DIMACS
DIMACS REU 2015

General Information

me
Student: Christine Wiersma
Office: CoRE 434, Wright Rieman Labs A209
School: Alma College
E-mail: wiersma1cl [at] alma [dot] edu
Project: Characterizing the Geometry and Topology of RNA

Project Description

RNA is a nucleic acid with many different variations and functions. The structure of individual molecules has a large effect on their function, making this an interesting topic to study. I am working to create a ribbon structure of RNA and to characterize the geometry and topology of the molecules. Using a previously established program I can identify junctions, which are important in the characterization of the whole molecule. I then can do an analysis of the data and create a mathematical model of the structure. The result may lead to a greater understanding of the function of RNA in cellular activities.


Weekly Log

Week 1:
This week I spent a lot of time reading papers to get an idea of what is already known about my project. I also met with Dr. Olson and received some guidence for the week. Finally, I prepared for and completed my first presentation.
Week 2:
I spent a lot of this week learning how to use Mathematica. Most of my research will involve working with code in Mathematica, so my mission this week was to become familiar with the commands and syntax. By the end of the week I was successful in constructing a simple ribbon model. In addition to working on my project, I attended a tutorial on using LaTeX and HTML, a tutorial on conditional lower bounds and participated in Cultural Day.
Week 3:
This week I worked to further understand RNA molecules using Mathematica. I began writing some code to compute various values that will help me understand the geometry and topology of the molecules. I also attended presentations and a tutorial on various topics. Finally, I participated in a field trip to the Cancer Institute of New Jersey.
Week 4:
I spent a lot of time troubleshooting in Mathematica this week. I ran into a few problems with my code simply because of my lack of experience with the program. I did manage to fix some of the problems though after many hours of carefully going through every character in sections of the code. So, while this week did not have any exciting milestones in it, I did learn a lot. I also attended two very interesting presentations.
Week 5:
This week I continued to work on my code. I worked through sections of my code to clean up some messy syntax and make the code function more efficiently. I also figured out a few problems that I had been having. A huge thank you to Richard Avelar for all your help this week! I am very close to finishing the code and I hope to start using it next week.
Week 6:
I spent a lot of time this week figuring out the computations for my junction analysis. In doing so, I discovered that some of the given data did not seem to match previously obtained data for the same molecule. Therefore, I was forced to figure out why it was different before proceeding. Even with all of the time I spent on unexpected problems, I did have one very successful computation this week, and I am really excited about that. I also attended a workshop on graduate school, which was very informative.
Week 7:
I spent this week continuing to work on correcting my code. I discovered a problem that occurred early on in the code and had a large effect on the computations. Correcting this took quite a bit of time, but I believe I was successful. Thank you to Andrew Wells for all your help! In addition to working on my code, I also prepared for and gave my final presentation this week.
Week 8:
This week was spent doing multiple checks to try to figure out whether or not my code was doing what I thought it should be doing. I calculated the same numbers multiple ways to determine if I was getting the correct values for my calculations. I am not done yet, but I think I am getting close to completing the code.
Week 9:
This was my final week at Rutgers. I continued to test my code and explore different possibilities involving a new molecule. I also spent a lot of time writing my final report and finalizing things here. I'm am going to continue my research after the program is over, so I had to take care of a few things to make that possible. Finally, I packed up my apartment and I am headed home on Friday.

Presentations


Additional Information