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• W2077250576 abstract "We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order $N$ methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various $T$ numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few $(ensuremath{sim}10)$ low-frequency modes that are global and cooperative." @default.
• W2077250576 created "2016-06-24" @default.
• W2077250576 creator A5028462860 @default.
• W2077250576 creator A5075598737 @default.
• W2077250576 date "2010-02-19" @default.
• W2077250576 modified "2023-09-25" @default.
• W2077250576 title "Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids" @default.
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• W2077250576 doi "https://doi.org/10.1103/physreve.81.021918" @default.
• W2077250576 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20365606" @default.
• W2077250576 hasPublicationYear "2010" @default.
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