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Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations
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10.1063/1.3514149
/content/aip/journal/jcp/134/2/10.1063/1.3514149
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/2/10.1063/1.3514149
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

The definition of the order parameters , , and used to analyze the dominant reaction pathways.

Image of FIG. 2.
FIG. 2.

Configurations on the dominant reaction pathway calculated ab initio. The colors on the surface represent the projection of the molecular electrostatic potential on the solvent accessible surface.

Image of FIG. 3.
FIG. 3.

(Upper-left panel) Evolution of the order parameter as a function of the reaction coordinate l for four different paths. (Upper-right panel) Evolution of the order parameter as a function of the reaction coordinate l for four different paths. (Lower-left panel) Evolution of the order parameter as a function of the reaction coordinate l for four different paths. (Lower-right panel) Evolution of the order parameter as a function of the reaction coordinate l for four different paths.

Image of FIG. 4.
FIG. 4.

Comparison of the dominant reaction pathways obtained from classical and ab initio DRP simulations, projected onto the plane selected by the and order parameters.

Image of FIG. 5.
FIG. 5.

Evolution of the partial charges of the O–6 and H–28 atoms (upper panel) and of the O–16 and H–38 atoms (lower panel), along the dominant reaction pathway. In both figures, the partial charge of the H atoms has been shifted by −0.42 a.u. for the sake of graphical clarity.

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/content/aip/journal/jcp/134/2/10.1063/1.3514149
2011-01-10
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/2/10.1063/1.3514149
10.1063/1.3514149
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