Microfabricated fused silica flow chambers were developed for applications in flow cytometry, a biomesurement technique for studying large numbers of cells or other biological particles individually as the flow single file past optical or electronic sensors. The flow cells were fabricated using two fused silica substrates with matched isotropically etched features. In addition to provisions for producing hydrodynamic focusing of the sample, the flow cells incorporated grooves for accurately positioning optical fibers that were used to illuminate the sample flow.

Three-dimensional finite element flow simulations were done to investigate the behavior of the sample flow. Results from these simulations together with a few simplifying assumptions allowed estimating the velocity and width of the sample flow as a function of streamwise position along the center flow axis of the device. The sample flow velocity was also used to compute suspended particle transit times as a function of position along the flow axis. These last results, coupled with a simple one dimensional diffusion model enabled the estimation of the transport of a fluorescent marker diluted in the sample flow.

The behavior of the sample flow was also studied experimentally using optical sectioning imaging techniques. These measurements yielded information about the three-dimensional structure of the sample flow and the influence of secondary flows on such structure. These effects were confirmed by the flow simulations.

Quantitative fluorescence data extracted from the flow images were compared to ransport simulations. These results showed similar trends and matched the data ly considering all the assumptions that were made for generating this model and possible artifacts in the measurements.

Resolution measurements using 2 um diameter calibrated fluorescent particles were used to evaluate the flow cells as part of a flow cytometry system. These measurements yielded a coefficient of variation (CV, standard deviation divided by the mean) of 7 to 8% using particles with a 2.6 % CV in size.

The technology, modeling, and methods developed for this thesis may be applied to many biomedical applications that require observing particles or exploiting transport of particles in steady flows. One possible application is the development of a precise mixer where the chemistry of the inner sample flow is controlled by the introduction of molecules dissolved in the surrounding sheath flow.