Control theory meets synthetic biology

D Del Vecchio, AJ Dy, Y Qian - Journal of The Royal …, 2016 - royalsocietypublishing.org
The past several years have witnessed an increased presence of control theoretic concepts
in synthetic biology. This review presents an organized summary of how these control …

Programmable protein circuit design

Z Chen, MB Elowitz - Cell, 2021 - cell.com
A fundamental challenge in synthetic biology is to create molecular circuits that can program
complex cellular functions. Because proteins can bind, cleave, and chemically modify one …

A universal biomolecular integral feedback controller for robust perfect adaptation

SK Aoki, G Lillacci, A Gupta, A Baumschlager… - Nature, 2019 - nature.com
Homeostasis is a recurring theme in biology that ensures that regulated variables robustly—
and in some systems, completely—adapt to environmental perturbations. This robust perfect …

Applications and advances of metabolite biosensors for metabolic engineering

D Liu, T Evans, F Zhang - Metabolic engineering, 2015 - Elsevier
Quantification and regulation of pathway metabolites is crucial for optimization of microbial
production bioprocesses. Genetically encoded biosensors provide the means to couple …

A quasi-integral controller for adaptation of genetic modules to variable ribosome demand

HH Huang, Y Qian, D Del Vecchio - Nature communications, 2018 - nature.com
The behavior of genetic circuits is often poorly predictable. A gene's expression level is not
only determined by the intended regulators, but also affected by changes in ribosome …

A cybergenetic framework for engineering intein-mediated integral feedback control systems

S Anastassov, M Filo, CH Chang… - Nature …, 2023 - nature.com
The ability of biological systems to tightly regulate targeted variables, despite external and
internal disturbances, is known as Robust Perfect Adaptation (RPA). Achieved frequently …

A hierarchy of biomolecular proportional-integral-derivative feedback controllers for robust perfect adaptation and dynamic performance

M Filo, S Kumar, M Khammash - Nature communications, 2022 - nature.com
Abstract Proportional-Integral-Derivative (PID) feedback controllers are the most widely used
controllers in industry. Recently, the design of molecular PID-controllers has been identified …

[HTML][HTML] Context-aware synthetic biology by controller design: Engineering the mammalian cell

N Shakiba, RD Jones, R Weiss, D Del Vecchio - Cell systems, 2021 - cell.com
The rise of systems biology has ushered a new paradigm: the view of the cell as a system
that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides …

[HTML][HTML] Biomolecular feedback controllers: from theory to applications

M Filo, CH Chang, M Khammash - Current Opinion in Biotechnology, 2023 - Elsevier
Highlights•Synthetic biomolecular feedback controllers have promising applications in
various fields.•Negative-feedback controllers enhance dynamic performance and reduce …

Cybergenetics: Theory and applications of genetic control systems

MH Khammash - Proceedings of the IEEE, 2022 - ieeexplore.ieee.org
There is no design template more important than DNA. Within the sequences of this
exquisite substance lie the design plans for each of us and for every living organism …