View source for Theory of incompatible substructure problem

== Schedule ==
*   19th December,  2014 : Submit final draft of incompatible substructure paper to Marco
*  30th November, 2014  : Finish results, create plots

== Todo ==

== Parameters ==
* Components
** Radius of each component: 25 mm
** Thickness of each component: '''8 mm'''
** Radius of magnet: 1.5 mm
** Strength of magnet: N48
** Polyamide

* Container
** Radius of container: 125 mm
** Depth of container: 9 mm
** Material: Acrylic

* Shaker
** Mode: Orbital shaking
** Speed: 300 rpm
** Duration for shaking: until stable structures are formed

== Variable(s) ==
* Number of components used in each experiment

== Experiments ==
* Simulated experiments
** Probability of the formation of 1, 2, 3, 4 and 5 targets for increasing number of components
* Physical experiments
** Probability of the formation of 1, 2, 3, 4 and 5 targets for increasing number of components

=== Particulars of simulation experiments (10000 trials each) ===
* Probability of the formation of 1 target structure in experiments with increasing number of components from 8 - 40
* Probability of the formation of 2 target structure in experiments with increasing number of components from 16 - 40
* Probability of the formation of 3 target structure in experiments with increasing number of components from 24 - 40
* Probability of the formation of 4 target structure in experiments with increasing number of components from 32 - 40
* Probability of the formation of 5 target structure in experiments with 40 components

=== Particulars of physical experiments (10 trials each) ===
* Photos of initial condition and final condition
* Assembly of one target structure
** Data to be collected: number of targets and number of incompatible substructures, time for steady state
* Assembly of two target structures
** Data to be collected: number of targets and number of incompatible substructures, time for steady state
* Assembly of three target structures
** Data to be collected: number of targets and number of incompatible substructures, time for steady state
* Assembly of four target structures 
** Data to be collected: number of targets and number of incompatible substructures, time for steady state
* Assembly of five target structures 
** Data to be collected: number of targets and number of incompatible substructures, time for steady state

* Results to show
** The simulated probability of the formation of 1, 2, 3, 4 and 5 target structures in self-assembly experiments
** Comparison of simulated probability vs. probability achieved in physical experiments
** Reasons for similarities and/or differences between simulated probability vs. probability of physical experiments

== Meeting points ==
In the case of the experiment where 24 components are used, if 2 target structures are formed (16 components consumed), then the third target structure will always form. This means that if the experiment is continued till the system reaches a steady state, then in the experiemnt with 24 components, there will never be a case where 2 target structures are formed. '''Doesn't this skew the probability graph? Also, how would this be reflected in the analysis? ''' . Obviously, this applies to the cases of 2, 4 and 5 target structures as well.