Precise spring constant assignment in elastic network model for identification of vibration frequency and modeshape

Mingwen Hu, Sharad Raj, Byung Kim, Wing Kam Liu, Seunghyun Baik, Taesung Kim, Byeong Soo Lim, Moon Ki Kim

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

We presented a feasible framework of studying dynamics of macromolecules by applying elastic network model (ENM) and vibration spectroscopy. We first identified the precise force constants of covalent bonds commonly observed in macromolecules by matching their reported Raman shifts data with predicted wavenumbers determined by normal mode analysis (NMA). Assigning the obtained spring constants to other small chemical compounds such as ethynyl isocyanide (C3HN) and diacetylene (C4H2), we not only predicted their vibration wavenumbers precisely but also identified their individual mode shapes from NMA. We extensively tested this chemical information based ENM with one of amino acids, cysteine. Subsequent comparison of frequencies and modeshapes also yields a strong agreement between computed and experimental data. Consequently, the proposed method enables us to identify low frequency modeshapes that are in general functionally important collective motions of macromolecules but have hardly been revealed experimentally even using terahertz spectroscopy.

Original languageEnglish (US)
Pages (from-to)1771-1780
Number of pages10
JournalJournal of Mechanical Science and Technology
Volume24
Issue number9
DOIs
StatePublished - 2010

Keywords

  • Elastic network model
  • Force constant calculation
  • Mode shape identification
  • Normal mode analysis
  • Spectroscopy

ASJC Scopus subject areas

  • Mechanics of Materials
  • Mechanical Engineering

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