Automated design of gene circuits with optimal mushroom-bifurcation behaviour
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Published version
Author(s)
Otero-Muras, Irene
Perez-Carrasco, Ruben
Banga, Julio R
Barnes, Chris P
Type
Journal Article
Abstract
Recent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation and generic multifunctional biocircuits. These novel applications require the design of gene circuits leading to sophisticated behaviours and functionalities. At the same time, designs need to be kept minimal to avoid compromising cell viability. Bifurcation theory addresses such challenges by associating circuit dynamical properties with molecular details of its design. Nevertheless, incorporating bifurcation analysis into automated design processes has not been accomplished yet. This work presents an optimization-based method for the automated design of synthetic gene circuits with specified bifurcation diagrams that employ minimal network topologies. Using this approach, we designed circuits exhibiting the mushroom bifurcation, distilled the most robust topologies and explored its multi-functional behavior. We then outline potential applications in biosensors, memory devices, and synthetic cell differentiation.
Date Issued
2023-06-16
Date Acceptance
2023-05-04
Citation
iScience, 2023, 26 (6), pp.1-15
ISSN
2589-0042
Publisher
Elsevier
Start Page
1
End Page
15
Journal / Book Title
iScience
Volume
26
Issue
6
Copyright Statement
© 2023 The Authors.
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
License URL
Identifier
https://www.sciencedirect.com/science/article/pii/S2589004223009136
Publication Status
Published
Article Number
106836
Date Publish Online
2023-05-09