Active Bacterial Bath in Droplets

Data Structure and Organization

Main Data File: Active_bacDrop_variables.mat All experimental data is stored in MATLAB cell arrays with systematic naming conventions:

Experimental Conditions:  Double Emulsion (DE): cells_per_mL_DE, variance, ro, ri, tau_bath, vbath, etc.

2D Particle Tracking: Variables suffixed with _part (e.g., cells_per_mL_part, variance_part, ro_part, ri_part)

3D Particle Tracking: Variables suffixed with _part_3d (e.g., cells_per_mL_part_3d, variance_part_3d, ro_part_3d, ri_part_3d)

 Key Data Arrays:  Raw trajectories: Time-series position data stored in cell arrays MSD data: MSDexp, t_MSD_exp, MSD_sim_part, MSD_sim_part_3d Fitted parameters: tau_bath, vbath, tau_sed_opt for all experimental conditions Simulation results: MSD_sim_adim_opt, t_MSD_sim_opt for model validation  

Bacterial concentrations: cells_per_mL_* arrays (converted to cells/μm³) Geometric parameters:  ro_*: Outer droplet radii (μm) ri_*: Inner particle radii (μm) R_*: Available space (ro - ri)   Bath properties:  tau_bath_*: Memory time τb (s) vbath_*: Characteristic velocity ub (μm/s) tau_sed_opt_*: Sedimentation time \tau (s)   Dimensionless parameters: best_pi1_=\tau_bath*, best_pi2_=\ell_b* for model fitting.

The trajectories should be in micrometers, otherwise the scale used in the experiments is  1/9.24 for micrometers.

Simulation Code Core Simulation Function: simulation_dimensionless_pi1pi2_reflective.m Implements the 3D stochastic model described in Methods (Equations 5-6):

MSD Calculation Function: msd_calculation.m