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.

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LinkedIn: https://www.linkedin.com/in/lucy-hodgins-733a30175/

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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

In this episode I interview Jonathan Mayo Maldonado about his work on applying the behavioural framework to modelling and controlling switched systems, as well as applying data-driven control to power systems!

You can engage with the podcast on

BlueSky: https://bsky.app/profile/coffee-and-control.bsky.social

Instagram: https://www.instagram.com/coffee_and_control_podcast/

Follow me on LinkedIn: https://www.linkedin.com/in/lucy-hodgins-733a30175/

Or email me at [email protected]

Jonathan Mayo-Maldonado: https://www.southampton.ac.uk/people/668pbh/doctor-jonathan-mayo-maldonado

PhD

PhD thesis: https://eprints.soton.ac.uk/383678/

Switched linear differential systems: https://arxiv.org/pdf/1303.0308

Dissipative switched linear differential systems: https://eprints.soton.ac.uk/386199/1/DissipativeSLDS-Rev5.pdf

DC-DC converters

Power shaping control: https://www.researchgate.net/publication/344671509_Power_shaping_control_of_DC-DC_converters_with_constant_power_loads

Paolo Rapisarda’s dissipativity paper: https://eprints.soton.ac.uk/271668/1/PublishedArticle.pdf

Lifted coordinates: https://www.researchgate.net/publication/344800256_Nonlinear_Stabilizing_Control_Design_for_DC-DC_Converters_Using_Lifted_Models

Episode with Chris on Non-minimum phase ILC: https://open.spotify.com/episode/0hLqV5hv5OeQO3gOE6aU9c

Direct voltage control of higher-order converters paper: https://www.researchgate.net/publication/359245867_Direct_Output-Voltage_Control_of_Non-Minimum_Phase_Higher-Order_DC-DC_Converters

Enrique Garza Arias PhD thesis: https://repositorio.tec.mx/items/6dfd5498-d0d4-417c-9e33-afb75930710a

Data-driven control

Active and reactive power analogy: https://www.youtube.com/watch?v=Tv_7XWf96gg

Data-driven D-PMU paper: https://www.researchgate.net/publication/339887346_Data-Driven_Framework_to_Model_Identification_Event_Detection_and_Topology_Change_Location_Using_D-PMUs

Voltage performance index tracking paper: https://ieeexplore.ieee.org/document/10517964

Extra questions

Advice from a young scientist to younger scientists article:https://medium.com/@jonathanmayo_75536/advice-from-a-young-scientist-to-younger-scientists-74d9aaf2d2f2

Arjan van der schafft: https://www.math.rug.nl/~arjan/index.html

Johann Kolar: https://pes.ee.ethz.ch/the-institute/People/prof-kolar2.html

Konstantinos Gatsis: https://kgatsis.github.io/

In this episode I talk to Professor Paolo Rapisarda about a bunch of interesting theoretical (but very useful) aspects of control, including his work on behavioural systems theory, model reduction, Willems’ fundamental lemma, and data-driven control.

You can engage with the podcast on

X: https://x.com/coffee_ctrl_pod

BlueSky: https://bsky.app/profile/coffee-and-control.bsky.social

Instagram: https://www.instagram.com/coffee_and_control_podcast/

Or email me at [email protected]

Paolo Rapisarda: https://www.southampton.ac.uk/people/5x2hb9/professor-paolo-rapisarda

Introduction

State maps for linear systems: https://eprints.soton.ac.uk/264646/1/State_maps.pdf

Harry Trentelman: https://research.rug.nl/en/persons/harry-trentelman

Jan Willems: https://homes.esat.kuleuven.be/~sistawww/smc/jwillems/

PhD thesis: https://research.rug.nl/en/publications/linear-differential-systems-2

Behavioural systems

Epic Jan Willems behavioural systems paper: https://skoge.folk.ntnu.no/prost/proceedings/cpc6-jan2002/willems.pdf

State maps

LTV paper:https://eprints.soton.ac.uk/457114/1/State_for_linear_discrete_time_varying_systems.pdf

