Eur. Phys. J. E (2015) 38: 89
https://doi.org/10.1140/epje/i2015-15089-0

Regular Article

Mesoscopic simulation of single DNA dynamics in rotational flows

Micro/nanofluidics Research Laboratory, Department of Mechanical Engineering, College of Engineering Trivandrum, Govermnet of Kerala, 695016, Thiruvananthapuram, India

^* e-mail: ranjith@cet.ac.in

Received: 12 April 2015
Revised: 11 June 2015
Accepted: 22 June 2015
Published online: 28 August 2015

Abstract

In this numerical study, the transport and dynamics of an isolated DNA in rotational flow generated in a microchannel have been investigated using dissipative particle dynamics. Often, inertial flow through microchannels with a sudden change in surface structure facilitates a re-circulation or vortex region. The conformation and mobility of the bio-polymer under the influence of such rotating fluid inside a square cavity of the microchannel is analyzed. The flexible polymer chain is found to migrate towards the rotating region and follows the vortex streamline. The orientation, size and tumbling period of polymer strands are affected by the strength of the microvortex. At elevated flow rates, the macromolecule prefers to remain inside the vortex and a hydrodynamic trap is formed. Moreover, residence time of the single molecule in the microcavity is significantly influenced by the chain length and flow strength. Further, it has been demonstrated that, such entrapment duration can be strategically altered by modifying the hydrophobicity of the microchannel.