A molecular dynamic modeling of hemoglobin-hemoglobin interactions

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

doi:10.1063/1.3452299

A molecular dynamic modeling of hemoglobin-hemoglobin interactions

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

Electrical and Computer Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	ISCM 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
Pages	89-94
Number of pages	6
Edition	PART 1
DOIs	https://doi.org/10.1063/1.3452299
State	Published - 2010
Event	2nd 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 2009 → Dec 3 2009

Publication series

Name	AIP Conference Proceedings
Number	PART 1
Volume	1233
ISSN (Print)	0094-243X
ISSN (Electronic)	1551-7616

Other

Other	2nd 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
Country/Territory	China
City	Hong Kong, Macau
Period	11/30/09 → 12/3/09

All Science Journal Classification (ASJC) codes

General Physics and Astronomy

Keywords

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

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10.1063/1.3452299

Cite this

Wu, T., Yang, Y., Sheldon Wang, X., Cohen, B., & Ge, H. (2010). A molecular dynamic modeling of hemoglobin-hemoglobin interactions. In ISCM 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 (PART 1 ed., pp. 89-94). (AIP Conference Proceedings; Vol. 1233, No. PART 1). https://doi.org/10.1063/1.3452299

Wu, Tao ; Yang, Ye ; Sheldon Wang, X. et al. / A molecular dynamic modeling of hemoglobin-hemoglobin interactions. ISCM 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. PART 1. ed. 2010. pp. 89-94 (AIP Conference Proceedings; PART 1).

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title = "A molecular dynamic modeling of hemoglobin-hemoglobin interactions",

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.",

keywords = "Molecular Dynamic Simulation, Principal Component Analysis, Protein Interaction, Singular Value Decomposition, coarse grained model",

author = "Tao Wu and Ye Yang and {Sheldon Wang}, X. and Barry Cohen and Hongya Ge",

note = "Copyright: Copyright 2010 Elsevier B.V., All rights reserved.; 2nd 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 ; Conference date: 30-11-2009 Through 03-12-2009",

year = "2010",

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series = "AIP Conference Proceedings",

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Wu, T, Yang, Y, Sheldon Wang, X, Cohen, B & Ge, H 2010, A molecular dynamic modeling of hemoglobin-hemoglobin interactions. in ISCM 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. PART 1 edn, AIP Conference Proceedings, no. PART 1, vol. 1233, pp. 89-94, 2nd 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, 11/30/09. https://doi.org/10.1063/1.3452299

A molecular dynamic modeling of hemoglobin-hemoglobin interactions. / Wu, Tao; Yang, Ye; Sheldon Wang, X. et al.
ISCM 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. PART 1. ed. 2010. p. 89-94 (AIP Conference Proceedings; Vol. 1233, No. PART 1).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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AU - Yang, Ye

AU - Sheldon Wang, X.

AU - Cohen, Barry

AU - Ge, Hongya

PY - 2010

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N2 - 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.

AB - 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.

KW - Molecular Dynamic Simulation

KW - Principal Component Analysis

KW - Protein Interaction

KW - Singular Value Decomposition

KW - coarse grained model

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Y2 - 30 November 2009 through 3 December 2009

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Wu T, Yang Y, Sheldon Wang X, Cohen B, Ge H. A molecular dynamic modeling of hemoglobin-hemoglobin interactions. In ISCM 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. PART 1 ed. 2010. p. 89-94. (AIP Conference Proceedings; PART 1). doi: 10.1063/1.3452299

A molecular dynamic modeling of hemoglobin-hemoglobin interactions

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