Synthetic biology outside the cell: linking computational tools to cell-free systems

Daniel D Lewis; Fernando D Villarreal; Fan Wu; Cheemeng Tan

doi:10.3389/fbioe.2014.00066

Synthetic biology outside the cell: linking computational tools to cell-free systems

Front Bioeng Biotechnol. 2014 Dec 9:2:66. doi: 10.3389/fbioe.2014.00066. eCollection 2014.

Authors

Daniel D Lewis¹, Fernando D Villarreal², Fan Wu², Cheemeng Tan²

Affiliations

¹ Integrative Genetics and Genomics, University of California Davis , Davis, CA , USA ; Department of Biomedical Engineering, University of California Davis , Davis, CA , USA.
² Department of Biomedical Engineering, University of California Davis , Davis, CA , USA.

Abstract

As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

Keywords: artificial cells; cell-free systems; computational modeling; deterministic and stochastic simulations; in vitro model; predictive modeling; synthetic biology.

Publication types

Review