Some swimming microorganisms are sensitive to light, and this can affect the way in which they negotiate their environment. In particular, photophobic cells are repelled from unfavourable light conditions, and in a quiescent fluid environment this can be observed as elevated cell levels in regions away from these light conditions. This photoresponsive effect is of interest due to its potential technological applications. For example, the use of light to focus and direct cells could be used as a convenient means to separate out the algae used in biofuel production (for example, hydrogen), or exploited within devices for biodetection of environmental contaminants. However, in these types of situations the swimming cells will usually be suspended in a flow with shear. In this environment, it has previously been shown that cells can become hydrodynamically trapped in regions of high fluid shear, and so the extent to which photofocusing can occur under these conditions is not immediately clear. Moreover, in applications where the light must pass through appreciable volumes of the suspension, cells will typically absorb light and so shade each other from the illumination. As such, the intensity at any point in the flow is dependent upon the global cell concentration. Hence, in this study we model the coupled influence of fluid shear and cell photosensitivity on a suspension of swimming microorganisms, and ask under what circumstances a suspension of photophobic cells might be focused into high concentration regions.

John Blake (1947–2016) was a leader in fluid mechanics, his two principal areas of expertise being biological fluid mechanics on microscopic scales and bubble dynamics. He produced leading research and mentored others in both Australia, his home country, and the UK, his adopted home. This article reviews John Blake’s contributions in biological fluid mechanics, as well as gives the author’s personal viewpoint as one of the many graduate students and researchers who benefitted from his supervision, guidance and inspiration. The key topics from biological mechanics discussed are: “squirmer” models of protozoa, the method of images in Stokes flow and the “blakelet” solution, discrete cilia modelling via slender body theory, physiological flows in respiration and reproduction, blinking stokeslets in microorganism feeding, human sperm motility and embryonic nodal cilia.

Incompressible flows with zero Reynolds number can be modeled by the Stokes equations. When numerically solving the Stokes flow in stream-vorticity formulation with high-order accuracy, it will be important to solve both the stream function and velocity components with the high-order accuracy simultaneously. In this work, we will develop a fifth-order spectral/combined compact difference (CCD) method for the Stokes equation in stream-vorticity formulation on the polar geometries, including a unit disk and an annular domain. We first use the truncated Fourier series to derive a coupled system of singular ordinary differential equations for the Fourier coefficients, then use a shifted grid to handle the coordinate singularity without pole condition. More importantly, a three-point CCD scheme is developed to solve the obtained system of differential equations. Numerical results are presented to show that the proposed spectral/CCD method can obtain all physical quantities in the Stokes flow, including the stream function and vorticity function as well as all velocity components, with fifth-order accuracy, which is much more accurate and efficient than low-order methods in the literature.

The Stokes axisymmetric flow of an incompressible viscous fluid past a micropolar fluid spheroid whose shape deviates slightly from that of a sphere is studied analytically. The boundary conditions used are the vanishing of the normal velocities, the continuity of the tangential velocities, continuity of shear stresses and spin-vorticity relation at the surface of the spheroid. The hydrodynamic drag force acting on the fluid spheroid is calculated. An exact solution of the problem is obtained to the first order in the small parameter characterizing the deformation. It is observed that due to increase spin parameter value, the drag coefficient decreases. Well known results are deduced and comparisons are made with classical viscous fluid and micropolar fluid.

A numerical method is presented for the computation of externally forced Stokes flows bounded by the plane z=0 and satisfying periodic boundary conditions in the x and y directions. The motivation for this work is the simulation of flows generated by cilia, which are hair-like structures attached to the surface of cells that generate flows through coordinated beating. Large collections of cilia on a surface can be modeled using a doubly-periodic domain. The approach presented here is to derive a regularized version of the fundamental solution of the incompressible Stokes equations in Fourier space for the periodic directions and physical space for the z direction. This analytical expression for û(k,m;z) can then be used to compute the fluid velocity u(x,y,z) via a two-dimensional inverse fast Fourier transform for any fixed value of z. Repeating the computation for multiple values of z leads to the fluid velocity on a uniform grid in physical space. The zero-flow condition at the plane z=0 is enforced through the use of images. The performance of the method is illustrated by numerical examples of particle transport by nodal cilia, which verify optimal particle transport for parameters consistent with previous studies. The results also show that for two cilia in the periodic box, out-of-phase beating produces considerablemore particle transport than in-phase beating.

