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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{Henrich:2018:epje/i2018-11669-8,
author = {Henrich, O and Gutiérrez, Fosado YA and Curk, T and Ouldridge, TE},
doi = {epje/i2018-11669-8},
journal = {European Physical Journal E. Soft Matter},
pages = {57--57},
title = {Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications},
url = {http://dx.doi.org/10.1140/epje/i2018-11669-8},
volume = {41},
year = {2018}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
AU  - Henrich,O
AU  - Gutiérrez,Fosado YA
AU  - Curk,T
AU  - Ouldridge,TE
DO  - epje/i2018-11669-8
EP  - 57
PY  - 2018///
SN  - 1292-8941
SP  - 57
TI  - Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications
T2  - European Physical Journal E. Soft Matter
UR  - http://dx.doi.org/10.1140/epje/i2018-11669-8
UR  - https://www.ncbi.nlm.nih.gov/pubmed/29748779
UR  - http://hdl.handle.net/10044/1/59745
VL  - 41
ER  -