Fig. 1
From: Single molecule dynamics in a virtual cell combining a 3-dimensional matrix model with random walks
Model description. (A) Cartoon of cell structures with single molecules (black and grey dots) moving within the cytosol or luminal spaces (ER, nucleus, filopodia) on membranes or along cytoskeletal tracks. (B) Flow-chart showing the typical iterative cycle of single molecule research which usually includes simulations as an important adjunct. (C) Here, we show a 2-dimensional slice of the structural model at coarse resolution. The value of each byte of computer memory represents one voxel in 3-dimensional (3-D) space, that is coded to represent material and chemical properties, e.g. different cytosolic classes occupy values from 1 to 20 (light grey), membranes are in the range 200–255 (dark grey) and extra cellular regions are set to zero (white). During the simulation, molecules diffuse through the virtual space and the 3-D map is used as a look-up table of physico-chemical properties at each time-step of the simulation. Molecules may either move freely through all voxels or, more realistically, may be entrapped within one class of voxel (here, black molecules move within membrane, grey within cytosol). (D) The model expanded to 3-D: A yeast cell (0.8 × 0.6 × 0.6 µm3) with simplified elliptical nucleus (diameter 400 nm, flattening = 0.8) populated by cell membrane molecules (blue circles), nuclear membrane molecules (green circles), and nucleoplasm molecules (red circles). Cell and nucleus membranes are 3 voxels thick.