Leibnitz rule: https://www.cuemath.com/calculus/leibniz-rule/

Dissipativity

Jan Willem’s paper: https://link.springer.com/article/10.1007/bf00276493

Jan Willem’s optimal control paper: https://ieeexplore.ieee.org/abstract/document/1099831

Quadratic differential forms: https://epubs.siam.org/doi/10.1137/S0363012996303062

Balancing

Siep Weiland: https://ieeexplore.ieee.org/author/37301202100

Keith Glover: https://www.eng.cam.ac.uk/profiles/kg103

H-infinity model order reduction: https://ieeexplore.ieee.org/document/701085

1980 Moore balancing paper: https://ieeexplore.ieee.org/document/1102568

Kalman decomposition: https://en.wikipedia.org/wiki/Kalman_decomposition

Arjan van der Schaft: https://scholar.google.nl/citations?user=BIPifjAAAAAJ&hl=en

Hamiltonian systems: https://www.unige.ch/~hairer/poly_geoint/week1.pdf

Port Hamiltonianity:https://www.annualreviews.org/content/journals/10.1146/annurev-control-081219-092250

Jacqueline Scherpen: https://research.rug.nl/en/persons/jacqueline-scherpen

Balancing of Port-Hamiltonian systems: https://research.rug.nl/files/2999949/2003ProcIFACWorkshopLHMNCLopezlena.pdf

Balancing for non-linear systems: https://research.rug.nl/files/3318296/1993ProcECCScherpen.pdf

Fundamental lemma

Ivan Markovski: https://scholar.google.com/citations?user=qSl_3FQAAAAJ&hl=en

Continuous-time work: https://www.sciencedirect.com/science/article/pii/S016769112400238X

Chebychev polynomials: https://mathworld.wolfram.com/ChebyshevPolynomialoftheFirstKind.html

Kanat Camblibel: https://scholar.google.com/citations?user=aeWjKPcAAAAJ&hl=en

Sufficient condition modification of Willems’s lemma: https://arxiv.org/abs/2405.18962

Experimental implementation: https://arxiv.org/abs/2407.12509

Data-driven control

Data-driven ILC:https://ieeexplore.ieee.org/abstract/document/10384133

DeePC: https://arxiv.org/abs/1811.05890

Jonathan Mayo-Maldonado: https://scholar.google.co.uk/citations?user=W-vnMBwAAAAJ&hl=en

Extra questions

Aizerman’s conjecture: https://en.wikipedia.org/wiki/Aizerman%27s_conjecture

In this episode I interview Professor Sabine Hauert about the super interesting work she does on the control of swarm robots, how considering nanoparticles as swarms can be used to treat cancer, and how morphogenesis can generate structure from random interactions.

You can follow us on Instagram (https://www.instagram.com/coffee_and_control_podcast/),BlueSky (https://bsky.app/profile/coffee-and-control.bsky.social) and X(https://x.com/coffee_ctrl_pod)for updates on episodes!

You can also connect with or follow me on LinkedIn: https://www.linkedin.com/in/lucy-hodgins-733a30175/

References

Sabine: https://hauertlab.com/

Podcasts/ TEDx talks

https://www.youtube.com/watch?v=sn1gmcs-HXU

https://www.youtube.com/watch?v=NBbYuzhxpE0

http://youtube.com/watch?v=vvknnV6325Q

Robot Talk: https://open.spotify.com/episode/0JWPnKQmwTQdM1K7247jkq

Complexity: https://open.spotify.com/episode/6nfcUpB3wesHqXP5XzSPAl

Engenius: https://open.spotify.com/episode/34jert4EQGBVrQBfS4OfxW

Research

Invertebrate inspiration review paper: https://iopscience.iop.org/article/10.1088/1748-3190/acc223/meta

Centipede control inspiration: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171421

