Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

Abstract

The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square-channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction of flow. Under the ideal solvent conditions, torsional twisting of the chain and aperiodic cyclical dynamics are observed for the end of the oligomer. Under poor solvent conditions, a metastable helix forms in the end of the chain despite the lack of any attractive potential between beads in the oligomeric chain. The formation of the helix is postulated to be the result of a solvent induced chain collapse that has been confined to a single dimension by a strong flow field.

15 pages, 13 figures, to appear in J. Chem. Phys., 2012

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