Search Results (11)

The velocity and trajectory of particles moving along the corrugated (rough) surface under the action of gravity is obtained by a modified Method of Fundamental Solutions (MFS). This physical situation is found often in biological systems and microfluidic devices. The Stokes equations with no-slip boundary conditions are solved using the Green’s function for Stokeslets. In the present study, the velocity of a moving particle under the action of the gravity force is not known and becomes a part of the MFS solution. This requires an adjustment of the matrix of the MFS linear system to include the unknown particle velocity and incorporate in the MFS the balance of hydrodynamic and gravity forces acting on the particle. The study explores the combination of the regularization of Stokeslets and placement of Stokeslets outside the flow domain to ensure the accuracy and stability of computations for particles moving in proximity to the wall. The MFS results are compared to prior published approximate analytical and experimental results to verify the effectiveness of this methodology to predict the trajectory of particles, including their deviation from the vertical trajectory, and select the optimal set of computational parameters. The developed MFS methodology is then applied to the sedimentation of a pair of two spherical particles in proximity to the corrugated wall, in which case, the analytical solution is not available. The MFS results show that particles in the pair deviate from the trajectory of a single particle: the particle located below moves farther away from vertical wall, and the particle located above shifts closer to the wall. Full article

Error in the method of regularized Stokeslets is highly dependent on the choice of the blob or regularization function that is utilized to handle singularities in the flow. In this work, we develop a general framework to choose regularizations at the level of the vector potential via smoothing factors. We detail the derivation for radial smoothing factors and specify properties which ensure that the solution is a regularized flow satisfying the incompressible Stokes equations. Error analysis is completed for both the far-field flow (away from the location of the forces) as well as at the location of the forces, relating our newly derived smoothing factors to commonly used blob functions and moment conditions. When forces are on a surface, we extend the radial smoothing factor case to the case of non-radial regularizations that are surface-oriented. We illustrate the utility of this framework by computing the forward and inverse problems of a translating sphere using radial and surface-oriented regularizations. Full article

Microorganisms often navigate a complex environment composed of a viscous fluid with suspended microstructures such as elastic polymers and filamentous networks. These microstructures can have similar length scales to the microorganisms, leading to complex swimming dynamics. Some microorganisms secrete enzymes that dynamically change the elastic properties of the viscoelastic networks through which they move. In addition to biological organisms, microrobots have been engineered with the goals of mucin gel penetration or dissolving blood clots. In order to gain insight into the coupling between swimming performance and network remodeling, we used a regularized Stokeslet boundary element method to compute the motion of a microswimmer consisting of a rotating spherical body and counter-rotating helical flagellum. The viscoelastic network is represented by a network of points connected by virtual elastic linkages immersed in a viscous fluid. Here, we model the enzymatic dissolution of the network by bacteria or microrobots by dynamically breaking elastic linkages when the cell body of the swimmer falls within a given distance from the link. We investigate the swimming performance of the microbes as they penetrate and move through networks of different material properties, and also examine the effect of network remodeling. Full article

Cell migration is critical for many vital processes, such as wound healing, as well as harmful processes, such as cancer metastasis. Experiments have highlighted the diversity in migration strategies employed by cells in physiologically relevant environments. In 3D fibrous matrices and confinement between two surfaces, some cells migrate using round membrane protrusions, called blebs. In bleb-based migration, the role of substrate adhesion is thought to be minimal, and it remains unclear if a cell can migrate without any adhesion complexes. We present a 2D computational fluid-structure model of a cell using cycles of bleb expansion and retraction in a channel with several geometries. The cell model consists of a plasma membrane, an underlying actin cortex, and viscous cytoplasm. Cellular structures are immersed in viscous fluid which permeates them, and the fluid equations are solved using the method of regularized Stokeslets. Simulations show that the cell cannot effectively migrate when the actin cortex is modeled as a purely elastic material. We find that cells do migrate in rigid channels if actin turnover is included with a viscoelastic description for the cortex. Our study highlights the non-trivial relationship between cell rheology and its external environment during migration with cytoplasmic streaming. Full article

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. Full article

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. Full article

We derive a new computational model for the simulation of viscous incompressible flows bounded by a thin, flexible, porous membrane. Our approach is grid-free and models the boundary forces with regularized Stokeslets. The flow across the porous membranes is modeled with regularized source doublets based on the notion that the flux velocity across the boundary can be viewed as the flow induced by a fluid source/sink pair with the sink on the high-pressure side of the boundary and magnitude proportional to the pressure difference across the membrane. Several validation examples are presented that illustrate how to calibrate the parameters in the model. We present an example consisting of flow in a closed domain that loses volume due to the fluid flux across the permeable boundary. We also present applications of the method to flow inside a channel of fixed geometry where sections of the boundary are permeable. The final example is a biological application of flow in a capillary with porous walls and a protein concentration advected and diffused in the fluid. In this case, the protein concentration modifies the pressure in the flow, producing dynamic changes to the flux across the walls. For this example, the proposed method is combined with finite differences for the concentration field. Full article

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. Full article

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. Full article

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 $\delta$, 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 $L^{\infty }$ bounds for the difference between regularized SBT and its classical counterpart in terms of $\delta$, $ϵ$, 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 $log(\delta /ϵ)$; in particular, $\delta =ϵ$ is necessary to avoid an $O\left(1\right)$ discrepancy between the theories. However, the flow at the surface of the fiber differs by an expression proportional to $log(1+{\delta }^2/{ϵ}^2)$, and any choice of $\delta \propto ϵ$ will result in an $O\left(1\right)$ discrepancy as $ϵ\to 0$. 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 $O\left(1\right)$ discrepancy but also indicate that the difference may have little impact in practice. Full article

A biologically-inspired micropumping model in a three-dimensional tube subjected to localized wall constrictions is given in this article. The present study extends our previous pumping model where a 3D channel with a square cross-section is considered. The proposed pumping approach herein applies to tubular geometries and is given to mimic an insect respiration mode, where the tracheal tube rhythmic wall contractions are used/hypothesized to enhance the internal flow transport within the entire respiration network. The method of regularized Stokeslets-mesh-free computations is used to reconstruct the flow motions induced by the wall movements and to calculate the time-averaged net flow rate. The time-averaged net flow rates from both the tube and channel models are compared. Results have shown that an inelastic tube with at least two contractions forced to move with a specific time lag protocol can work as a micropump. The system is simple and expected to be useful in many biomedical applications. Full article