Chemical and hydrodynamic alignment of an enzyme.

Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with short-range surface interactions. An asymmetric dumbbell consisting of two unequal subunits, in a nonuniform suspension of a solute with which it interacts via hydrodynamic interactions as well as non-contact surface interactions, is shown to have two alignment mechanisms due to the two types of interactions. In addition to alignment, the chemical gradient results in a drift velocity that is modified by hydrodynamic interactions between the constituents of the enzyme.

Probing passive diffusion of flagellated and deflagellated Escherichia coli.

Using particle-tracking techniques, the translational and rotational diffusion of paralyzed E. coli with and without flagella are studied experimentally. The position and orientation of the bacteria are tracked in the lab frame and their corresponding mean-square displacements are analyzed in the lab frame and in the body frame to extract the intrinsic anisotropic translational diffusion coefficients as well as the rotational diffusion coefficient for both strains. The deflagellated strain is found to show an anisotropic translational diffusion, with diffusion coefficients that are compatible with theoretical estimates based on its measured geometrical features. The corresponding translational diffusion coefficients of the flagellated strain have been found to be reduced as compared to those of the deflagellated counterpart. Similar results have also been found for the rotational diffusion coefficients of the two strains. Our results suggest that the presence of flagella --even as a passive component-- has a significant role in the dynamics of E. coli, and should be taken into account in theoretical studies of its motion.

Three-sphere low-Reynolds-number swimmer with a cargo container.

A recently introduced model for an autonomous swimmer at low Reynolds number that is comprised of three spheres connected by two arms is considered when one of the spheres has a large radius. The Stokes hydrodynamic flow associated with the swimming strokes and net motion of this system can be studied analytically using the Stokes Green's function of a point force in front of a sphere of arbitrary radius R provided by Oseen. The swimming velocity is calculated, and shown to scale as 1/R3 with the radius of the sphere.

The interfacial behaviour of single poly(N,N-dimethylacrylamide) chains as a function of pH.

We have studied the pH-dependent conformational behaviour of poly(N,N-dimethylacrylamide) (PDMAc) at silicon and gold surfaces using single-molecule force spectroscopy and a quartz crystal microbalance (QCM). Despite the pH dependence, nuclear magnetic resonance and titration experiments demonstrate that PDMAc is not a weak polybase. The interaction between single chains and a silicon surface (with native oxide layer intact) in aqueous solution was investigated using force spectroscopy. Single-molecule force measurements were performed using thiol-functionalized PDMAc and gold-coated AFM cantilevers. The forces of interaction between PDMAc and the native oxide-coated silicon surface vary with the pH. The shape of the retraction curve for low pH solution includes a greater number of 'train' conformations, which suggests a stronger interaction with the surface relative to the surrounding media at low pH. The adsorption behaviour of PDMAc, from liquid onto silicon surfaces, was monitored using a QCM, which shows greater PDMAc adsorption onto silicon at low pH. The force spectroscopy and QCM investigations confirm that the PDMAc chain is more extended and stiffer in low pH solution. We attribute the pH-dependent behaviour to an increased number of hydrogen bonding sites on the silicon surface at low pH.

Liquid rope coiling on a solid surface.

We present an experimental study of the coiling instability of a liquid "rope" falling on a solid surface. Coiling can occur in three different regimes--viscous, gravitational, or inertial--depending on the fluid viscosity and density, the fall height, and the flow rate. The competition among the different forces causes the coiling frequency first to decrease and subsequently to increase with increasing height. We also observe an oscillation between two coiling states in the gravitational-to-inertial transitional range, reflecting the multivaluedness of the dependence of coiling frequency on fall height. The data can be rescaled in a universal way, and agree very well with numerically predicted coiling frequencies.

Nonlinear mechanical response of DNA due to anisotropic bending elasticity.

