Conformation dependence of DNA electrophoretic mobility in a converging channel.

The electrophoresis of lambda-DNA is observed in a microscale converging channel where the center-of-masses trajectories of DNA molecules are tracked to measure instantaneous electrophoretic (EP) mobilities of DNA molecules of various stretch lengths and conformations. Contrary to the usual assumption that DNA mobility is a constant, independent of field and DNA length in free solution, we find DNA EP mobility varies along the axis in the contracting geometry. We correlate this mobility variation with the local stretch and conformational changes of the DNA, which are induced by the electric field gradient produced by the contraction. A "shish-kebab" model of a rigid polymer segment is developed, which consists of aligned spheres acting as charge and drag centers. The EP mobility of the shish-kebab is obtained by determining the electrohydrodynamic interactions of aligned spheres driven by the electric field. Multiple shish-kebabs are then connected end-to-end to form a freely jointed chain model for a flexible DNA chain. DNA EP mobility is finally obtained as an ensemble average over the shish-kebab orientations that are biased to match the overall stretch of the DNA chain. Using physically reasonable parameters, the model agrees well with experimental results for the dependence of EP mobility on stretch and conformation. We find that the magnitude of the EP mobility increases with DNA stretch, and that this increase is more pronounced for folded conformations.

The hydrodynamics of a run-and-tumble bacterium propelled by polymorphic helical flagella.

To study the swimming of a peritrichous bacterium such as Escherichia coli, which is able to change its swimming direction actively, we simulate the "run-and-tumble" motion by using a bead-spring model to account for: 1), the hydrodynamic and the mechanical interactions among the cell body and multiple flagella; 2), the reversal of the rotation of a flagellum in a tumble; and 3), the associated polymorphic transformations of the flagellum. Because a flexible hook connects the cell body and each flagellum, the flagella can take independent orientations with respect to the cell body. This simulation reproduces the experimentally observed behaviors of E. coli, namely, a three-dimensional random-walk trajectory in run-and-tumble motion and steady clockwise swimming near a wall. We show that the polymorphic transformation of a flagellum in a tumble facilitates the reorientation of the cell, and that the time-averaged flow-field near a cell in a run has double-layered helical streamlines, with a time-dependent flow magnitude large enough to affect the transport of surrounding chemoattractants.

Shear-induced chiral migration of particles with anisotropic rigidity.

We report that an achiral particle with anisotropic rigidity can migrate in the vorticity direction in shear flow. A minimal "tetrumbbell" model of such a particle is constructed from four beads and six springs to make a tetrahedral structure. A combination of two different spring constants corresponding to "hard" and "soft" springs yields ten distinguishable tetrumbbells, which when simulated in shear flow with hydrodynamic interactions between beads but no Brownian motion at zero Reynolds number, produces five different types of behavior in which seven out of ten tetrumbbell structures migrate in the vorticity direction due to shear-induced chirality. Some of the structures migrate in the same direction along the vorticity direction even when the shear flow is reversed, which is impossible for permanently chiral objects.

Fluidic trapping of deformable polymers in microflows.

We report that a polymer molecule can be trapped spatially and conformationally using a microflow that has at least two stagnation points (or two points with equal velocity) and a net flow orthogonal to the line connecting them. Examples include a Taylor vortex flow and an electro-osmotic flow in a channel with surfaces that have a sinusoidal charge. Simulating the motion of a polymer molecule in these flows using Brownian dynamics, we find that such flows produce a curved polymer conformation, leading to an elastic force that drives migration against the flow, thus stabilizing this conformation. Simulations with hydrodynamic interactions confirm these predictions and show that there exists a repulsive interaction between two trapped polymers.

Simulation of DNA motion in a microchannel using stochastic rotation dynamics.

The authors propose a method to simulate the DNA motion in microchannels of complex geometry. It is based on stochastic rotation dynamics using a new scheme for the boundary condition. The method enables them to define a boundary wall of arbitrary shape and to describe a wall moving at an arbitrary velocity. As an application, they simulate the motion of DNA in Poiseuille flow between two parallel planes and show that DNA molecules tend to concentrate near the center of the channel in agreement with experimental results.