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Essential Concepts in Theoretical Biophysics

Module PH2306

This module handbook serves to describe contents, learning outcome, methods and examination type as well as linking to current dates for courses and module examination in the respective sections.

Basic Information

PH2306 is a semester module in language at Master’s level which is offered irregularly.

This Module is included in the following catalogues within the study programs in physics.

  • Specific catalogue of special courses for Biophysics
  • Complementary catalogue of special courses for condensed matter physics
  • Complementary catalogue of special courses for nuclear, particle, and astrophysics
  • Complementary catalogue of special courses for Applied and Engineering Physics

If not stated otherwise for export to a non-physics program the student workload is given in the following table.

Total workloadContact hoursCredits (ECTS)
150 h  h 5 CP

Responsible coordinator of the module PH2306 is Ulrich Gerland.

Content, Learning Outcome and Preconditions

Content

• 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

Learning Outcome

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.

Preconditions

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

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

Learning and Teaching Methods

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. 

Media

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

Literature

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

Module Exam

Description of exams and course work

There will be an oral exam of 25 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.

Exam Repetition

The exam may be repeated at the end of the semester.

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