Difference between revisions of "Conformational Switching"

From IridiaWiki
Jump to navigationJump to search
 
(12 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
== Schedule ==
 
== Schedule ==
  +
* TBD
* 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 ==
 
== Todo ==
  +
* Finalise pendulum design
* Outline by 8th November
 
  +
* Run experiments
* Mount existing container on shaker
 
   
 
== Experiments ==
 
== Experiments ==
  +
* Self-assembly experiment at different speeds:
* Speed test
 
  +
** Result: self-assembly time distribution for each speed; use in experiments speed with lowest average time to completion + 2 std. dev.
* Time test
 
* Test to verify role of seed
+
* Test to verify role of seed:
 
** Passive components, no seed
 
** Passive components, no seed
 
** Passive components, AND seed
 
** Passive components, AND seed
   
== Particulars of experiments (10 trials each) ==
+
=== 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)
 
* 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''
** Simple
 
  +
** All components are seeds
 
** Passive components, no seed
 
** Passive components, no seed
 
** Passive components, AND 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)
 
* 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
** Simple
 
  +
** All components are seeds
 
** Passive components, no seed
 
** Passive components, no seed
 
** Passive components, AND 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 ==
 
== Meeting minutes ==

Latest revision as of 15:36, 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