Research

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs

Advait A Apte¹ , John W Cain^2,3 , Danail G Bonchev^2,3 and Stephen S Fong^1,3

¹  Department of Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, VA 23284, USA

²  Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, P.O. Box 842014, Richmond, VA 23284, USA

³  Center for the Study of Biological Complexity, Virginia Commonwealth University, P.O. Box 842030, Richmond, VA 23284, USA

author email corresponding author email

Journal of Biological Engineering 2008, 2:2doi:10.1186/1754-1611-2-2

Published:	27 February 2008

Abstract

Background

Feed-forward motifs are important functional modules in biological and other complex networks. The functionality of feed-forward motifs and other network motifs is largely dictated by the connectivity of the individual network components. While studies on the dynamics of motifs and networks are usually devoted to the temporal or spatial description of processes, this study focuses on the relationship between the specific architecture and the overall rate of the processes of the feed-forward family of motifs, including double and triple feed-forward loops. The search for the most efficient network architecture could be of particular interest for regulatory or signaling pathways in biology, as well as in computational and communication systems.

Results

Feed-forward motif dynamics were studied using cellular automata and compared with differential equation modeling. The number of cellular automata iterations needed for a 100% conversion of a substrate into a target product was used as an inverse measure of the transformation rate. Several basic topological patterns were identified that order the specific feed-forward constructions according to the rate of dynamics they enable. At the same number of network nodes and constant other parameters, the bi-parallel and tri-parallel motifs provide higher network efficacy than single feed-forward motifs. Additionally, a topological property of isodynamicity was identified for feed-forward motifs where different network architectures resulted in the same overall rate of the target production.

Conclusion

It was shown for classes of structural motifs with feed-forward architecture that network topology affects the overall rate of a process in a quantitatively predictable manner. These fundamental results can be used as a basis for simulating larger networks as combinations of smaller network modules with implications on studying synthetic gene circuits, small regulatory systems, and eventually dynamic whole-cell models.