Model for Polymorphic Transitions in Bacterial Flagella

Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes in solution temperature and ionic strength, and point substitutions in the amino acid sequence of the protein subunits that make up the filament. To explain polymorphism, we propose a new coarse-grained continuum rod theory based on the quaternary structure of the filament. The model has two molecular switches. The first is a double-well potential for the extension of a protofilament, which is one of the eleven almost longitudinal columns of subunits. Curved filament shapes occur in the model when there is a mismatch strain, i.e. when inter-subunit bonds in the inner core of the filament prefer a subunit spacing which is intermediate between the two spacings favored by the double-well potential. The second switch is a double-well potential for twist, due to lateral interactions between neighboring protofilaments. Cooperative interactions between neighboring subunits within a protofilament are necessary to ensure the uniqueness of helical ground states. We calculate a phase diagram for filament shapes and the response of a filament to external moment and force.Comment: 17 pages, 21 figure

Determining the Anchoring Strength of a Capillary Using Topological Defects

We consider a smectic-A* in a capillary with surface anchoring that favors parallel alignment. If the bulk phase of the smectic is the standard twist-grain-boundary phase of chiral smectics, then there will be a critical radius below which the smectic will not have any topological defects. Above this radius a single screw dislocation in the center of the capillary will be favored. Along with surface anchoring, a magnetic field will also suppress the formation of a screw dislocation. In this note, we calculate the critical field at which a defect is energetically preferred as a function of the surface anchoring strength and the capillary radius. Experiments at a few different radii could thus determine the anchoring strength.Comment: Plain TeX (macros included), 8 pages, 2 included ps figures. Revision includes a new figure and a textual modificatio

Swimming near Deformable Membranes at Low Reynolds Number

Microorganisms are rarely found in Nature swimming freely in an unbounded fluid. Instead, they typically encounter other organisms, hard walls, or deformable boundaries such as free interfaces or membranes. Hydrodynamic interactions between the swimmer and nearby objects lead to many interesting phenomena, such as changes in swimming speed, tendencies to accumulate or turn, and coordinated flagellar beating. Inspired by this class of problems, we investigate locomotion of microorganisms near deformable boundaries. We calculate the speed of an infinitely long swimmer close to a flexible surface separating two fluids; we also calculate the deformation and swimming speed of the flexible surface. When the viscosities on either side of the flexible interface differ, we find that fluid is pumped along or against the swimming direction, depending on which viscosity is greater

Helical swimming in Stokes flow using a novel boundary-element method

We apply the boundary-element method to Stokes flows with helical symmetry, such as the flow driven by an immersed rotating helical flagellum. We show that the two-dimensional boundary integral method can be reduced to one dimension using the helical symmetry. The computational cost is thus much reduced while spatial resolution is maintained. We review the robustness of this method by comparing the simulation results with the experimental measurement of the motility of model helical flagella of various ratios of pitch to radius, along with predictions from resistive-force theory and slender-body theory. We also show that the modified boundary integral method provides reliable convergence if the singularities in the kernel of the integral are treated appropriately.Comment: 30 pages, 10 figure

Locomotion of helical bodies in viscoelastic fluids: enhanced swimming at large helical amplitudes

The motion of a rotating helical body in a viscoelastic fluid is considered. In the case of force-free swimming, the introduction of viscoelasticity can either enhance or retard the swimming speed and locomotive efficiency, depending on the body geometry, fluid properties, and the body rotation rate. Numerical solutions of the Oldroyd-B equations show how previous theoretical predictions break down with increasing helical radius or with decreasing filament thickness. Helices of large pitch angle show an increase in swimming speed to a local maximum at a Deborah number of order unity. The numerical results show how the small-amplitude theoretical calculations connect smoothly to the large-amplitude experimental measurements

Enhancement of microorganism swimming speed in active matter

We study a swimming undulating sheet in the isotropic phase of an active nematic liquid crystal. Activity changes the effective shear viscosity, reducing it to zero at a critical value of activity. Expanding in the sheet amplitude, we find that the correction to the swimming speed due to activity is inversely proportional to the effective shear viscosity. Our perturbative calculation becomes invalid near the critical value of activity; using numerical methods to probe this regime, we find that activity enhances the swimming speed by an order of magnitude compared to the passive case.Comment: 5 pages, 5 figure