David Garzon-Ramos: https://dgarzonramos.com/

Puzzle/ Problem/mess paper: https://arxiv.org/abs/2410.22478

Dario Floriano: https://people.epfl.ch/dario.floreano?lang=en

Manuela Veloso: https://engineering.cmu.edu/directory/bios/veloso-manuela.html

PhD

PhD thesis: https://infoscience.epfl.ch/entities/publication/dbb9fe40-930c-4e54-a5c0-10b62ebb6d1c
Robot swarm video: https://www.youtube.com/watch?v=n_qRuHkD5lc

Onboard evolution of swarm behaviours: https://advanced.onlinelibrary.wiley.com/doi/pdf/10.1002/aisy.201900031

Supervisory control papers: https://research-information.bris.ac.uk/files/229980063/Paper_SWARM2019.pdf

MAP-elites algorithm: https://link.springer.com/chapter/10.1007/978-3-319-77538-8_49

Morphogenesis

James Sharpe: https://www.embl.org/people/person/james-sharpe/

Original paper: https://www.science.org/doi/full/10.1126/scirobotics.aau9178

Controllability of morphogenesis: https://research-information.bris.ac.uk/en/publications/toward-controllable-morphogenesis-in-large-robot-swarms

Controllability in control theory: https://en.wikipedia.org/wiki/Controllability

Steve Brunton controllability Gramian video: https://www.youtube.com/watch?v=ZNHx62HbKNA

Alan Turing reaction diffusion paper: https://www.dna.caltech.edu/courses/cs191/paperscs191/turing.pdf

Nanoswarms

Sangita Bhatia: https://ki.mit.edu/people/faculty/sangeeta-bhatia

Nanoswarm papers: https://pmc.ncbi.nlm.nih.gov/articles/PMC4295824/

John Ives: https://www.bristol.ac.uk/people/person/Jonathan-Ives-fa38de81-8d34-4978-a99d-1f55efe2e0f4/

Matimba Swana: https://research-information.bris.ac.uk/en/persons/matimba-c-swana

Outreach

AIhub.org: https://aihub.org/

Robohub.org: https://robohub.org/

Drones for 3D printing buildings: https://robohub.org/five-ways-drones-will-change-the-way-buildings-are-designed/

AI environmental impact: https://aihub.org/2025/02/06/explained-generative-ais-environmental-impact/

AI for drug development: https://aihub.org/2025/01/09/will-ai-revolutionize-drug-development-researchers-explain-why-it-depends-on-how-its-used/

Extra questions

Radhika Nagpal: https://www.radhikanagpal.org/

Dot robots: https://arxiv.org/pdf/2203.13809

In this episode, I talk to Professor William Holderbaum about some of the many fascinating areas of research he’s involved in, including Boolean control, geometric control, and control of electroactive polymer gels—plus a lot more!

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PhD research

FES work

FES muscle fatigue papers

Geometric control

Control of RTG cranes

Electroactive polymer gels

In this episode I talk to Dr Zehor Belkhatir about her fascinating

You can follow us on Instagram, BlueSky, and X for updates on episodes!

In this episode we interview Professor Matthew Turner, professor in the Cyber Physical Systems group at the university of Southampton, about his fascinating work on aircraft control, anti-windup, Lur’e systems, and his recent research into applying techniques from control theory to the analysis of neural networks.

Contact me at: [email protected]

We have an Instagram now!

References:

Other cool neural network/ control papers

In this first episode, I talk to Chris Freeman, professor of applied control at the University of Southampton and expert on all things related to iterative learning control and its application in rehabilitation.

References:

People Chris worked with throughout his PhD:

Rehabilitation robotics folks:

Tremor suppression:

Multiple model ILC:

Electrode arrays:

Biomedical contexts of ILC:

EDI:

Other projects:

Trailer for my new control-related podcast! Epsiodes will be released on the 1st of each month.

You can check out inControl here: https://www.incontrolpodcast.com/

inControl episodes tend to be realeased during the middle of the month, so you could subscribe to both!

(Please bear with me regarding the strange background noises and general awkwardness - I'm still learning how podcast making works!)