Chapter 1 - Introduction
Administrative stuff
On biological machines
E.coli book-keeping
Molecular length- and time scales, forces, energies

dietz ph.tum.de

Chapter 2 - Life in bitumen
Fluid dynamics:
- Navier-Stokes Equation
- Flow through narrow channels
- The Reynolds Number
- The Low-Reynolds regime: Life in bitumen.

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

END OF PART I

dietz ph.tum.de

Part II - Motors, membranes, and biological design principles
Administrative stuff, syllabus, and course calendar
- contains instructions for how to prepare the seminar project

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

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

dietz ph.tum.de

Chapter 15 - How cytoskeletal filaments might form
Polymerization kinetics
- The equilibrium polymer
- Nucleated growth
- Treadmilling
- Dynamic instability
- Multi-stranded filaments
- Propulsion by polymerization

dietz ph.tum.de

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.

dietz ph.tum.de

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

dietz ph.tum.de