Confined subdiffusion in three dimensions

The three-dimensional (3D) Fick's diffusion equation and fractional diffusion equation are solved for different reflecting boundaries. We use the continuous time random walk model (CTRW) to investigate the time averaged mean square displacement (MSD) of 3D single particle trajectory. Theoretical results show the ensemble average of the time averaged MSD can be expressed analytically by a Mittag-Leffler function. Our new expression is in agreement with previous formulas in two limiting cases which are $< \overline{\delta^2} > \sim\Delta$ in short lag time and $< \overline{\delta^2}> \sim\Delta^{1-\alpha}$ in long lag time. We also simulate the experimental data of mRNA diffusion in living E. coli using 3D CTRW model under confined and crowded conditions. The simulated results are well consistent with experimental results. The calculations of power spectral density (PSD) indicate further the subdiffsive behavior of individual trajectory.