(89i) Applications of the Telegraph Model for Nanochannel Confined DNA

The study of nanochannel-confined polymers, in particular DNA, has received substantial attention in the past decade owing to its application in the field of genome mapping. Recently, a weakly-correlated telegraph model was proposed to describe the extension of the DNA molecules stretched under confinement using a single scaling parameter, and this model was solved asymptotically in the limit relevant to genome mapping. We will present an analysis of the applicability of the telegraph model to both simulation and experimental data. On the computational front, we have compared the predicted distribution of fractional extensions obtained by an asymptotic solution to the telegraph model to computational results using pruned-enriched Rosenbluth method (PERM) simulations for the same conditions. We find good agreement between the two methods. On the experimental front, we used recent results of a large dataset of fractional extension values as a function of the ionic strength to study the telegraph model predictions spanning several decades in its scaling parameter. We find good agreement at the smaller values of the scaling parameter where the telegraph model is expected to hold. The agreement between the model and experiments is considerably worse at larger values of the scaling parameter, which correspond to small effective channel sizes.