Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] adtv_v2_0.tar.gz(1491 Kbytes)|
|Manuscript Title: tweezercalib 2.0: Faster version of MatLab package for precise calibration of optical tweezers|
|Authors: Poul Martin Hansen, Iva Marija Tolic-Nørrelykke, Henrik Flyvbjerg, Kirstine Berg-Sørensen|
|Program title: tweezercalib|
|Catalogue identifier: ADTV_v2_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 174(2006)518|
|Programming language: MatLab (Mathworks Inc.), standard licence.|
|Computer: General computer running MatLab (Mathworks Inc.).|
|Operating system: Windows2000, Windows-XP, linux.|
|RAM: Of order four times the size of the data file.|
|Keywords: Power spectrum analysis, precision calibration of optical tweezers.|
|PACS: 87.80.-y, 06.20.Dk, 07.60.-j, 05.40.Jc.|
|Classification: 3, 4.14, 18, 23.|
Does the new version supersede the previous version?: yes
Nature of problem:
Calibrate optical tweezers with precision by fitting theory to experimental power spectrum of position of bead doing Brownian motion in incompressible fluid, possibly near microscope cover slip, while trapped in optical tweezers. Thereby determine spring constant of optical trap and conversion factor for arbitrary-units-to-nanometers for detection system.
Elimination of cross-talk between quadrant photo-diode's output channels for positions (optional). Check that distribution of recorded positions agrees with Boltzmann distribution of bead in harmonic trap. Data compression and noise reduction by blocking method applied to power spectrum. Full accounting for hydrodynamic effects; Frequency-dependent drag force and interaction with nearby cover slip (optional). Full accounting for electronic filters (optional), for "virtual filtering" caused by detection system (optional). Full accounting for aliasing caused by finite sampling rate (optional). Standard non-linear least-squares fitting. Statistical support for fit is given, with several plots facilitating inspection of consistency and quality of data and fit.
Summary of revisions:
A faster fitting routine, adapted from [1,2], is applied. It uses fewer function evaluations, and the remaining function evaluations have been vectorized. Calls to routines in Toolboxes not included with a standard MatLab licence have been replaced by calls to routines that are included in the present package. Fitting parameters are rescaled to ensure that they are all of roughly the same size (of order 1) while being fitted. Generally, the program package has been updated to comply with MatLab, vs. 7.0, and optimized for speed.
Data should be positions of bead doing Brownian motion while held by optical tweezers. For high precision in final results, data should be time series measured over a long time, with sufficiently high experimental sampling rate; The sampling rate should be well above the characteristic frequency of the trap, the so-called corner frequency. Thus, the sampling frequency should typically be larger than 10 kHz. The Fast Fourier Transform used works optimally when the time series contain 2n data points, and long measurement time is obtained with n>12-15. Finally, the optics should be set to ensure a harmonic trapping potential in the range of positions visited by the bead. The fitting procedure checks for harmonic potential.
|||Jorge Nocedal and Ya xiang Yuan. Combining trust region and line search techniques. Technical Report OTC 98/04, Optimization Technology Center, 1998.|
|||W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. Numerical Recipes. The Art of Scientific Computing. Cambridge University Press, Cambridge, 1986.|
|||(The theoretical underpinnings for the procedure) Kirstine Berg-Sørensen and Henrik Flyvbjerg. Power spectrum analysis for optical tweezers. Rev. Sci. Ins., 75 594-612, 2004.|
|Disclaimer | ScienceDirect | CPC Journal | CPC | QUB|