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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{Kuntz:2021,
author = {Kuntz, J and Thomas, P and Stan, G-B and Barahona, M},
journal = {SIAM Review},
title = {Stationary distributions of continuous-time Markov chains: a review of  theory and truncation-based approximations},
url = {http://arxiv.org/abs/1909.05794v1},
year = {2021}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Computing the stationary distributions of a continuous-time Markov chaininvolves solving a set of linear equations. In most cases of interest, thenumber of equations is infinite or too large, and cannot be solved analyticallyor numerically. Several approximation schemes overcome this issue by truncatingthe state space to a manageable size. In this review, we first give acomprehensive theoretical account of the stationary distributions and theirrelation to the long-term behaviour of the Markov chain, which is readilyaccessible to non-experts and free of irreducibility assumptions made instandard texts. We then review truncation-based approximation schemes payingparticular attention to their convergence and to the errors they introduce, andwe illustrate their performance with an example of a stochastic reactionnetwork of relevance in biology and chemistry. We conclude by elaborating oncomputational trade-offs associated with error control and some open questions.
AU  - Kuntz,J
AU  - Thomas,P
AU  - Stan,G-B
AU  - Barahona,M
PY  - 2021///
SN  - 0036-1445
TI  - Stationary distributions of continuous-time Markov chains: a review of  theory and truncation-based approximations
T2  - SIAM Review
UR  - http://arxiv.org/abs/1909.05794v1
UR  - http://hdl.handle.net/10044/1/81806
ER  -

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