An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System

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Title An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System
Authors Zoltan A. Tuza, Vipul Singhal, Jongmin Kim, Richard M. Murray
Source 2013 Conference on Decision and Control (CDC)
Abstract In this paper, we develop an experimentally val- idated MATLAB software toolbox as an accompaniment to an in vitro cell-free biomolecular “breadboard” system. The toolbox gives insight into the dynamics of unmeasured states in the cell-free system, accounting especially for the resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid ill-conditioning. The toolbox allows for most applications to be implemented with standard set of commands for ease of use. Due to the breadboarding nature of the underlying cell-free sys- tem, the toolbox provides a general framework for experiment planning and predictive modeling for synthetic biomolecular circuits cell-free systems, accelerating our capacity to rationally design circuits from well characterized parts.
Type Conference paper
URL http://www.cds.caltech.edu/~murray/preprints/tskm13-cdc_s.pdf
Tag tskm13-cdc
ID 2013b
Funding
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