# The fluid dynamics of flagellar swimming by microorganisms and harmonic generation by reflecting internal, ocean-like waves

## Abstract

This dissertation includes two fluid dynamics studies that involve fluid flows on vastly different scales, and therefore vastly different physics. The first study is of bacterial swimming using a flagellum for propulsive motion. Because bacteria are only about 10 [micrometers] in length, they swim in a very low Reynolds number (10⁻⁴) world, which is described by the linear set of governing equations known as the Stokes equations, that are a simplified version of the Navier-Stokes equations. The second study is of harmonic generation from nonlinear effects in internal, ocean-like wave beams that reflect from boundaries in a density stratified fluid. Internal wave reflection is an important oceanic process and may help sustain ocean circulation and affect global weather patterns. Such ocean processes have typical Reynold's numbers of 10¹⁰ or more and are only described by the full, nonlinear Navier-Stokes equations. In the low Reynolds number study, I examine theories by Gray et al.(1956) and Lighthill (1975) that describe swimming microorganisms using a helical flagellum for propulsive motion. I determine the resistance matrix, which can fully describe the dynamics of a flagellum, for flagella with different geometries, defined by: filament radius a, helical radius R, helical pitch [lambda], and axial length L. I use laboratory experiments and numerical simulations conducted in collaboration with Dr. Hepeng Zhang. The experiments, conducted with assistance from a fellow graduate student Chih-Hung Chen, use macroscopic scale models of bacterial flagella in a bath of highly viscous silicone oil. Numerical simulations use the Regularized Stokeslet method, which approximates the Stokeslet representation of an immersed body in a low Reynolds number flow. My study covers a biologically relevant parameter regime: 1/10R < a < 1/25R, R < [lambda] < 20R, and 2R< L <40R. I determine the three elements of the resistance matrix by measuring propulsive force and torque generated by a rotating, non-translating flagellum, and the drag force on a translating, non-rotating flagellum. I investigate the dependences of the resistance matrix elements on both the flagellum's axial length and its wavelength. The experimental and numerical results are in excellent agreement, but they compare poorly with the predictions of resistive force theory. The theory's neglect of hydrodynamic interactions is the source of the discrepancies in both the length dependence and wavelength dependence studies. I show that the experimental and simulation data scale as L/ln(L/r), a scaling analytically derived from slender body theory by my other collaborator Dr. Bin Liu. This logarithmic scaling is new and missing from the widely used resistive force theory. Dr. Zhang's work also includes a new parameterized version of resistive force theory. The second part of the dissertation is a study of harmonic generation by internal waves reflected from boundaries. I conduct laboratory experiments and two-dimensional numerical simulations of the Navier-Stokes equations to determine the value of the topographic slope that gives the most intense generation of second harmonic waves in the reflection process. The results from my experiments and simulations agree well but differ markedly from theoretical predictions by Thorpe (1987) and by Tabaei et al. (2005), except for nearly inviscid, weakly nonlinear flow. However, even for weakly nonlinear flow (where the dimensionless Dauxois-Young amplitude parameter value is only 0.01), I find that the ratio of the reflected wavenumber to the incoming wavenumber is very different from the prediction of weakly nonlinear theory. Further, I observe that for incident beams with a wide range of angles, frequencies, and intensities, the second harmonic beam produced in reflection has a maximum intensity when its width is the same as the width of the incident beam. This observation yields a prediction for the angle corresponding to the maximum in second harmonic intensity that is in excellent accord with my results from experiments and numerical simulations.