Molecular Programming Architectures, Abstractions, Algorithms, and Applications

This is a joint project between Caltech, Harvard, U. Washington and UCSF. This page primarily describes the work done in Richard Murray's group; see the MPP homepage for a description of the complete project.

Project participants: Samuel Clamons (Alumni, BE) Andrew Montequin (Alumni, BE) Anu Thubagere (Alumni, BE) Jongmin Kim (postdoc, BE) Additional participants: William Poole (Alumni, CNS)

Collaborators Niles Pierce (Caltech BBE) Erik Winfree (Caltech CNS/BE)

Overview

Molecular programming involves the specification of structures, circuits, and behaviors both within living and non-living systems—systems in which computing and decision-making will carried out by chemical processes themselves. Our work focuses on the development of in vitro circuits that demonstrate the principles of feedback in biomolecular systems and the application of cell-free assays as a "biomolecular breadboard" for molecular programming.

Publications

• Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts. Wolfgang Halter, Frank Allgower, Richard M. Murray and Andras Gyorgy. To appear, 2018 Conference on Decision and Control (CDC).
• An analytical approach to bistable biological circuit discrimination using real algebraic geometry. Dan Siegal-Gaskins, Elisa Franco, Tiffany Zhou, Richard M. Murray. J. R. Soc. Interface 2015 12 20150288; DOI: 10.1098/rsif.2015.0288..
• Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively. Xianglin Meng, Ania A. Baetica, Vipul Singhal, and Richard M. Murray. Presented, 2016 Winter q-Bio Conference.
• Rapid in vitro engineering of 16 two-input logic gates. Clarmyra A. Hayes, Emmanuel L.C. de los Santos, Enoch Yeung, Sean R. Sanchez, Seung Y. Lee, and Richard M. Murray. Presented, 2016 Winter q-Bio.
• Design of a Toolbox of RNA Thermometers. Rohit Satija, Shaunak Sen, Dan Siegal-Gaskins, Richard M. Murray. Presented at Synthetic Biology: Engineering, Evolution and Design (SEED), 10-13 June 2015.
• Synthetic logic circuits using RNA aptamer against T7 RNA polymerase. Jongmin Kim, Juan F Quijano, Enoch Yeung, Richard M Murray. bioRxiv, 4 Sep 2014.
• Synthetic circuit for exact adaptation and fold-change detection. Jongmin Kim, Ishan Khetarpal, Shaunak Sen and Richard M. Murray. Nucleic Acids Research, 42(9):6078-6089, 2014.

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Research supported by the National Science Foundation award number 1317694.

Agency: NSF Grant number: 1317694

Start date: 1 Oct 2013 End date: 30 Sep 2018

Support: shared students/postdocs + supplies Reporting: annually in September