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Modal Reduction of Mathematical Models of Biological Molecules

[+] Author Affiliations
Aiqin Li, Earl H. Dowell

Duke University, Durham, NC

Paper No. DETC2005-84056, pp. 1801-1815; 15 pages
doi:10.1115/DETC2005-84056
From:
  • ASME 2005 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 1: 20th Biennial Conference on Mechanical Vibration and Noise, Parts A, B, and C
  • Long Beach, California, USA, September 24–28, 2005
  • Conference Sponsors: Design Engineering Division and Computers and Information in Engineering Division
  • ISBN: 0-7918-4738-1 | eISBN: 0-7918-3766-1
  • Copyright © 2005 by ASME

abstract

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. Also a modal reduction method combining POD and component modal synthesis(CMS) 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(ROM) is valid for small amplitude excitation and low frequency excitation. It is found that a nonlinear ROM based on POD modes provides a good approximation even for large excitation while the nonlinear ROM using linear eigenmodes as the basis vectors is less effective for modeling molecules with a strong nonlinearity. The ROM based on CMS 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.

Copyright © 2005 by ASME

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