Nonequilibrium associative retrieval of multiple stored self-assembly targets - Simulation Engine

Nonequilibrium associative retrieval of multiple stored self-assembly targets - Simulation Engine
This Git channel contains the nonequilibrium self-assembly research conducted in the Bisker Lab, Tel-Aviv University
This work contains contributions by Michael Faran (PhD student) and Ohad Nir & Noam Raviv- graduate students.

Click here for the canonical article, which contains the simulation details.

At the moment there is a short description of each MATLAB and Python file use in the "CodeExplanation.docx" file.

Name		Name	Last commit message	Last commit date
Beast		Beast
Key Figures		Key Figures
Sankey/Sankey		Sankey/Sankey
fullscreen		fullscreen
github_repo		github_repo
knee_pt		knee_pt
mArrow3		mArrow3
mi		mi
partitions		partitions
rp-master/rp-master		rp-master/rp-master
slprj/sim/varcache/TF_SISO_orig_test/tmwinternal		slprj/sim/varcache/TF_SISO_orig_test/tmwinternal
.gitignore		.gitignore
AddLetters2Plots.m		AddLetters2Plots.m
BubblePlot.m		BubblePlot.m
CallBubblePlot.m		CallBubblePlot.m
CodeExplanation.docx		CodeExplanation.docx
Collection_Tfas_DATA.m		Collection_Tfas_DATA.m
Fisher_resid_bu.m		Fisher_resid_bu.m
FitEXPDecaytoData.m		FitEXPDecaytoData.m
Gather_Tfas_DATA_Many_Drives.m		Gather_Tfas_DATA_Many_Drives.m
Gather_Tfas_DATA_Single_Drive.m		Gather_Tfas_DATA_Single_Drive.m
GetFullPath.m		GetFullPath.m
Initial_Seed_Start_Results.m		Initial_Seed_Start_Results.m
InstallMex.m		InstallMex.m
LogTFasDraftEstimation_LOGTriangulationUP_Many_DrivesWith2D.m		LogTFasDraftEstimation_LOGTriangulationUP_Many_DrivesWith2D.m
Mat2Py.py		Mat2Py.py
MovieMakerCall.m		MovieMakerCall.m
MovieMakerCallUP.m		MovieMakerCallUP.m
PeakDetector.m		PeakDetector.m
PlotAllMovieUPDATED.m		PlotAllMovieUPDATED.m
PlotFigure2a_Left_Side_GiliOriginalPaper.m		PlotFigure2a_Left_Side_GiliOriginalPaper.m
PlotFigure2a_Right_Side_GiliOriginalPaper.m		PlotFigure2a_Right_Side_GiliOriginalPaper.m
Plot_All_SImulation_Macro_Parameters_Figures.m		Plot_All_SImulation_Macro_Parameters_Figures.m
Plot_Histograms_KLD.m		Plot_Histograms_KLD.m
Plot_Histograms_KLD_mu_sigma.m		Plot_Histograms_KLD_mu_sigma.m
PlottingBEASTEnergyTrajectories.m		PlottingBEASTEnergyTrajectories.m
Plotting_Tracjectories_Ensemble_No_BEAST.m		Plotting_Tracjectories_Ensemble_No_BEAST.m
README.md		README.md
ReadResultsFromFoldersJfunction__tfas_results_Js.m		ReadResultsFromFoldersJfunction__tfas_results_Js.m
ReadResultsFromFoldersJfunction__tfas_results_mu.m		ReadResultsFromFoldersJfunction__tfas_results_mu.m
RecurruenceRateETC.m		RecurruenceRateETC.m
Resize_figure_for_full_screen_attempt.m		Resize_figure_for_full_screen_attempt.m
SeedJson.py		SeedJson.py
Smoothing_Using_Mutual_Information.m		Smoothing_Using_Mutual_Information.m
TF_SISO_orig_test.mdl		TF_SISO_orig_test.mdl
TF_SISO_orig_test.slxc		TF_SISO_orig_test.slxc
TFasDraftEstimation_LOGTriangulationUP_Many_DrivesWith2D.m		TFasDraftEstimation_LOGTriangulationUP_Many_DrivesWith2D.m
TFasDraftEstimation_LOGTriangulation_Many_DrivesWith2D_simple_figures.m		TFasDraftEstimation_LOGTriangulation_Many_DrivesWith2D_simple_figures.m
TdraftEstimation_add_on_Weighted_Euclidian_Matrix.m		TdraftEstimation_add_on_Weighted_Euclidian_Matrix.m
Tfas_Distrubtion_Drives_Margi_UPDATED.m		Tfas_Distrubtion_Drives_Margi_UPDATED.m
The_one_choosen_trajectory.asv		The_one_choosen_trajectory.asv
The_one_choosen_trajectory.m		The_one_choosen_trajectory.m
Time_Lag_Visual_Recuurence_Plot.m		Time_Lag_Visual_Recuurence_Plot.m
TrajectoryPlot.m		TrajectoryPlot.m
TrajectoryPlotVecs.m		TrajectoryPlotVecs.m
TrajectoryPlotVecs4TfasMap.m		TrajectoryPlotVecs4TfasMap.m
board.py		board.py
buseg.m		buseg.m
centerOfMass.m		centerOfMass.m
cfg.json		cfg.json
entropy.py		entropy.py
exceptions.py		exceptions.py
fnn_deneme.m		fnn_deneme.m
fnn_deneme_call.m		fnn_deneme_call.m
fullscreen.m		fullscreen.m
give_vecs.m		give_vecs.m
mArrow3.m		mArrow3.m
main.py		main.py
mat2np.m		mat2np.m
particle.py		particle.py
partitions.m		partitions.m
partitions_demo.m		partitions_demo.m
scriptToExc		scriptToExc
seed.json		seed.json
shade.m		shade.m
simulation_cfg.py		simulation_cfg.py
stdshade.m		stdshade.m
take_change_points.m		take_change_points.m
take_change_points_option2.m		take_change_points_option2.m
target.py		target.py
turn_callbacks.py		turn_callbacks.py
uTest_GetFullPath.m		uTest_GetFullPath.m
utils.py		utils.py

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