More and more experimental evidence demonstrates that the slip boundary condition plays an important role in the study of nano- or micro-scale fluid. We propose a homogenization approach to study the effective slippage problem. We show that the effective slip length obtained by homogenization agrees with the results obtained by the traditional method in the literature for the simplest Stokes flow; then we use our approach to deal with two examples which seem quite hard by other analytical methods. We also include some numerical results to validate our analytical results.

The Kelvin–Helmholtz flow is a shearing instability that occurs at the interface between two fluids moving with different speeds. Here, the two fluids are each of finite depth, but are highly viscous. Consequently, their motion is caused by the horizontal speeds of the two walls above and below each fluid layer. The motion of the fluids is assumed to be governed by the Stokes approximation for slow viscous flow, and the fluid motion is thus responsible for movement of the interface between them. A linearized solution is presented, from which the decay rate and the group speed of the wave system may be obtained. The nonlinear equations are solved using a novel spectral representation for the streamfunctions in each of the two fluid layers, and the exact boundary conditions are applied at the unknown interface location. Results are presented for the wave profiles, and the behaviour of the curvature of the interface is discussed. These results are compared to the Boussinesq–Stokes approximation which is also solved by a novel spectral technique, and agreement between the results supports the numerical calculations.

In this paper, an improved singular boundary method (SBM), viewed as one kind of modified method of fundamental solution (MFS), is firstly applied for the numerical analysis of two-dimensional (2D) Stokes flow problems. The key issue of the SBM is the determination of the origin intensity factor used to remove the singularity of the fundamental solution and its derivatives. The new contribution of this study is that the origin intensity factors for the velocity, traction and pressure are derived, and based on that, the SBM formulations for 2D Stokes flow problems are presented. Several examples are provided to verify the correctness and robustness of the presented method. The numerical results clearly demonstrate the potentials of the present SBM for solving 2D Stokes flow problems.

The study of vesicles, capsules and red blood cells (RBCs) under flow is a field of active research, belonging to the general problematic of fluid/structure interactions. Here, we are interested in modeling vesicles, capsules and RBCs using a boundary integral formulation, and focus on exact singularity subtractions of the kernel of the integral equations in 3D. In order to increase the precision of singular and near-singular integration, we propose here a refinement procedure in the vicinity of the pole of the Green-Oseen kernel. The refinement is performed homogeneously everywhere on the source surface in order to reuse the additional quadrature nodes when calculating boundary integrals in multiple target points. We also introduce a multi-level look-up algorithm in order to select the additional quadrature nodes in vicinity of the pole of the Green-Oseen kernel. The expected convergence rate of the proposed algorithm is of order while the computational complexity is of order , where N is the number of degrees of freedom used for surface discretization. Several numerical tests are presented to demonstrate the convergence and the efficiency of the method.

We investigate several robust preconditioners for solving the saddle-point linear systems that arise from spatial discretization of unsteady and steady variable-coefficient Stokes equations on a uniform staggered grid. Building on the success of using the classical projection method as a preconditioner for the coupled velocity pressure system [B. E. Griffith, J. Comp. Phys., 228 (2009), pp. 7565-7595], as well; established techniques for steady and unsteady Stokes flow in the finite-element literature, we construct preconditioners that employ independent generalized Helmholtz and Poisson solvers for the velocity and pressure subproblems. We demonstrate that only a single cycle of a standard geometric multigrid algorithm serves as an effective inexact solver for each of these subproblems. Contrary to traditional wisdom, we find that the Stokes problem can be solved nearly as efficiently as the independent pressure and velocity subproblems, making the overall cost of solving the Stokes system comparable to the cost of classical projection or fractional step methods for incompressible flow, even for steady flow and in the presence of large density and viscosity contrasts. Two of the five preconditioners considered here are found to be robust to GMRES restarts and to increasing problem size, making them suitable for large-scale problems. Our work opens many possibilities for constructing novel unsplit temporal integrators for finite-volume spatial discretizations of the equations of low Mach and incompressible flow dynamics.

