High-Resolution Simulations of Chromatin on Federated Infrastructures

Overview of the Project:

We are going to study nucleosome arrays with different nucleosome spacings (i.e., DNA linker lengths) using Monte Carlo simulations based on a base-pair resolution mesoscale model. The model accounts for the elasticity of nucleosome-free DNA and for the electrostatics interactions between the proteins and the DNA. Excluded-volume effects are incorporated into the simulations with the use of a collision-detection method (based on ODE: Open Dynamics Engine). Chemical modifications at the nucleosome level, such as histone tails modifications, can also be incorporated into the simulations to study the influence of these modifications on the overall chromatin architecture. These simulations will give us the opportunity to study the interplay between nucleosome positioning and chromatin architecture over a biologically relevant range of DNA linker lengths. The synergy between nucleosome positioning and chromatin architecture is a crucial mechanism in the packaging and processing of genomic material within cell nuclei. In order to perform those simulations in a reasonable timeframe, we need to aggregate resources to enhance our computational capabilities. This project will use CometCloud to run the simulations across federated resources.

Collaborators

1) Nicolas Clauvelin, Wilma Olson from BioMaPS Institute for Quantitative Biology, Rutgers University

2) Javier Diaz-Montes, Manish Parashar, Jaroslaw Zola from  Rutgers Discovery Informatics Institute, Dept. of Electrical and Computer Engineering, Rutgers University

Relevant Publications

1.)N. Clauvelin, P. Lo, O. I. Kulaeva, E. V. Nizovtseva, J. Diaz-Montes, J .Zola, M. Parashar, V. M. Studitsky, W. K. Olson, “Nucleosome positioning and composition modulate in silico chromatin flexibility,” Journal of Physics: Condensed Matter, Vol. 27, Issue 6, pp. 1-12, 2015. 

2.)J. Diaz-Montes, Y. Xie, I. Rodero, J. Zola, Ganapathysubramanian, M. Parashar, "Federated Computing for the Masses - Aggregating Resources to Tackle Large-scale Engineering Problems", IEEE Computing in Science and Engineering (CiSE) Magazine, Vol. 16, Issue 4, 2014.

3.)J. Diaz-Montes, Y. Xie, I. Rodero, J. Zola, B. Ganapathysubramanian, and M. Parashar, "Exploring the Use of Elastic Resource Federations for Enabling Large-scale Scientific Workflows", In Proc. of Workshop on Many-Task Computing on Clouds, Grids, and Supercomputers (MTAGS). Co-located with Supercomputing/SC 2013, Denver, Colorado, November 2013. (Best Paper Award Finalist)