Automated Procedure for FE-based Modular Analysis of Biomolecular Structures

Abstract

Dynamic behavior of biomolecular structures plays an essential role in a variety of way in living organism. Molecular dynamics simulation provide valuable information about dynamic characteristic of biomolecular structure but time and length scale have limits due to computational complexity. Therefore, coarse-grained modeling techniques such as elastic network model and finite element model have been successfully used for analysis of dynamic properties of biomolecular structures. However, analysis of biomolecular structure which have high molecular weight is still challenging even using these coarse-grained modeling approaches due to its huge number of DOFs. In order to handle this problem, I introduce component mode synthesis (CMS) that is a popular reduced order modeling technique to generate reduced model. Reduced model consist of subunits whose dynamics is dominated by low frequency normal modes of substructure. In this study I suggest an automated procedure for FE-based dynamic analysis of biomolecular structures applying the Craig-Bampton method, a widely used CMS, and relative eigenvalue estimator to determine the proper number of low-frequency normal mode dominating dynamics of biomolecular structures.