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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| − | * 22nd November, 2014 : Finish first draft of Conformational Switching paper |
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| − | * 8th November, 2014 : Finalise results, create plots |
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| − | * 1st November, 2014 : Finalise plan for experiments and collect preliminary data |
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== Todo == |
== Todo == |
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| + | * Finalise pendulum design |
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| − | * Outline by 8th November |
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| + | * Run experiments |
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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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| − | * Setting of the speed for experiments |
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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. |
** 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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| − | * Test to verify role of seed |
+ | * Test to verify role of seed: |
** Passive components, no seed |
** Passive components, no seed |
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** Passive components, AND seed |
** Passive components, AND seed |
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=== Particulars of experiments (10 trials each) === |
=== Particulars of experiments (10 trials each) === |
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| ⚫ | |||
| ⚫ | |||
| + | * Self-assembly experiment at different speeds: |
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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 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) |
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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 |
** All components are seeds |
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** Passive components, no seed |
** Passive components, no 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) |
* 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 |
** All components are seeds |
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** Passive components, no seed |
** Passive components, no seed |
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** Passive components, AND seed |
** Passive components, AND seed |
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| − | |||
| ⚫ | |||
* Results to show |
* Results to show |
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** Experiments for setting parameter (shaking speed) |
** Experiments for setting parameter (shaking speed) |
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** Time evolution of self-assembly |
** Time evolution of self-assembly |
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| − | ** |
+ | ** Conformational switching eliminates incompatible structures |
** Scaling |
** Scaling |
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** Removing the acceleration rump-up phase |
** 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 == |
== Meeting minutes == |
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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.
