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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{Papadimitriou:2013:10.1371/journal.pone.0053591,
author = {Papadimitriou, KI and Stan, G-B and Drakakis, EM},
doi = {10.1371/journal.pone.0053591},
journal = {PLoS ONE},
title = {Systematic computation of non-linear cellular and molecular dynamics with low-power cytomimetic circuits: A simulation study},
url = {http://dx.doi.org/10.1371/journal.pone.0053591},
volume = {8},
year = {2013}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented.
AU  - Papadimitriou,KI
AU  - Stan,G-B
AU  - Drakakis,EM
DO  - 10.1371/journal.pone.0053591
PY  - 2013///
SN  - 1932-6203
TI  - Systematic computation of non-linear cellular and molecular dynamics with low-power cytomimetic circuits: A simulation study
T2  - PLoS ONE
UR  - http://dx.doi.org/10.1371/journal.pone.0053591
UR  - http://hdl.handle.net/10044/1/63623
VL  - 8
ER  -

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