Inverse Problems in Pump–Probe Spectroscopy
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript titled “Inverse problems in pump-probe spectroscopy” by Tikhonov, Garg, and Schnell provides an extremely comprehensive description of fitting, their new developed software, and use cases. I believe this manuscript must be published in Photochem, and I expect that this will be standard reading for any scientist entering the field of pump-probe spectroscopy and associated data analysis. The terminology and equations are clear, consistent, and well-explained. The new software PP(MC)3, which uses least-squares fitting and Markov chain Monte Carlo sampling to fit any data set encountered in pump-probe spectroscopy, will be a useful tool for the growing community in this field.
Comments on the Quality of English LanguageJust some minor polishing needed.
Author Response
Thank you for your decision and suggestions. We checked the text once again, improving the minor language issues.
Reviewer 2 Report
Comments and Suggestions for AuthorsIn their manuscript, Tikhonov et al. describe in detail an approach for fitting pump-probe spectroscopy data (in a broad sense) by kinetic models. The approach is based on regularized Markov Chain Monte Carlo sampling. The authors have used the software to analyse their xuv-ir data (Ref. 6), and in this paper they present the full description, with examples and, crucially, accompanied by a ready-to-use Python implementation.
Considering the importance, popularity and omnipresence of the pump-probe spectroscopy together with the generality of the approach, the pump-probe multi-channel Markov chain Monte Carlo software has the potential to become the tool of choice and thus have a significant impact on the scientific community. As such, the paper should definitely be published.
This said, the paper would certainly benefit in putting into the context of existing pump-probe analysis approaches. In its current form, the paper is written in a completely self-standing way (reads almost like a thesis). While this is very useful concerning definitions and derivation of expressions, the reader does not know which concepts are new and what is already established and used. There are several popular ways to analyse pump-probe data. These include, among else, lifetime map analysis (Holzwarth et al., Biophys. J. 90, 552 (2006)) and global/target analysis (Ref. 32 of this manuscript). The latter is especially popular and recently got a Python implementation as well (Photochem Photobiol Sci 22, 2413 (2023)). In order to convince the scientific audience to adopt their approach and use the PP(MC)^3 software, the authors should put their work in such context and discuss the differences and similarities with existing approaches, possibly emphasizing the advantages of the presented approach. This could be either included in a separate Discussion section, or at least in the Conclusion/Introduction parts and the appropriate places throughout the text.
I have further one specific remark:
In pump-probe spectroscopy (transient absorption) with spectrally overlapping pump/probe pulses, an additional type of response localized near the pump-probe overlap is the so-called coherent artifact. It is often this (typically oscillatory) feature that limits the practical time resolution of the experiment. Can the current approach address this feature often present in the pump-probe data?
Minor:
p. 39, l.: 1125: "... setting the non-diagonal elements ..." setting to what - zero? does it?
Author Response
Thank you for your decision and suggestions.
Point #1
In its current form, the paper is written in a completely self-standing way (reads almost like a thesis). While this is very useful concerning definitions and derivation of expressions, the reader does not know which concepts are new and what is already established and used.
The most important new concept is the fitting procedure and its software implementation. All the concepts presented as theoretical background are known. The following sentences were added to a conclusion to highlight the newer (minor) results introduced in the theory section.
Here, we provided rigorous proof that the classical set of model functions used to fit the pump-probe experimental data is sufficient to describe any pump-probe observables, given that only first-order reactions are possible (Appendix A.8). In addition, we have extended the standard set of the basis functions used to fit the pump-probe dynamics with two additional ones, describing coherent oscillations in the dataset (Equations 82 and 83).
Point #2
The paper would certainly benefit in putting into the context of existing pump-probe analysis approaches. <...> This could be either included in a separate Discussion section, or at least in the Conclusion/Introduction parts and the appropriate places throughout the text.
We have added the following part in the Conclusion section.
The presented PP(MC)3 Fitting software is a complementary addition to the existing methods used to analyze experimental pump-probe data. Examples of such approaches include global and target analysis,[32,38,74] KiMoPack,[33] lifetime density maps analysis,[75–77] and Maxwell-Bloch equation modeling.[4,34] Adding the PP(MC)3 Fitting to the listed set of methods can be useful for the ultrafast community to robustly and effectively tackle complicated experimental pump-probe results with various dynamical observables.
Point #3
In pump-probe spectroscopy (transient absorption) with spectrally overlapping pump/probe pulses, an additional type of response localized near the pump-probe overlap is the so-called coherent artifact. It is often this (typically oscillatory) feature that limits the practical time resolution of the experiment. Can the current approach address this feature often present in the pump-probe data?
Yes, a similar treatment to the one used for the coherent oscillations analysis (Section 6.3) can be used to work with the coherent artifacts. The following sentence was added at the end of Section 6.3 to highlight this fact:
The same procedure can also treat other unaccounted features in the experimental pump-probe data. One example is the presence of so-called coherent artifacts, which appear near the temporal overlap of the pump and probe pulses.[69–72]
Point #4
p. 39, l.: 1125: "... setting the non-diagonal elements ..." setting to what - zero? does it?
Yes, it was to zero. Thank you. The following sentence was corrected as
This result can also be obtained by setting the non-diagonal elements to zero in the density matrix in Equation 47, which is known to lead to a classical regime of the quantum system.[78,79]