PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data

PLoS Computational Biology
Gabriel F DorlhiacJasper J van Thor

Abstract

Ultrafast spectroscopy offers temporal resolution for probing processes in the femto- and picosecond regimes. This has allowed for investigation of energy and charge transfer in numerous photoactive compounds and complexes. However, analysis of the resultant data can be complicated, particularly in more complex biological systems, such as photosystems. Historically, the dual approach of global analysis and target modelling has been used to elucidate kinetic descriptions of the system, and the identity of transient species respectively. With regards to the former, the technique of lifetime density analysis (LDA) offers an appealing alternative. While global analysis approximates the data to the sum of a small number of exponential decays, typically on the order of 2-4, LDA uses a semi-continuous distribution of 100 lifetimes. This allows for the elucidation of lifetime distributions, which may be expected from investigation of complex systems with many chromophores, as opposed to averages. Furthermore, the inherent assumption of linear combinations of decays in global analysis means the technique is unable to describe dynamic motion, a process which is resolvable with LDA. The technique was introduced to the field of photosynthe...Continue Reading

References

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Jan 26, 2017·Biophysical Journal·Marius KaucikasJasper J van Thor

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Citations

Aug 11, 2020·The Journal of Chemical Physics·Kenji Katayama
Nov 28, 2019·Physical Chemistry Chemical Physics : PCCP·Charlotte L SmithAlexander J Cowan
Sep 2, 2020·Proceedings of the National Academy of Sciences of the United States of America·Noura ZamzamJasper J van Thor
Jan 1, 2021·The Journal of Chemical Physics·David BuhrkePeter Hamm
Aug 18, 2020·The Journal of Physical Chemistry. B·Clyde FareJasper J van Thor
May 23, 2020·The Journal of Physical Chemistry Letters·Yangzhong QinDaniel G Nocera
Nov 9, 2021·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Christopher D M HutchisonJasper J van Thor

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Software Mentioned

NumPy
LDA
IPython
SciPy
LASSO
PyLDM
Matplotlib
OPTIMUS

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