Teaching


Please refer to campus.tum.de for lectures & seminars that are taught currently by members of this laboratory. Below please find the lecture material for the course on mechanics and dynamics of biomacromolecules taught by HD within the biophysics master's program of TUM. 

Biophysics of the Cell I+II

This course should contain most of what you should know about the physical and chemical aspects of biological macromolecules (and their interactions) to carry out research in molecular and cellular biophysics. The author of the lecture files is H.Dietz, but some of the slides contain privileged material from other sources. The files are for your personal use only.


Chapter 1 - Introduction

Administrative stuff

On biological machines

E.coli book-keeping

Molecular length- and time scales, forces, energies

Download
lecture file
biocell_1_ws1415_hd_vo1.pdf
Adobe Acrobat Dokument 20.2 MB

Chapter 2 - Life in bitumen

Fluid dynamics:

- Navier-Stokes Equation

- Flow through narrow channels

- The Reynolds Number

- The Low-Reynolds regime: Life in bitumen.

 

Download
lecture file
biocell_1_ws1011_hd_vo2.pdf
Adobe Acrobat Dokument 3.0 MB

Chapter 3 - Life in a thermal hurricane

Basics of diffusion:

- The microscopic perspective

- Smoluchowski Equation / Diffusion Equation

- Transport with Fokker-Planck

- Einstein Relation

- Crowded Environments

- Diffusion as Transport Mechanism

 

Download
lecture file
biocell_1_ws1011_hd_vo3.pdf
Adobe Acrobat Dokument 4.0 MB

Chapter 4 - Interlude: Gene regulation

The regulation of lactose metabolism in E.coli. (descriptive)

- Regulated recruitment

- RNA polymerase, Lac repressor, CAP activator

- Protein-DNA recognition

- Detection of physiological signals

 

Download
lecture file
biocell_1_ws1011_hd_vo4.pdf
Adobe Acrobat Dokument 2.7 MB

Chapter 5 - Macromolecule meets macromolecule

Fundamental reaction speed limits:

- Free diffusion to capture

- Free diffusive release

- Diffusion to capture / release in potentials

- Reduction of dimensionality

- Kramers and Arrhenius

 

Download
lecture file
biocell_1_ws0910_hd_vo5.pdf
Adobe Acrobat Dokument 2.4 MB

Chapter 6 - Lost in transition

Rate equations and equilibrium aspects of:

- Irreversible Decay 

- Reversible two-state system

- Two-state systems under force: shifted equilibrium, accelerated rates

 

Interlude 2:

- Protein unfolding under force

- Case study: 3D Mechanics of Green Fluorescent Protein

 

Download
lecture file
biocell_1_ws0910_hd_vo6.pdf
Adobe Acrobat Dokument 6.8 MB

Chapter 7 - Let's stick together

Dynamics of bimolecular reactions:

- Steady-state characteristics, Gibbs Free Energy 

- Equilibration time scales 

- Concentration / Affinity jumps

- Cooperative binding: Molecular logic

- Response function of a repressed gene

- Response function of a gene controlled by an activator

 

Download
lecture file
biocell_1_ws0910_hd_vo7.pdf
Adobe Acrobat Dokument 2.9 MB

Chapter 8 - Enzyme kinetics

Dynamics of enzymatic catalysis:

- How enzymes can speed up chemical reactions

- Michaelis-Menten enzyme kinetics 

- Non-Michealis-Menten kinetics

- Enzyme activation 

- Energy available for work by substrate flux

- Examples: ATP Synthase, Kinesin

 

Download
lecture file
biocell_1_ws0910_hd_vo8.pdf
Adobe Acrobat Dokument 3.7 MB

Chapter 9 - Polymer elasticity and molecular random walks

Shape and mechanics of polymeric chains:

- The 1D random chain: end-to-end distance, entropic elasticity

- The freely-jointed chain model

- Bending mechanics of slender rods

- Persistence length as a measure for stiffness

- The worm-like chain

 

Download
lecture file
biocell_1_ws0910_hd_vo9.pdf
Adobe Acrobat Dokument 5.3 MB

Chapter 10 - Beams and polymers are everywhere!

