1. Filaments in the cycloskeleton; Major types:
   • Actin filaments
     • Structure
     • Treadmilling and driving mechanism, and regulation
   • Intermediate filaments
   • Microtubules
2. Microtubule structure:
• Tubulin subunits
• Protofilaments, nucleation and growth
• Polarity
3. Dynamic Instability [Mitchison & Kirchner, Nature 312, 237 (1984)]
• Model of growth and regulation (Leibler, et al)   [JCB 118, 1097 (1992)] [PRL70, 1347 (1993).]
• Model of catastrophes [H. Flyvbjerg, TE Holy, & S. Leibler, PRL73, 2372 (1994).]
4. Search strategy
   • Mitosis (animation)
   • Condensation of RecA on ssDNA as a tool for computation by stochastic assembly
   • Kinetic proof-reading
5. Self-organization of microtubules and motors in vitro

1. Molecular motors:
   • Kinesin and Dynein move in opposite directions along microtubules consuming ATP
   • Myosin moves on actin filaments
   • Animation of motion of kinesin on a microtubule (offline)
2. General scheme of motor transport:
• Asymmetry for directionality
• Rectification of fluctuations by consumption of energy
3. Motion in a noisy environment

• Feynman's ratchet and pawl:                       
• Simulation of a Brownian motor
• From the web-page of George Oster:
  • "Ratchets, power strokes, and molecular motors," H. Wang & G. Oster, Appl. Phys. A 75, 315 (2002).
  • "The physics of molecular motors," C. Bustamante, D. Keller, & G. Oster, Acc. Chem. Res. 34, 412, (2001),
  • Animation of energy landscape for a rotary motor
4. Asymmetric hopping models:
• "The force exerted by a molecular motor," M.E. Fisher & A.B. Kolomeisky, PNAS 96, 6597 (1999).
• Multiple internal states
• Solution with two internal state
• Einstein force, stalling force

1. Brownian motion: (offline)
   • Movies of  milk droplets in water, beads in water & DNA, DNA tethered bead, bead capture
   • Animated simulation (see also Applet#2, Applet#3)
   • Langevin description
   • Fokker-Planck descrition
   • Thermal equilibrium and the Einsten relation
   • Lecture notes on Dissipative Dynamics
2. Crawling cells
   • Remodelling of actin cycloskeleton
   • Crawling Neutrophil Chasing a Bacterium
   • Actin-based motility (Listeria)
   • More from the Theriot lab movie collection
   • Latex beads coated with ActA protein: motion and spontaneous symmetry breaking
3. Swimming cells:
• Life at Low Reynolds Number (E.M. Purcell)
• The scallop theorem: impossibility of reciprocal motion
• Flagellar rotary motion (efficiency)
• Chemotaxis by runs and tumbles- why?

[Lecture Notes]

[Exercises]

Related links

• Microtubule links
• Nonosimulations of the cytoskeleton (a PhD thesis by Christopher Betts)
• Steve Berg's animations
• Kinesin Home Page
• Dynein Home Page
• Myosin Home Page
• Kinesin Motors - the Movies
• Vale lab movies (e.g. MT gliding)
• The inner life of a cell
• Lecture at Delft by Gerrit E.W. Bauer
• Capturing and viewing single molecules:
  • Optical tweezers
  • Fluorescent light microscopy