Optimization of E. coli Tip-Sonication for High-Yield Cell Free Extract
using Finite Element Modeling
Abstract
Optimal tip sonication settings, namely tip position, input power, and
pulse durations, are necessary for temperature sensitive procedures like
preparation of viable cell extract. In this paper, the optimum tip
immersion depth (20-30% height below the liquid surface) is estimated
which ensures maximum mixing thereby enhancing thermal dissipation of
local cavitation hotspots. A finite element (FE) heat transfer model is
presented, validated experimentally with (R2 > 97%) and
used to observe the effect of temperature rise on cell extract
performance of E. coli BL21 DE3 star strain and estimate the temperature
threshold. Relative yields in the top 10% are observed for solution
temperatures maintained below 32°C; this reduces below 50% relative
yield at temperatures above 47°C. A generalized workflow for direct
simulation using the COMSOL code as well as master plots for estimation
of sonication parameters (power input and pulse settings) is also
presented.