PassiveCalibrationModel

lumicks.pylake.PassiveCalibrationModel

class PassiveCalibrationModel(bead_diameter, viscosity=None, temperature=20, hydrodynamically_correct=False, distance_to_surface=None, rho_sample=None, rho_bead=1060.0, fast_sensor=False, axial=False)

Model to fit data acquired during passive calibration.

The power spectrum calibration algorithm implemented here is based on a number of publications by the Flyvbjerg group at DTU 1 2 3 4 5 6.

References

1

Berg-Sørensen, K. & Flyvbjerg, H. Power spectrum analysis for optical tweezers. Rev. Sci. Instrum. 75, 594 (2004).

2

Tolić-Nørrelykke, I. M., Berg-Sørensen, K. & Flyvbjerg, H. MatLab program for precision calibration of optical tweezers. Comput. Phys. Commun. 159, 225–240 (2004).

3

Hansen, P. M., Tolic-Nørrelykke, I. M., Flyvbjerg, H. & Berg-Sørensen, K. tweezercalib 2.1: Faster version of MatLab package for precise calibration of optical tweezers. Comput. Phys. Commun. 175, 572–573 (2006).

4

Berg-Sørensen, K., Peterman, E. J. G., Weber, T., Schmidt, C. F. & Flyvbjerg, H. Power spectrum analysis for optical tweezers. II: Laser wavelength dependence of parasitic filtering, and how to achieve high bandwidth. Rev. Sci. Instrum. 77, 063106 (2006).

5

Tolić-Nørrelykke, S. F, and Flyvbjerg, H, “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 (2010)

6

Tolić-Nørrelykke S. F, Schäffer E, Howard J, Pavone F. S, Jülicher F and Flyvbjerg, H. Calibration of optical tweezers with positional detection in the back focal plane, Review of scientific instruments 77, 103101 (2006).

bead_diameter

Bead diameter [um].

Type

float

viscosity

Liquid viscosity [Pa*s]. When omitted, the temperature will be used to look up the viscosity of water at that particular temperature.

Type

float, optional

temperature

Liquid temperature [Celsius].

Type

float, optional

hydrodynamically_correct

Enable hydrodynamic correction.

Type

bool, optional

distance_to_surface

Distance from bead center to the surface [um]. When specifying None, the model will use an approximation which is only suitable for measurements performed deep in bulk.

Type

float, optional

rho_sample

Density of the sample [kg/m^3]. Only used when using hydrodynamic corrections.

Type

float, optional

rho_bead

Density of the bead [kg/m^3]. Only used when using hydrodynamic corrections.

Type

float, optional

fast_sensor

Fast sensor? Fast sensors do not have the diode effect included in the model.

Type

bool

axial

Is this an axial force model?

Type

bool

__call__(f, fc, diffusion_constant, *filter_params)

Call self as a function.

calibration_results(fc, diffusion_constant_volts, filter_params, fc_err, diffusion_constant_volts_err, filter_params_err)

Compute calibration parameters from cutoff frequency and diffusion constant.

Parameters

• fc (float) – Corner frequency, in Hz.

• diffusion_constant_volts (float) – Diffusion constant, in V^2/s

• filter_params (list of float) – Parameters for the filter model.

• fc_err (float) – Corner frequency standard error, in Hz

• diffusion_constant_volts_err (float) – Diffusion constant standard error, in Hz

• filter_params_err (list of float) – Standard errors for the filter model