Designing Conservation Relations in Layered Synthetic Biomolecular Networks

In Synthetic Biology, biomolecular networks are designed and constructed to perform specified tasks. Design strategies for these networks tend to center on tuning the parameters of mathematical models to achieve a specified behavior, and implementing these parameters experimentally. This design stra...

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Bibliographic Details
Published in:IEEE transactions on biomedical circuits and systems 2015-08, Vol.9 (4), p.572-580
Main Authors: Prescott, Thomas P., Papachristodoulou, Antonis
Format: Article
Language:English
Subjects:
Biology
Conservation
Conservation relations
Constraining
Design engineering
Gene Regulatory Networks - physiology
Genetics
layers
Mathematical model
Mathematical models
Models, Biological
Networks
Null space
Proteins - metabolism
Reduced order systems
singular perturbation
Strategy
synthetic biology
Synthetic Biology - methods
Trajectory
Transient analysis
Tuning
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Summary:In Synthetic Biology, biomolecular networks are designed and constructed to perform specified tasks. Design strategies for these networks tend to center on tuning the parameters of mathematical models to achieve a specified behavior, and implementing these parameters experimentally. This design strategy often assumes a fixed network structure that defines the possible behaviors, which may be too restrictive for our purposes. This paper investigates the extent to which the state space of a synthetic network can also be designed and shaped by parametric tuning. We exploit timescale separation to implement new, nonlinear, tunable conservation relations that hold for all times beyond a fast transient. We demonstrate an application of this design strategy by flexibly constraining the possible behaviors of a gene regulatory network through the design of fast protein interactions.
ISSN:1932-4545
1940-9990
DOI:10.1109/TBCAS.2015.2460376