Heterogeneity and multi-scale dynamics in the molecular bearing of the bacterial flagellum

# README # Heterogeneity and Multi-scale Dynamics in the Molecular Bearing of the Bacterial Flagellum Martin Rieu, Daping Xu, Gunasekaran Subramaniam, Ashley L. Nord, Alexis Courbet, Hafez El Sayyed, Richard M. Berry* **Corresponding author:** Prof. Richard M. Berry ([e-mail]) --- ## Repository Structure This repository is organised into two main folders: - `data/` Contains the raw and processed datasets used throughout the analysis pipeline and supplementary calibration/control experiments. - `source_data/` Contains the processed numerical data used to generate the plots presented in the manuscript and supplementary figures. --- ## Data Structure (`data/`) - `data/` - `main_motors/` - `raw/` Raw `.tdms` polarization recordings and companion `_cor.npy` correction files for motor experiments. These files are the starting point for `preprocessing_and_angle_extraction.py`. - `phi_unwrapped/` Extracted unwrapped azimuthal phase traces stored as `.npy`. These are the first processed orientation outputs from Fourkas extraction. - `step_filtered/` Step-detection results stored as `.npz`, containing filtered phase traces, `time_boundaries`, and `levels` generated by `step_detection.py`. In these `.npz` files: - step boundary indices are saved under the key `peaks` - detected level values are saved under the key `m` - `mapped_to_global_states/` Global state mapping outputs for selected datasets. `map_local_to_global_states.py` identifies KDE global states from `phi_unwrapped` and maps detected step levels to those global angular states. - `free_gold/` Freely rotating gold nanorod datasets used for Supplementary Figure S7. Includes: - raw `.tdms` files - `_cor.npy` correction files - selected extracted `.npy` traces - `fixed_rods/` Stuck-on-surface gold nanorod datasets used for Supplementary Figure S3. Includes: - raw `.tdms` files - `_cor.npy` correction files - `figure_1/` Data used to plot the small segment of raw polarization traces and projected angle shown in Figure 1d,e of the main manuscript. This dataset illustrates the analysis pipeline used for angle extraction. - `Calibration/` Data used for Supplementary Figure S5: *Calibration of recovered rod angle*. - `rod/` Data used in panels b (blue), c, and d. - `not_rod/` Control data used in panel b (grey) as a contrast. Both datasets contain short recordings and associated images acquired at each imposed slide rotation angle. - `Heating/` Data used for Supplementary Figure S6: *Estimation of possible laser heating*. - `fixed_power/` Long recordings acquired at fixed laser power values, used in panel a: > “Long traces of the azimuthal angle ϕ of a streptavidin gold nanorod (“rod 0”) non-specifically stuck to the coverglass” - `changing_power/` Recordings where the laser power was changed approximately every 40 s. These datasets are used in panels b–d to verify that the long-term effects observed in panel a do not significantly affect drag estimation, demonstrating that laser heating effects are minimal. --- ## Source Data (`source_data/`) This folder contains all processed numerical data used to generate the plots presented in the paper, including both the main figures and supplementary figures. All files are provided in either `.xlsx` or `.npz` format unless otherwise specified. - `.xlsx` files can be opened using spreadsheet software such as Microsoft Excel or LibreOffice Calc. - `.npz` files are NumPy compressed arrays and can be loaded in Python using the NumPy library: ```python import numpy as np data = np.load(filepath) ``` --- ## Supplementary Notes S8 The files associated with **Supplementary Notes S8** are National Instruments `.vi` files. These files can be opened using **LabVIEW version 2021 or later**.