This repository contains experimental data, analysis scripts, and computational models supporting the PNAS publication: Miles CE, Renda F, Tikhonenko I, Alfieri A, Mogilner A, and Khodjakov A. "The kinetochore corona orchestrates chromosome congression through transient microtubule interactions." PNAS (2026). Repository Structure .├── data/ # Experimental chromosome tracking data├── processing/ # MATLAB scripts for experimental data analysis└── sim/ # Computational models and simulations Data Files (data/) Six .mat files containing experimental chromosome trajectory data: rpe_ctr_all.mat - Wild-type RPE1 control cells rpe_prc_all.mat - RPE1 cells depleted of PRC1 (microtubule crosslinker) rpe_gsk_all.mat - RPE1 cells with CENP-E inhibited (GSK923295) rpe_kid_all.mat - RPE1 cells depleted of Kid (chromokinesin) rod_ctr_all.mat - RPE1 Rod-/- cells (corona deficient) rod_gsk_all.mat - RPE1 Rod-/- cells with CENP-E inhibited Each file contains: chr_pos_cyl - Chromosome positions in cylindrical coordinates [time, coordinate, chromosome] Coordinate 1: theta (angle) Coordinate 2: rho (radial distance from spindle axis) Coordinate 3: z (axial position along pole-pole axis) biorient_time - Time of biorientation for each chromosome (seconds) sp_length - Spindle length over time [time, cell] nCells - Number of cells in dataset bad_chroms - Indices of chromosomes excluded from analysis chroms_range - Range of chromosome indices for each cell [2, nCells] chroms_total - Total number of chromosomes tracked Processing Scripts (processing/) MATLAB scripts for analyzing experimental chromosome trajectories: mono_dynamics.m - Analyzes monooriented chromosome dynamics (population-level) mono_dynamics_per_cell.m - Analyzes monooriented chromosome dynamics (single-cell) velocity_at_distance_v2.m - Calculates velocity-distance relationships positions_movie_normZ.m - Generates chromosome position movies (normalized Z) positions_movie_per_cell.m - Generates position movies for individual cells quiver_movie_normZ.m - Generates velocity field quiver plot movies Usage: Run scripts from the processing/ directory. Edit the exp_class variable at the top of each script to select which dataset to analyze (e.g., 'rpe_ctr', 'rod_ctr'). Simulation Scripts (sim/) MATLAB scripts implementing computational models of chromosome congression: Main Simulation Script run_models.m - Master script that runs all models and generates figures comparing experimental data with model predictions Model Implementations simulate_transient_model_saturated.m - Transient interactions with saturated binding (control cells) simulate_transient_model_unsaturated.m - Transient interactions with unsaturated binding (directed microtubules) simulate_stable_model.m - Stable attachment model (for comparison) Analysis and Visualization process_trajectories.m - Processes simulated/experimental trajectories and calculates velocity statistics plot_velocity_profiles.m - Generates velocity vs. distance plots plot_colored_trajectories.m - Visualizes chromosome trajectories colored by velocity calculate_analytical_velocities.m - Computes theoretical velocity predictions generate_streamplot_figures.m - Creates mean-field velocity streamplots streamplot.m - Streamplot visualization utility load_experimental_data.m - Loads experimental data files Usage: Run run_models.m from the sim/ directory. The script will: Load experimental data from ../data/ Run multiple simulation scenarios Generate comparison plots Save figures to sim/figs/ (created automatically) Getting Started Requirements MATLAB (tested with R2020b and later) Statistics and Machine Learning Toolbox Curve Fitting Toolbox Parallel Computing Toolbox (optional, for faster simulations) Running the Analysis Process experimental data: cd processingmono_dynamics % Analyze monoorientation dynamicsvelocity_at_distance_v2 % Compute velocity-distance relationships Run computational models: cd simrun_models % Run all models and generate comparison figures Generate streamplot figures: cd simgenerate_streamplot_figures % Create mean-field velocity visualizations Data Format Notes Chromosome positions in all data files use cylindrical coordinates (z, r, theta) centered on the spindle, where z is the axial position (equator at z=0), r is the radial distance from the spindle axis, and theta is the angular position. Contact For questions about the code or data: Christopher E. Miles: chris.miles@utah.edu