An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system
- 1 December 2013
- conference paper
- conference paper
- Published by Institute of Electrical and Electronics Engineers (IEEE)
- p. 1404-1410
- https://doi.org/10.1109/cdc.2013.6760079
Abstract
In this paper, we develop an experimentally validated 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 resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid ill-conditioning. The toolbox provides a general framework for experiment planning and predictive modeling for synthetic biomolecular circuits in cell-free systems, accelerating our capacity to rationally design circuits from well characterized parts.Keywords
This publication has 28 references indexed in Scilit:
- Real-Time mRNA Measurement during an in Vitro Transcription and Translation Reaction Using Binary ProbesACS Synthetic Biology, 2012
- Competition for Catalytic Resources Alters Biological Network DynamicsPhysical Review Letters, 2012
- Coarse-Grained Dynamics of Protein Synthesis in a Cell-Free SystemPhysical Review Letters, 2011
- Interdependence of Cell Growth and Gene Expression: Origins and ConsequencesScience, 2010
- Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70Journal of Biological Engineering, 2010
- An integrated cell‐free metabolic platform for protein production and synthetic biologyMolecular Systems Biology, 2008
- The λ Gam Protein Inhibits RecBCD Binding to dsDNA EndsJournal of Molecular Biology, 2007
- Regeneration of adenosine triphosphate from glycolytic intermediates for cell‐free protein synthesisBiotechnology & Bioengineering, 2001
- Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymeraseNucleic Acids Research, 2000
- Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elementsNucleic Acids Research, 1997