DIMACS
DIMACS REU 2013

General Information

me
Student: Priscilla Lo
Office: Hill 359 ; Wright-Rieman A204
School: Rutgers University
E-mail: ppl19@dimacs.rutgers.edu
Project: Chromatin Folding

Project Description

Gene expression requires proteins at separate sites on DNA to come together which results in DNA looping. This DNA looping is affected by chromatin architecture such as the interactions between nucleosomes on chromatin and nucleosome spacing. By studying how these nucleosomes interact with one another an effective potential (covariance analysis) can be found.


Weekly Log

Week 1:
I moved into Rutgers and met with the other participants in the program. Throughout the week, I read some material to understand the structure of DNA and chromatin and met with my mentors to discuss the problem that I will be solving. A presentation was given on Friday.
Week 2:
My mentors were in Albany for a conference. I was introduced to the data which consisted of simulations of chromatin for different DNA linker lengths. The data for each of these simulations consisted of many configurations for the nucleosomes. Using Mathematica, I calculated the rotation matrix and the angle and axis representation for each pair of nucleosomes.
Week 3:
For the rotation matrix for each pair of nucleosome, I finished calculating the axis and angle of rotation. From the axis of rotation, I was able to obtain spherical coordinates to describe that vector (axis of rotation) with respect to its corresponding nucleosome frame.
Week 4:
After creating the Mathematica script for the axis and angle representation of the nucleosomes pairs, I ran the data for the nucleosome frames for 15, 20, 25, 30, 35, 40, 45, 50, and 55 linker lengths to obtain the corresponding axis and angle representation for each of the different linker lengths. From this, I looked at the histograms for the different types of angles between the pairs of nucleosome frames. I also calculated the distance between the origins of the nucleosome frames and looked at their distribution.
Week 5:
I obtained the spherical coordinates for the distance between the origins of the nucleosome frames and began calculating the correlation of the components of the parameter which consisted of the axis and angles representation of the rotation matrices and the spherical coordinates for the translation of the nucleosome frames.
Week 6:
I finished calculating the correlation between the different parameters for each nucleosome frame pair and created the chromatin fiber correlation matrix which contained all of the nucleosome frame pairs and for each of these frame pairs the correlation for the parameters.
Week 7:
I looked for patterns in the chromatin fiber correlation matrix and compared the correlation matrices for the different linker lengths. Also, I prepared for my final presentation on Friday.
Week 8:
The last week was spent writing my final report and fixing my code so there would not be any imaginary numbers in my calculations.

Presentations


Additional Information