Figure 2 : Modeling effect of tip depth on mixing. a) Circulation zone (yellow) and dead zone (gray) with different tip depths for 1.5 mL Microcentrifuge tube obtained from simulation. b) Percentage of volume in circulation zone with changing tip height for four sizes of tubes 1.5,1.5, 5, 15, and 50 mL with 1.5,1, 5, 10, 15 mL sample respectively.
For the common 1.5 mL snap-cap microcentrifuge tubes the vessel cavity is narrow (low clearance between tip and wall) and the liquid has a smaller circulation zone; when the tip depth is more than 60% of the liquid height, the circulation zone percentage falls below 50% of the total capacity, in simulation. Another interesting observation is reduced mixing at the shallower tip depths for the 15 mL centrifuge tube; this tube has the highest length to diameter aspect ratio of the tubes screened and we observe a dead zone build up at bottom of the tube if the depth is less than 20% from the top; likewise, there is reduced mixing if depth is more than 40% (dead zone near the top surface). The 50 mL tube is the only one simulated that can achieve nearly 100% mixing (at depths less than 40% total fluid height). We attribute this to the superior circulation zone observed in this vessel size. However, the 50 mL tube has the limitation of poorer heat dissipation (smaller area to volume ratio) leading to greater potential of heat build-up and damage to cell extract preparation. This laminar model does not take into account the improved mixing cause by turbulent eddies caused by sonication; thus we progress to the heat transfer model by making the assumption of complete mixing for all tubes and then use experimental validation to confirm use of this assumption.