TUTORIAL:

"pyglotaran: a lego-like Python framework for global and target analysis of time resolved spectra"

Ivo H.M. van Stokkuma, Jörn Weißenborna, Sebastian Weiganda,b, Joris J. Snellenburga
aDepartment of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
bFakultät II Institut für Festkörperphysik, Technische Universität Berlin

Email: i.h.m.van.stokkum@vu.nl
Date: Wednesday, October 9, from 14:30 to 18:00, with a Coffee break from 16-16h30.
Zoom: https://uva-live.zoom.us/my/ivo.van.stokkum

A hands-on tutorial
The case studies will be demonstrated in the PaN-Training e-Learning platform and explained, using a pyglotaran image Jupyterlab environment.
https://github.com/glotaran/pyglotaran/blob/main/README.md

Abstract:
The dynamics of molecular systems can be studied with time-resolved spectroscopy combined with model-based analysis. A Python framework for global and target analysis of time resolved spectra is introduced with the help of four case studies. The first study introduces the principles of global and target analysis. The second study concerning broadband absorption of intersystem crossing in 4-thiothymidine, demonstrates the framework's ability to resolve vibrational wavepackets with a time resolution of ≈10 fs using damped oscillations and their associated spectra and phases. Thereby a parametric description of the “coherent artefact” is crucial. The third study addresses multichromophoric systems composed of two perylene bisimide chromophores. Here, pyglotaran's guidance spectra and lego-like model composition enable the integration of spectral and kinetic properties of the parent chromophores, revealing a loss process, the undesired production of a radical pair, that reduces the light harvesting efficiency. In the fourth, time-resolved emission case study of whole photosynthetic cells, a megacomplex containing ≈500 chromophores of five different types is described by a combination of the kinetic models for its elements. As direct fitting of the data by theoretical simulation is unfeasible, our global and target analysis methodology provides a useful ‘middle ground’ where the theoretical description and the fit of the experimental data can meet. The pyglotaran framework enables the lego-like creation of kinetic models through its modular design and seamless integration with the rich Python ecosystem, particularly Jupyter notebooks. With extensive documentation and a robust validation framework, pyglotaran ensures accessibility and reliability for researchers, serving as an invaluable tool for understanding complex molecular systems.
 
BIO:
Ivo van Stokkum (1962) is an associate professor in biophysics of photosynthesis. Systems biophysics of photosynthesis aims to develop models that describe complex photosynthetic systems. Such models are based upon measured time-resolved absorption and emission spectra, which are two-dimensional data sets. Theoretical methods and software have been developed to identify the model and estimate the biophysical parameters that describe all data. These methods are termed global and target analysis. The key ingredients are compartmental, spectral, and thermodynamic models