A few examples on where bending and stretching matters:

- Beams in gene regulation: the case of the lac repressor and other suspects

- Beams in the cytoskeleton: Actin structure and mechanics, other filaments

- Fiber stretching and molecular unfolding in blood clotting

- Polymer elasticity as a molecular ruler for structure determination.

- A few afterwords

 

 

Download
lecture file
biocell_1_ws0910_hd_vo10.pdf
Adobe Acrobat Dokument 9.4 MB

Part II

Part II - Motors, membranes, and biological design principles

Administrative stuff, syllabus, and course calendar

- contains instructions for how to prepare the seminar project

 

 

Download
lecture file
biocell_2_ss10_hd_vo0.pdf
Adobe Acrobat Dokument 3.1 MB

Chapter X -Stochastic Chemical Kinetics

- Reminder probability theory

- Specifying a chemical system

- The specific probability rate constant

- Collisions with impact threshold

- The chemical master equation (CME)

- Solving the CME

- The Gillespie algorithm

 

Download
lecture file
biocell_2_ss13_hd_stochastic_kinetics.pd
Adobe Acrobat Dokument 11.2 MB

Chapter 11 - Translational molecular motors: an overview

A crash-course in molecular motor traffic:

- Types of motors

- Methods of experimental analysis

- Kinesin: structure, stepping behaviour etc

- Dynein: structure, stepping behaviour etc

- Myosin: structure, stepping behaviour etc

 

Download
lecture file
biocell_2_ss10_hd_vo11.pdf
Adobe Acrobat Dokument 10.2 MB

Chapter 12 - Molecular motors as random walkers

Understanding molecular motor behaviour:

- The one-state-model

- The one-state-motor under force

- Ratchet-shaped energy profiles

- Fluctuation analysis

- The two-state-model

 

Download
lecture file
biocell_2_ss10_hd_vo12.pdf
Adobe Acrobat Dokument 3.0 MB

Chapter 13 - ATP Hydrolysis as a source of energy

The molecular details of ATP hydrolysis

- ΔG when ATP is split into ADP and P

- Motors move along a ΔG gradient

- Motors move faster with higher [ATP]

- Structure of ATP and the hydrolysis reaction

- At least 8 distinct states are involved in motor stepping

- Case study: the complete ATP hydrolysis cycle of Myosin II

 

Download
lecture file
biocell_2_ss10_hd_vo13.pdf
Adobe Acrobat Dokument 3.4 MB

Chapter 14 - ATP Synthesis by ATP Synthase

ATP Synthase: a marvelous mechano-chemical factory

- Structure of ATP Synthase

- F1-Motor catalyzes ATP hydrolysis and synthesis

- Experimental evidence

- F1 ATPase hydrolysis cycle

- F0-Motor rotation mechanism

- Minimum delta pH for ATP synthesis

 

Download
lecture file
biocell_2_ss10_hd_vo14.pdf
Adobe Acrobat Dokument 5.6 MB

Chapter 15 - How cytoskeletal filaments might form

Polymerization kinetics

- The equilibrium polymer

- Nucleated growth

- Treadmilling

- Dynamic instability

- Multi-stranded filaments

- Propulsion by polymerization

 

Download
lecture file
biocell_2_ss11_hd_vo15.pdf
Adobe Acrobat Dokument 5.3 MB

Chapter 16 - Kinetic Proofreading & Robustness

The concept of proofreading in

- protein translation

- immuno recognition

The concept of robustness in 

- bacterial chemotaxis

And some notes on translocation ratchets.

 

Download
lecture file
biocell_2_ss11_hd_vo16.pdf
Adobe Acrobat Dokument 5.2 MB

Chapter 17 - Reaction and Diffusion.

More on reactions.

- beyond bimolecular reactions

- feedback, oscillations

 

Reminder on diffusion.

Reaction - Diffusion Equations

- typical structure

- spatial and temporal discretization

 

Download
lecture file
biocell_2_ss11_hd_vo17.pdf
Adobe Acrobat Dokument 2.1 MB