Abstract
In this paper,we simply review a variety of atomistic modeling techniques for macromolecular structures including proteins,DNA and RNA.To compromise modeling accuracy with computational efficiency,various coarse-graining methods have been introduced to represent a biomolecule as a mass-spring system called elastic network model.Both conventional mechanical vibration analysis and topology optimization method have been applied to investigate macromolecular dynamics in terms of thermal fluctuations and conformational changes,respectively,all of which are strongly related with biological functions in macromolecules.In addition,the proposed computational methods were recently extended to the study of DNA nanoengineering in which self-assembly mechanism of various DNA tiles was successfully elucidated and the simulation results showed good agreement with experimental evidences.
