In this paper, we present a mixed-technology micro-system for electronically manipulating and optically detecting virusscale particles in fluids that is designed using 3D integrated circuit technology. During the 3D fabrication process, the top-most chip tier is assembled upside down and the substrate material is removed. This places the polysilicon layer, which is used to create geometries with the process' minimum feature size, in close proximity to a fluid channel etched into the top of the stack. By taking advantage of these processing features inherent to "3D chip-stacking" technology, we create electrode arrays that have a gap spacing of 270 nm. Using 3D CMOS technology also provides the ability to densely integrate analog and digital control circuitry for the electrodes by using the additional levels of the chip stack. We show simulations of the system with a physical model of a Kaposi's sarcoma-associated herpes virus, which has a radius of approximately 125 nm, being dielectrophoretically arranged into striped patterns. We also discuss how these striped patterns of trapped nanometer scale particles create an effective diffraction grating which can then be sensed with macro-scale optical techniques.
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