Design-dependent shear and liquid media transport characteristics in microfluidic U-shaped cell traps

Single-cell analysis has become central to fields ranging from cancer biology to drug screening. To exploit its potential, tools that can isolate individual cells and maintain them under controlled conditions are needed. Microfluidic platforms are an ideal fit for this, offering precise control over microenvironments. In these systems, cell behavior is shaped by parameters such as fluid shear stress (the mechanical force exerted by flow) and the transport of soluble factors (nutrients and signaling molecules). However, both are set by flow velocity, so they cannot be tuned independently. Here, we present a systematic characterization of the fluid mechanical environment in microfluidic devices featuring U-shaped traps in two distinct designs: slit traps, employing vertical slits to retain cells while maintaining lateral flow through the slits, and gap traps, using a shallow bottom gap to allow vertical flow beneath the cells. Using microparticle tracking velocimetry in microfabricated fluidic chips combined with COMSOL Multiphysics simulations, we quantify shear rates and Péclet numbers across a wide range of trap geometries and pump flow rates. Shear stress scales linearly with the applied flow rate in all configurations, accessing biologically relevant shear stress levels while mainly remaining below the threshold for adverse cellular responses. The Péclet number increases exponentially with the slit/gap size for both trap types. We further show that capture efficiency scales with slit or gap size but is independent of pump flow rate, offering an additional, orthogonal design parameter. Furthermore, we demonstrate successful trapping of cells from different cell lines in the different device types. The presented work provides a quantitative framework for the design of trap geometry and flow rate to achieve optimal cell culture conditions in microfluidic chips.