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].

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¶

BSF04: Kirstine Berg-Sørensen and Henrik Flyvbjerg. Power spectrum analysis for optical tweezers. Review of Scientific Instruments, 75(3):594–612, 2004.
BSPW+06: Kirstine Berg-Sørensen, Erwin JG Peterman, Tom Weber, Christoph F Schmidt, and Henrik Flyvbjerg. Power spectrum analysis for optical tweezers. ii: laser wavelength dependence of parasitic filtering, and how to achieve high bandwidth. Review of scientific instruments, 77(6):063106, 2006.
BKSW16(1,2,3): Onno D Broekmans, Graeme A King, Greg J Stephens, and Gijs JL Wuite. Dna twist stability changes with magnesium (2+) concentration. Physical review letters, 116(25):258102, 2016.
BvBulowH20: Jakob Tómas Bullerjahn, Sören von Bülow, and Gerhard Hummer. Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics, 153(2):024116, 2020.
Cav97: Joseph E Cavanaugh. Unifying the derivations for the akaike and corrected akaike information criteria. Statistics & Probability Letters, 33(2):201–208, 1997.
GLO+11: Peter Gross, Niels Laurens, Lene B Oddershede, Ulrich Bockelmann, Erwin JG Peterman, and Gijs JL Wuite. Quantifying how dna stretches, melts and changes twist under tension. Nature Physics, 7(9):731–736, 2011.
HTNFBS06: Poul Martin Hansen, Iva Marija Tolić-Nørrelykke, Henrik Flyvbjerg, and Kirstine Berg-Sørensen. Tweezercalib 2.0: faster version of matlab package for precise calibration of optical tweezers. Computer physics communications, 174(6):518–520, 2006.
HPL+09: Marcia L Huber, Richard A Perkins, Arno Laesecke, Daniel G Friend, Jan V Sengers, Marc J Assael, Ifigenia N Metaxa, Eckhard Vogel, R Mareš, and Kiyoshi Miyagawa. New international formulation for the viscosity of h 2 o. Journal of Physical and Chemical Reference Data, 38(2):101–125, 2009.
KJC+19: Harpreet Kaur, Fatemehsadat Jamalidinan, Samson G. F. Condon, Alessandro Senes, and Aaron A. Hoskins. Analysis of spliceosome dynamics by maximum likelihood fitting of dwell time distributions. Methods, 153:13–21, 2019.
MHS+16: Tim Maiwald, Helge Hass, Bernhard Steiert, Joep Vanlier, Raphael Engesser, Andreas Raue, Friederike Kipkeew, Hans H Bock, Daniel Kaschek, Clemens Kreutz, and others. Driving the model to its limit: profile likelihood based model reduction. PloS one, 2016.
MPP16: Pierre Mangeol, Bram Prevo, and Erwin JG Peterman. Kymographclear and kymographdirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs. Molecular biology of the cell, 27(12):1948–1957, 2016.
MS95: John F Marko and Eric D Siggia. Stretching dna. Macromolecules, 28(26):8759–8770, 1995.
Mic10: Xavier Michalet. Mean square displacement analysis of single-particle trajectories with localization error: brownian motion in an isotropic medium. Physical Review E, 82(4):041914, 2010.
MB12: Xavier Michalet and Andrew J Berglund. Optimal diffusion coefficient estimation in single-particle tracking. Physical Review E, 85(6):061916, 2012.
MCSF10: Kim I. Mortensen, L. Stirling Churchman, James A. Spudich, and Henrik Flyvbjerg. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nature Methods, 7(5):377–381, 2010.
NF10: Simon F Nørrelykke and Henrik Flyvbjerg. Power spectrum analysis with least-squares fitting: amplitude bias and its elimination, with application to optical tweezers and atomic force microscope cantilevers. Review of Scientific Instruments, 81(7):075103, 2010.
Odi95: Theo Odijk. Stiff chains and filaments under tension. Macromolecules, 28(20):7016–7018, 1995.
PT90: William H Press and Saul A Teukolsky. Numerical recipes. Computers in Physics, 4(6):669–672, 1990.
QSE91: Hong Qian, Michael P Sheetz, and Elliot L Elson. Single particle tracking. analysis of diffusion and flow in two-dimensional systems. Biophysical journal, 60(4):910–921, 1991.
RKM+09: Andreas Raue, Clemens Kreutz, Thomas Maiwald, Julie Bachmann, Marcel Schilling, Ursula Klingmüller, and Jens Timmer. Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics, 25(15):1923–1929, 2009.
SK05: Ivo F Sbalzarini and Petros Koumoutsakos. Feature point tracking and trajectory analysis for video imaging in cell biology. Journal of structural biology, 151(2):182–195, 2005.
SchafferNorrelykkeH07: Erik Schäffer, Simon F Nørrelykke, and Jonathon Howard. Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers. Langmuir, 23(7):3654–3665, 2007.
SCB96: Steven B Smith, Yujia Cui, and Carlos Bustamante. Overstretching b-dna: the elastic response of individual double-stranded and single-stranded dna molecules. Science, 271(5250):795–799, 1996.
Ste98: Carsten Steger. An unbiased detector of curvilinear structures. IEEE Transactions on pattern analysis and machine intelligence, 20(2):113–125, 1998.
TolicNorrelykkeSchafferH+06: Simon F Tolić-Nørrelykke, Erik Schäffer, Jonathon Howard, Francesco S Pavone, Frank Jülicher, and Henrik Flyvbjerg. Calibration of optical tweezers with positional detection in the back focal plane. Review of scientific instruments, 77(10):103101, 2006.
TNBSF04: Iva Marija Tolić-Nørrelykke, Kirstine Berg-Sørensen, and Henrik Flyvbjerg. Matlab program for precision calibration of optical tweezers. Computer physics communications, 159(3):225–240, 2004.
Ves16: Christian L Vestergaard. Optimizing experimental parameters for tracking of diffusing particles. Physical Review E, 94(2):022401, 2016.
VBF14: Christian L Vestergaard, Paul C Blainey, and Henrik Flyvbjerg. Optimal estimation of diffusion coefficients from single-particle trajectories. Physical Review E, 89(2):022726, 2014.
VPMF15: Christian L Vestergaard, Jonas N Pedersen, Kim I Mortensen, and Henrik Flyvbjerg. Estimation of motility parameters from trajectory data. The European Physical Journal Special Topics, 224(7):1151–1168, 2015.
WYL+97(1,2): Michelle D Wang, Hong Yin, Robert Landick, Jeff Gelles, and Steven M Block. Stretching dna with optical tweezers. Biophysical journal, 72(3):1335, 1997.
WLG+16: Michael S. Woody, John H. Lewis, Michael J. Greenberg, Yale E. Goldman, and E. Michael Ostap. Memlet: an easy-to-use tool for data fitting and model comparison using maximum-likelihood estimation. Biophysical Journal, 111(2):273–282, 2016.