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

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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.

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Authors and Affiliations

  1. Department of Mechanical and Industrial Engineering, University of Massachusetts, 160 Governors Dr., Amherst, MA, 01003, USA

    Mingwen Hu, Sharad Raj & Byung Kim

  2. Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA

    Wing Kam Liu

  3. School of Mechanical Engineering, Sungkyunkwan University, 300 Cheoncheon-dong, Suwon, 440-746, Korea

    Seunghyun Baik, Taesung Kim, Byeong-Soo Lim & Moon Ki Kim

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  1. Mingwen Hu
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Correspondence to Moon Ki Kim.

Additional information

This paper was recommended for publication in revised form by Associate Editor Yong-Tae Kim

Mingwen Hu received the B.S. degree in Mechanical Engineering from Yuan Ze University in 2002 and then the M.S. degree in Mechanical and Mechatronic Engineering from National Taiwan Ocean University in 2004. He is currently pursuing the Ph.D. degree in Mechanical and Industrial Engineering, University of Massachusetts-Amherst. His researches focus on investigating macromolecules by experimental and theoretical approaches which include vibrational spectroscopy and elastic network model.

Byung Kim received the B.S. in Mechanical Engineering from UC Berkeley in 1978, M.S. and Ph.D. in Mechanical Engineering from MIT in 1980 and 1983, respectively. He has joined the faculty member in the department of Mechanical and Industrial Engineering at the University of Massachusetts, Amherst since 1983. His research interests are in the area of micro and nanomanufacturing, SERS, protein dynamics.

Wing Kam Liu obtained by B.S. with the highest honor from from the University of Illinois at Chicago Circle in 1976 and received his M.S in 1977 and Ph.D. in 1981, both from California Institute of Technology. He is the Walter P. Murphy Professor of Mechanical Engineering Department of Northwestern University, Founding Director of the NSF Summer Institute on Nano Mechanics and Materials, and Founding Chairman of the prestigious ASME NanoEngineering Council. Multiresolution continuum theory and immersed finite element method are his main research interests.

Moon Ki Kim received the B.S. and M.S. degrees in Mechanical Engineering from Seoul National University in 1997 and 1999, respectively, and the M.S.E. and Ph.D. degrees from The Johns Hopkins University in 2002 and 2004, respectively. He had been an Assistant Professor in the department of Mechanical and Industrial Engineering at University of Massachusetts, Amherst from 2004 to 2008. He has worked for School of Mechanical Engineering at Sungkyunkwan University as an associate professor since 2009. His research interests are focused on computational structural biology based on robot kinematics, bioinstrumentations, and multiscale modeling and simulation.

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Hu, M., Raj, S., Kim, B. et al. Precise spring constant assignment in elastic network model for identification of vibration frequency and modeshape. J Mech Sci Technol 24, 1771–1780 (2010). https://doi.org/10.1007/s12206-010-0631-x

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