Chemical Engineering Seminar

Nanochannels are emerging as a new technology for obtaining large-scale genomic information where the DNA is stretched and fluorescent genomic information is optically "read" from the linearized DNA. These applications motivated renewed interest in the basic physics of confined polymers, where DNA plays the role of a model polymer. While the scaling laws for strong (Odijk) and weak (de Gennes) confinement were established decades ago, recent experiments have illuminated the complex physics arising between these limiting cases for semi-flexible chains such as DNA. I will present our recent results in this area, which take advantage of a DNA model that accurately reproduces the free solution radius of gyration and diffusivity. Using a combination of Monte Carlo models and hydrodynamics calculations, we are exploring both the statics and dynamics of confined DNA. Our results provide clear evidence for the existence of two transition regimes between the Odijk and de Gennes regimes, thereby resolving the apparent contradiction between these scaling theories and the corresponding experiments by Austin and coworkers. We have also identified surprising dynamic results arising from the interplay between the semi-flexible nature of the chain and the hydrodynamic interactions.