Direct simulations of large populations of confined hydrodynamically interacting swimming particles at low Reynolds number are performed. Hydrodynamic coupling between the swimmers leads to large-scale coherent vortex motions in the flow and regimes of anomalous diffusion that are consistent with experimental observations. At low concentrations, swimmers propelled from behind (like spermatazoa) strongly migrate toward solid surfaces in agreement with simple theoretical considerations; at higher concentrations this localization is disrupted by the large-scale coherent motions.

Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro-and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.

We present a fully parametrized bead-spring chain model for stained -phage DNA. The model accounts for the finite extensibility of the molecule, excluded volume effects, and fluctuating hydrodynamic interactions ͑HI͒. Parameters are determined from equilibrium experimental data for 21 m stained -phage DNA, and are shown to quantitatively predict the non-equilibrium behavior of the molecule. The model is then used to predict the equilibrium and nonequilibrium behavior of DNA molecules up to 126 m. In particular, the HI model gives results that are in quantitative agreement with experimental diffusivity data over a wide range of molecular weights. When the bead friction coefficient is fit to the experimental relaxation time at a particular molecular weight, the stretch in shear and extensional flows is adequately predicted by either a free-draining or HI model at that molecular weight, although the fitted bead friction coefficients for the two models differ significantly. In shear flow, we find two regimes at high shear rate (␥ ) that follow different scaling behavior. In the first, the viscosity and first normal stress coefficient scale roughly as ␥ Ϫ6/11 and ␥ Ϫ14/11 , respectively. At higher shear rates, these become ␥ Ϫ2/3 and ␥ Ϫ4/3 . These regimes are found for both free-draining and HI models and can be understood based on scaling arguments for the diffusion of chain ends.

Populations of swimming micro-organisms produce fluid motions that lead to dramatically enhanced diffusion of tracer particles. Using simulations of suspensions of swimming particles in a periodic domain, we capture this effect and show that it depends qualitatively on the mode of swimming: swimmers "pushed" from behind by their flagella show greater enhancement than swimmers that are "pulled" from the front. The difference is manifested by an increase, that only occurs for pushers, of the diffusivity of passive tracers and the velocity correlation length with the size of the periodic domain. A physical argument supported by a mean field theory sheds light on the origin of these effects.

In this work, a continuum theory is developed for the behavior of flowing dilute polymer solutions near solid surfaces, using a bead-spring dumbbell model of the dissolved polymer chains. Hydrodynamic interactions between the chains and the wall lead to migration away from the wall in shear flow. At steady state, this hydrodynamic effect is balanced by molecular diffusion; an analytical expression for the resulting concentration profile is derived. It is shown that the depletion layer thickness is determined by the normal stresses that develop in flow and can be much larger than the size of the polymer molecule. The transient development of this depletion layer is also studied, as well as the spatial development downstream from an entrance. Numerical and similarity solutions in these cases show that the developing concentration profile generally displays a maximum at an intermediate distance from the wall.