Essential Concepts in Theoretical Biophysics

• Binding specificity and discrimination
• Kinetic proofreading
• Coupled disequilibria
• Target search and facilitated diffusion
• Chemotaxis
• Adaptation
• Elasticity and shape
• Robustness
• Positional information and morphogen gradients
• Polarity
• Oscillations and limit cycles
• Pattern formation
• Evolution and evolvability

After successful completion of the module the students are able to:

1. Illustrate general biophysical concepts present in a multitude of biological systems
2. Exemplify and discuss strategies of biological systems to achieve and regulate their function reliably under noisy and changing conditions.
3. Explain and compare different mechnisms employed in biological systems to break symmetries, form and manipulate patterns and shapes as well as react to and interact with their surroundings.
4. Elaborate different schemes of finding targets in space.
5. Explain the prerequisits, causes, mechanisms and effects on changes of gene pools and individual genes
6. Use the basic methods of literature retrieval, condense their knowlegde from scientific papers into a presentation and obtain presentation skills.

Familiarity with the basic concepts of statistical physics on bachelor level (PH0008) is required. 

This module consists of a lecture and a seminar

In the thematically structured lecture the theoretical contents are developed and discussed. Relevant experimental results from biology and biophysics are also presented. Building on that the theoretical models for their description are developed on the blackboard or using a slideshow together with the students. A dialogical structure of the lecture is emphasized to advance the analytic-physics intellectual power of the students and to encourage a critical scrutinization of the chosen approaches.

In the framework of the seminar students have the opportunity to learn under the supervision of a tutor how to retrieve scientific literature, critically read and extract the relevant information from research articles, and condense this information into a presentation understandable to a broad audience. They subsequently present their findings and recieve feedback on their presentation skills. 

Blackboard Presentations, Slide Shows, Online-Meetings, Scientific Literature

• "Biophysics: Searching for Principles" by William Bialek
• "Models of Life: Dynamics and Regulation in Biological Systems" by Kim Sneppen

There will be an oral exam of 45 minutes duration. Therein the achievement of the competencies given in section learning outcome is tested exemplarily at least to the given cognition level using comprehension questions and sample calculations.

For example an assignment in the exam might be:

• Explain how bacteria are able to control their movement to move up chemical concentration gradients.
• Discuss how a developing organism is able differentiate its cells differently at different spatial locations in a reliable manner.