abstract: Single cell phenotypic heterogeneity studies reveal more information about the pathogenesis process than conventional bulk methods. Furthermore, investigation of the individual cellular response mechanism during rapid environmental changes can only be achieved at single cell level. By enabling the study of cellular morphology, a single cell three-dimensional (3D) imaging system can be used to diagnose fatal diseases, such as cancer, at an early stage. One proven method, CellCT, accomplishes 3D imaging by rotating a single cell around a fixed axis. However, some existing cell rotating mechanisms require either intricate microfabrication, and some fail to provide a suitable environment for living cells. This thesis develops a microvorterx chamber that allows living cells to be rotated by hydrodynamic alone while facilitating imaging access. In this thesis work, 1) the new chamber design was developed through numerical simulation. Simulations revealed that in order to form a microvortex in the side chamber, the ratio of the chamber opening to the channel width must be smaller than one. After comparing different chamber designs, the trapezoidal side chamber was selected because it demonstrated controllable circulation and met the imaging requirements. Microvortex properties were not sensitive to the chambers with interface angles ranging from 0.32 to 0.64. A similar trend was observed when chamber heights were larger than chamber opening. 2) Micro-particle image velocimetry was used to characterize microvortices and validate simulation results. Agreement between experimentation and simulation confirmed that numerical simulation was an effective method for chamber design. 3) Finally, cell rotation experiments were performed in the trapezoidal side chamber. The experimental results demonstrated cell rotational rates ranging from 12 to 29 rpm for regular cells. With a volumetric flow rate of 0.5 µL/s, an irregular cell rotated at a mean rate of 97 ± 3 rpm. Rotational rates can be changed by altering inlet flow rates. / Dissertation/Thesis / Video of the irregular cell rotation / M.S. Bioengineering 2011

abstract: Volumetric cell imaging using 3D optical Computed Tomography (cell CT) is advantageous for identification and characterization of cancer cells. Many diseases arise from genomic changes, some of which are manifest at the cellular level in cytostructural and protein expression (functional) features which can be resolved, captured and quantified in 3D far more sensitively and specifically than in traditional 2D microscopy. Live single cells were rotated about an axis perpendicular to the optical axis to facilitate data acquisition for functional live cell CT imaging. The goal of this thesis research was to optimize and characterize the microvortex rotation chip. Initial efforts concentrated on optimizing the microfabrication process in terms of time (6-8 hours v/s 12-16 hours), yield (100% v/s 40-60%) and ease of repeatability. This was done using a tilted exposure lithography technique, as opposed to the backside diffuser photolithography (BDPL) method used previously (Myers 2012) (Chang and Yoon 2004). The fabrication parameters for the earlier BDPL technique were also optimized so as to improve its reliability. A new, PDMS to PDMS demolding process (soft lithography) was implemented, greatly improving flexibility in terms of demolding and improving the yield to 100%, up from 20-40%. A new pump and flow sensor assembly was specified, tested, procured and set up, allowing for both pressure-control and flow-control (feedback-control) modes; all the while retaining the best features of a previous, purpose-built pump assembly. Pilot experiments were performed to obtain the flow rate regime required for cell rotation. These experiments also allowed for the determination of optimal trapezoidal neck widths (opening to the main flow channel) to be used for cell rotation characterization. The optimal optical trap forces were experimentally estimated in order to minimize the required optical power incident on the cell. Finally, the relationships between (main channel) flow rates and cell rotation rates were quantified for different trapezoidal chamber dimensions, and at predetermined constant values of laser trapping strengths, allowing for parametric characterization of the system. / Dissertation/Thesis / Demonstration of process flow in the microvortex chip / Cell rotation in a 50 microns wide (at the neck) trapezoidal chamber,at a flow rate of 95 microliters/min at approximately 0.25 rev/s / Cell rotation in a 70 microns wide (at the neck) trapezoidal chamber,at a flow rate of 7 microliters/min at approximately 0.125 rev/s / M.S. Bioengineering 2013

abstract: Single cell analysis has become increasingly important in understanding disease onset, progression, treatment and prognosis, especially when applied to cancer where cellular responses are highly heterogeneous. Through the advent of single cell computerized tomography (Cell-CT), researchers and clinicians now have the ability to obtain high resolution three-dimensional (3D) reconstructions of single cells. Yet to date, no live-cell compatible version of the technology exists. In this thesis, a microfluidic chip with the ability to rotate live single cells in hydrodynamic microvortices about an axis parallel to the optical focal plane has been demonstrated. The chip utilizes a novel 3D microchamber design arranged beneath a main channel creating flow detachment into the chamber, producing recirculating flow conditions. Single cells are flowed through the main channel, held in the center of the microvortex by an optical trap, and rotated by the forces induced by the recirculating fluid flow. Computational fluid dynamics (CFD) was employed to optimize the geometry of the microchamber. Two methods for the fabrication of the 3D microchamber were devised: anisotropic etching of silicon and backside diffuser photolithography (BDPL). First, the optimization of the silicon etching conditions was demonstrated through design of experiment (DOE). In addition, a non-conventional method of soft-lithography was demonstrated which incorporates the use of two positive molds, one of the main channel and the other of the microchambers, compressed together during replication to produce a single ultra-thin (<200 µm) negative used for device assembly. Second, methods for using thick negative photoresists such as SU-8 with BDPL have been developed which include a new simple and effective method for promoting the adhesion of SU-8 to glass. An assembly method that bonds two individual ultra-thin (<100 µm) replications of the channel and the microfeatures has also been demonstrated. Finally, a pressure driven pumping system with nanoliter per minute flow rate regulation, sub-second response times, and < 3% flow variability has been designed and characterized. The fabrication and assembly of this device is inexpensive and utilizes simple variants of conventional microfluidic fabrication techniques, making it easily accessible to the single cell analysis community. / Dissertation/Thesis / M.S. Bioengineering 2012