, to the interaction of human populations with the environment. Thus one needs to understand how on the smallest scale conformational changes of molecules plus their interaction give rise to collective phenomena.

Literature

Part of the lectures is based on
Theoretical Molecular Biophysics Series: Biological and MedicalPhysics, Biomedical Engineering
Scherer, Philipp, Fischer, Sighart F.
1st Edition., 2010, XIII, 371 p. 250 illus., 3 in color., Hardcover ISBN: 978-3-540-85609-2

You can access the electronic version of the book via
 
Springerlink

Due to restrictions by Springer, the electronic version will not be available. At least one hardcopy will be available at the ITP library Philosophenweg 16.

Projects

You can find the list of projects as well as the references here.

Lecture notes:

The Hidden Markov Model lecture.

The full script version (but still very sketchy). Return frequently for an updated version.


Contents:

  1. Introduction
  2. Macromolecules
    • General Properties of Macromolecules
      • Freely jointed chain
      • The Gaussian chain model
      • Elastic rod model
      • Self Avoiding Chains
      • Conformations and Energy Lanscapes
      • Macromolecules in Solution
      • Macromolecules at a Surface
    • Intermolecular interactions and electrostatic screening
    • Helix-Coil Transition
    • DNA Melting
    • Polyelectrolytes
      • The Poisson-Boltzmann equation
    • Proteins
      • Protein folding
      • Numerical approaches
      • Folding as a spin glass problem
      • Protein-protein interactions
    • Chromatin
      • Chromatin Models
      • Force-extension behavior of folded macromolecules
    • Genes
      • Gene expression and genetic code
  3. Membranes
    • Self–assembly of micelles
    • Surface Behavior of Lipids
      • Differential geometry of surfaces
      • Membrane elasticity and bending energy
      • Membrane fluctuations
    • Structure of Lipids
    • Cell Membranes
  4. Transport
    • Diffusion
    • Polymer dynamics
      • Rouse Model
      • Hydrodynamic interactions
      • Reptation
  5. Networks
    • Gels
    • Metabolic Networks
      • Boolean Networks
      • Scale-free Networks
      • Robustness of Networks
  6. Molecular Motors
    • Polymerization of cell filaments
    • Brownian ratchet
    • A basic model of a molecular motor
  7. Statistical Analysis
    • A first example
    • Bayesian Analysis
    • Monte Carlo Methods
    • Hidden Markov Models

Literature: