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Research

Biological systems - including the simplest cells - exhibit a broad range of functions to thrive in their environment. Research in the Imperial College Centre for Synthetic Biology is focused on the possibility of engineering the underlying biochemical processes to solve many of the challenges facing society, from healthcare to sustainable energy. In particular, we model, analyse, design and build biological and biochemical systems in living cells and/or in cell extracts, both exploring and enhancing the engineering potential of biology.

As part of our research we develop novel methods to accelerate the celebrated Design-Build-Test-Learn synthetic biology cycle. As such research in the Centre for Synthetic Biology highly multi- and interdisciplinary covering computational modelling and machine learning approaches; automated platform development and genetic circuit engineering ; multi-cellular and multi-organismal interactions, including gene drive and genome engineering; metabolic engineering; in vitro/cell-free synthetic biology; engineered phages and directed evolution; and biomimetics, biomaterials and biological engineering.

Publications

Citation

BibTex format

@article{Sootla:2016:10.1016/j.automatica.2015.10.037,
author = {Sootla, A and Oyarzun, DA and Angeli, D and Stan, GB},
doi = {10.1016/j.automatica.2015.10.037},
journal = {Automatica},
pages = {254--264},
title = {Shaping Pulses to Control Bistable Systems: Analysis, Computation and Counterexamples},
url = {http://dx.doi.org/10.1016/j.automatica.2015.10.037},
volume = {63},
year = {2016}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - In this paper we study how to shape temporal pulses to switch a bistable system between its stable steady states. Our motivation forpulse-based control comes from applications in synthetic biology, where it is generally difficult to implement real-time feedback controlsystems due to technical limitations in sensors and actuators. We show that for monotone bistable systems, the estimation of the set ofall pulses that switch the system reduces to the computation of one non-increasing curve. We provide an efficient algorithm to computethis curve and illustrate the results with a genetic bistable system commonly used in synthetic biology. We also extend these results tomodels with parametric uncertainty and provide a number of examples and counterexamples that demonstrate the power and limitationsof the current theory. In order to show the full potential of the framework, we consider the problem of inducing oscillations in a monotonebiochemical system using a combination of temporal pulses and event-based control. Our results provide an insight into the dynamics ofbistable systems under external inputs and open up numerous directions for future investigation.
AU  - Sootla,A
AU  - Oyarzun,DA
AU  - Angeli,D
AU  - Stan,GB
DO  - 10.1016/j.automatica.2015.10.037
EP  - 264
PY  - 2016///
SN  - 1873-2836
SP  - 254
TI  - Shaping Pulses to Control Bistable Systems: Analysis, Computation and Counterexamples
T2  - Automatica
UR  - http://dx.doi.org/10.1016/j.automatica.2015.10.037
UR  - http://hdl.handle.net/10044/1/27308
VL  - 63
ER  -