Henry Shum

University of Waterloo | UWaterloo · Department of Applied Mathematics

The controllability of a fully three-dimensional $N$ N -link swimmer is studied. After deriving the equations of motion in a low Reynolds number fluid by means of Resistive Force Theory, the controllability of the minimal 2-link swimmer is tackled using techniques from Geometric Control Theory. The shape of the 2-link swimmer is described by two an...

Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures ( Vibrio natri...

The controllability of a fully three-dimensional $N$-link swimmer is studied. After deriving the equations of motion in a low Reynolds number fluid by means of Resistive Force Theory, the controllability of the minimal $2$-link swimmer is tackled using techniques from Geometric Control Theory. The shape of the $2$-link swimmer is described by two a...

To navigate in complex fluid environments, swimming organisms like fish or bacteria often reorient their bodies antiparallel or against the flow, more commonly known as rheotaxis. This reorientation motion enables the organisms to migrate against the fluid flow, as observed in salmon swimming upstream to spawn. Rheotaxis can also be realized in art...

Many theoretical studies of bacterial locomotion adopt a simple model for the organism consisting of a spheroidal cell body and a single corkscrew-shaped flagellum that rotates to propel the body forward. Motivated by experimental observations of a group of magnetotactic bacterial strains, we extended the model by considering two flagella attached...

Mechanical and electrical pumps are conventionally used to drive fluid flow in microfluidic devices; these pumps require external power supplies, thus limiting the portability of the devices. Harnessing catalytic reactions in solution allows pumping to be shifted into the chemical realm and alleviates the need for extraneous equipment. Chemical "pu...

By harnessing biochemical signaling and chemotaxis, unicellular slime molds can aggregate on a surface to form a long, vertical stalk. Few synthetic systems can self-organize into analogous structures that emerge out of the plane. Through computational modeling, we devise a mechanism for assembling tower-like structures using microcapsules in solut...

We use boundary element simulations to study the interaction of model microswimmers with a neutrally buoyant spherical particle. The ratio of the size of the particle to that of the swimmer is varied from $R^\mathrm{P} / R^\mathrm{S} \ll 1$, corresponding to swimmer--tracer scattering, to $R^\mathrm{P} / R^\mathrm{S} \gg 1$, approximately equivalen...

Biological quorum sensing refers to the ability of cells to gauge their population density and collectively initiate a new behavior once a critical density is reached. Designing synthetic materials systems that exhibit quorum sensing-like behavior could enable the fabrication of devices with both self-recognition and self-regulating functionality....

Immobilized enzymes generate net fluid flow when exposed to specific reagents in solution. Thus, they function as self-powered platforms that combine sensing and on-demand fluid pumping. To uncover the mechanism of pumping, we examine the effects of solutal and thermal buoyancy on the behavior of phosphatase-based micropumps, using a series of reac...

The directed transport of microparticles in microfluidic devices is vital for efficient bioassays and fabrication of complex microstructures. There remains, however, a need for methods to propel and steer microscopic cargo that do not require modifying these particles. Using theory and experiments, we show that catalytic surface reactions can be us...

The video (a snapshot is shown in Supplementary Figure 1) shows convective transport of 500 tracers in a three-dimensional rectangular domain (3 mm × 1 mm × 3 mm). The enzyme (catalase) on the bottom plane coats a pattern consisting of parallel stripes oriented along the z-direction (similar to the experimental setup shown in Fig. 6). The stripe wi...

The video (a snapshot is shown in Supplementary Figure 2) shows convective transport of 500 tracers in a three-dimensional rectangular domain (3 mm × 1 mm × 3 mm) with catalase homogeneously coating the whole bottom plane. The reaction rate per unit area on the bottom is rmax= 0.85×10−3 molm−2s−1, which is half of the rate used on the stripes in Su...

The urease pump is comprised of strips of gold with enzymes attached to them and the gel is soaked with 500 mM urea in phosphate buffer. 2 μm (radius) tracer particles demonstrate the direction of the flow after 5 min. As we change the focal plane and move vertically in the system, the reversal of the direction of tracer particles is seen, due to f...

Supplementary Notes and Supplementary Figures

The video shows results presented in Fig. 2 for C0= 0.1 M and rmax= 1.7×10−5 mol m−2s−1. The results presented in Fig. 3, 4, and 5 for C0= 0.1 M at other reaction rates demonstrate similar behavior.

The video shows results presented in Fig. 5 for C0= 0.2 M and rmax= 1.7×10−2 mol m−2s−1. The results presented in Fig. 5 for C0= 0.2 M at other reaction rates demonstrate similar behavior.

The platinum pump is comprised of strips of platinum and the gel is soaked with 0.59 M H2O2. 2 μm (radius) tracer particles demonstrate the direction of the flow after 5 min. As we change the focal plane and move vertically in the system, the reversal of the direction of tracer particles is seen, due to fluid continuity.

The platinum pump is comprised of strips of platinum and the gel is soaked with 0.29 M H2O2. The video was taken after 60 min. As we move along the pattern, the settled tracers can be seen and the changes in their density can be measured.

The video shows results presented in Fig. 5 for C0= 0.05 M and rmax= 1.7×10−2 mol m−2s−1. The results presented in Fig. 5 for C0= 0.05 M at other reaction rates demonstrate similar behavior.

The platinum pump is comprised of strips of platinum and the gel is soaked with DI water. 2 μm (radius) tracer particles demonstrate the absence of the flow after 5 min, with the tracers undergoing Brownian diffusion.

