RM+FSM+Fundamental+Knowledge

RM's Milestone Report Home

I have accomplished all of these milestones, learning them mostly from interactions with my mentor and my experience at the lab. It took a while for the information to sink in, especially as it was not presented in this order. I feel confident about these milestones and know they will provide a solid foundation.

The purpose is for smaller electronics, and in particular, for smaller circuit boards. We are using silicon because it's a semi-conductor, which is a necessary property for modifying the board, as is later explained. So, first, a polymer is spread on the silicon, in order that the pattern for the circuit board can be etched into it (the pattern cannot be etched into the surface of silicon). This is done using electro-beam lithography, which must bee used on a semi-conductor to work. Assume that this pattern consists of rectangles spaced every 3-4 nanometers. Thus, at each of these spaces, a rectangle is etched into the polymer surface and the area of polymer within the rectangle is removed. Thus, there are bare, rectangular silicon areas visible across the surface of the sample. Next, the APTES is applied to the bare silicon areas. After that, the rest of the polymer is destroyed from the surface using an organic solvent. Now, the DNA rectangles, used as scaffolding, are placed on the bare silicon surface that has APTES deposited in specific places. The APTES attracts the DNA, so that the DNA accumulates where the pattern has been implanted. Now, nanoparticles can be attached to the DNA scaffolding in order to transmit signals, etc. From there, you can custom your circuit board.
 * State the purpose of project and its applications to the future.**

Obviously, AFM stands for Atomic Force Microscope or Microscopy. The AFM can scan conducting and non-conducting samples, making it an excellent tool for biological research. It takes an image of a sample from above, and a color key codes the different heights of the surface. Also, you can obtain the cross sectionional images as well has a 3-D graphic image. From an image of a sample, you can zoom in or out. More will be described in the technological section, when a person comes into contact with the AFM and learns to use it.
 * Describe the functions of AFM.**

//Tapping mode//- the cantilever "taps" the surface between 50,000- 500, 000 times per second. This does not damage the surface by dragging; therefore, this mode is used to scan surfaces that may move, surfaces that are already damaged, and surfaces that are inherently difficult to scan. //Contact mode//- the tip drags across the surface at a desired voltage. If, through the feedback loop, the deflection is discovered to be different, the feedback amplifier highers or lowers the voltage applied to the piezo, thus lowering or raising the sample surface. As a result, these changes measure the height(s) of the sample. //Non-contact mode-// the cantilever does not touch the surface, but hovers about 50-150 Angstroms above the surface and attempts to scan the surface from above by detecting the van de Waals forces. Unfortunately, this is not always used because contaminant layers on the surface of a sample can interfere with the attraction between the tip and surface, and therefore images obtained are not optimal. This information was found [|here].
 * Explain the tapping, contact, and non-contact modes.**

APTES - aminopropyl triethoxysilane. The APTES solution acts as a postive layer for the DNA to bind to. The silicon layer and DNA both have negative charges; therefore, to bind them together, the APTES needs to be present so that the DNA and silicon don't repel each other.
 * Explain what APTES stands for and its function between DNA and silicon.**

DNA plasmid is a round, double-stranded, DNA molecule that exists in the plasma of cells. Thus, it is not chromosomal DNA, but it can still reproduce. The reason we use plasmids is that they are cheap and easily accessible, two helpful properties for research materials. We use the "pUC-19" plasmid that has over 2,000 base pairs.
 * Describe what a DNA plasmid is and why it is used for research.**

If the DNA is coiled or "scrunched up" on a surface, it doesn't make very good building blocks. When DNA is relaxed and linear, it will be a stable, reliable building block. Right now, the DNA just ends up on the surface in the way it falls. If it can be influenced to linearize and relax, it would be a remakable achievement.
 * Explain why we want "linearized" DNA.**

Restriction enzymes "cut" double-stranded DNA at specific points, called "restriction sites". These enzymes are specifically fixed to identify a portion of the DNA and cut it. Thus, many restriction enzymes are sold today to make specific incisions. The restriction enzyme used in this project is called kp 1, although we're probably going to use different types, depending on how relaxed the DNA becomes after being cut by certain enzymes.
 * Describe the functions of restriction enzymes, which type is used in this project, and why.**

The plasmids have a negative charge, as explained before. Thus, as the silicon is also negative, the plasmids are repelled from the surface. As a result, the APTES solution, which has a positive charge, adheres to the silicon surface and DNA adheres to the APTES solution. APTES acts as a sort of "glue" between the silicon surface and DNA.
 * Explain the plasmids' relationship to the silicon surface and APTES.**

The Technology