ArticleBiomicrofluidics2013
Modeling the relaxation time of DNA confined in a nanochannel.
Article in Biomicrofluidics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 44 citations in OpenAlex.
- Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene.Materials today. Chemistry · 2021Article
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- A nanofluidic knot factory based on compression of single DNA in nanochannels.Nature communications · 2018Article
- Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel.Macromolecules · 2018Article
- The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.Journal of biomechanical engineering · 2018Article
- Simulations of knotting of DNA during genome mapping.Biomicrofluidics · 2017Article
- Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels.Biomicrofluidics · 2016Article
- Modeling the relaxation of internal DNA segments during genome mapping in nanochannels.Biomicrofluidics · 2016Article
- Measurements of DNA barcode label separations in nanochannels from time-series data.Biomicrofluidics · 2015Article
- DNA Brushing Shoulders: Targeted Looping and Scanning of Large DNA Strands.Nano letters · 2015Article
- Kirkwood diffusivity of long semiflexible chains in nanochannel confinement.Macromolecules · 2015Article
- Evaluation of the Kirkwood approximation for the diffusivity of channel-confined DNA chains in the de Gennes regime.Biomicrofluidics · 2015Article
- Hydrodynamics of DNA confined in nanoslits and nanochannels.The European physical journal. Special topics · 2014Article
- Mixed confinement regimes during equilibrium confinement spectroscopy of DNA.The Journal of chemical physics · 2014Article
- Interplay between chain stiffness and excluded volume of semiflexible polymers confined in nanochannels.The Journal of chemical physics · 2014Article
- Simulations of DNA stretching by flow field in microchannels with complex geometry.Biomicrofluidics · 2014Article
- Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels.Biomicrofluidics · 2013Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 (2012)], which have been difficult to validate due to the lack of direct experimental data. Furthermore, the model calculation shows that as the channel size passes below approximately 100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping.
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