RM's+Overview+of+AFM+Research

Back to RM's 2008-2009 Research

Here, I've compiled the basic information you would need to begin this project on nanotechnology at Notre Dame. From the materials to the learning process, I've provided on overview on what to expect. To be more specific, this project, as a whole, utlizes a special DNA molecule as the focus of creating a nano-scale circuit board, which can used in future nano-electronics. (Here's a [|video] that gives a very basic view of the kind of molecular nanoelectronics being pursued at Notre Dame.) My specific focus was to determine the polymerization pattern of the DNA, because based on that, a circuit board can be constructed once it's known how DNA rafts form chains and organize.


 * The Basics:**

//Atomic Force Microscope (AFM)://
 * A very high-resolution microscope that can scan samples at a nanoscale. It is the descendant of the Scanning Tunneling Microscope (STM) and "feels" the surface by contacting the sample surface intermittently. This particular mode of scanning the surface, termed "tapping mode" was used in my research.
 * The microscope is attached to a computer and has special software in order to produce an image of the sample surface on the computer screen. Using the software, I can find the length, height, and width of individual particles. Additionally, many other tools can be used to analyze the sample surface.
 * It took me about a full school year working in the lab to feel comfotable with setting up the microscope and scanning a sample. After a school year using the microscope under my mentor's supervision, I passed a test to use the microscope by myself.
 * Check out these website to learn more about the instrument!
 * http://en.wikipedia.org/wiki/Atomic_force_microscope
 * http://www.nanoscience.com/education/AFM.html
 * http://www.mih.unibas.ch/Booklet/Booklet96/Chapter3/Chapter3.html

//The Learning Process://
 * As mentioned, it took me nearly a year to become familiar with the equipment and to be allowed to conduct this part of the research by myself.
 * Learning the structure of DNA, and especially the structure of the specific double cross-over molecule used is very important. Additionally, I would say that a year of chemistry and biology are both important to have before embarking on this project because it involves biochemistry.
 * Here's a link on the double crossover molecule : http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302964
 * Also, creating samples is another important step. The process is simple, but careful attention must be paid to cleaning the mica chips (on which the DNA is mounted) and handling the materials.
 * We use mica (as opposed to silicon in some studies) because it is cheaper and an easier surface on which to prepare a sample because cleaning it is very easy.
 * Another important step is being able to clean samples in the special Cleaning Room located in the engineering building at Notre Dame.
 * For this, a special pass must be issued, and a full bunny-suit and goggles are required.
 * The cleaning room is a very sterile environment, but it holds very dangerous chemical. Therefore, a person has to go through cleaning room training procedures and pass another test to demostrate that he/she follows the safety precautions and procedures.
 * Just remember, the process may seem tedious, and it requires patience....but the benefits of doing research independently later on is an incentive!
 * If you can, try to do research during the summer! I learned so much during my time over the summer, and my project advanced much more, as well.
 * The specific program that I went through was the RET program at Notre Dame. Someone on the Notre Dame faculty has to recommend you for the opportunity.

//The Future://
 * There is a lot of potential for this project in the future. First, my research over the summer should be re-tested, just to be certain that my results were not anomalies.
 * If the results match with mine (i.e. step-growth polymerization v. chain-growth polymerization), then more research should go into identifying how the DNA rafts could be defected, and how to eliminate or diminish that factor in the research and results.
 * If the results do not match with mine (i.e. chain-growth polymerization was discovered, not step-growth), then that could mean one of many things. For example, finding chain-growth polymerization is ideal in the creation of circuit boards and nano-electrics because the growth can be predicted easily, which is ideal in the mass-production of anything.

//Other Information://
 * Mentors: Dr. Marya Lieberman (Notre Dame) and Dr. Koshala Sarveswaran (Notre Dame)
 * Since this project is conducted outside of school, it is helpful to drive, since you travel to Notre Dame (usually after school) to do research. Parking is the easiest in the Notre Dame parking lot near the library.
 * It's usually good to conduct research at least twice a week for about 2-3 hours, because as you will soon learn, that is hardly enough time to accomplish a lot.