Computer simulation of the directional displacement of rod-shaped, arc-shaped, and circular objects in an array of obstacles, representing a simple model for the gel electrophoresis of small DNA.

The gel electrophoresis of DNA of identical length but various static conformations was simulated using a two-dimensional model of the movement of rod-shaped, arc-shaped, and circular objects through random arrays of disk-shaped obstacles. At low obstacle density, the displacement rate of these objects decreases from the rod-shaped to the circular to the arc-shaped objects. At high obstacle densities, the displacement rate of circular objects approaches zero. The alignment of the arc-shaped objects along the axis of the directional movement of the objects were retarded in their movement by collisions with the obstacles; the number of collisions of the former, in view of their greater ability to align, was less than that of the latter. Circular objects were exclusively retarded by collisions, while the arc-shaped objects exhibited an additional retarding mechanism, viz. the suspension ("hanging") on the obstacles. When the rigid objects were made flexible, their displacement increased. The increase was most pronounced with the circular objects, allowing them to penetrate at obstacle densities from which the rigid objects were excluded.