Using confined bacteria as building blocks to generate fluid flow

Synchronized oscillations in swarms of nematode Turbatrix aceti

There is a recent surge of interest in the behavior of active particles that can at the same time align their direction of movement and synchronize their oscillations, known as swarmalators. While theoretical and numerical models of such systems are now abundant, no real-life examples have been shown to date. We present an experimental investigation of the collective motion of the nematode Turbatrix aceti that self-propel by body undulation. We discover that these nematodes can synchronize their body oscillations, forming striking traveling metachronal waves, which produces strong fluid flows. We uncover that the location and strength of this collective state can be controlled through the shape of the confining structure; in our case the contact angle of a droplet. This opens a way for producing controlled work such as on-demand flows or displacement of objects. We illustrate this by showing that the force generated by this state is sufficient to change the physics of evaporation of fluid droplets, by counteracting the surface-tension force, which allow us to estimate its strength. The relatively large size and ease of culture make Turbatrix aceti a promising model organism for experimental investigation of swarming and oscillating active matter capable of producing controllable work.

Boids in a loop: Self-propelled particles within a flexible boundary

We numerically explore the behavior of repelling and aligning self-propelled polar particles (boids) in two dimensions enclosed by a damped flexible and elastic loop-shaped boundary. We observe disordered, polar ordered, jammed, and circulating states. The latter produce a rich variety of boundary shapes, including circles, ovals, irregulars, ruffles, or sprockets, depending upon the bending moment of the boundary and the boundary to particle mass ratio. With the exception of the circulating states with nonround boundaries, states resemble those exhibited by attracting self-propelled particles, but here the confining boundary acts in place of a cohesive force. We attribute the formation of ruffles to instability mediated by pressure on the boundary when the speed of waves on the boundary approximately matches the self-propelled particle's swim speed.

Transition to bound states for bacteria swimming near surfaces

It is well known that flagellated bacteria swim in circles near surfaces. However, recent experiments have shown that a sulfide-oxidizing bacterium named Thiovulum majus can transition from swimming in circles to a surface bound state where it stops swimming while remaining free to move laterally along the surface. In this bound state, the cell rotates perpendicular to the surface with its flagella pointing away from it. Using numerical simulations and theoretical analysis, we demonstrate the existence of a fluid-structure interaction instability that causes cells with relatively short flagella to become surface bound.

A robot made of robots: Emergent transport and control of a smarticle ensemble

Robot locomotion is typically generated by coordinated integration of single-purpose components, like actuators, sensors, body segments, and limbs. We posit that certain future robots could self-propel using systems in which a delineation of components and their interactions is not so clear, becoming robust and flexible entities composed of functional components that are redundant and generic and can interact stochastically. Control of such a collective becomes a challenge because synthesis techniques typically assume known input-output relationships. To discover principles by which such future robots can be built and controlled, we study a model robophysical system: planar ensembles of periodically deforming smart, active particles—smarticles. When enclosed, these individually immotile robots could collectively diffuse via stochastic mechanical interactions. We show experimentally and theoretically that directed drift of such a supersmarticle could be achieved via inactivation of individual smarticles and used this phenomenon to generate endogenous phototaxis. By numerically modeling the relationship between smarticle activity and transport, we elucidated the role of smarticle deactivation on supersmarticle dynamics from little data—a single experimental trial. From this mapping, we demonstrate that the supersmarticle could be exogenously steered anywhere in the plane, expanding supersmarticle capabilities while simultaneously enabling decentralized closed-loop control. We suggest that the smarticle model system may aid discovery of principles by which a class of future “stochastic” robots can rely on collective internal mechanical interactions to perform tasks.

A dynamic preferred direction model for the self-organization dynamics of bacterial microfluidic pumping

It is known that some flagellated bacteria like Serratia marcescens, when deposited and affixed onto a surface to form a "bacterial carpet", self-organize in a collective motion of the flagella that is capable of pumping fluid through microfluidic channels. We set up a continuum model comprising two macroscopic variables that is capable of describing this self-organization mechanism as well as quantifying it to the extent that an agreement with the experimentally observed channel width dependence of the pumping is reached. The activity is introduced through a collective angular velocity of the helical flagella rotation, which is an example of a dynamic macroscopic preferred direction. Our model supports and quantifies the view that the self-coordination is due to a positive feedback loop between the bacterial flagella and the local flow generated by their rotation. Moreover, our results indicate that this biological active system is operating close to the self-organization threshold.

Helical micropumps near surfaces

Recent experiments proposed to use confined bacteria in order to generate flows near surfaces. We develop a mathematical and a computational model of this fluid transport using a linear superposition of fundamental flow singularities. The rotation of a helical bacterial flagellum induces both a force and a torque on the surrounding fluid, both of which lead to a net flow along the surface. The combined flow is in general directed at an angle to the axis of the flagellar filament. The optimal pumping is thus achieved when bacteria are tilted with respect to the direction in which one wants to move the fluid, in good agreement with experimental results. We further investigate the optimal helical shapes to be used as micropumps near surfaces and show that bacterial flagella are nearly optimal, a result which could be relevant to the expansion of bacterial swarms.

Applications of Microfluidics in Quantitative Biology

Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future.

Device and programming abstractions for spatiotemporal control of active micro-particle swarms

We present a hardware setup and a set of executable commands for spatiotemporal programming and interactive control of a swarm of self-propelled microscopic agents inside a microfluidic chip. In particular, local and global spatiotemporal light stimuli are used to direct the motion of ensembles of Euglena gracilis, a unicellular phototactic organism. We develop three levels of programming abstractions (stimulus space, swarm space, and system space) to create a scripting language for directing swarms. We then implement a multi-level proof-of-concept biotic game using these commands to demonstrate their utility. These device and programming concepts will enhance our capabilities for manipulating natural and synthetic swarms, with future applications for on-chip processing, diagnostics, education, and research on collective behaviors.