We focus on the problem of evaluating the velocity field outside a solid object moving in an incompressible Stokes flow using the boundary integral formulation. For points near the boundary, the integral is nearly singular, and accurate computation of the velocity is not routine. One way to overcome this problem is to regularize the integral kernel. The method of regularized Stokeslet (MRS) is a systematic way to regularize the kernel in this situation. For a specific blob function which is widely used, the error of the MRS is only of first order with respect to the blob parameter. We prove that this is the case for radial blob functions with decay property ϕ(r)=O(r−3−α) when r→∞ for some constant α>1. We then find a class of blob functions for which the leading local error term can be removed to get second and third order errors with respect to blob parameter. Since the addition of these terms might give a flow field that is not divergence free, we introduce a modification of these terms to make the divergence of the corrected flow field close to zero while keeping the desired accuracy. Furthermore, these dominant terms are explicitly expressed in terms of blob function and so the computation time is negligible.

We present a hybrid numerical method for simulating fluid flow through a compliant, closed tube, driven by an internal source and sink. Fluid is assumed to be highly viscous with its motion described by Stokes flow. Model geometry is assumed to be axisymmetric, and the governing equations are implemented in axisymmetric cylindrical coordinates, which capture 3D flow dynamics with only 2D computations. We solve the model equations using a hybrid approach: we decompose the pressure and velocity fields into parts due to the surface forcings and due to the source and sink, with each part handled separately by means of an appropriate method. Because the singularly-supported surface forcings yield an unsmooth solution, that part of the solution is computed using the immersed interface method. Jump conditions are derived for the axisymmetric cylindrical coordinates. The velocity due to the source and sink is calculated along the tubular surface using boundary integrals. Numerical results are presented that indicate second-order accuracy of the method.

In this study, we examine a steady two-dimensional slow flow past a rigid cylinder coated with a thin layer of immiscible fluid. The Reynolds number for the external bulk flow is assumed small and flow within the film is driven by the action of the bulk fluid’s tangential viscous stress acting at the interface. Using double asymptotic expansions based on the bulk fluid’s Reynolds number and the aspect ratio of the film thickness to the cylinder’s radius, we derive the leading- and first-order equations governing the steady-state film dynamics, and obtain analytical solutions, in terms of the film thickness, for the bulk flow. We solve the governing film equations, finding that solutions feature a drained region. We briefly discuss the influence of the Capillary number and fluid viscosities, and conclude by showing how the presence of the film affects the drag on the film-coated cylinder.

The immersed boundary method has been extensively used to simulate the motion of elastic structures immersed in a viscous fluid. For some applications, such as modeling biological materials, capturing internal boundary viscosity is important. We present numerical methods for simulating Kelvin-Voigt and standard linear viscoelastic structures immersed in zero Reynolds number flow. We find that the explicit time immersed boundary update is unconditionally unstable above a critical boundary to fluid viscosity ratio for a Kelvin-Voigt material. We also show there is a severe time step restriction when simulating a standard linear boundary with a small relaxation time scale using the same explicit update. A stable implicit method is presented to overcome these computation challenges.

