Extracting bulk properties of self-assembling systems from small simulations

Ouldridge, Thomas E.; Louis, Ard A.; Doye, Jonathan P. K.

doi:10.1088/0953-8984/22/10/104102

Cited by 66 publications

(97 citation statements)

References 50 publications

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“…The relative probabilities of bound and unbound states can than be related to the bulk yields f ∞ as described in Ref. 62. Extrapolating our results to the conditions of Ref.…”

Section: A Topologically Unlinked Complex; Lk =mentioning

confidence: 63%

The effect of topology on the structure and free energy landscape of DNA kissing complexes

Romano

Hudson

Doye

et al. 2012

The Journal of Chemical Physics

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We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers −1, 0, or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from −1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.

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“…The relative probabilities of bound and unbound states can than be related to the bulk yields f ∞ as described in Ref. 62. Extrapolating our results to the conditions of Ref.…”

Section: A Topologically Unlinked Complex; Lk =mentioning

confidence: 63%

The effect of topology on the structure and free energy landscape of DNA kissing complexes

Romano

Hudson

Doye

et al. 2012

The Journal of Chemical Physics

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“…However, the statistical distribution of various clusters of strands within a simulation volume obtained from a single-target simulation is different from the distribution that would be obtained from a bulk simulation of the same model (at the same concentration and temperature). 93,108 Physically, the difference arises because concentration fluctuations are suppressed. For example, in the case of a single duplex, there would always be one strand of each type in the simulated volume, whereas for the same volume in a bulk system there are many other possibilities.…”

Section: Rare-event Methodsmentioning

confidence: 99%

Coarse-graining DNA for simulations of DNA nanotechnology

Doye¹,

Ouldridge²,

Louis³

et al. 2013

Phys. Chem. Chem. Phys.

190

220

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To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

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“…35,39,[50][51][52]54 These examples involve dimers and clusters of a single species, which we analysed in our earlier work. 63 Interesting structures, however, are not exclusively dimers or formed from identical subunits. DNA nanostructures, such as polyhedra, 65,66 often involve several different single strands.…”

Section: Systems In the Canonical Ensemblementioning

confidence: 99%

Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble

Ouldridge¹

2012

The Journal of Chemical Physics

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In this paper we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling systems of characteristic finite size. In particular, schemes for extrapolating the results of simulations of a single self-assembling object to the bulk limit are established in three cases: for assembly involving multiple particle species, for systems with one species localized in space and for simulations in the grand canonical ensemble. Furthermore, methodologies are introduced for evaluating the accuracy of these extrapolations. Example systems demonstrate that differences in cluster concentrations between simulations of a single self-assembling structure and bulk studies of the same model under identical conditions can be large, and that convergence on bulk results as system size is increased can be slow and non-trivial.

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Extracting bulk properties of self-assembling systems from small simulations

Cited by 66 publications

References 50 publications

The effect of topology on the structure and free energy landscape of DNA kissing complexes

The effect of topology on the structure and free energy landscape of DNA kissing complexes

Coarse-graining DNA for simulations of DNA nanotechnology

Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble

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