The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend coupling that can lead to the formation of kinks and modulations in the curvature and/or in the twist, depending on the values of the elastic constants and the imposed deflection angle. The typical wavelength for the modulations, or the distance between the neighboring kinks is found to be set by half of the DNA pitch.

Radial distribution function of rod-like polyelectrolytes.

We study the effect of electrostatic interactions on the distribution function of the end-to-end distance of a single polyelectrolyte chain in the rod-like limit. The extent to which the radial distribution function of a polyelectrolyte is reproduced by that of a wormlike chain with an adjusted effective persistence length is investigated. Strong evidence is found for a universal scaling formula connecting the effective persistence length of a polyelectrolyte with the strength of the electrostatic interaction and the Debye screening length.

Dissipation in dynamics of a moving contact line.

The dynamics of the deformations of a moving contact line is studied assuming two different dissipation mechanisms. It is shown that the characteristic relaxation time for a deformation of wavelength 2pi/|k| of a contact line moving with velocity v is given as tau(-1)(k)=c(v)|k|. The velocity dependence of c(v) is shown to depend drastically on the dissipation mechanism: we find c(v)=c(v=0)-2v for the case in which the dynamics is governed by microscopic jumps of single molecules at the tip (Blake mechanism), and c(v) approximately c(v=0)-4v when viscous hydrodynamic losses inside the moving liquid wedge dominate (de Gennes mechanism). We thus suggest that the debated dominant dissipation mechanism can be experimentally determined using relaxation measurements similar to the Ondarcuhu-Veyssie experiment [T. Ondarcuhu and M. Veyssie, Nature 352, 418 (1991)].

Casimir torques between anisotropic boundaries in nematic liquid crystals.

Fluctuation-induced interactions between anisotropic objects immersed in a nematic liquid crystal are shown to depend on the relative orientation of these objects. The resulting long-range "Casimir" torques are explicitly calculated for a simple geometry where elastic effects are absent. Our study generalizes previous discussions restricted to the case of isotropic walls, and leads to new proposals for experimental tests of Casimir forces and torques in nematics.

Probing the strong boundary shape dependence of the Casimir force.

We study the geometry dependence of the Casimir energy for deformed metal plates by a path integral quantization of the electromagnetic field. For the first time, we give a complete analytical result for the deformation induced change in Casimir energy delta E in an experimentally testable, nontrivial geometry, consisting of a flat and a corrugated plate. Our results show an interesting crossover for delta E as a function of the ratio of the mean plate distance H, to the corrugation length lambda: For lambda<>H.

Casimir dispersion forces and orientational pairwise additivity

A path-integral formulation is used to study the fluctuation-induced interactions between manifolds of arbitrary shape at large separations. It is shown that the form of the interactions crucially depends on the choice of the boundary condition. In particular, whether or not the Casimir interaction is pairwise additive is shown to depend on whether the "metallic" boundary condition corresponds to a "grounded" or an "isolated" manifold.

Statistical mechanics of semiflexible ribbon polymers.

The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from one type of short-range order to a fundamentally different sort of short-range order. In the high temperature regime, the two-point correlation functions of the object are identical to wormlike chains, while in the low temperature regime they are different due to a twist structure. The crossover happens when the persistence length of individual strands becomes comparable to the thickness of the ribbon. In the low temperature regime, the ribbon is observed to have a "kink-rod" structure with a mutual exclusion of twist and bend in contrast to smooth wormlike chain behavior. This is due to its anisotropic rigidity and corresponds to an infinitely strong twist-bend coupling. The double-stranded polymer is also studied in a confined geometry. It is shown that when the polymer is restricted in a particular direction to a size less than the bare persistence length of the individual strands, it develops zigzag conformations which are indicated by an oscillatory tangent-tangent correlation function in the direction of confinement. Increasing the separation of the confining plates leads to a crossover to the free behavior, which takes place at separations close to the bare persistence length. These results are expected to be relevant for experiments that involve complexation of two or more stiff or semiflexible polymers.