The creeping flow of an incompressible viscous liquid past a porous approximately spherical shell is considered. The flow in the free fluid region outside the shell and in the cavity region of the shell is governed by the Navier–Stokes equations. The flow within the porous annular region of the shell is governed by Brinkman’s model. The boundary conditions used at the interface are continuity of the velocity, continuity of the pressure and Ochoa-Tapia and Whitaker’s stress jump condition. An exact solution for the problem and an expression for the drag on the porous approximately spherical shell are obtained. The drag is evaluated numerically for several values of the parameters governing the flow.

In this paper, we numerically investigate the effects of surfactant on drop-drop interactions in a 2D shear flow using a coupled level-set and immersed interface approach proposed in (Xu et al., J. Comput. Phys., 212 (2006), 590-616). We find that surfactant plays a critical and nontrivial role in drop-drop interactions. In particular, we find that the minimum distance between the drops is a non-monotone function of the surfactant coverage and Capillary number. This non-monotonic behavior, which does not occur for clean drops, is found to be due to the presence of Marangoni forces along the drop interfaces. This suggests that there are non-monotonic conditions for coalescence of surfactant-laden drops, as observed in recent experiments of Leal and co-workers. Although our study is two-dimensional, we believe that drop-drop interactions in three-dimensional flows should be qualitatively similar as the Maragoni forces in the near contact region in 3D should have a similar effect.

We present two-dimensional simulations of chemotactic self-propelled bacteria swimming ina viscous fluid. Self-propulsion is modelled by a couple of forces of same intensity andopposite direction applied on the rigid bacterial body and on an associated region in thefluid representing the flagellar bundle. The method for solving the fluid flow and themotion of the bacteria is based on a variational formulation written on the whole domain,strongly coupling the fluid and the rigid particle problems: rigid motion is enforced bypenalizing the strain rate tensor on the rigid domain, while incompressibility is treatedby duality. This model allows to achieve an accurate description of fluid motion andhydrodynamic interactions in moderate to concentrated active suspensions. A mesoscopicmodel is also used, in which the size of the bacteria is supposed to be much smaller thanthe elements of fluid: the perturbation of the fluid due to propulsion and motion of theswimmers is neglected, and the fluid is only subjected to the buoyant forcing induced bythe presence of the bacteria, which are denser than the fluid. Although this model doesnot accurately take into account hydrodynamic interactions, it is able to reproducecomplex collective dynamics observed in concentrated bacterial suspensions, such asbioconvection. From a mathematical point of view, both models lead to a minimizationproblem which is solved with a standard Finite Element Method. In order to ensurerobustness, a projection algorithm is used to deal with contacts between particles. Wealso reproduce chemotactic behaviour driven by oxygen: an advection-diffusion equation onthe oxygen concentration is solved in the fluid domain, with a source term accounting foroxygen consumption by the bacteria. The orientations of the individual bacteria aresubjected to random changes, with a frequency that depends on the surrounding oxygenconcentration, in order to favor the direction of the concentration gradient.

Shear flow over a solid surface containing perforations or patches of zero shear stress is discussed with a view to evaluating the slip velocity. In both cases, the functional dependence of the slip velocity on the solid fraction of the surface strongly depends on the surface geometry, and a universal law cannot be established. Numerical results for flow over a plate with circular or square perforations or patches of zero shear stress, and flow over a plate consisting of separated square or circular tiles corroborate the assertion.

The reduced basis element method is a new approach for approximating the solution of problems described by partial differential equations. The method takes its roots in domain decomposition methods and reduced basis discretizations. The basic idea is to first decomposethe computational domain into a series of subdomains that are deformationsof a few reference domains (or generic computational parts). Associated with each reference domain are precomputed solutions corresponding to the same governing partial differential equation,but solved for different choices of deformations of the referencesubdomains and mapped onto the reference shape.The approximation corresponding to a new shape is then taken to be a linear combination of the precomputed solutions, mappedfrom the generic computational part to the actual computational part.We extend earlier work in this direction to solve incompressible fluid flow problems governed by the steady Stokes equations. Particular focus is given to satisfying the inf-sup condition,to a posteriori error estimation, and to “gluing” the local solutions together in the multidomain case.