Details

Last Updated: Friday, 06 October 2017 11:59

Written by Chavdar Slavov

Artifact analysis

It is common in ultrafast transient absorption experiments to observe distortions in the recorded signal around the time zero position commonly called coherent artifact (CA) (for more information see Kovalenko et al, 1999; Slavov et al., 2015). The CA contribution to the sample measurements is typically estimated by performing a solvent measurements under the same experimental conditions. The transient absorption signal from the solvent can then be subtracted from the sample measurement (for example using the 'Combine datasets' module of OPTIMUS). Alternatively, the CA can be analysed directly by approximating its contribution with a function composed of a Gaussian and/or its first and second derivative (for details see Artifact analysis) as is done in this module and in the GLA module of OPTIMUS

In addition to the CA, time-resolved measurements on the sub-ps timescale are often affected by group velocity dispersion and self-phase modulation of light, which lead to a wavelength dependence of the time zero position (chirp). This dependence is modeled in OPTIMUS by a a polynomial function (for details see Artifact analysis).

The 'Artifact analysis' module of OPTIMUS allows analysis of solvent measurements to obtain information useful later on in the data analysis of the sample measurements, e.g. the FWHM of the IRF and the chirp parameters. The solvent measurements should be supplied in the form of .ana files.

Module layout

Tips

The 'Artifact analysis' module is very intuitive and self-explanatory. Nevertheless, here are provided some tips on how to use it.

1. The lower (lb) and upper (ub) boundary as well as the starting value (start) of each fit parameter in the 'Artifact analysis' module of OPTIMUS are specified using a series of edit boxes. The fit value is given in a text box or push button located next to the corresponding start value edit box.
2. Panel - Specify general settings
   1. Edit box: Wavelength range (nm) and Exclude wavelength ranges (nm) - Specify a wavelength range of interest. Dismiss wavelength regions (Format: e.g. 310:350, 420:460, meaning dismiss wavelength regions 310-350 nm and 420-450 nm) where no relevant signal is present.
   2. Edit box - Time range - Specify the time range (typically you can use the complete time range of your measurement).
   3. Popup menu - Background offset - Background offset option is included in case the data contains a background offset. However, this is rarely the case, thus typically this option is not used.
3. Panel - Specify IRF and artifact settings
   1. Popup menu - IRF with variable FWHMs - Specify whether the IRF FWHM should be varied over the selected wavelength range and if so what kind of variation should be used: i) independent for each wavelength (Option: yes); ii) dispersed (Option: dispersed).
   2. Pushbuttons - Load and Save - The fitted widths of the IRF can be save in a text file (.wirf), which then can be loaded again. This option allows estimating the IRF widths on a solvent measurements and then use these widths as fixed (option in the Popup menu - IRF with variable FWHMs ) in the analysis of the sample measurements. Note, the .wirf file contains only IRF widths for the analyzed wavelength channels.
   3. Edit boxes - IRF FWHM (ps) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the IRF width. 
   4. Popup menu - # of artifact components - Specify the number of artifact components to be used in approximating the CA (for details see Artifact analysis). Typically, setting '3' is used.
   5. Push button- Relative shift - An option is included to allow variation between the center position in time of the different artifact components. Typically the three components should have the same position in time coinciding with the position of the IRF maximum. Thus, this option is almost never used but is included as an option in case it is needed.
4. Panel - Specify fit parameters for 'time 0' dispersion
1. Popup menu - Dispersion order - Specify the dispersion order to be used for apporximaing the chirp polynomial (for details see Artifact analysis). Order '2' is typically sufficient, while in rear case where the chirp is relatively large also order '3' might be used (e.g. like in the example CA file included with the program).
2. Edit boxes - Center (nm) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the center position of the polynomial approximating the chirp. This boxes are initially set using the wavelength information from the loaded dataset.
3. Edit boxes - Time offset (ps) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the time zero offset. The starting value should be roughly assigned to the time point of the rise of the signal at the center wavelength (Center (nm)). The boundaries should be set wider enough to allow the program to find the time zero offset.
4. Edit boxes - Dispersion - specifying lower (lb) and upper (ub) boundary and starting value (start) for the coefficients of the chirp polynomial (should be between -1 and 1).
5. Please note that if in Panel: Specify IRF and artifact settings the option dispersed is selected for the varying the IRF FWHM in dependence of the wavelength, a pushbutton will appear in the Panel: Specify fit parameters for 'time 0' dispersion that will allow setting up dispersion fit parameters also for the IRF width.
5. 3D plot and 2D plot pushbuttons - at the top-center of the GUI for the this module act as tabs for switching between viewing the 3D plots for the dataset and the fit and the 2D plots comparing data and fit traces.
6. Additional push buttons are provided for saving the presented figures in a variety of file formats (please explore the options). Push buttons: Save 3D data, Save 3D fit, Residuals, Save 2D plots.
7. Pressing 'Save 3D data', 'Save 3D fit' or 'Residuals' push button brings up a new GUI with enlarged 3D plot.
8. Pressing 'Save 2D plots' push button brings up a new GUI for exploring the rests.