helixmc.fitfxn.wlc_bouchiat

helixmc.fitfxn.wlc_bouchiat(A, L, z, kT=41.164043971999995)

Worm-like chain fitting formula described in Bouchiat et al. 1999 paper. Assumes the chain has constant length (inextensive model). For fitting force-extension curve in low-to-medium force regime (< 10 pN).

Parameters:

A : float

Bending persistence length, in Å.

L : float

Contour length, in Å.

z : float or 1D ndarray

Average Z-extension of the helix, in Å.

kT : float, optional

Temperature times Boltzmann constant, in pN.Å. Default is 298.15 K.

Returns:

F : float or 1D ndarray

Z-direction stretching force, in pN.

See also

wlc_bouchiat_impl

Implict worm-like chain fitting formula described in Bouchiat et al.

f_wlc_bouchiat_impl

Approximately solve the force from implicit wlc model by grid search.

Notes

The fitting function [1] is

\[F = \frac{kT}{A} \left[ \frac{1}{4 (1 - z / L)^2} - \frac{1}{4} + \frac{z}{L} + \sum\limits_{i=2}^{i \le 7} { \alpha_i {\left( \frac{z}{L} \right)}^i} \right]\]

Where \(\alpha\) = [-0.5164228, -2.737418, 16.07497, -38.87607, 39.49944, -14.17718] for i = 2~7.

References

[1]	Bouchiat C, Wang MD, Allemand J, Strick T, Block SM, et al. (1999) Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys. J. 76: 409-413.