Mathias Foo (River systems and biochemical control)

In this episode I interview Dr Mathias Foo about his fascinating research on controlling river systems, implementing control systems using DNA, and gene network rewiring. Basically applying control to a bunch of different systems that you weren’t expecting.

You can find the transcript for this episode at: https://docs.google.com/document/d/1cWRFK20bWm64k7MCghI82eJ3-FjTt3hK0VEpQ-VE0Og/edit?usp=sharing

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References

Dr Mathias Foo: https://warwick.ac.uk/fac/sci/eng/people/mathias_foo/

PhD

PhD thesis: https://scholar.google.com/citations?view_op=view_citation&hl=en&user=H5eLRq4AAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=H5eLRq4AAAAJ:2osOgNQ5qMEC

Nadia Bedjaoui: https://www.linkedin.com/in/nadia-bedjaoui-39862110/

Observers for leak detection in irrigation channels: https://www.sciencedirect.com/science/article/abs/pii/S0967066110001498

MPC using reverse engineering paper: https://ieeexplore.ieee.org/abstract/document/6114363
Maciejowski MPC book: https://www.amazon.com/Predictive-Control-Constraints-Jan-Maciejowski/dp/0201398230

Maciejowski inverse optimal control paper: https://www.sciencedirect.com/science/article/pii/S1474667015366180

DNA strand displacement reactions

Oishi and Klavins paper: https://www.dna.caltech.edu/courses/cs191/paperscs191/Oishi2011linear.pdf

DNA amplifiers: https://www.science.org/doi/10.1126/science.1148532

DNA Logic gates: https://www.science.org/doi/10.1126/science.1132493

DNA Detectors: https://www.dna.caltech.edu/Papers/Nucleation_DNA10.pdf

PID control using DSD reactions: https://ieeexplore.ieee.org/document/8721529

Nuno Paulino: https://scholar.google.com/citations?user=FKL-xegAAAAJ&hl=en&oi=ao

DNA programmable gate arrays: https://www.nature.com/articles/s41586-023-06484-9

Theoretical DNA feedback paper: https://www.mdpi.com/2306-5354/10/4/466

DNA stability paper: https://www.sciencedirect.com/science/article/pii/S0005109820303010

SSV DNA robustness paper: https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8619072

Gomez-Uribe covalent modification cycle paper: https://pubmed.ncbi.nlm.nih.gov/18159939/

Quasi sliding-model controller paper: https://ieeexplore.ieee.org/document/7833853

Design based on covalent modification cycle: https://link.springer.com/article/10.1186/s13036-016-0036-1

PI-degradation controllers: https://warwick.ac.uk/fac/sci/eng/staff/dgb/077972431.pdf

Gene regulatory networks

Voit S-system paper: https://doi.org/10.1042/bse0450029

Modelling and control using S-system models: https://ieeexplore.ieee.org/abstract/document/8254368

Extended S-system model for restoring circadian cycles: https://www.nature.com/articles/s41540-022-00216-x

Uri Alon gene regulation paper: https://www.nature.com/articles/nrg2102

Network re-wiring paper: https://pubs.acs.org/doi/full/10.1021/acssynbio.8b00037

Reverse-engineering Hill-type models paper: https://royalsocietypublishing.org/doi/abs/10.1098/rsif.2024.0811

2009 Cell optimisation paper: https://www.sciencedirect.com/science/article/pii/S0092867409007120

Briat antithetic integral control paper: https://www.cell.com/fulltext/S2405-4712(16)00005-3

Professor Declan Bates: https://warwick.ac.uk/fac/sci/eng/staff/dgb/

Steve Brunton: https://www.youtube.com/@Eigensteve

Control bootcamp series: https://www.youtube.com/watch?v=Pi7l8mMjYVE&list=PLMrJAkhIeNNR20Mz-VpzgfQs5zrYi085m

Physics-informed machine learning series: https://www.youtube.com/watch?v=JoFW2uSd3Uo&list=PLMrJAkhIeNNQ0BaKuBKY43k4xMo6NSbBa

Probability and statistics series: https://www.youtube.com/watch?v=sQqniayndb4&list=PLMrJAkhIeNNR3sNYvfgiKgcStwuPSts9V