Simulated Molecular Biology

Glorious Tsui, in Christian Jacob's lab at the The University of Calgary, has used breve to simulate the molecular workings of a virus.

The lambda-switch is one of the most studied gene regulatory systems of a virus called lambda. The switch determines whether the virus will reproduce and destroy the host cell, or hide in the cell's DNA and await another opportunity. This simulation makes use of breve's 3D simulation engine and its object-oriented programming language, steve, to model the lambda-switch. RepressorDimer agents (objects consisting of two spheres joined by a black string), CroDimer agents (green spheres) and the RNApolymerase agents (purple rectangular blocks) compete for binding to the binding sites at the control area (three stationary blue rectangles) of the DNA segment. The control area determines whether the CI gene (yellow stationary block) or the CRO gene (orange stationary block) gets read by the RNApolymerase agents, thus determining the fate of the cell.