Hydrodynamic effects in driven soft matter

Abstract

Recent theoretical works exploring the hydrodynamics of soft material in non-equilibrium situations are reviewed. We discuss the role of hydrodynamic interactions for three different systems: i) the deformation and orientation of sedimenting semiflexible polymers, ii) the propulsion and force-rectification with a nano-machine realized by a rotating elastic rod, and iii) the deformation of a brush made of grafted semiflexible polymers in shear flows. In all these examples deformable polymers are subject to various hydrodynamic flows and hydrodynamic interactions. Perfect stiff nano-cylinders are known to show no orientational effects as they sediment through a viscous fluid, but it is the coupling between elasticity and hydrodynamic torques that leads to an orientation perpendicular to the direction of sedimentation. Likewise, a rotating stiff rod does not lead to a net propulsion in the Stokes limit, but if bending is allowed an effective thrust develops whose strength and direction is independent of the sense of rotation and thus acts as a rectification device. Lastly, surface-anchored polymers are deformed by shear flows, which modifies the effective hydrodynamic boundary condition in a non-linear fashion. All these results are obtained with hydrodynamic Brownian dynamics simulation techniques, as appropriate for dilute systems. Scaling analyses are presented when possible. The common theme is the interaction between elasticity of soft matter and hydrodynamics, which can lead to qualitatively new effects.

DNA denaturation bubbles: Free-energy landscape and nucleation/closure rates

“…The use of all-atom simulations, or CG models considering explicitly stacking interaction in the single-stranded domain 16,19 , coupled to metadynamics, would be interesting, as a second step, to support our mechanism. Furthermore, the role of hydrodynamics interactions 46 , which might accelerate the closure, would be also relevant. Finally, let us comment on the potential biological implications of this work.…”

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“…2,16 For D(r), kinetic theory had limited success at high fluid packing densities, largely because of the complexity of the molecular motions in dense fluids resulting from their many-body character. At the other extreme, details of the molecular struca) jeetain@lehigh.edu.…”

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