User:Brian P. Josey/Notebook/2010/06/29

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Checking Calculations with Experiment

Now that my emulsions are coming along, the next step is to move forward and check my theoretical calculations against the results from the experiments. There is still the issue of the drift that I observed yesterday, but because it is over a large time frame and is very slight, running shorter experiments and paying closer attention should take care of it for now. However, I will return to this issue later.

I eventually hope to get a program running, like the one used on the microtubules, that I could plug in the images I take and get out the data I need. This may take a while, and for now, it is more efficient to do the process by hand than to teach myself LabVIEW and write the software from scratch. Although, I will try to pick some up in the process. To get to this point, my goals for the next couple of days are to:

  • Build a model in FEMM of the objective and magnet
  • Run simulations of this model with various magnetizations and orientations
  • Process the data from the simulations to calculate forces
  • Estimate the size and speed of ferritin droplets by hand, and
  • Account for the influence of Brownian motion and the drifting

After I complete these several steps, I should have an adequate way to measure the average terminal velocity a droplet moves at, and with its size, the force that ferritin exerts on it. Then, depending on the results, I can run it against my simulations and see if they agree.

Objective Measurements

Using the digital calibers, I was able to make some measurements of the objective lens. For the sake of keeping them in one place I've created a table listing the measured values, in mm:

Base To Distance Negative Distance Diameter Radius
Lip 34 -16 28 14
First Angle 42.5 -7.5 30 15
Second Angle 46.8 -3.2 22 11
Angle Break 47.8 -2.2 17.6 8.8
Lens 50 0 8.32 4.16

"Negative distance" is what I use when placing the nodes into FEMM to account for my centering of the simulation. Generally, I place the zero at the center of one of the things I'm looking at, and at its end. To get the location of my nodes, the z-coordinate is the "negative distance" and the r-coordinate is the "radius".

FEMM and Mindmap

Here is an image of what the objective looks like in FEMM with the above nodes:

6-29-10 objective FEMM.JPG

The problem is axisymetric, and is defined in mm. Towards the bottom of the objective, I simplified the design, replacing the threaded part that attaches to the microscope with a cylinder. I also generated a mind map of things that I need to keep in mind, and would like to accomplish:

<html> <iframe id='xmindshare_embedviewer' src='http://xmind.net/share/_embed/brianjosey/ferritin-force/' width='900px' height='300px' frameborder='0' scrolling='no'></iframe> </html>

Tomorrow, I hope to run a couple of quick two minute experiments to use as my data, and finish the FEMM model in the afternoon.