SupportingDataset Identification and Quantification of Within-Burst Dynamics in Singly-Labeled Single-Molecule Fluorescence Lifetime Experiments

The Jupyter notebooks and resulting files used to demonstrate divisor-based mpH²MM. The analysis is demonstrated with both simulations and analyses of alpha-synuclein. <em><strong>Notebooks.zip</strong></em>:* Zip file containing the Jupyter notebooks for producing, analyzing and visualizing the simulated photon trajectories. Note: this folder contains all code needed to reproduce simulations. All other files related to the simulations are produced by one of the notebooks in this trajectory. However, as simulations can take a long time, the various results files are included in this repository so that notebooks can be run from intermediate steps. <strong>1-PIFE-pybromo-sims.ipynb</strong> : The code for producing simulated diffusion trajectories and photon-HDF5 files of two-state systems undergoing transition dynamics (the results of this notebook are stored in the sub-folder <em>PyBroMo_photonHDF5</em>) <strong>2-PIFE-mpH2MM-sim-[lifetime components].ipynb </strong>: Notebooks performing divisor-based mpH²MM on simulated datasets for a given combination of lifetime states. (these notebooks store files that are contained in the sub-folder <em>H2MMresults</em>) <strong>3-PIFE-mpH2MM-compiled-plots.ipynb</strong> : Jupyter notebook for producing figures comparing all results globally <strong>532nm_IRF_19-10-2021.csb</strong>: the file containing the experimental IRF used in the simulations <em><strong>PyBroMo_photonHDF5.zip</strong></em>:* Zip file containing the simulated results of <em>1-PIFE-pybromo-sims</em> notebook as photon-HDF5 files (1 file per transition rate/lifetime combination) <strong>PIFE-sim-dynamicmix_[lifetime components]_result.hdf5</strong>: special HDF5 files containing the results of each notebook in <em>Notebooks</em>, which are used by <em>3-PIFE-mpH2MM-compiled-plots</em> <strong>PIFE-mpH2MM-alpha-syn-vFinal.ipynb</strong>: divisor-based mpH²MM analysis of alpha-synuclein smPIFE data <strong>H2MM-Lifetime_example.ipynb</strong>: A demonstration of divisor-based mpH²MM using nsALEX-smFRET data. This method could potentially demonstrate states differentiated in lifetimes independently of potential changes in E &amp; S. <strong>Template_ltH2MM.ipynb</strong>: An easy-to-follow implementation of divisor-based mpH²MM demonstrated on a single alpha-synuclein experimental data acquisition file. This can be used for learning how to implement and analyze single dye fluorescence lifetime data with mpH²MM * For running these notebooks, generally, all files in <em>PyBroMo_photonHDF5.zip</em> should be placed into a single directory (i.e., the files in <em>Notebooks</em>.<em>zip</em> should be placed into the same directory as the files in <em>PyBroMo_photonHDF5</em>.<em>zip</em>) as the notebooks are set to read in files from their current directory.