The urease pump is comprised of strips of gold with enzymes attached to them and the gel is soaked with phosphate buffer only. 2 μm (radius) tracer particles demonstrate the absence of the flow after 5 min, with the tracers undergoing Brownian diffusion.

The urease pump is comprised of strips of gold with enzymes attached to them and the gel is soaked with 500 mM urea in phosphate buffer. The video was taken after 60 min. As we move along the pattern, the settled tracers can be seen and the changes in their density can be measured.

By developing new computational models, we examine how enzymatic reactions on an underlying surface can be harnessed to direct the motion and organization of reagent-laden microcapsules in a fluid-filled microchannel. In the presence of appropriate reagents, surface-bound enzymes can act as pumps, which drive large-scale fluid flows. When the reage...

Surface-bound enzymes can act as pumps that drive large-scale fluid flows in the presence of their substrates or promoters. Thus, enzymatic catalysis can be harnessed for "on demand" pumping in nano- and microfluidic devices powered by an intrinsic energy source. The mechanisms controlling the pumping have not, however, been completely elucidated....

The influence of nearby solid surfaces on the motility of bacteria is of fundamental importance as these interactions govern the ability of the microorganisms to explore their environment and form sessile colonies. Reducing biofouling in medical implants and controlling the transport of bacterial cells in a microfluidic device are two applications...

Systems of motile microscopic particles can exhibit behaviors that resemble those of living microorganisms, including cooperative motion, self-organization, and adaptability to changing environments. Using mesoscale computational modeling, we design synthetic microswimmers and microcapsules that undergo controllable, self-propelled motion in soluti...

Biological self-healing involves the autonomous localization of healing agents at the site of damage. Herein, we design and characterize a synthetic repair system where self-propelled nanomotors autonomously seek and localize at microscopic cracks and thus mimic salient features of biological wound healing. We demonstrate that these chemically powe...

Inspired by the collective behavior of slime molds and amoebas, we designed synthetic cell-like objects that move and self-organize in response to self-generated chemical gradients, thereby exhibiting "auto-chemotaxis". Using computational modeling, we specifically focused on microcapsules that encompass a permeable shell and are localized on an ad...

One of the intriguing challenges in designing active matter is devising systems that not only self-organize, but also exhibit self-regulation. Inspired by biological regulatory networks, we design a collection of self-organizing, self-regulating microcapsules that move in response to self-generated chemical signals. Three microcapsules act as local...

The motility of swimming bacteria near solid surfaces has implications in a wide range of scenarios, including water treatment facilities, microfluidics, and biomedical implants. Using the boundary element method to numerically solve the equations of low Reynolds number fluid flow, we investigate the dynamics of a model swimmer propelled by rotatin...

This manuscript is a summary of a set of lectures given at the Geilo School 2013 Soft Matter Confinement: from Biology to Physics. It aims to provide an introduction to the hydrodynamics that underlies the way in which microorganisms, such as bacteria and algae, and fabricated microswimmers, swim. We focus on two features peculiar to bacterial swim...

Biological cilia play a critical role in a stunning array of vital functions, from enabling marine organisms to trap food and expel fouling agents to facilitating the effective transport of egg cells in mammals. Inspired by the performance of these microscopic, hair-like filaments, researchers are synthesizing artificial cilia for use in lab-on-a-c...

Inspired by marine organisms that utilize active cilia to prevent the biofouling of their surfaces, we use computational and theoretical modeling to determine if passive cilia, which are driven to undulate by an oscillatory shear flow, can be harnessed for antifouling applications. By modeling the oscillating shear flow near a ciliated wall within...

Continually moving cilia on the surface of marine organisms provide a natural defense against biofouling. To probe the physical mechanisms underlying this antifouling behavior, we integrate the lattice Boltzmann and immersed boundary methods and undertake the first computational studies of the interactions between actuated, biomimetic cilia and a m...

Cilia are filamentous organelles found in many organisms for achieving locomotion or for driving fluid flows within the body. Cilia-like structures can be constructed and have potential for application in microfluidics, where they may be used to locally control flow and the motion of particles in the fluid. We implement a lattice Boltzmann method t...

Biofouling by micro-organisms is problematic on scales from microfluidic devices to the largest ships in the ocean. One solution found in nature for clearing undesired material from surfaces is to employ active cilia, for example, in the respiratory tract. It is feasible to fabricate surfaces covered with artificial cilia actuated by an externally...

We discuss the path of a tracer particle as a microswimmer moves past on an infinite straight trajectory. If the tracer is sufficiently far from the path of the swimmer it moves in a closed loop. As the initial distance between the tracer and the path of the swimmer $\rho$ decreases, the tracer is displaced a small distance backwards (relative to t...

A crucial structure in the motility of flagellated bacteria is the hook, which connects the flagellum filament to the motor in the cell body. Early mathematical models of swimming bacteria assume that the helically shaped flagellum rotates rigidly about its axis, which coincides with the axis of the cell body. Motivated by evidence that the hook is...

A recent study by Elgeti et al. used multiparticle collision dynamics to simulate a long-standing problem: the approach of sperm to surfaces, and subsequent accumulation. The authors highlight differences in their predictions with those of the earlier Stokes flow simulations of Smith et al. attributing the differences to methodological flaws in the...

We describe a boundary-element method used to model the hydrodynamics of a bacterium propelled by a single helical flagellum. Using this model, we optimize the power efficiency of swimming with respect to cell body and flagellum geometrical parameters, and find that optima for swimming in unbounded fluid and near a no-slip plane boundary are nearly...