A notebook implementing the algorithm to correct an energy landscape, as measured by particle tracking, for static and dynamic errors.
Errors in energy landscapes measured with particle tracking
Michał J. Bogdan and Thierry Savin, Biophys. J. 115:139-149 (2018)
http://doi.org/10.1016/j.bpj.2018.05.035
@article{Bogdan:2018,
author = {Bogdan, Micha\l{} J. and Savin, Thierry},
title = {Errors in energy landscapes measured with particle tracking},
volume = {115},
number = {1},
pages = {139--149},
year = {2018},
doi = {10.1016/j.bpj.2018.05.035},
URL = {http://doi.org/10.1016/j.bpj.2018.05.035},
eprint = {http://www.cell.com/biophysj/fulltext/S0006-3495(18)30675-1},
journal = {Biophysical Journal}
}
- Wolfram Mathematica is required to execute the notebook. It can be obtained from http://www.wolfram.com/mathematica.
- The input data files should be provided as three columns .csv files:
- 1st column: locations at which the apparent potential is measured;
- 2nd column: values of the measured potential;
- 3rd column: error bars on the potential's measurements.
- "
Potential-Correction.nb
" is a Mathematica notebook implementing the true potential reconstruction algorithm using Eqs. (15) & (16) of the article referenced above; - "
Examples/
" contains 8 example data files, with the simulation results used to generate Fig. 5 of the article; the names of the files provide information about which of the curves the data refers to: for example, "Data_fig5a_sig0.1_eps0.3_p10.csv
" contains the data for Fig. 5a, with the dimensionless shutter timesigma=0.1
, the dimensionless static localisation uncertaintyepsilon=0.3
, and the optimal polynomial order of potential fittingp=10
.
- The section INPUTS specifies the information to be entered by the user;
- The section CALCULATIONS performs the reconstruction algorithm;
- The section OUTPUTS plots the reconstructed potential compared to the apparent measured potential, and gives the polynomial coefficients of the reconstructed potential.