ArticlePhotochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology2023
Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra.
Article in Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 25 citations in OpenAlex.
- Effect of Al-Doping of Faceted SrTiOThe journal of physical chemistry. C, Nanomaterials and interfaces · 2026Article
- Photochemistry of Aromatic N-Oxides in Water Probed by Time-Resolved X-ray Absorption Spectroscopy.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Far-red chlorophyll d clusters extend photosystem I absorption toward the red limit.Science advances · 2026Article
- Ultrafast Excited-State Dynamics of Dithienyltetrazine-Based Donor-Acceptor Copolymers.The journal of physical chemistry. B · 2026Article
- Characterization of Parameter Uncertainty in Global Analysis for Ultrafast Spectroscopy Using Markov Chain Monte Carlo Sampling.Precision chemistry · 2026Article
- A design principle for tuning far-red absorption of chlorophyll a in light-harvesting complexes.Communications chemistry · 2026Article
- Unraveling Charge-Transfer States and Their Ultrafast Dynamics in Artificial Light-Harvesting Complexes.ACS physical chemistry Au · 2026Article
- Cryo-EM structure of photosystem II supercomplex from a green microalga with extreme phototolerance.Nature communications · 2026Article
- Dynamic control of electron correlations in photodoped charge-transfer insulators.Science advances · 2025Article
- Acclimation to white light in a far-red light specialist: insights from Acaryochloris marina MBIC11017.The New phytologist · 2025Article
- Cyanobacteria dynamically regulate phycobilisome-to-photosystem excitation energy transfer.iScience · 2025Article
- Retinal to Retinal Energy Transfer in a Bistable Microbial Rhodopsin Dimer.Journal of the American Chemical Society · 2025Article
- Target Analysis Resolves the Ground and Excited State Properties from Femtosecond Stimulated Raman Spectra.The journal of physical chemistry letters · 2024Article
- Energy Transfer and Radical-Pair Dynamics in Photosystem I with Different Red ChlorophyllInternational journal of molecular sciences · 2024Article
- Coloring Outside the Lines: Exploiting Pigment-Protein Synergy for Far-Red Absorption in Plant Light-Harvesting Complexes.Journal of the American Chemical Society · 2024Article
- Article
- Energy transfer from phycobilisomes to photosystem I at room temperature.Frontiers in plant science · 2023Article
- KiMoPack: A python Package for Kinetic Modeling of the Chemical Mechanism.The journal of physical chemistry. A · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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 three case studies. The first 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 artifact" is crucial. The second 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 third, 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.
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