Generate trajectories in cylindrical substrate

[astamm]

The function simulate_bundle() generates a cylindrical substrate. We can initialise a number of water molecules in there with subject to Brownian motion with a given free diffusion coefficient and let them diffuse for a given time. We can then calculate the mean square displacement in the direction parallel to the cylinders' axis and in the direction perpendicular to it which are by definition the apparent axial and radial diffusion coefficient. This can be done in the extra-axonal space as well as in the intra-axonal space.