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Below please find information on classes and seminars. Refer to TUM Molecular and Cellular Biophysics for information on lectures / courses offered by other faculty members from experimental biophysics.

Winter 2010/2011

Biophysics in the Cell I + II - Lecture transcripts:

Note 1: Seminar series 'Biophysics of the Cell' part I: Calendar + Topics.
Note 2: Not all chapters currently come with a 'problems sheet'.

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.

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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

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Chapter 4
Chapter 4 -- No Problems

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

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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

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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

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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

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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

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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

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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


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

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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

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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

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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
- Motor 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

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Chapter 14 - Strange molecular transport mechanisms
Pushing and Pulling by
- translocation ratchets
- polymerization ratchets
- DNA polymerase as a polymerization ratchet

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Modern fluorescence methods
Introduction into fluorescence phenomena
- Atomic orbitals
- Electronic transitions and optical transitions
- Fluorophores and fluorophore spectra
- Solvent effects

Methods for detecting fluorescence
- Spectrophotometers
- Fluorescence microscopy
- Resolution and other aspects of optical microscopy

Optical microscopy beyond the diffraction limit:
- Fluorescence resonance energy transfer (FRET)
- FRAP and FCS

The physics of FRET redux
- Why and how does it work
- Some applications of FRET

Total internal reflection + Ellipsometry

thorsten.hugel ph.tum.de

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