We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an  Escherichia coli  bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon.  Prokaryo , our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes.
['Afshin Esmaeili', 'Timothy Davison', 'Andrew Wu', 'Joenel Alcantara', 'Christian Jacob']
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli