Figure 1.
Virtual cytoplasm model in a cubic box of length 406 Å.
Each protein is represented by a collection of spheres representing the volume and approximate shape of a particular macromolecule.
Figure 2.
Model for the calculation of local volume fraction for the sphere i.
In this model, Rcut is 4 times radius of central sphere i, and j and k are spheres that lie completely inside and partially inside Rcut, respectively.
Figure 3.
Scaling of the mean-squared displacement as a function of time.
Figure 4.
Diffusion coefficient values of the particles corresponding to GFP, CheY and FabD plotted against time.
Table 1.
Diffusion coefficient values for three proteins with and without considering hydrodynamic interactions (HI). SD represents standard deviation.
Figure 5.
Correlation function of successive displacements (eq. 11) for different time lags (see text) ranging from 100 ns to 1000 ns.
Figure 6.
Anomalous subdiffusion occurring over short time regimes, tending to normal Brownian motion at larger time differences.
Diffusion is subdiffusive anomalous for t<3 on the log scale. After this time, the diffusion is approximately "normal" Brownian motion.
Figure 7.
Correlation function of successive displacements (eq. 11) for simulation with and without hydrodynamic interactions.
Figure 8.
Correlation function of successive displacements (eq. 11) with and without repulsive interactions (both are without hydrodynamic interactions).
Figure 9.
Correlation function of successive displacements (eq. 11) for two different repulsive force constants (both are with hydrodynamic interactions).
Inset shows the same figure for a smaller range of y-axis.
Figure 10.
Correlation function of successive displacements (eq. 11) showing the effect of stationary and mobile crowders.