This page lists references used for implementing specific functionality into Pylake. Please see below for more information on these topics.
Force Calibration¶
The passive force calibration method was based on a number of publications by the Flyvbjerg group [BSF04, BSPW+06, HTNFBS06, TNBSF04].
F,d Fitting¶
Several polymer models from literature were included. These include Odijk’s extensible worm-like chain model [Odi95, WYL+97], the Freely Jointed Chain model [SCB96, WYL+97], the Marko-Siggia interpolation model [MS95] and the twistable worm-like chain model [BKSW16, GLO+11].
We used [BKSW16] as reference material throughout the implementation of the F,d fitting routines, both as a starting point for the model implementations as well as for the procedure on how to reliably fit the twistable worm-like chain model (via its inverted form). For the twistable worm-like chain, we perform model inversion via interpolation rather than point-wise inversion through optimization analogously to [BKSW16]. Parameter estimation is performed via Maximum Likelihood Estimation [MHS+16, RKM+09]. We also implemented several asymptotic information criteria for ranking model fits [Cav97].
Kymotracker¶
The line algorithm was based on sections 1, 2 and 3 from [Ste98] to find line centers based on local geometric considerations. The greedy algorithm was based on two papers. It initially detects feature points based on [SK05], followed by line tracing inspired by [MPP16]. Instead of subtracting the background and thresholding the values below zero to zero, we perform a bias correction for background by symmetrizing the used window ([BMML08]).
Diffusion constant estimation¶
The unweighted ordinary least squares estimation method (including the optimal number of lag computation) is implemented from [MB12]. The generalized least squares method was based on [BvBulowH20]
References¶
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