# 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:

- Introduction
- The Physics Chromosomes
- Week 1 : Freely jointed chain, contour length, end-to-end distance, radius of gyration, Kuhn segment length, persistence length, lattice chains
- Week 2 : Gaussian chain model, Worm-like chain model, relation to Heisenberg model
- Week 3 : Self avoiding random walk, n-vector model, energy landscape, random heteropolymer, REM model, glas transition temperature
- Week 4 : macromolecules in solution, Flory-Huggins theory, theta-temperature, phase transitions, intermolecular potentials, electrostatic screening, helix-coil transition
- Week 5: helix-coil transition, Zimm Bragg model, DNA melting, Poland-Scheraga-model, Kittel zipper-model
- Week 6: polyelectrolytes, Poisson-Boltzmann equation, Debye-screening length, Bjerrum length, Manning parameter, protein, primary structure, secondary structure, beta-sheets, tertiary structure, force fields
- Week 7: protein folding, numerical methods, Molecular Dynamics, Langevin Dynamics, Monte Carlo
- Week 8: Lattice models, HP-model, LS-model, designability of proteins, spin-glas, pivot-algorithm, simulated annealing, chromatin, two-angle model, phase diagram for chromatin
- Week 9: Membranes, surfaces, random surface, curvature, bending rigdity, Hausdorff dimension, phase transition
- Week 10: Recap
- Week 11 : Macromolecular dynamics, diffusion, Hydrodynamics, Rouse dynamics
- Week 12 : Networked systems, gel, Flory-Stockmayer theory, percolation, site percolation, bond percolation, electrophoresis
- Week 13: Bayesian inference, Bayesian networks, gene regulatory networks, random boolean network
- Week 14: Here are some online references to further online material concerning networks
- Bibliography and key word list : Will be updates continuously and may not match with the reference number in the notes at this stage!

The Hidden Markov Model lecture.

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

## Contents:

- Introduction
- 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

- General Properties of Macromolecules
- 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

- Transport
- Diffusion
- Polymer dynamics
- Rouse Model
- Hydrodynamic interactions
- Reptation

- Networks
- Gels
- Metabolic Networks
- Boolean Networks
- Scale-free Networks
- Robustness of Networks

- Molecular Motors
- Polymerization of cell filaments
- Brownian ratchet
- A basic model of a molecular motor

- Statistical Analysis
- A first example
- Bayesian Analysis
- Monte Carlo Methods
- Hidden Markov Models

## Literature:

- Harvey Lodish, Arnold Berk, Paul Matsudaira, Molecular Cell Biology, W.H. Freeman and Co, ISBN: 071676152, 5th Edition 2004
- Philip Nelson, Biological Physics: Energy, Information, Life, Publisher: W H Freeman and Co, 2003
- P. Nelson, Biological physics, W.H.Freeman, 2004
- David Boal, Mechanics of the Cell, Cambridge University Press, 2002.
- Roland Glaser, Biophysics, New York : Springer, 2001.
- Rodney Cotterill, Biophysics : An introduction, Chichester ; New York : Wiley, 2002