Propulsion by a Helical Flagellum in a Capillary Tube

We study the microscale propulsion of a rotating helical filament confined by a cylindrical tube, using a boundary-element method for Stokes flow that accounts for helical symmetry. We determine the effect of confinement on swimming speed and power consumption. Except for a small range of tube radii at the tightest confinements, the swimming speed at fixed rotation rate increases monotonically as the confinement becomes tighter. At fixed torque, the swimming speed and power consumption depend only on the geometry of the filament centerline, except at the smallest pitch angles for which the filament thickness plays a role. We find that the `normal' geometry of \textit{Escherichia coli} flagella is optimized for swimming efficiency, independent of the degree of confinement. The efficiency peaks when the arc length of the helix within a pitch matches the circumference of the cylindrical wall. We also show that a swimming helix in a tube induces a net flow of fluid along the tube.Comment: 13 pages, 5 figure

Wrinkling of a thin film on a nematic liquid crystal elastomer

Wrinkles commonly develop in a thin film deposited on a soft elastomer substrate when the film is subject to compression. Motivated by recent experiments [Agrawal et al., Soft Matter 8, 7138 (2012)] that show how wrinkle morphology can be controlled by using a nematic elastomer substrate, we develop the theory of small-amplitude wrinkles of an isotropic film atop a nematic elastomer. The directors of the nematic elastomer are assumed to lie in a plane parallel to the plane of the undeformed film. For uniaxial compression of the film along the direction perpendicular to the elastomer directors, the system behaves as a compressed film on an isotropic substrate. When the uniaxial compression is along the direction of nematic order, we find that the soft elasticity characteristic of liquid crystal elastomers leads to a critical stress for wrinkling which is very small compared to the case of an isotropic substrate. We also determine the wavelength of the wrinkles at the critical stress, and show how the critical stress and wavelength depend on substrate depth and the anisotropy of the polymer chains in the nematic elastomer

Locomotion and transport in a hexatic liquid crystal

The swimming behavior of bacteria and other microorganisms is sensitive to the physical properties of the fluid in which they swim. Mucus, biofilms, and artificial liquid-crystalline solutions are all examples of fluids with some degree of anisotropy that are also commonly encountered by bacteria. In this article, we study how liquid-crystalline order affects the swimming behavior of a model swimmer. The swimmer is a one-dimensional version of G. I. Taylor's swimming sheet: an infinite line undulating with small-amplitude transverse or longitudinal traveling waves. The fluid is a two-dimensional hexatic liquid-crystalline film. We calculate the power dissipated, swimming speed, and flux of fluid entrained as a function of the swimmer's waveform as well as properties of the hexatic film, such as the rotational and shear viscosity, the Frank elastic constant, and the anchoring strength. The departure from isotropic behavior is greatest for large rotational viscosity and weak anchoring boundary conditions on the orientational order at the swimmer surface. We even find that if the rotational viscosity is large enough, the transverse-wave swimmer moves in the opposite direction relative to a swimmer in an isotropic fluid

Dynamic supercoiling bifurcations of growing elastic filaments

Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The structures may be solenoids or plectonemes, with or without branches in the latter case. Any microscopic theory of these morphological instabilities must address the nature of pattern selection in the presence of growth, for growth renders the problem nonautonomous and the bifurcations dynamic. To gain insight into these phenomena, we formulate a general theory for growing elastic filaments with bending and twisting resistance in a viscous medium, and study an illustrative model problem: a growing filament with preferred twist, closed into a loop. Growth depletes the twist, inducing a twist strain. The closure of the loop prevents the filament from unwinding back to the preferred twist; instead, twist relaxation is accomplished by the formation of supercoils. Growth also produces viscous stresses on the filament which even in the absence of twist produce buckling instabilities. Our linear stability analysis and numerical studies reveal two dynamic regimes. For small intrinsic twist the instability is akin to Euler buckling, leading to solenoidal structures, while for large twist it is like the classic writhing of a twisted filament, producing plectonemic windings. This model may apply to situations in which supercoils form only, or more readily, when axial rotation of filaments is blocked. Applications to specific biological systems are proposed.Comment: 35 pages, 11 figure