Optical Microscopy: Part 4 Report Outline

7. Viscosity
   1. Procedure
      • Document the samples you prepared and used and how you captured images (camera settings including frame acquisition rate, number of frames, number of particles in the region of interest, choice of sample plane, etc)
   2. Data
   • Include a snapshot of the 0.84 μm fluorescent beads monitored.
   • Plot an example bead trajectory in the X-Y plane.
   • Plot the beads' MSD vs time interval (τ) data on log-log axes.
   3. Analysis and Results
   • Provide a bullet point outline of all calculations and data processing steps.
   • Explain how you can use the mean squared displacement data to extract D, the diffusion coefficient of a purely viscous fluid. What equation relates D and η, the fluid's viscosity?
   • Estimate diffusion coefficient and viscosity for each water-glycerin mixture sample (A, B, C and D).
   • Comment on results, specifically how they are influenced by microscope stability and resolution.
   4. Discussion
   • How do your viscosity calculations compare to your expectations? (This chart is a useful reference.)
   • Comment extensively on sources of error and approaches to minimize them, both utilized and proposed. Categorize the sources of error as systematic, random, or just mistakes (so-called "illegitimate" errors).
8. Bacteria behavior
   1. Model
      • Based on the simple classic model of the diffusion-convection equation and presuming oxygen is an attractant to Vibrio alginolyticus, what distribution B(x) do you expect at steady state for the bacteria in suspension in a microchannel with boundary conditions "air = 20% oxygen" on one side and "nitrogen = 0% oxygen" on the other side? Express your result B(x)as a function of μ, the diffusivity of the bacteria, V_c, their drift or convection velocity, and x, the space coordinate across the microchannel width.
      • Count the bacteria present in a few example pictures taken at various x-locations in the microchannel (from small x values near the air-PDMS wall to large x values closer to the nitrogen-PDMS wall). Does the actual bacteria population agree with your theoretical model?