Difference between revisions of "Conformational Switching"

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== Schedule ==
  
== Schedule ==
  +
* TBD
−
* 1st December, 2014 : Submit final draft of Conformational Switching paper to Marco
  
  +
−
* 1st November, 2014 : Finalise results and finish first draft of Conformational Switching paper
  
  +
== Todo ==
−
* 15th October, 2014 : Finalise experiments
  
−
* 1st October, 2014 : Finalise conformational switching component design
 +
* Finalise pendulum design
  +
* Run experiments
−
* 18th September, 2014 : Return from PPSN
  
   
 
== Experiments ==
  
== Experiments ==
  +
* Self-assembly experiment at different speeds:
−
* Test to verify role of seed
  
  +
** Result: self-assembly time distribution for each speed; use in experiments speed with lowest average time to completion + 2 std. dev.
−
** Components with seed
  
−
** Components without seed
 +
* Test to verify role of seed:
  +
** Passive components, no seed
−
* Assembly of one target structure
  
  +
** Passive components, AND seed
⚫
** Conformational switching
  
  +
−
** Simple
  
  +
=== Particulars of experiments (10 trials each) ===
−
* Assembly of multiple target structures
  
  +
* Video recording of experiments, probably one frame every second (1 fps).
−
** Conformational switching
  
  +
* Self-assembly experiment at different speeds:
−
** Simple
  
  +
** 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 ==
 
[[File:Meeting1.jpg|250px|thumb|left|Meeeting 1 whiteboard capture]]
  
[[File:Meeting1.jpg|250px|thumb|left|Meeeting 1 whiteboard capture]]
 
[[File:Meeting2.jpg|250px|thumb|left|Meeeting 2 whiteboard capture]]
  
[[File:Meeting2.jpg|250px|thumb|left|Meeeting 2 whiteboard capture]]

Latest revision as of 16:36, 20 April 2016

Schedule

  • TBD

Todo

  • Finalise pendulum design
  • Run experiments

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
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