ORCID Profile
0000-0001-9111-182X
Current Organisations
University of Minnesota System
,
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
,
University of Oxford
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Publisher: AIP Publishing
Date: 03-2018
DOI: 10.1063/1.5018787
Abstract: If a semiflexible polymer confined to a narrow channel bends around by 180°, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here, we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte-Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.
Publisher: Zenodo
Date: 2018
Publisher: AIP Publishing
Date: 03-2015
DOI: 10.1063/1.4917269
Abstract: We use Brownian dynamics with hydrodynamic interactions to calculate both the Kirkwood (short-time) diffusivity and the long-time diffusivity of DNA chains from free solution down to channel confinement in the de Gennes regime. The Kirkwood diffusivity in confinement is always higher than the diffusivity obtained from the mean-squared displacement of the center-of-mass, as is the case in free solution. Moreover, the ergence of the local diffusion tensor, which is non-zero in confinement, makes a negligible contribution to the latter diffusivity in confinement. The maximum error in the Kirkwood approximation in our simulations is about 2% for experimentally relevant simulation times. The error decreases with increasing confinement, consistent with arguments from blob theory and the molecular-weight dependence of the error in free solution. In light of the typical experimental errors in measuring the properties of channel-confined DNA, our results suggest that the Kirkwood approximation is sufficiently accurate to model experimental data.
Publisher: Zenodo
Date: 2018
Publisher: Zenodo
Date: 2018
Location: United States of America
Location: No location found
Location: Netherlands
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Maria J. Cruz.