Chapter 1: additional files of interest

Matlab Figs

Chapter 1 Part 1 – updated on 8.30.17 @ 6:20pm

Slide 1-8: no comments

Slide 9: I want you to know the relative scales of the different entities discussed. Know how many orders of magnitude are covered as well as the estimated scales for each.

Slide 10: I want you to know what imposes the lower and upper limits on the size of cells and what the lower and upper limit of the cells are.

Slide 11: No comment.

Slide 12: I want you to know what these two different instruments are and how they work. I want you to know the equations involved in each and what the limitations of each are.

Slide 13: Know RMS and GM equations and everything on the slide. What happens to values that are extreme? Be able to answer the rhetorical questions.

Slide 14: This is a picture of what I want you to replicate in MatLab which will be one of the problems for Ch. 6. You can download the associated files above (MatLab figures) and I want you to be able to replicate these figures with your program. The purpose of doing this is to quantify what the theoretical distances traveled would be. Know how to do this for 1-D, 2-D, and 3-D. How does the in silico values compare to your program?

Chapter 1 Part 2 – updated on 8.30.17 @ 6:20pm

Slide 1: Another figure (follow-up to the slide 14 above.

Slide 2: Know everything on this slide. I want you to know what the slopes mean for the correlation function in time. I want you to draw what a larger and smaller particle would look like. I want you to be able to draw what a more heterogenous population of particles would look like, in comparison to a more homogeneous population.

Slide 3: I want you to know what the absolute and relative values are for the different entities discussed; as well as how the shown diffusivity equation changes in 1-D, 2-D, and 3-D.

Slide 4: These are simple examples of what can be calculated. I want you to be able to do this, however. I want you to know that diffusion can be more effective for shorter distances than longer distances. The facts about the bugs are interesting to think about why it is physiologically possible to have no heart, single-chambered hearts, etc.

Slide 5: Know the units of viscosity, density, and kinematic viscosity. Know everything on this slide.

Slide 6: Know this.

Slide 7: Know what the units of flux are and what multiple types of units there can be. Know what the gradient symbol is and how to expand it. Know what Fick’s first law is and how to use it.

Slide 8: No comment.

Slide 9: Simple calculations.

Slide 10: Know Fick’s 2nd law and what the delta symbol is in the gradient-squared sense. Know how to expand the equation and how to use it. We will be discussing how to solve this partial differential equation for C in the not so distant future.

Slide 11: Know the analogous forms of this equation and what the units are for each. Be able to answer the rhetorical questions.

Slide 12: Know this.

Slide 13: Know rough estimate of MW for each and the Diffusivities for each. Know the diameters discussed as well (also mentioned in an earlier slide). Be able to estimate diffusion times and how to calculate the Pe #s (see upcoming slide in regards to Pe #) based on the information given. See caption.

Slide 14: Know everything on this slide. Know what the Re # is useful for.

Slide 15: Know everything on this slide. Know what the Pe # is useful for.

Slide 16: State the meaning of the plot in words (absolute values are unimportant here).

Slide 17: State the meaning of the plot in words.

Slide 18: Know what MM kinetics are and what the Hill equation is and what cooperativity is and how to caculate it. Be able to draw what positive cooperativity is, no cooperativity, as well as negative cooperativity (with units on axes, etc.). Know the linear form of the Hill equation.

Supplemental NTA information:

http://www.me.umn.edu/centers/cdr/reports/NanoSightPaper.pdf

Supplemental DLS information:

http://www.nano.wustl.edu/doc/Instrument%20Manuals%20and%20Protocols/DLS%20Final.pdf

Interesting and not required:

http://bio.classes.ucsc.edu/bio131/Thometz%20Website/Ponganis%202011%20Diving%20Mammal%20Review.pdf