Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a few static and dynamic systems that are dominated by charge effects. One class comprises complexation between oppositely charged objects, for example the adsorption of charged ions or charged polymers on oppositely charged substrates of different geometry. Here the main questions are whether adsorption occurs and what the effective charge of the resulting complex is. We explicitly discuss the adsorption behavior of polyelectrolytes on substrates of planar, cylindrical and spherical geometry with specific reference to DNA adsorption on supported charged lipid layers, DNA adsorption on oppositely charged cylindrical dendro-polymers, and DNA binding on globular histone proteins, respectively. In all these systems salt plays an important role, and some of the important features can already be obtained on the linear Debye-Hückel level. The second class comprises effective interactions between similarly charged objects. Here the main theme is to understand the experimental finding that similarly and highly charged bodies attract each other in the presence of multi-valent counterions. This is demonstrated using field-theoretic arguments as well as Monte-Carlo simulations for the case of two homogeneously charged bodies. Realistic surfaces, on the other hand, are corrugated and also exhibit modulated charge distributions, which is important for static properties such as the counterion-density distribution, but has even more pronounced consequences for dynamic properties such as the counterion mobility. More pronounced dynamic effects are obtained with highly condensed charged systems in strong electric fields. Likewise, an electrostatically collapsed highly charged polymer is unfolded and oriented in strong electric fields. All charged systems occur in water, and water by itself is not a very well understood material. At the end of this review, we give a very brief and incomplete account of the behavior of water at planar surfaces. The coupling between water structure and charge effects is largely unexplored, and a few directions for future research are sketched. On an even more nanoscopic level, we demonstrate using ab-initio methods that specific interactions between oppositely charged groups (which occur when their electron orbitals start to overlap) are important and cause ion-specific effects that have recently moved into the focus of interest.

Spurred by an experimental controversy in the literature, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations and dynamic mean-field theory. Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) 〈r 2 (t)〉 ~ t 1/2 at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling 〈r 2 (t)〉 ~ t 2/3 in the same time range. Using hydrodynamic simulations, analytical and scaling theories, we find a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, α(t) = d log〈r 2 (t)〉/d log t, drops below the Zimm value of 2/3 for sufficiently long chains. The deviation from the Zimm prediction increases with chain length, though it does not reach the Rouse limit of 1/2. The qualitative features of this intermediate regime, found in simulations and in an improved mean-field theory for semiflexible polymers, in particular the variation of α(t) with chain and persistence lengths, can be reproduced through a heuristic scaling argument. Anomalously low values of the effective exponent α are explained by hydrodynamic effects related to the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger length scales.

The dynamics of a rotating elastic filament is investigated using Stokesian simulations. The filament, straight and tilted with respect to its rotation axis for small driving torques, undergoes at a critical torque a strongly discontinuous shape bifurcation to a helical state. It induces a substantial forward propulsion whatever the sense of rotation: a nanomechanical force-rectification device is established.

Using hydrodynamic simulation methods and scaling arguments, we consider an elastic rod which is moving in a gravitational or electric field through a quiescent fluid in the low-Reynolds-number limit. Hydrodynamic effects lead to rod bending and orientation perpendicular to the direction of motion, similar to what is seen in anomalous electric birefringence experiments on TM and FD viruses or polyelectrolytes. Static and dynamic scaling relations for the mean orientation as a function of rod length and elasticity are established.

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.