Kirkwood diffusivity of long semiflexible chains in nanochannel confinement

Abhiram Muralidhar, Kevin D. Dorfman

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

We compute the axial diffusivity of asymptotically long semiflexible polymers confined in square channels. Our calculations employ the Kirkwood approximation of the mobility tensor by combining computational fluid dynamics (CFD) calculations of the hydrodynamic tensor in channel confinement with the pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model. Three key results emerge from our study. First, for the classic de Gennes regime, we confirm that Brochard and de Gennes' blob theory correctly predicts the scaling of the axial diffusivity, contrary to the conclusions of previous analyses. Second, for the extended de Gennes regime, we show that a modified blob theory, which has been used to incorporate the effect of local stiffness on DNA diffusion in nanoslits, explains the deviation from the prediction of classic blob theory for diffusion in nanochannels. Third, we provide a calculation similar to the modified blob theory to explain the relative insensitivity of the diffusivity to channel size for channels between the extended de Gennes regime and the Odijk regime, which is the most relevant regime for experiments and technological applications of DNA confinement in nanochannels. Our results not only are relevant to the dynamics of confined semiflexible polymers such as DNA but also reveal interesting analogies between confinement in channels and slits.

Original languageEnglish (US)
Pages (from-to)2829-2839
Number of pages11
JournalMacromolecules
Volume48
Issue number8
DOIs
StatePublished - Apr 28 2015

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