MOLECULAR DYNAMICS SIMULATIONS OF NUCLEIC ACIDS: STRUCTURE, MOTIONS, SOLVATION

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our proposed research involves studies of the dynamical structures of DNA and RNA nucleic acids and their complexes with proteins based on molecular modeling via computer simulation and related theoretical approaches. The overall reliability of molecular modeling and simulation on DNA and RNA systems depends critically on the demonstrable accuracy of the calculated results. Thus, one of the focal points of this research is critical validation and assessment of one of most detailed form of computational modeling, all-atom molecular dynamics (MD) simulation. An additional emphasis in the proposed project period will be the articulation of free energy calculations with MD in order to approach more directly diverse questions about stability and conformational equilibria of nucleic acids structures and their complexes.