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Theoretical Biophysics

Module PH2017

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.

Module version of WS 2021/2 (current)

There are historic module descriptions of this module. A module description is valid until replaced by a newer one.

Whether the module’s courses are offered during a specific semester is listed in the section Courses, Learning and Teaching Methods and Literature below.

available module versions
WS 2021/2WS 2010/1

Basic Information

PH2017 is a semester module in English or German language at Master’s level which is offered in winter semester.

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 60 h 5 CP

Responsible coordinator of the module PH2017 is Martin Zacharias.

Content, Learning Outcome and Preconditions

Content

  • Structure and function of biomolecules, Structure determination
  • How to determine a biomolecule structure by X-ray crystallography
  • How to obtain a protein structure by NMR spectroscopy
  • Principles of structure determination by CryoEM
  • Theory of macromolecular chain models, Folding and unfolding of biomolecules
  • Inter- and intramolecular interactions that drive folding and association
  • Solvation of biomolecules
  • Electrostatic interactions
  • Protonation of biomolecules
  • Hydrophobic effect
  • Thermodynamics of structural transitions and folding
  • Conformational dynamic
  • Energy landscape models of folding
  • Theoretical methods to predict protein and nucleic acid structures
  • Computersimulation of structure formation
  • Methods of secondary structure prediction
  • Tertiary structure predictions of proteins
  • RNA/DNA secondary and tertiary structure calculation
  • Theory of biomolecular binding and association
  • Theory of methods to obtain binding affinities and kinetics of binding
  • How to calculate and predict binding affinities
  • Prediction of Biomolecular complexes and protein-ligand binding
  • Molecular Dynamics simulation of biomolecular binding
  • Binding prediction by Docking methods
  • Prediction using machine learning approaches
  • Calculation of binding kinetics

Learning Outcome

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

  1. Understand the most important structure determination methods and when to use it.
  2. Have a fundamental understanding of the various inter- and intramolecular forces that drive structure formation of biomolecules.
  3. Know the concepts to describe conformational states of biomolecules and conformational transitions.
  4. Understand the most important methods for structure prediction.
  5. The student is able to apply theoretical concepts to analyse the thermodynamics and kinetics of biomolecular association.

Preconditions

Some knowledge of biomolecules can be helpful but is not necessary. No prerequisites beyond the qualification for master level studies in physics are required.

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

TypeSWSTitleLecturer(s)DatesLinks
VO 2 Theoretical Biophysics Zacharias, M. Fri, 10:00–12:00, PH HS2
UE 2 Exercise to Theoretical Biophysics
Responsible/Coordination: Zacharias, M.

Learning and Teaching Methods

Lecture: In the thematically structured lecture the learning content is presented. Both beamer presentations as well as writing on the board will be used. The close connection of the learning content with topics in physics from electrodynamics/statics, quantum mechanics and statistical mechanics will be demonstrated. Example applications and example calculations will deepen the learning content. In scientific discussions the students are involved to stimulate their analytic-physics intellectual power. In the exercise the learning content will be deepened and extended by student presentations such that the students are able to explain and apply the learned physics and explain results independently. This includes literature study of manuscripts that directly relate to the lecture and example excercises that relate to the lecture.

Media

writing on board

PowerPoint presentation

practise sheets

scientific publications related to the lecture content

Literature

  • Michel Daune, Molekulare Biophysik, Vieweg Verlag
  • Jacob Israelachvelli, Intermolecular and surface forces, Academic Press
  • Charles Cantor and Paul Schimmel, Biophysical Chemistry, part II, Freeman Press
  • Erich Sackmann, Rudolf Merkel, Lehrbuch der Biophysik, Wiley, VCH

Module Exam

Description of exams and course work

There will be an oral exam of 30 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:

  • How can one solve the phase problem in X-ray crystallography of proteins
  • Why is the diffusion of an ion through a membrane so slow?

In the exam no learning aids are permitted.

Participation in the exercise classes is strongly recommended since the exercises prepare for the problems of the exam and rehearse the specific competencies.

Exam Repetition

The exam may be repeated at the end of the semester. There is a possibility to take the exam in the following semester.

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