Due to the role of ClO and BrO in the rate-limiting step of the catalytic cycles enabling ozone loss, measurement of concentrations of these halogen molecules is of critical importance to understanding the loss rate of ozone in the stratosphere. A key advantage of in situ measurements is that these rate-limiting molecules can be observed simultaneously with ozone in the same volume element of the stratosphere, with high spatial and temporal resolution. Historically, these in situ measurements were made using instruments on the NASA ER-2 flight platform for a few hours at a time. However, the development and advancement of a high-altitude long-endurance (HALE) solar aircraft has made it possible to monitor these radicals continuously in the stratosphere. The slower flight speeds of the HALE aircraft will greatly improve molecule detection sensitivity and spatial resolution. To ensure proper mixing and accurate measurements, a quantitative dissection of the flow dynamics within the instrument architecture is required. Of particular importance are the turbulent behavior and the boundary layer growth, both of which affect measurement quality. The geometry of the NO injector used for titration is studied as a function of its solidity and the flight airspeed, to understand its effect on turbulence and boundary layer growth. A 3D Computational Fluid Dynamics simulation of an Eulerian mixture model is used to analyze the advection-dominated mixing inside the instrument. The injector inside the instrument is found to act as a flow-conditioning device, with a lower solidity causing the downstream flow to be increasingly turbulent. Additionally, a quantitative relationship between the Reynolds number of the inlet air and the volume fraction of the flow is demonstrated. Analysis of the boundary layer dependencies demonstrates that the boundary layer does not encroach on the optical sensing area in any of the cases.