Modified mechanical mass-spring model of biomolecules for understanding dynamics of proteins

Kilho Eom, Jeong Hee Ahn, Jae In Kim, Gwon Chan Yoon, Sungsoo Na

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

A dynamic model applicable to biomolecular structures for understanding the dynamics and the vibrational behaviors of protein is considered. A mechanical mass-spring model represented by point masses and harmonic springs is presented. The biomolecular structure may be envisioned by a mass and spring system with multi-degrees-of-freedom because dominant atoms in protein may be considered to be point masses, and bonding and non-bonding interactions between atoms of interest and surrounding atoms within some critical distances are implemented by a spring. Furthermore, a model condensation scheme is to be introduced because most proteins have large degree of freedom requiring large computation time and memory, which results in reducing computational cost and maintaining the accurate predictions. From solving the corresponding eigenvalue problem constructed from a multi-degree-of-freedom system, our results show the modified mechanical spring-mass model of a biostructure through a condensation scheme is very successful in predicting the dynamics of molecular structures in terms of thermal fluctuations and eigenmode, etc.

Original languageEnglish
Pages (from-to)506-513
Number of pages8
JournalJournal of Mechanical Science and Technology
Volume22
Issue number3
DOIs
Publication statusPublished - 2008 Mar

Keywords

  • Biomolecular structure
  • Eigenvalue problem
  • Mass-spring model
  • Model condensation
  • Multi-degree-of-freedom system

ASJC Scopus subject areas

  • Mechanics of Materials
  • Mechanical Engineering

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