Difference between revisions of "Optical Microscopy: Part 4 Report Outline"
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| − | </li> <li>Viscosity | + | </li> <li>Viscosity and viscoelasticity |
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<li>Procedure | <li>Procedure | ||
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<ul> | <ul> | ||
<li>Include a snapshot of the 0.84 μm fluorescent beads monitored.</li> | <li>Include a snapshot of the 0.84 μm fluorescent beads monitored.</li> | ||
| − | <li>Plot an example bead trajectory in the X-Y plane.</li> | + | <li>Plot an example bead trajectory and an example differential trajectory in the X-Y plane.</li> |
| − | <li>Plot the | + | <li>Plot the ''differential'' MSD vs time interval (τ) data on log-log axes, for beads tracked in glycerol:water mixtures and on a separate figure for beads tracked in polyacrylamide gels.</li> |
</ul> | </ul> | ||
<li>Analysis and Results</li> | <li>Analysis and Results</li> | ||
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<li>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?</li> | <li>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?</li> | ||
<li>Estimate diffusion coefficient and viscosity for each water-glycerin mixture sample (A, B, C and D).</li> | <li>Estimate diffusion coefficient and viscosity for each water-glycerin mixture sample (A, B, C and D).</li> | ||
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</ul> | </ul> | ||
<li>Discussion</li> | <li>Discussion</li> | ||
<ul> | <ul> | ||
<li>How do your viscosity calculations compare to your expectations? (This [https://dl.dropboxusercontent.com/u/12957607/Viscosity%20of%20Aqueous%20Glycerine%20Solutions.pdf chart] is a useful reference.)</li> | <li>How do your viscosity calculations compare to your expectations? (This [https://dl.dropboxusercontent.com/u/12957607/Viscosity%20of%20Aqueous%20Glycerine%20Solutions.pdf chart] is a useful reference.)</li> | ||
| + | <li>Comment on viscoelasticity results, specifically on the divergence in viscoelastic behavior of the PAGs at various total acrylamide concentrations, and the existence of an elastic plateau characteristic of solid-like material for some cross-linking percentages but not others.</li> | ||
| + | <li>Could this passive microrheology approach be used to study cellular biomechanics? Under what assumptions could the intracellular viscoelasticity be quantified by monitoring beads embedded in the cytoskeleton?</li> | ||
| + | <li>How are your results affected by microscope stability and resolution?</li> | ||
<li>Comment extensively on significant 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). Do not comment on insignificant sources of error. To determine which error sources are significant, and which are not, you must think carefully about the uncertainty related to each error source and estimate its magnitude and sign. Include these estimates in your report along with the combine, total uncertainty.</li> | <li>Comment extensively on significant 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). Do not comment on insignificant sources of error. To determine which error sources are significant, and which are not, you must think carefully about the uncertainty related to each error source and estimate its magnitude and sign. Include these estimates in your report along with the combine, total uncertainty.</li> | ||
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Revision as of 17:49, 9 March 2015
- Viscosity and viscoelasticity
- 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)
- Data
- Include a snapshot of the 0.84 μm fluorescent beads monitored.
- Plot an example bead trajectory and an example differential trajectory in the X-Y plane.
- Plot the differential MSD vs time interval (τ) data on log-log axes, for beads tracked in glycerol:water mixtures and on a separate figure for beads tracked in polyacrylamide gels.
- 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).
- Discussion
- How do your viscosity calculations compare to your expectations? (This chart is a useful reference.)
- Comment on viscoelasticity results, specifically on the divergence in viscoelastic behavior of the PAGs at various total acrylamide concentrations, and the existence of an elastic plateau characteristic of solid-like material for some cross-linking percentages but not others.
- Could this passive microrheology approach be used to study cellular biomechanics? Under what assumptions could the intracellular viscoelasticity be quantified by monitoring beads embedded in the cytoskeleton?
- How are your results affected by microscope stability and resolution?
- Comment extensively on significant 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). Do not comment on insignificant sources of error. To determine which error sources are significant, and which are not, you must think carefully about the uncertainty related to each error source and estimate its magnitude and sign. Include these estimates in your report along with the combine, total uncertainty.
- Procedure
- Conclusion
- Take a step back to reflect on the Optical Microscopy module of 20.309: what did you accomplish and learn through your work?
