A molecular dynamic modeling of hemoglobin-hemoglobin interactions

Tao Wu, Ye Yang, X. Sheldon Wang, Barry Cohen, Hongya Ge

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

In this paper, we present a study of hemoglobin-hemoglobin interaction with model reduction methods. We begin with a simple spring-mass system with given parameters (mass and stiffness). With this known system, we compare the mode superposition method with Singular Value Decomposition (SVD) based Principal Component Analysis (PCA). Through PCA we are able to recover the principal direction of this system, namely the model direction. This model direction will be matched with the eigenvector derived from mode superposition analysis. The same technique will be implemented in a much more complicated hemoglobin-hemoglobin molecule interaction model, in which thousands of atoms in hemoglobin molecules are coupled with tens of thousands of T3 water molecule models. In this model, complex inter-atomic and inter-molecular potentials are replaced by nonlinear springs. We employ the same method to get the most significant modes and their frequencies of this complex dynamical system. More complex physical phenomena can then be further studied by these coarse grained models.

Original languageEnglish (US)
Title of host publicationISCM II and EPMESC XII - Proc. of the 2nd Int. Symposium on Computational Mechanics and the 12th Int. Conf. on the Enhancement and Promotion of Computational Methods in Engineering and Science
Pages89-94
Number of pages6
EditionPART 1
DOIs
StatePublished - 2010
Event2nd International Symposium on Computational Mechanics, ISCM II, and the 12th International Conference on the Enhancement and Promotion of Computational Methods in Engineering and Science, EPMESC XII - Hong Kong, Macau, China
Duration: Nov 30 2009Dec 3 2009

Publication series

NameAIP Conference Proceedings
NumberPART 1
Volume1233
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Other

Other2nd International Symposium on Computational Mechanics, ISCM II, and the 12th International Conference on the Enhancement and Promotion of Computational Methods in Engineering and Science, EPMESC XII
CountryChina
CityHong Kong, Macau
Period11/30/0912/3/09

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)

Keywords

  • Molecular Dynamic Simulation
  • Principal Component Analysis
  • Protein Interaction
  • Singular Value Decomposition
  • coarse grained model

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