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Theoretical physicists working at a blackboard collaboration pod in the Beecroft building.
Credit: Jack Hobhouse

Ard Louis

Professor of Theoretical Physics

Research theme

  • Biological physics

Sub department

  • Rudolf Peierls Centre for Theoretical Physics

Research groups

  • Condensed Matter Theory
ard.louis@physics.ox.ac.uk
Louis Research Group members
Louis Research Group
  • About
  • Research
  • Publications on arXiv/bioRxiv
  • Publications

DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

Nucleic Acids Research 43:13 (2014) 6181-6190

Authors:

JS Schreck, Thomas Ouldridge, F Romano, P Sulc, L Shaw, AA Louis, Jonathan Doye

Abstract:

The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grainedmodel of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ~100 and ~2000. This surprisingly large speedup occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.

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DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

(2014)

Authors:

John S Schreck, Thomas E Ouldridge, Flavio Romano, Petr Sulc, Liam Shaw, Ard A Louis, Jonathan PK Doye
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A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure

Journal of The Royal Society Interface The Royal Society 11:95 (2014) 20140249

Authors:

Sam F Greenbury, Iain G Johnston, Ard A Louis, Sebastian E Ahnert
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A nucleotide-level coarse-grained model of RNA

Journal of Chemical Physics American Institute of Physics 140:23 (2014) 235102

Authors:

P Šulc, F Romano, TE Ouldridge, JP Doye, Adriaan Louis

Abstract:

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.
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Correlation of automorphism group size and topological properties with program-size complexity evaluations of graphs and complex networks

Physica A Statistical Mechanics and its Applications Elsevier 404 (2014) 341-358

Authors:

Hector Zenil, Fernando Soler-Toscano, Kamaludin Dingle, Ard A Louis
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