# Research Journal

Week 1 |Week 2 | Week 3 | Week 4 | Return to Index |

## Week of July 21, 2009

(July 22) (July 23) (July 24)

July 22
Determining index of refraction of unknown material:

(K.D. Alexopoulos)

As the above image shows, there is an angle of minimum deviation, where the rate of change of the angle of the refracted ray is zero (derivative is zero). What to get from that image is that epsilon is the angle of deviation. When the ray inside the prism is parallel to the base of the prism (or when the entering and exiting angles are the same), the angle of minimum deviation is achieved. It's useful because it can be used to determine the index of refraction of an unknown material using the following relationship:

n=sin[(D+a)/2]/sin(a/2)

Where n is the index of refraction of the material, "a" is the angle between the two faces of the prism the beam passes through, and D is the angle of minimum deviation (as measured from an extension of the original incident ray).

There is a simple applet on this page which demonstrates the angle of minimum deviation well.

Also, this is a useful concept to remember: The angle made by the reflected beam is twice the angle of tilt of the mirror.

July 23

I decided that now would be a good opportunity to try and learn some things about Linux, considering I need to use a Linux shell to edit this webpage and associated files. Also, it's something I've been meaning to learn about anyway because MIT's computing environment, Athena, is Linux-based.

July 24
 Okay, most useful commands: cd - change directory ls - list files in current directory. Modify with -l for "long," -a for "all" (including .files), or combinations. pwd - indicates current directory pushd and popd - "stacks" directories and returns to original directory, respectively pico - accesses text editor find [starting directory] -name [filename] OR -ctime [days old] OR -size [kb] touch - creates new file or updates modification time of existing file "rm -i" removes file and asks for confirmation! mkdir - creates new directory. rmdir removes a directory. cp [sourcefile] [destinationfile] to copy to same directory. cp [sourcefile] [destinationdirectory] will copy to desired directory. Random file succesfully destroyed forever

## Week of July 27

(July 27) (July 30)

July 27 More Linux commands:

• "mv" [newname] [newdirectory] moves files.
• less [filename] displays file content page by page.
• emacs - much more complicated file editor than pico (but on Athena has games)
• vi - quick and dirty file editing

And a bit on molecular anisotropy: Directionally dependent properties of molecules, including self-assembling biomolecules like membraneous phospholipids and cholesterol-based molecules in liquid crystals. Nucleotides also follow this "Janus" principle to allow for DNA assembly. Self assembly has tons of applications in biomedicine and industry, from targeted drug treatments to solar cells.

 Phospholipids have a hyrdophillic head and a hydrophobic tail, which causes self-assembly when these molecules are in water Janus, Roman god of gates and doorways

 July 30 Some interesting things:

 Photorefractive keratectomy (PRK) - use of an excimer laser for corneal ablation to correct near- or farsightedness (similar to LASIK). In PRK, ethanol is used to dissolve the outer protective layer of the eye, the conjunctiva, which is then scraped off. An excimer (excited dimer) laser (whose particular wavelength is optimal for breaking biomolecular bonds without damaging nearby tissue) is used to ablate the outer layer of the cornea (compared to the inner layer, the stroma, in LASIK). The degree of ablation is unique to each patient depending upon the refractive index the doctor wants to achieve. When I had this surgery performed, I was moderately myopic, so my cornea was ablated to decrease its refractive index. And while this would be a really cool thing to look in to, the kind of equipment and materials available in the lab probably couldnt accomodate such an experiment.

And here's a pretty good video of the procedure being performed:

## Week of August 3

August 4 - Newton's Rings

Newton's Rings are a similar phenomenon to thin-film interference, where light rays reflect off two surfaces and either constructively or destructively interfere with one another to produce a series of light and dark "rings" (or colors with multichromatic light). The below diagram illustrates this principle:

The "green" rays are out of phase with the "blue" rays because they had to travel further. When the distance they had to travel puts the "green" rays half of a wavelength out of phase with the "blue" rays, they interfere destructively and black rings are seen. With multichromatic light, different wavelengths need to travel different distance to constructively/destructively interfere, which results in a rainbow of colors instead of distinct rings (note: the rays aren't necessarily incident at an angle, an observer could be looking at the setup from directly above. The diagram is merely meant to illustrate the concept).

Unfortunately, we could not get this setup to work in the lab with a convex lens and a glass plate, probably for a variety of reasons. We did not have a good method of securing the lens to the plate tightly, nor did we have a good way to actually visualize the rings (such as a microscope with a monochromatic light source).

*Update (8/6/09)* - Able to see Newton's rings between two slightly curved glass plates, when viewed under white fluorescent light, up close, at the correct angle. A more distinct rainbow "ring" pattern could also be seen when I switched the top lens for a thinner and slightly more curved lens (but again, only from the proper viewing angle).

## Week of August 10

Photoelectric effect in an arc lamp

We observed a unique phenomenon with the sodium lamp the other day - it would immediately activate in the presence of light but otherwise would take much longer to start up. It wasn't how the lamp was designed, surely, but it was an interesting confirmation of the photoelectric effect ("quantized" light particles). Shining a light on the lamp ejected electrons and consequently activated the lamp (either by completing a circuit or through some chemical interaction, I'm not quite sure how the lamp itself works). A multichromatic flashlight provided wavelengths with enough energy, as did a green laser, but a red laser was totally ineffective (again an effect of "quantized" light "particles").