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A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology

Marken, John P. and Xiao, Fangzhou and Murray, Richard M. (2020) A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200220-083645813

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Abstract

Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system's structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.02.18.953620DOIDiscussion Paper
ORCID:
AuthorORCID
Marken, John P.0000-0001-9696-088X
Xiao, Fangzhou0000-0002-5001-5644
Murray, Richard M.0000-0002-5785-7481
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. February 17, 2020. J.P.M. is supported by a National Science Foundation Graduate Research Fellowship, and F.X. is partially funded by the Defense Advanced Research Projects Agency (Agreement HR0011-16-2- 0049 and Agreement HR0011-17-2-0008). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0008
Record Number:CaltechAUTHORS:20200220-083645813
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200220-083645813
Official Citation:A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology. John P Marken, Fangzhou Xiao, Richard M Murray. bioRxiv 2020.02.18.953620; doi: https://doi.org/10.1101/2020.02.18.953620
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101413
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:20 Feb 2020 17:21
Last Modified:20 Feb 2020 17:21

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