Conformational Switching

Schedule

• 1st December, 2014 : Submit final draft of Conformational Switching paper to Marco
• 22nd November, 2014 : Finish first draft of Conformational Switching paper
• 8th November, 2014 : Finalise results, create plots
• 1st November, 2014 : Finalise plan for experiments and collect preliminary data

Todo

• Outline by 8th November
• Mount existing container on shaker

Experiments

• Self-assembly experiment at different speeds:
  • Result: self-assembly time distribution for each speed; use in experiments speed with lowest average time to completion + 2 std. dev.
• Test to verify role of seed:
  • Passive components, no seed
  • Passive components, AND seed

Particulars of experiments (10 trials each)

• Video recording of experiments, probably one frame every second (1 fps).
• Self-assembly experiment at different speeds:
  • Run each experiment till self-assembly of one target structure
    • All components are seeds
    • Passive components, no seed
    • Passive components, AND seed
  • Use different speeds starting from lowest speed (= when components start to move) and increment speed by 25 rpm till target structure breaks.

• Assembly of one target structure (Data to be collected: number of individual components, number of compatible substructures, number of incompatible substructures, number of targets)
  • The results of the experiment where all the components are seeds and the experiment where there are passive components and a seed should have the same yield
  • All components are seeds
  • Passive components, no seed
  • Passive components, AND seed

• Assembly of two target structures (Data to be collected: number of individual components, number of compatible substructures, number of incompatible substructures, number of targets)
  • When there are components (only seeds) enough to make more than one target structure, the incompatible substructure problem is observed
  • All components are seeds
  • Passive components, no seed
  • Passive components, AND seed

• Results to show
  • Experiments for setting parameter (shaking speed)
  • Time evolution of self-assembly
  • Conformational switching eliminates incompatible structures
  • Scaling
  • Removing the acceleration rump-up phase
  • Plot of Gibbs free energy
    • Gibbs free energy related to the number of available bonding sites.

Meeting minutes

Meeeting 1 whiteboard capture

Meeeting 2 whiteboard capture