Develop a suite of software for the analysis of time-resolved WAXS data incorporating molecular dynamics simulations.
The ESRF team has, in collaboration with UGOT and CNRS, added new functionality to the WAXSGUI, a program originally written by Marco Cammarata in 2009 at the ESRF.
The software reduces raw images to radial intensity curves while correcting for the flatness of the detector, the thickness of the phosphor screen, sample absorption and the polarization of the x-ray beam.
The corrected curve is proportional to the intrinsic scattering function S (Q) for the sample (solute in solution). In the GUI window, the user first selects the data files to analyze. Then the Region-of-Interest (ROI) of the image is defined which is typically used to avoid the data behind the laser and x-ray beamstops.
The Rayonix firmware automatically subtracts the dark image associated with the given exposure time (~ 1-100 s) after which it add 10 to all pixes to avoid having negative intensities.
In pump-probe experiments, the time delay between the laser and the x-ray pulse is scanned over a wide range of time, from 100 picosecond to 1 millisecond in a typical experiment. Each delay is measured several times to improve the signal-to-noise ratio.
The merging and averaging of radial curves is now done in the following way:
- Merging of all the data folders for a given sample into one hdf5 file
- Merging of repeated time delays into one file for that delay
- Kinetics analysis by singular-value-decomposition on the averaged data
- Outlier identification caused by beam instability, laser drif, radiation damage and flow-cell failure
- Plots for assessing if further improvement in S/N is achievable within a reasonable time.
The differential scattering curves dS (q,t) in laser/x-ray pump probe experiments are usually compared with the molecular dynamics simulations (MD) of excited-state solutes in solution. MD can predict the packing of the solvent around excited state molecules that are calculated by Density Functional Theory (DFT). At the ESRF we are using the DFT code Gaussian and the MD code Moldy.
The ESRF has a license to Materials Studio, which incorporates a number of MD codes for small, medium and large molecules. Linking the WAXSGUI to Moldy and Gaussian is work in progress.
The achievement of this milestone witnesses the progress towards deliverable D2.3 “WAXS software suite”.
Presently the software is available for ID09 ESRF users ant it will be soon publicly distributed
