Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways

Project description (typically about a paragraph)

Current participants: Additional participants:

Collaborators: Past participants: Zoila Jurado (Alumni, CMS) Joe Meyerowitz (Alumni, BMB) Ayush Pandey (Alumni, CDS) Xinying (Cindy) Ren (Alumni, CDS)

Objectives

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Description of the main objectives of the project

References

• A chemical reaction network model of PURE. Zoila Jurado, Ayush Pandey, Richard M. Murray. BioRxiv preprint, 2023.
• BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts. William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M. Murray. PLoS Computational Biology, 18(4), e1009987, 2022.
• Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline. Ayush Pandey, Makena L. Rodriguez, William Poole, Richard M. Murray. ACS Synthetic Biology, 12(2):511–523, 2023.
• Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models. Ayush Pandey, Richard M. Murray. International Journal on Robust and Nonlinear Control (IJRNC), 1-29, 2022.
• Robustness Guarantees for Structured Model Reduction of Dynamical Systems. Ayush Pandey, Richard M. Murray. IEEE Conference on Decision and Control (CDC), 2021.
• Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits. Ayush Pandey, Richard M. Murray. 2020 Winter q-bio.

Agency: NSF Grant number:

Start date: 1 Jul 2019 End date: 30 Jun 2023

Support: 1 graduate student Reporting: Annual reports