Modal reduction of mathematical models of biological molecules


Journal Article

This paper reports a detailed study of modal reduction based on either linear normal mode (LNM) analysis or proper orthogonal decomposition (POD) for modeling a single α-d-glucopyranose monomer as well as a chain of monomers attached to a moving atomic force microscope (AFM) under harmonic excitations. Also a modal reduction method combining POD and component modal synthesis is developed. The accuracy and efficiency of these methods are reported. The focus of this study is to determine to what extent these methods can reduce the time and cost of molecular modeling and simultaneously provide the required accuracy. It has been demonstrated that a linear reduced order model is valid for small amplitude excitation and low frequency excitation. It is found that a nonlinear reduced order model based on POD modes provides a good approximation even for large excitation while the nonlinear reduced order model using linear eigenmodes as the basis vectors is less effective for modeling molecules with a strong nonlinearity. The reduced order model based on component modal synthesis using POD modes for each component also gives a good approximation. With the reduction in the dimension of the system using these methods the computational time and cost can be reduced significantly. © 2005 Elsevier Inc. All rights reserved.

Full Text

Duke Authors

Cited Authors

  • Li, A; Dowell, EH

Published Date

  • January 1, 2006

Published In

Volume / Issue

  • 211 / 1

Start / End Page

  • 262 - 288

Electronic International Standard Serial Number (EISSN)

  • 1090-2716

International Standard Serial Number (ISSN)

  • 0021-9991

Digital Object Identifier (DOI)

  • 10.1016/

Citation Source

  • Scopus