title: Mathematical modeling: bridging the gap between concept and realization in synthetic biology.
abstract: Mathematical modeling plays an important and often indispensable role in synthetic biology because it serves as a crucial link between the concept and realization of a biological circuit. We review mathematical modeling concepts and methodologies as relevant to synthetic biology, including assumptions that underlie a model, types of modeling frameworks (deterministic and stochastic), and the importance of parameter estimation and optimization in modeling. Additionally we expound mathematical techniques used to analyze a model such as sensitivity analysis and bifurcation analysis, which enable the identification of the conditions that cause a synthetic circuit to behave in a desired manner. We also discuss the role of modeling in phenotype analysis such as metabolic and transcription network analysis and point out some available modeling standards and software. Following this, we present three case studies-a metabolic oscillator, a synthetic counter, and a bottom--up gene regulatory network--which have incorporated mathematical modeling as a central component of synthetic circuit design.
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Maryland, 1208D, Chemical and Nuclear Engineering Building 090, College Park, MD 20742, USA.
authors.forename: Yuting
authors.initials: Y
authors.lastname: Zheng
authors.forename: Ganesh
authors.initials: G
authors.lastname: Sriram
mesh_terms: D057005:Bioengineering; D008954:Models, Biological; D015233:Models, Statistical; D015398:Signal Transduction; D049490:Systems Biology