Divide-and-Conquer Based Adaptive Coarse Grained Simulation of RNA

Molecular modeling has gained increasing importance in recent years for predicting important structural properties of large biomolecular systems such as RNA which play a critical role in various biological processes. Given the complexity of biopolymers and their interactions within living organisms, efficient and adaptive multi-scale modeling approaches are necessary if one is to reasonably perform computational studies of interest. These studies nominally involve multiple important physical phenomena occurring at different spatial and temporal scales. These systems are typically characterized by large number of degrees of freedom O(10³) – O(10⁷). The temporal domains range from sub-femto seconds (O(10⁻¹⁶)) associated with the small high frequency oscillations of individual tightly bonded atoms to milliseconds (O(10⁻³)) or greater for the larger scale conformational motion. The traditional approach for molecular modeling involved fully atomistic models which results in fully decoupled equations of motion. The problems with this approach are well documented in literature.