Length-Dependence of DNA mechanical properties
I establish the collaboration with Ramin Golestanian, who has expertise in polymer science, with the idea to understand the 2 kinds of experimental data that describe contradictory mechanical properties of DNA, since they use fragments from different lengths. The Length Dependent Elastic Model (LDEM) that I developed at Sheffield first and then at Oxford provides a systematic description of how the effective elastic properties of DNA are built from the single base-pair level by probing the conformation and fluctuations of DNA at different scales using atomistic MD simulations (Noy and Golestanian, PRL, 2012). By capturing structured molecular motions with different characteristic correlation length scales, the LDEM reveals that the elastic constants vary on the molecule’s length in surprising ways which are hard to predict, thus unravelling the experimental contradiction. This is due to the fact that DNA is not a straight, uniform polymer but it is a chiral double-helix with distinct minor and major grooves.
Lately, I employed the DNA-LDEM to assess the parmbsc1, a new force-field for DNA atomistic simulation. Ivani et al Nat Methods (2016).