Assignment 5, Part 1: viscosity and diffusivity in glycerolwater mixtures
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This is Part 1 of Assignment 5.
Estimating the diffusion coefficient by tracking suspended microspheres
1. Track some 0.84μm Nile Red Spherotech polystyrene beads in waterglycerin mixtures (Samples A and B contain 30% and 50% glycerin, respectively).
 Notes: Fluorescent microspheres have been mixed for you by the instructors into waterglycerin solutions A and B. (a) Vortex the stock Falcon tube, and then (b) transfer the bead suspension into its imaging chamber (consisting of a microscope slide, doublesided tape delimiting a 2mm channel, and a 22mm x 40mm No. 1.5 coverslip, and sealed at both ends nail polish).
 Tip 1: Do not choose to monitor particles that remain stably in focus: these are likely to be 'sitting on the coverslip' and their motion will not be representative of diffusion in the viscous waterglycerol fluid.
 Tip 2: Limit the ROI to a region with only 3 or 4 particles. Long movies with the whole field of view is a sure way to make MATLAB complain.
2. Estimate the diffusion coefficient of these samples: MSD = $ \left \langle {\left  \vec r(t+\tau)\vec r(t) \right \vert}^2 \right \rangle=2Dd\tau $, where r(t) = position, d = number of dimensions, D = diffusion coefficient, and $ \tau $= time interval.
Turn in for the viscosity part:

 Overview
 Part 1: Viscosity of glycerol
 Part 2: Live cell particle tracking of endocytosed beads
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