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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{Sengar:2021:10.3389/fmolb.2021.693710,
author = {Sengar, A and Ouldridge, TE and Henrich, O and Rovigatti, L and Sulc, P},
doi = {10.3389/fmolb.2021.693710},
journal = {Frontiers in Molecular Biosciences},
pages = {1--22},
title = {A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results},
url = {http://dx.doi.org/10.3389/fmolb.2021.693710},
volume = {8},
year = {2021}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - The oxDNA model of DNA has been applied widely to systems in biology,biophysics and nanotechnology. It is currently available via two independentopen source packages. Here we present a set of clearly-documented exemplarsimulations that simultaneously provide both an introduction to simulating themodel, and a review of the model's fundamental properties. We outline howsimulation results can be interpreted in terms of -- and feed into ourunderstanding of -- less detailed models that operate at larger length scales,and provide guidance on whether simulating a system with oxDNA is worthwhile.
AU  - Sengar,A
AU  - Ouldridge,TE
AU  - Henrich,O
AU  - Rovigatti,L
AU  - Sulc,P
DO  - 10.3389/fmolb.2021.693710
EP  - 22
PY  - 2021///
SN  - 2296-889X
SP  - 1
TI  - A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
T2  - Frontiers in Molecular Biosciences
UR  - http://dx.doi.org/10.3389/fmolb.2021.693710
UR  - http://arxiv.org/abs/2104.11567v1
UR  - https://www.frontiersin.org/articles/10.3389/fmolb.2021.693710/full
UR  - http://hdl.handle.net/10044/1/89298
VL  - 8
ER  -