Examples & Applications

The examples below from Monnier et al, BiophysJ 2012 illustrate how to apply the MSD-Bayes package to MSD curves to obtain model probabilities for a set of motion models. The necessary input files can be found in the 'examples' folder in the MSD-Bayes code package.

## Example 1: Diffusion-flow simulations

Figure 2A in the paper demonstrates the effect of varying velocity on the ability to resolve the diffusion plus flow (DV) model. Particles were simulated undergoing diffusion with a superimposed velocity v. As described in the text, the relative contributions of the diffusive and directed motions of the particle to the mean square displacement (MSD) are equal when the ratio 6D/v^2 equals the timelag tau. When this ratio is much greater or much less than the tau values sampled in the MSD curve, diffusive or directed motion (respectively) dominates the MSD curve and the DV model is rejected in favor of the simpler models pure diffusion (D) or pure flow (V), which are more likely to explain the observed MSD curve given the level of noise.

To reproduce the figure panel below, the 'simulation_example.m' script loads the series of MSD curves that were obtained from the simulated trajectories at each velocity value and iteratively calls the MSD-Bayes package to evaluate the corresponding model probabilities.

## Example 2: Starfish chromosomes

Figure 4C in the paper shows the results of analyzing experimental chromosome trajectories with different trajectory groupings. Groupings are in order of distance from the animal pole of the starfish oocyte, since chromosome velocity is known to increase along this axis. This experimental dataset demonstrates two important priciples of MSD-Bayes analysis: (1) the sampling noise in the mean MSD curve increases with smaller groups of trajectories (less averaging power), illustrated by the trend towards simpler models (D and V) from top to bottom in the figure; and (2) the probability of the D model is higher at low velocities and the V model is higher at large velocities (left to right in the figure), consistent with the simulation results above.

To reproduce this figure, the 'chromosome_example.m' script loads the MSD curves obtained from the experimental chromosome trajectories and calls the MSD-Bayes package with a series of different groupings of the MSD curves.