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WIREs Syst Biol Med
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Mathematical models in biology: from molecules to life

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Abstract A vexing question in the biological sciences is the following: can biological phenotypes be explained with mathematical models of molecules that interact according to physical laws? At the crux of the matter lies the doubt that humans can develop physically faithful mathematical representations of living organisms. We discuss advantages that synthetic biological systems confer that may help us describe life's distinctiveness with tractable mathematics that are grounded on universal laws of thermodynamics and molecular biology. WIREs Syst Biol Med 2011 3 314–322 DOI: 10.1002/wsbm.142 This article is categorized under: Analytical and Computational Methods > Analytical Methods Models of Systems Properties and Processes > Organismal Models

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Screenshots of steps a user takes in SynBioSS Designer to build a model. Users may enter the DNA sequence of molecular components in their synthetic construct (Step 1), enter biomolecular interactions information (Step 2), and save the reaction network Designer generates automatically in SBML format (Step 3).

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Comparison of model (first panel) and experimental results (second panel) for the TTL AND gate. The x and y axes form a grid of inducer concentrations: aTc (0–200 ng/ml) and IPTG (0–1 mM). The color scheme reflects the average strength of fluorescence from the experiments or the average number of GFP molecules in the simulations, scaled by the maximum strength/number of GFP molecules. The third panel shows the difference between experiments and simulations. In all cases, behavior is depicted 6 h after induction. The plotted model values are the means of 1000 independent stochastic kinetic simulations, whereas experimental values are the means of 100,000 Fluorescence‐activated cell sorting (FACS) observations.

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Schematic representation of the synthetic logic‐AND gate promoter.

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