BOOK CHAPTER R. Mukherjee and T.C. Bishop. “Nucleosomal DNA: Kinked, Not Kinked, or Self-Healing Material?” Frontiers in Nucleic Acids, Chapter 5, pp 69–92.

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BOOK CHAPTER R. Mukherjee and T.C. Bishop. “Nucleosomal DNA: Kinked, Not Kinked, or Self-Healing Material?” Frontiers in Nucleic Acids, Chapter 5, pp 69–92. Chapter DOI: /bk ch005 ACS Symposium Series, Vol ISBN13: eISBN: JOURNALS High Performance Computing R. Mukherjee, A. Thota, H. Fujioka, T. C. Bishop, S. Jha, 2012, “Running Many Molecular Dynamics Simulations on Many Supercomputers”, in preparation CONFERENCES T. C. Bishop, R. Mukherjee, “Nucleosomal DNA: Kinked, not kinked, or self-healing material ”, SWRM and SERM of ACS, Nov 30 – Dec 4, 2010, New Orleans, LA R. Mukherjee, T. C. Bishop, “Computational Study of Nucleosome Positioning and Stability”, Biophysical Journal, vol. 100, issue 3, pp. 67a-67a R. Mukherjee, H. Fujioka, A. Thota, S. Jha, T. C. Bishop, “The Nucleosome Simulator: 100 Nucleosomes; 2 Microseconds and Counting”, Albany2011, Conversation17, June T. C. Bishop, R. Mukherjee, H. Fujioka, A. Thota, S. Jha, “High Throughput Atomistic Simulations of the Nucleosome”, CECAM-HQ-EPFL, August 30, 2011 to September 2, 2011, Lausanne, Switzerland R. Mukherjee, A. Thota, H. Fujioka, T. C. Bishop, S. Jha, 2011, “Many Big jobs on Distributed Cyberinfrastructure”, Proceedings of Louisiana EPSCoR RII LA-SiGMA 2011 Symposium R. Mukherjee, H. Fujioka, T. C. Bishop, 2012, “High Performance High Throughput Computing of Positioned Nucleosomes on LONI”, Mardi Gras Conference -- Computational Materials & Biosystems, February 16-18, 2012, Baton Rouge, LA

All atom Molecular Dynamics Simulations of Nucleosomes Obtain the crystal structure from PDB. Include our sequence which has the same helical parameter configuration as the protein structure and create the all atom structure The system is solvated (added water) and ions added The whole simulation is broken into 1 ns trajectory and the simulation is carried out using nanoscale molecular dynamics (NAMD): a scalable MD simulator

Trajectory file We save the trajectory of the coordinates every picoseconds in (*.dcd files) and velocity in (*.dvd files) The raw trajectories are in /simulations/ From the *.dcd files, we strip of the water using (/projects/rmukhe1/TERAGRID/floer-sims- analysis/utils/01-nowat.tcsh) which uses the VMD script (/home/rmukhe1/bin/strip-wat.vmd) creating *.nowat.dcd

Extracting Helical Parameters From the nowater trajectory, we extract the 12 helical parameter using /projects/rmukhe1/TERAGRID/floer-sims- analysis/utils/07-par.tcsh that uses the VMD script /home/rmukhe1/bin/dcds2par.vmd the VMD script uses 3DNA. This program creates 12 (*.par.dat) files, one for each helical parameters and one sequence file.

Analysis of Helical Parameters The helical parameters gives the structural form of the DNA for each basepair step at every picoseconds. The analysis is performed on the atom coordinate to find the RMSD and on helical parameters to find max, min, mean, stdev, of each and every helical parameters and compare it with that of free DNA using /projects/rmukhe1/TERAGRID/floer-sims- analysis/utils/09-analy.tcsh The RMSD is calculated using VMD code /home/rmukhe1/bin/dcds2rmsd.vmd And helical parameter analysis using FORTRAN code /projects/rmukhe1/TERAGRID/floer-sims- analysis/utils/analysis.f

Analysis The analysis.f also calculates the kink by comparing the helical parameters; Slide, Roll and Twist values with that of free DNA. Kink, as it appears at every timeframe are shown /projects/rmukhe1/TERAGRID/floer-sims- analysis/utils/09-analy.tcsh Also does the Fourier knock-out knock-in using mean values of the helical parameters 02-ko.tcsh, 03- ko.rmsd.tcsh, 04-ki.tcsh, 05-ki.rmsd.tcsh

Essential Dynamics Analysis The appearance of kink which is high deformation of the helical parameter may alter the mean and affect Fourier analysis. It is important to identify the essential dynamics that constitutes the kink. /projects/rmukhe1/TERAGRID/floer-sims-analysis/utils/27- pca.tcsh Is used to calculated the covariance, eigenvalues and eigenvectors of the helical parameters and calculate the amplitude of the essential dynamics using the python code: fei2evecsonly1.py

Essential Dynamics Analysis The covariance and eigenvector are also used to calculate overlap of different trajectory and consistency of the same trajectory using matlab code. I will change these with python code, as these are simple matrix operations.