AUTHOR=Lewis Daniel D. , Villarreal Fernando D. , Wu Fan , Tan Cheemeng TITLE=Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems JOURNAL=Frontiers in Bioengineering and Biotechnology VOLUME=2 YEAR=2014 URL=https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2014.00066 DOI=10.3389/fbioe.2014.00066 ISSN=2296-4185 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.