Weekly Progress

Week 1:

I arrived at Rutgers on Sunday; Monday and Tuesday DIMACS held an orientation to the program. During the remainder of the week, I met Dr. Olson's graduate reserach group and went to a few DIMACS seminars. I also read several articles and scientific papers to familiarize myself with nucleosomes and the epigenome.

Week 2:

In addition to going to two DIMACS seminars this week, I studied the Matlab and Python programming languages. Using Excel, I created a table of parameters that could be input into the w3dna website to generate 3D images of the specified DNA strand. An example of these first images is to the left. Student Presentations were held on the Friday of this week, and I participated by giving an introductory PowerPoint presentation, which can be accessed from the link below: Presentation I

Week 3:

After studying Matlab for much of the beginning of this week, I decided that the implementation of my program (which was to randomly place nucleosomes on a DNA strand according to observed probabilities and then generate output parameter files describing the topology of the strand) would be completed more easily using Python. Thus, I switched gears and began focusing solely on Python. By Friday, I had a basic working program that would generate a single file of parameters with each run.

Week 4:

I used this week to improve my program and was able to make many output files of parameters at once. These parameter files containing the relationship of DNA base-pairs to each other could be rebuilt using an existing computer program to create files describing the topology of the DNA strand at the atomic level. Using Pymol, I was able to generate 3D images of the DNA. Such an image can be seen to the right. On Tuesday, two scientists from the UK came to visit Dr. Olson's lab, and I attended their seminar with Dr. Olson and her reserach group. I concluded the week by beginning to write HTML code for my REU webpage.

Week 5:

On Monday of this week I reviewed my original program and added new code to create more realistic images of the DNA. Originally I had worked under the assumption that free DNA was perfectly straight, but this is not truly the case. Thus, the new image on the left, the parameters of which were generated by my program and used as input into Pymol, represents a more faithful rendering of the DNA strand. Having finished my program on Monday, I changed focus entirely. For the remainder of the week I read background material on DNA supercoiling and studied the mathematical methods used to describe the topology of circular DNA molecules. My reading took its form in two books: Unraveling DNA by M. Frank-Kamenetskii and Topology and Physics of Circular DNA by A. Vologodskii. An interesting lecture on the subject can be found at the link below: Lecture on DNA Twisting, Coiling, & Knotting

Week 6:

I continued to do background reading on DNA loops this week and focused particularly on several papers describing the mathematics behind computations involving twist, writhe, and link. In addition to attending a seminar and a field trip to Bell Labs, I also started modifying a shell script written by Lauren Britton later this week. This script automatically rebuilt the parameter files my program created into xyz-coordinate files. These files could then be used to calculate the end-to-end distance of each DNA strand in the hopes of finding closed loops.

Week 7:

Early this week I finished modifying Lauren Britton's shell script and wrote a short Python program to calculate the end-to-end distances of DNA strands. I then ran the script overnight to generate 5000 sample structures. Unfortunately, none of these structures represented closed DNA loops, so I was unable to calculate their writhe values. Nevertheless, I created a histogram to illustrate the frequency of different end-to-end distances occuring. The image to the right shows the DNA structure with the smallest end-to-end distance I was able to find, and the histogram I constructed is below. Final student presentations were held on Friday of this week, and I participated by describing the work I did this summer via a PowerPoint presentation. It can be accessed from the link below: Presentation II

---

Week 8:

This was my last week at Rutgers University, and I used it to wrap up my REU project and say goodbye to the program. I spent time fulfilling my responsibilities to DIMACS and wrote up a final report on my summer research. In addition, I went back to the code I created to add comments and formatting so it would remain useful to future students.