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######### Directory structure ##########
########################################

1. ./LengthAndAngleRuns			- Contains all the simulation data of the FFEA simulations used to parameterise the axonemal dynein 
					  model based on experimental observations

   ./LengthAndAngleRuns/ADPVI		- Contains all of the simulation input files for the ADPVI model
   ./LengthAndAngleRuns/APO		- Contains all of the simulation input files for the APO model


2. ./AxonemeExploration			- Contains all the simulation data of the FFEA simulations used to predict the crowded diffusional 
					  behaviour of the axonemal dynein model when confined in the axonemal structure

   ./AxonemeExploration/Interaction0	- Contains all of the simulation input files for models with zero interaction with the axoneme
   ./AxonemeExploration/Interaction1e14	- Contains all of the simulation input files for models with a weak interaction with the axoneme
   ./AxonemeExploration/Interaction1e15	- Contains all of the simulation input files for models with a strong interaction with the axoneme

3. ./ChemomechanicalSwitching		- Contains all the simulation data of the FFEA simulations used to mimic the chemo-mechanical cycle  
					  of the axonemal dynein model when confined in the axonemal structure

   ./ChemomechanicalSwitching/scripts	- Contains the FFEA input scripts for the axonemal dynein chemomechanical cycle model
   ./ChemomechanicalSwitching/axoneme	- Contains the FFEA structure and kinetics files for the axonemal dynein chemomechanical cycle model




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### Simulation and Analysis Protocol ###
########################################

Dependencies:

	Dependencies for entire simulation suite

	Cmake
	g++
	FFEA (https://bitbucket.org/FFEA/ffea/branches/, axoneme_switch branch)
		Eigen (3.3.7)
		Boost (1.69)


###### Length and Angle Fluctuations ######

1. Run FFEA simulation sweep

	# This is a bash script method. If uncomfortable, you can run them manually

	cd ./LengthAndAngleRuns
	./build_and_run.sh


###### Axonemal exploration ######

1. Run the FFEA simulation for each model system (run multiple copies for statistics)

	cd ./AxonemeExploration/Interaction0
	ffea ADPVI_axoneme.ffea

	cd ./AxonemeExploration/Interaction1e14
	ffea ADPVI_axoneme.ffea

	cd ./AxonemeExploration/Interaction1e15
	ffea ADPVI_axoneme.ffea

###### Chemo-kinetic cycle ######

1. Run the FFEA simulation for the model (rates can be altered in the .ffea script if required)

	cd ./ChemomechanicalSwitching/scripts
	ffea chemo_axoneme_switching.ffea