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Document Type

Open Access

Degree Program

Mechanical Engineering

Degree Type

Master of Science in Mechanical Engineering (M.S.M.E.)

Year Degree Awarded

2013

Month Degree Awarded

February

Keywords

protein normal mode analysis, finite element analysis, protein elastic network model

Abstract

This study proposed a finite element procedure for protein normal mode analysis (NMA). The finite element model adopted the protein solvent-excluded surface to generate a homogeneous and isotropic volume. A simplified triangular approximation of coarse molecular surface was generated from the original surface model by using the Gaussian-based blurring technique. Similar to the widely adopted elastic network model, the finite element model holds a major advantage over standard all-atom normal mode analysis: the computationally expensive process of energy minimization that may distort the initial protein structure has been eliminated. This modification significantly increases the efficiency of normal mode analysis. In addition, the finite element model successfully brings out the capability of normal mode analysis in low-frequency/high collectivity molecular motion by capturing protein shape properties. Fair results from six protein models in this study have fortified the capability of the finite element model in protein normal mode analysis.

First Advisor

Byung H. Kim

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