This paper presents a numerical framework for design-based analyses of electrokinetic flow in interconnects. Electrokinetic effects, which can be broadly divided into electrophoresis and electroosmosis, are of importance in providing a transport mechanism in microfluidic devices for both pumping and separation. Models for the electrokinetic effects can be derived and coupled to the fluid dynamic equations through appropriate source terms. In the design of practical microdevices, however, accurate coupling of the electrokinetic effects requires the knowledge of several material and physical parameters, such as the diffusivity and the mobility of the solute in the solvent. Additionally wall-based effects such as chemical binding sites might exist that affect the flow patterns. In this paper, we address some of these issues by describing a synergistic numerical/experimental process to extract the parameters required. Experiments were conducted to provide the numerical simulations with a mechanism to extract these parameters based on quantitative comparisons with each other. These parameters were then applied in predicting further experiments to validate the process. As part of this research, we have created NetFlow, a tool for micro-fluid analyses. The tool can be validated and applied in existing technologies by first creating test structures to extract representations of the physical phenomena in the device, and then applying them in the design analyses to predict correct behavior.
A second generation optical design for the ABI PRISM<SUP>TM</SUP> 377 DNA sequencer enhances sensitivity and increases sequencing throughput by taking advantage of simultaneous four color detection using a spectrograph and CCD array. On-axis laser illumination using a small turning mirror to excite sample fluorescence replaces the Brewster's angle geometry of the first generation sequencer. The small turning mirror blocks direct reflection of laser light from the collection path. Alignment precision and mechanical stability must be sufficient to avoid image wander on the spectrograph slit which would add noise. The spectrograph slit is underfilled to maximize signal strength and reduce mechanical vibration sensitivity. The primary noise sources have been identified and minimized such that the instrument is shot noise limited. The instrument may be reconfigured through software for use of additional or different fluorescent dye labels as required by new genetic analysis applications. The overall result is a flexible instrument platform with increased throughput, improved sensitivity and longer sequences read.