An investigation of cyclic flow within an optical water analog engine oriented horizontally and with a square cross-section has been carried out using a computational code, KIVA, and compared with particle image velocimetry results. The simulation results highlight the ambiguity with regard to the velocity direction in the experiment and provide more insight into the velocity profile at the latter part of the intake stroke. The computational work is found to not adequately capture the higher order turbulence statistics obtained in the experimental results. The study concludes that the Reynolds stress transport is the dominant component of the equation of motion near the piston surface and causes the turbulent mixing responsible for the mixing and combustion efficiency in an engine.