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The alpha-helix is coarse-grained to beads 0.5 nm apart (mass 400 amu) interacting through a four-segment piecewise-linear tensile law plus a three-body bending term; the plateau force at the onset of unfolding is about 200 pN (the asymptotic value at vanishing pulling rate), backbone rupture is set at about 5,500 pN from ReaxFF results, the mesh side is 12 nm, and the time step is 15 fs.
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Notation basis: The parameter values and the description (four spring constants switched on by Heaviside functions; bending energy of bead triplets) are in the prose; equations (6)–(10) are images and the exact spring constants are in a table not in the vendored text. The multilinear form written here follows the prose description.
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Mesoscale bead model: 0.5 nm beads, multilinear tensile law, 200 pN unfolding plateau, 5,500 pN backbone rupture
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F(r) = \sum_{i=1}^{4} k_i\,(r - r_{i-1})\,H(r - r_{i-1})H(r_i - r)\ (\text{multilinear});\quad r_0 = 0.5\ \mathrm{nm},\ F_{\alpha\to\beta} \approx 200\ \mathrm{pN},\ F_{\mathrm{break}} \approx 5500\ \mathrm{pN},\ \Delta t = 15\ \mathrm{fs}
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Theodor Ackbarow et al., “Alpha-Helical Protein Networks Are Self-Protective and Flaw-Tolerant”, PLoS ONE 4, e6015 (2009), doi:10.1371/journal.pone.0006015; Materials and Methods. Scope: Coarse-grained alpha-helix filament model (LAMMPS)
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Theodor Ackbarow, Dipanjan Sen, Christian Thaulow, Markus J. Buehler. Alpha-Helical Protein Networks Are Self-Protective and Flaw-Tolerant. PLoS ONE 4, e6015 (2009). doi:10.1371/journal.pone.0006015
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Theodor Ackbarow, Dipanjan Sen, Christian Thaulow, Markus J. Buehler
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Alpha-Helical Protein Networks Are Self-Protective and Flaw-Tolerant
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Full text of Alpha-Helical Protein Networks Are Self-Protective and Flaw-Tolerant, as read
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Quoted from the full text (cc by licence), paragraph 43–45 of 2009-helical-networks.txt (sha256 d35d9ea109c79b04ca4f44608c823ee0ab4e43a642147772bb6b89e3fe2d734f), vendored from Europe PMC PMC2696088 by build/resolve.py and checked by build/check.py.
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We choose r 0 = 0.5 nm per bead, providing significant computational speedup while maintaining a sufficiently fine discretization of the alpha-helical protein (leading to a bead particle mass m = 400 amu).
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Theodor Ackbarow et al. 2009 claim: Mesoscale bead model: 0.5 nm beads, multilinear tensile law, 200 pN unfolding plateau, 5,500 pN backbone rupture
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