List of Figures
  1. (a) Schematic depicting cell lysis by tip sonication: (i) sonicator tip is inserted into the sonication vessel, submerging tip in liquid. (ii) Controller for specifying pulse, amplitude & duration iii) The tube sits in ice-bath for cooling iv) Input energy from controller (ii) is set as a function of signal amplitude (translates to tip power based on fluid volume and vessel), pulse durations, and total sonication time v) Thermal energy transfers to ice-bath from cell suspension domain vi) The sonicated liquid is divided into circulated zone & dead zone (b) Axis-symmetric models (right half) of common laboratory tubes: i) 1.5 mL microcentrifuge tube ii) 5 mL microcentrifuge tube iii) 15 mL Falcon tube iv) 50 mL Falcon tube.
  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.
  3. Temperature rise over time determined experimentally (blue line) and estimated with the finite element simulation (orange line). a) 1.5 mL microcentrifuge tube with 1.5 mL sample at 50% amplitude using a 3mm tip (corresponding to ~5.5 Watt) and 10 second on and 10 second off pulse, initial temperature 1.6C. b) 1.5 mL microcentrifuge tube with 1.5 mL sample at 50% amplitude using a 3mm tip (corresponding to ~5.5 Watt) and 20 second on and 20 second off pulse, initial temperature 3.4C. c) 1.5 mL microcentrifuge tube with 1.5 mL sample at 25% amplitude using a 3mm tip (corresponding to ~2 Watt) and 10 second on and 10 second off pulse, initial temperature 1.1C. d) 5 mL microcentrifuge tube with 5 mL sample at 50% amplitude using a 6mm tip (corresponding to ~12.5 Watt) and 20 second on and 20 second off pulse, initial temperature at 14.4 C.
  4. a) Heat map of normalized sfGFP yield from BL21 DE3 Star cell extracts prepared at different volumes and total energies, with z-axis color bar presenting relative amounts of expression (replotted from (Kwon & Jewett, 2015)). Thick dashed lines depict temperatures (K) at these sonication conditions obtained by the finite element simulation. Thin solid lines indicate energy density values (J/mL). b) The same normalized yield data plotted in a more generalized fashion as power density vs. total energy; dashed lines again show temperatures estimated by simulation.
  5. Workflow diagram to obtain optimized sonication parameters for temperature sensitive procedure using the finite element model directly (access to COMSOL required to run provided process code).
  6. Maximum temperature (y-axis) estimated for different power density (x-axis) and pulse time (5-10,10-10,15-10 and 20-10 on-off pulses respectively) for each of the four tubes – a) 1.5 mL microcentrifuge tube b) 5 mL microcentrifuge tube c) 15 mL conical tube d) 50mL conical tube.
  7. Model drawing in COMSOL with specified boundary conditions for a) Pressure acoustics, b) Laminar flow and c) Heat transfer