Modelling Multi-Pulse Population Dynamics from Ultrafast Spectroscopy

Abstract

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments.

Excited‐State Deactivation of Branched Phthalocyanine Compounds

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Ground-state proton transfer in the photoswitching reactions of the fluorescent protein Dronpa

“…Pump-on minus pump-off difference spectra were obtained by shot-to-shot referencing and on the fly-signal discrimination to reject outliers. Transient absorption measurements were analysed by global analysis, using a previously reported ultrafast spectroscopy modelling toolbox 26 . Data treatment included the fitting of instrument response function (about 100 fs) and chirp, and applied a sequential model, using coupled differential equations, to retrieve the speciesassociated difference spectra relative to the ground state, which correspond to the dominant time constants that describe the full time-resolved data set.…”

Excited-state absorption and ultrafast relaxation dynamics of protoporphyrin IX and hemin

“…14 Charge transfer (CT) and (d,d) states, energetically below Q, are believed to be responsible for the effect. 46 The analysis is performed by using a sequential model as already reported for other iron- 52,53,65 The kinetic traces in Fig.…”