1. Amphiphiles Copyright Stuart Lindsay 2008 Hydrophobic tail Polar head Phospholipid

2. Self-assembled amphiphilic structures Copyright Stuart Lindsay 2008 (From Molecular Cell Biology, 4 th ed. By H. Lodish, A. Berk, S.L. Zipursky, P. Matsudara, D. Baltimore, J. Darnell. © 2000, W.H. Freeman and Company. Used with permission)

3. MD Simulation of vesicle formation Copyright Stuart Lindsay 2008 (Reprinted with permission from Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail, A.H de Vries et al., A.E. Mark, and S.J. Marrink, J. Am. Chem. Soc. 2004 126: 4488. Published 2006 by American Chemical Society)

4. Association Kinetics Single-step aggregation To dissociate into N monomers divide aggregate concentration by N to get monomer equivalent In equilibrium the two rates are equal so the equilibrium constant is Association rateDissociation rate

6. Critical Micelle Concentration In units of mole fraction the total mole fraction of solute is: The maximum value of C-X 1 is unity Above this critical micelle concentration all added monomer is turned into aggregates Copyright Stuart Lindsay 2008

7. Chemical potential must be lower in aggregate! For: with X 1 <1Monomers predominte!

8. Size-dependent chemical potential The chemical potential depends on the size of the aggregate: Chemical potential for an infinite N aggregate Bond energy (in KT units) p p : dimensionality and shape of the aggregate

9. For a spherical aggregate: γ = interfacial energy And so:

10. Critical Micelle Concentration Revisited Since X N can never exceed 1, X 1 cannot exceed exp( -  ) and: for a spherical aggregate For a water/methane interface: γ ≈50mJ·m -2, r≈0.2 nm, T=300K α ≈ 6

11. Packing effects depend on geometry a0a0 l c is the length of the hydrocarbon chain  is the volume occupied by the hydrocarbon chain A 0 is the area of the head group Shape of aggregates

12. Spherical micelles Non-spherical micelles Vesicles or bilayers ‘Inverted cones’ A dimensionless shape factor Short hydrocarbon chains Long or double hydrocarbon chains

13. Lipid bilayer structure – the mitochondrian Pyruvate oxidation – 30 ATPs vs 2 Copyright Stuart Lindsay 2008 (EM image is reproduced with permission from Chapter 4 of The genetic basis of human disease by G. Wallis published by the Biochemical Society 1999. Copyrighted by the Biochemical Society. http://www.biochemj.org.)

14. Self-assembled monolayers Copyright Stuart Lindsay 2008

15. Chemisorption of long-chain amphiphilic molecules (both hydrophobic and hydrophilic functionalities) at surfaces. → creation of long-range order active head group for chemisorption activated surfaces Self-assembled monolayers

16. long-chain alkanethiolates (SH end group)

17. STM image of a dodecanthiol SAM on Au(111) (40nm·40nm)

18. I step: attachment of the sulfur atom to the gold surface driving force: Au-S interaction (≈40 kcal·mol -1 ) X(CH 2 ) n SH + Au 0 → X(CH 2 ) n S - + Au + + ½H 2 Sulfur atoms for long.chain alkanethiolates (n>11) formed a hexagonally packed arrangement on the Au(111) surface.

19. Kinetic studies on SAM formation show that the adsorption process is consistent with a first-order Langmuir isotherm: the growth rate is proportional to the number of unoccupied gold sites.

20. The methylene groups tilt at an angle of 30° degrees from the surface normal to maximize the favorable Van der Waals interactions between adjacent chains. Bulky or polar groups terminating the alkyl chain may reduce the packing density and overall order of the SAM. Long-lasting self-healing dynamics II step: lateral organization of the alkyl chains to form a densely packed monolayer. driving force: Van der Waals lateral interactions

21. A series of STM images of a single octanedithiol molecule inserted into an octanethiol monolayer. Sulfur with the gold atom attached to it moves over the surface in almost liquid-like manner. The consequence of the mobility of the sulfur-gold bond is a substantial restructuring of the gold surface resulting in the formatiion of pits on the surface that are one gold atom in depth.

22. Nanoparticles kinetically trapped CdSe quantum dots from two phase synthesis with Ostwald ripening (diameter: 8 nm) Si nanowires from Au/Si eutectic seeded on Au NP

23. Copyright Stuart Lindsay 2008 Helix repeat: 3.4 nm

24. DNA Nanotechnology Copyright Stuart Lindsay 2008 About 8 bases must be paired for a double helix to be stable at room Temperature.

25. Copyright Stuart Lindsay 2008 A DNA-based four-way crossover structures producing a rigid planar tile. The distance between adjacent tile is 20nm. The structure, imaged by AFM, is produced by spontaneous self- assembly of the individual crosses.

26. DNA Origami Copyright Stuart Lindsay 2008 A long template strand is annealed with a numebr of short strands that either form cross-links at fixed points (loops) or fill regions to form double helices.