Difference between revisions of "Conformational Switching"
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== Schedule == |
== Schedule == |
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| + | * TBD |
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| − | * 1st December, 2014 : Submit final draft of Conformational Switching paper to Marco |
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| − | * 1st November, 2014 : Finalise results and finish first draft of Conformational Switching paper |
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| − | * 15th October, 2014 : Finalise experiments |
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| − | * 1st October, 2014 : Finalise conformational switching component design |
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| − | * 18th September, 2014 : Return from PPSN |
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== Todo == |
== Todo == |
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| + | * Finalise pendulum design |
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| − | * Outline by 6th September |
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| + | * Run experiments |
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| − | * Send container designs |
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| − | * Run trials |
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| − | * Mount existing container on shaker |
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== Experiments == |
== Experiments == |
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| + | * Self-assembly experiment at different speeds: |
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| − | * Test to verify role of seed |
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| + | ** Result: self-assembly time distribution for each speed; use in experiments speed with lowest average time to completion + 2 std. dev. |
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| − | ** Components with seed |
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| − | + | * Test to verify role of seed: |
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| + | ** Passive components, no seed |
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| − | * Assembly of one target structure |
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| + | ** Passive components, AND seed |
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| ⚫ | |||
| − | ** Simple |
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| − | * Assembly of multiple target structures |
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| − | ** Conformational switching |
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| − | ** Simple |
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| + | === Particulars of experiments (10 trials each) === |
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| + | * Video recording of experiments, probably one frame every second (1 fps). |
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| + | * Self-assembly experiment at different speeds: |
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| + | ** Run each experiment till self-assembly of one target structure |
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| + | *** All components are seeds |
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| + | *** Passive components, no seed |
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| + | *** Passive components, AND seed |
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| + | ** Use different speeds starting from lowest speed (= when components start to move) and increment speed by 25 rpm till target structure breaks. |
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| + | |||
| + | * Assembly of one target structure (Data to be collected: number of individual components, number of compatible substructures, number of incompatible substructures, number of targets) |
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| + | ** 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'' |
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| + | ** All components are seeds |
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| + | ** Passive components, no seed |
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| + | ** Passive components, AND seed |
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| + | |||
| + | * Assembly of two target structures (Data to be collected: number of individual components, number of compatible substructures, number of incompatible substructures, number of targets) |
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| + | ** When there are components (only seeds) enough to make more than one target structure, the incompatible substructure problem is observed |
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| + | ** All components are seeds |
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| + | ** Passive components, no seed |
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| + | ** Passive components, AND seed |
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| + | |||
| + | * Results to show |
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| + | ** Experiments for setting parameter (shaking speed) |
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| + | ** Time evolution of self-assembly |
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| ⚫ | |||
| + | ** Scaling |
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| + | ** Removing the acceleration rump-up phase |
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| + | ** Plot of Gibbs free energy |
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| + | *** Gibbs free energy related to the number of available bonding sites. |
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| + | |||
| + | == Meeting minutes == |
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[[File:Meeting1.jpg|250px|thumb|left|Meeeting 1 whiteboard capture]] |
[[File:Meeting1.jpg|250px|thumb|left|Meeeting 1 whiteboard capture]] |
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[[File:Meeting2.jpg|250px|thumb|left|Meeeting 2 whiteboard capture]] |
[[File:Meeting2.jpg|250px|thumb|left|Meeeting 2 whiteboard capture]] |
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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.
- Run each experiment till self-assembly of one target structure
- 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.
