Publications
75 results found
Sulc P, Romano F, Ouldridge TE, et al., 2014, A nucleotide-level coarse-grained model of RNA, JOURNAL OF CHEMICAL PHYSICS, Vol: 140, ISSN: 0021-9606
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- Citations: 84
Ć ulc P, Ouldridge TE, Romano F, et al., 2014, Simulating a burnt-bridges DNA motor with a coarse-grained DNA model, Natural Computing, Vol: 13, Pages: 535-547, ISSN: 1567-7818
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a ‘burnt-bridges’ DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful steps due to the build up of unfavourable tension. The mechanism of suppression suggests that varying the distance between stators could be used as a method for improving signal-to-noise ratios for motors that are required to make a decision at a junction of stators.
Srinivas N, Ouldridge TE, Sulc P, et al., 2013, On the biophysics and kinetics of toehold-mediated DNA strand displacement, NUCLEIC ACIDS RESEARCH, Vol: 41, Pages: 10641-10658, ISSN: 0305-1048
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- Citations: 319
Ouldridge TE, Sulc P, Romano F, et al., 2013, DNA hybridization kinetics: zippering, internal displacement and sequence dependence, NUCLEIC ACIDS RESEARCH, Vol: 41, Pages: 8886-8895, ISSN: 0305-1048
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- Citations: 159
Ouldridge TE, Hoare RL, Louis AA, et al., 2013, Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker, ACS NANO, Vol: 7, Pages: 2479-2490, ISSN: 1936-0851
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- Citations: 77
Romano F, Chakraborty D, Doye JPK, et al., 2013, Coarse-grained simulations of DNA overstretching, JOURNAL OF CHEMICAL PHYSICS, Vol: 138, ISSN: 0021-9606
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- Citations: 59
Doye JPK, Ouldridge TE, Louis AA, et al., 2013, Coarse-graining DNA for simulations of DNA nanotechnology, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 15, Pages: 20395-20414, ISSN: 1463-9076
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- Citations: 143
Ouldridge TE, 2012, Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble, JOURNAL OF CHEMICAL PHYSICS, Vol: 137, ISSN: 0021-9606
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- Citations: 16
Sulc P, Romano F, Ouldridge TE, et al., 2012, Sequence-dependent thermodynamics of a coarse-grained DNA model, JOURNAL OF CHEMICAL PHYSICS, Vol: 137, ISSN: 0021-9606
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- Citations: 218
Matek C, Ouldridge TE, Levy A, et al., 2012, DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 116, Pages: 11616-11625, ISSN: 1520-6106
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- Citations: 33
Romano F, Hudson A, Doye JPK, et al., 2012, The effect of topology on the structure and free energy landscape of DNA kissing complexes, JOURNAL OF CHEMICAL PHYSICS, Vol: 136, ISSN: 0021-9606
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- Citations: 24
Ouldridge TE, Louis AA, Doye JPK, 2011, Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model, JOURNAL OF CHEMICAL PHYSICS, Vol: 134, ISSN: 0021-9606
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- Citations: 315
Ouldridge TE, Louis AA, Doye JPK, 2010, DNA Nanotweezers Studied with a Coarse-Grained Model of DNA, PHYSICAL REVIEW LETTERS, Vol: 104, ISSN: 0031-9007
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- Citations: 142
Ouldridge TE, Louis AA, Doye JPK, 2010, Extracting bulk properties of self-assembling systems from small simulations, JOURNAL OF PHYSICS-CONDENSED MATTER, Vol: 22, ISSN: 0953-8984
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- Citations: 40
Ouldridge TE, Johnston IG, Louis AA, et al., 2009, The self-assembly of DNA Holliday junctions studied with a minimal model, JOURNAL OF CHEMICAL PHYSICS, Vol: 130, ISSN: 0021-9606
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- Citations: 31
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