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Abstract

Hydrogels—crosslinked polymer networks swollen by aqueous solvents—have become important components in biomicrofluidic devices due to their softness, biocompatibility, porosity, and ready availability. This thesis presents an integrated theoretical and computational investigation into the complex mechanical interactions between hydrogels, embedded biological cells, and surrounding fluid flows. By developing a robust poroelastic model coupled with an advanced finite-element numerical framework implemented using the deal.II library, fluid-hydrogel interface dynamics are accurately resolved via a fixed-mesh arbitrary Lagrangian-Eulerian approach. The reliability and precision of this computational method are rigorously validated through benchmark problems, including hydrogel compression, two-layer shear flow, and the deformation of gel particles in planar elongational flow. Leveraging this validated computational platform, the study systematically explores fluid-induced deformation of hydrogels and the consequent mechanical responses of single embedded cells subjected to shear and normal perfusion flows. Results highlight the critical role of interstitial fluid pressure in governing cellular deformation, closely matching experimental observations from biomicrofluidic assays. Extending this analysis, the thesis investigates the more intricate scenario of mechanical interactions among multiple cells embedded within the hydrogel. These simulations uncover the formation of tension ribbons—regions of aligned tensile stress within the hydrogel matrix—that mediate intercellular mechanical communication and contribute to collective cell behavior and tissue morphogenesis. Overall, the thesis provides both robust computational tools and fundamental mechanistic insights that enhance the design and optimization of biomicrofluidic systems, significantly advancing our understanding of mechanotransduction within cellular microenvironments.