Optimal Design of Bacterial Carpets for Fluid Pumping

In this work, we outline a methodology for determining optimal helical flagella placement and phase shift that maximize fluid pumping through a rectangular flow meter above a simulated bacterial carpet. This method uses a Genetic Algorithm (GA) combined with a gradient-based method, the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm, to solve the optimization problem and the Method of Regularized Stokeslets (MRS) to simulate the fluid flow. This method is able to produce placements and phase shifts for small carpets and could be adapted for implementation in larger carpets and various fluid tasks. Our results show that given identical helices, optimal pumping configurations are influenced by the size of the flow meter. We also show that intuitive designs, such as uniform placement, do not always lead to a high-performance carpet.

Using Experimentally Calibrated Regularized Stokeslets to Assess Bacterial Flagellar Motility Near a Surface

The presence of a nearby boundary is likely to be important in the life cycle and evolution of motile flagellate bacteria. This has led many authors to employ numerical simulations to model near-surface bacterial motion and compute hydrodynamic boundary effects. A common choice has been the method of images for regularized Stokeslets (MIRS); however, the method requires discretization sizes and regularization parameters that are not specified by any theory. To determine appropriate regularization parameters for given discretization choices in MIRS, we conducted dynamically similar macroscopic experiments and fit the simulations to the data. In the experiments, we measured the torque on cylinders and helices of different wavelengths as they rotated in a viscous fluid at various distances to a boundary. We found that differences between experiments and optimized simulations were less than 5% when using surface discretizations for cylinders and centerline discretizations for helices. Having determined optimal regularization parameters, we used MIRS to simulate an idealized free-swimming bacterium constructed of a cylindrical cell body and a helical flagellum moving near a boundary. We assessed the swimming performance of many bacterial morphologies by computing swimming speed, motor rotation rate, Purcell’s propulsive efficiency, energy cost per swimming distance, and a new metabolic energy cost defined to be the energy cost per body mass per swimming distance. All five measures predicted that the optimal flagellar wavelength is eight times the helical radius independently of body size and surface proximity. Although the measures disagreed on the optimal body size, they all predicted that body size is an important factor in the energy cost of bacterial motility near and far from a surface.

Flagellar Cooperativity and Collective Motion in Sperm

Sperm have thin structures known as flagella whose motion must be regulated in order to reach the egg for fertilization. Large numbers of sperm are typically needed in this process and some species have sperm that exhibit collective or aggregate motion when swimming in groups. The purpose of this study is to model planar motion of flagella in groups to explore how collective motion may arise in three-dimensional fluid environments. We use the method of regularized Stokeslets and a three-dimensional preferred curvature model to simulate groups of undulating flagella, where flagellar waveforms are modulated via hydrodynamic coupling with other flagella and surfaces. We find that collective motion of free-swimming flagella is an unstable phenomenon in long-term simulations unless there is an external mechanism to keep flagella near each other. However, there is evidence that collective swimming can result in significant gains in velocity and efficiency. With the addition of an ability for sperm to attach and swim together as a group, velocities and efficiencies can be increased even further, which may indicate why some species have evolved mechanisms that enable collective swimming and cooperative behavior in sperm.

Regularized Stokeslets Lines Suitable for Slender Bodies in Viscous Flow

Slender-body approximations have been successfully used to explain many phenomena in low-Reynolds number fluid mechanics. These approximations typically use a line of singularity solutions to represent flow. These singularities can be difficult to implement numerically because they diverge at their origin. Hence, people have regularized these singularities to overcome this issue. This regularization blurs the force over a small blob and thereby removing divergent behaviour. However, it is unclear how best to regularize the singularities to minimize errors. In this paper, we investigate if a line of regularized Stokeslets can describe the flow around a slender body. This is achieved by comparing the asymptotic behaviour of the flow from the line of regularized Stokeslets with the results from slender-body theory. We find that the flow far from the body can be captured if the regularization parameter is proportional to the radius of the slender body. This is consistent with what is assumed in numerical simulations and provides a choice for the proportionality constant. However, more stringent requirements must be placed on the regularization blob to capture the near field flow outside a slender body. This inability to replicate the local behaviour indicates that many regularizations cannot satisfy the no-slip boundary conditions on the body’s surface to leading order, with one of the most commonly used blobs showing an angular dependency of velocity along any cross section. This problem can be overcome with compactly supported blobs, and we construct one such example blob, which can be effectively used to simulate the flow around a slender body.

Remarks on Regularized Stokeslets in Slender Body Theory

We remark on the use of regularized Stokeslets in the slender body theory (SBT) approximation of Stokes flow about a thin fiber of radius ϵ>0. Denoting the regularization parameter by δ, we consider regularized SBT based on the most common regularized Stokeslet plus a regularized doublet correction. Given sufficiently smooth force data along the filament, we derive L∞ bounds for the difference between regularized SBT and its classical counterpart in terms of δ, ϵ, and the force data. We show that the regularized and classical expressions for the velocity of the filament itself differ by a term proportional to log(δ/ϵ); in particular, δ=ϵ is necessary to avoid an O(1) discrepancy between the theories. However, the flow at the surface of the fiber differs by an expression proportional to log(1+δ2/ϵ2), and any choice of δ∝ϵ will result in an O(1) discrepancy as ϵ→0. Consequently, the flow around a slender fiber due to regularized SBT does not converge to the solution of the well-posed slender body PDE which classical SBT is known to approximate. Numerics verify this O(1) discrepancy but also indicate that the difference may have little impact in practice.

The art of coarse Stokes: Richardson extrapolation improves the accuracy and efficiency of the method of regularized stokeslets

The method of regularized stokeslets is widely used in microscale biological fluid dynamics due to its ease of implementation, natural treatment of complex moving geometries, and removal of singular functions to integrate. The standard implementation of the method is subject to high computational cost due to the coupling of the linear system size to the numerical resolution required to resolve the rapidly varying regularized stokeslet kernel. Here, we show how Richardson extrapolation with coarse values of the regularization parameter is ideally suited to reduce the quadrature error, hence dramatically reducing the storage and solution costs without loss of accuracy. Numerical experiments on the resistance and mobility problems in Stokes flow support the analysis, confirming several orders of magnitude improvement in accuracy and/or efficiency.