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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{Fonseca:2018:10.1063/1.5019344,
author = {Fonseca, P and Romano, F and Schreck, JS and Ouldridge, TE and Doye, JPK and Louis, AA},
doi = {10.1063/1.5019344},
journal = {Journal of Chemical Physics},
title = {Multi-scale coarse-graining for the study of assembly pathways in  DNA-brick self assembly},
url = {http://dx.doi.org/10.1063/1.5019344},
volume = {148},
year = {2018}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Inspired by recent successes using single-stranded DNA tiles to producecomplex structures, we develop a two-step coarse-graining approach that usesdetailed thermodynamic calculations with oxDNA, a nucleotide-based model ofDNA, to parametrize a coarser kinetic model that can reach the time and lengthscales needed to study the assembly mechanisms of these structures. We test themodel by performing a detailed study of the assembly pathways for atwo-dimensional target structure made up of 334 unique strands each of whichare 42 nucleotides long. Without adjustable parameters, the model reproduces acritical temperature for the formation of the assembly that is close to thetemperature at which assembly first occurs in experiments. Furthermore, themodel allows us to investigate in detail the nucleation barriers and thedistribution of critical nucleus shapes for the assembly of a single targetstructure. The assembly intermediates are compact and highly connected(although not maximally so) and classical nucleation theory provides a good fitto the height and shape of the nucleation barrier at temperatures close towhere assembly first occurs.
AU  - Fonseca,P
AU  - Romano,F
AU  - Schreck,JS
AU  - Ouldridge,TE
AU  - Doye,JPK
AU  - Louis,AA
DO  - 10.1063/1.5019344
PY  - 2018///
SN  - 0021-9606
TI  - Multi-scale coarse-graining for the study of assembly pathways in  DNA-brick self assembly
T2  - Journal of Chemical Physics
UR  - http://dx.doi.org/10.1063/1.5019344
UR  - http://arxiv.org/abs/1712.02161v1
UR  - http://hdl.handle.net/10044/1/58303
VL  - 148
ER  -