Computational Models for Nucleic Acid Assembly Processes at Bio-Nano-Interfaces

Nucleic acids, specifically DNA, have become a common material in the field of nanotechnology whether it is in DNA based materials or the recognition and separation of carbon nanotubes.  Many of these systems have been characterized experimentally, but there is currently an information gap between what happens and why.  Molecular modeling poses a convenient method for better understanding some of these DNA-interface interactions, but the systems of interest are too large for all-atom models to test a useful timescale to observe these phenomena.  A coarse-grained model could be used to overcome this computational barrier, however, there is not a model in the current literature that is versatile enough while maintaining the simplicity required to sample such large systems.  We have proposed and characterized a minimal model that can adequately characterize both ssDNA and dsDNA, as both are important in DNA-interface interactions.