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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{Davidchack:2017:10.1063/1.4999771,
author = {Davidchack, RL and Ouldridge, TE and Tretyakov, MV},
doi = {10.1063/1.4999771},
journal = {Journal of Chemical Physics},
title = {Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions},
url = {http://dx.doi.org/10.1063/1.4999771},
volume = {147},
year = {2017}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - We introduce new Langevin-type equations describing the rotational andtranslational motion of rigid bodies interacting through conservative andnon-conservative forces, and hydrodynamic coupling. In the absence ofnon-conservative forces the Langevin-type equations sample from the canonicalensemble. The rotational degrees of freedom are described using quaternions,the lengths of which are exactly preserved by the stochastic dynamics. For theproposed Langevin-type equations, we construct a weak 2nd order geometricintegrator which preserves the main geometric features of the continuousdynamics. A number of numerical experiments are presented to illustrate boththe new Langevin model and the numerical method for it.
AU  - Davidchack,RL
AU  - Ouldridge,TE
AU  - Tretyakov,MV
DO  - 10.1063/1.4999771
PY  - 2017///
SN  - 0021-9606
TI  - Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions
T2  - Journal of Chemical Physics
UR  - http://dx.doi.org/10.1063/1.4999771
UR  - http://hdl.handle.net/10044/1/54738
VL  - 147
ER  -

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