Description
Studies of microbial behavior often require trapping and steering single cells while preserving their motility and stimulus–response dynamics. Existing manipulation techniques achieve precise control using optical, acoustic, electric, or magnetic fields, but these approaches introduce additional forces that can conflate field-mediated microbial responses and limit the interpretation of microbial behavior. Hydrodynamic confinement, by contrast, relies only on the fluid environment experienced by the cell and is therefore minimally invasive; however, it has so far lacked the fast, programmable, closed-loop control needed for robust manipulation of active microorganisms.
Here, we present a microfluidic platform that enables real-time trapping and steering of single passive particles and motile microbes using only pressure-driven flows. Time-varying flow fields are shaped through model predictive control with update rates of 20–35 Hz, enabling robust closed-loop manipulation without external fields. This platform enables systematic and quantitative investigation of microbial decision-making in response to time-dependent stimuli, including chemical and phototactic cues. The device consists of a Hele–Shaw microfluidic chamber formed by two PMMA (acrylic) plates separated by an adjustable gap height (100–500 μm). One plate incorporates multiple microscale inlets, whose layout and chamber geometry can be customized. Flow rates through these inlets are continuously adjusted by a controller that explicitly accounts for the dynamics of the actuation system.
First, we achieve precise trapping and steering of a passive tracer bead (≈11 μm diameter). The bead can be moved over several millimeters in 5 s to a new prescribed position with 2 microns accuracy and can be trapped for tens of minutes. By translating the setpoint in time, particles can be guided along prescribed trajectories. Next, we use our platform as a “soft” hydrodynamic trap for the motile green alga Chlamydomonas reinhardtii in dark light conditions. While hydrodynamically confined, the stochastic motility of the swimmers leads to a bounded diffusive behavior around the trapping location. Trajectory statistics reveal a mean position centered at the setpoint and a mean-squared displacement that is ballistic at short times and saturates at long times, consistent with an active Brownian particle confined by a harmonic potential.
Finally, we extend the platform toward single-cell stimulus–response measurements by integrating a localized optical stimulus delivered through a fiber-coupled LED while maintaining hydrodynamic trapping. The trapped swimmer exhibits negative phototaxis, manifested as a steady positional offset from the hydrodynamic setpoint and a reduction in oscillation amplitude and frequency with increasing light intensity. Interpreting this offset as a balance between phototactic swimming and hydrodynamic restoring velocities enables quantitative estimation of the phototactic drive as a function of light intensity, wavelength, and stimulus location.