I developed a base-pair resolution model for chromatin, and use it to perform Monte Carlo simulations. This model makes it possible to study chromatin constructs with different nucleosome positioning. Chemical modifications at the nucleosome level, such as histone tails modifications, can be incorporated into the simulations to study the influence of these modifications onto the chromatin architecture. The model accounts for the elasticity of the DNA and for the electrostatics interactions between the proteins and the DNA. I am currently focusing on the influence of nucleosome positioning on chromatin architecture and fiber properties (stiffness and geometry).
Average chromatin architectures for different nucleosome positioning (from left to right the nucleosome spacing is: 25 base pairs, 30-bp, 32-bp, 25-bp, 37-bp, 40-bp and 45-bp).
Fluctuating chromatin construct with 13 nucleosomes (nucleosome spacing is 25-bp).