Research output per year
Research output per year
Personal profile
Personal information
From 1979 until 1984 he studied physics at the Radboud University Nijmegen. Bachelors degree in physics and chemistry in 1982 (cum laude). Masters degree in experimental physics in 1984 (cum laude). Ph.D. degree in natural sciences on September 13, 1989 Analysis of auditory brainstem neurons in the grassfrog (Ph.D. advisor Prof. dr. C.C.A.M. Gielen). In December 1989 he became UD (universitair docent, comparable to assistant professor) in the Department of Physics and Astronomy, Faculty of Sciences, of the Vrije Universiteit, Amsterdam. First in the Physics Applied Computer Science group, since October 2005 in the Biophysics of photosynthesis group. Since July 2014 UHD (universitair hoofddocent, comparable to associate professor).
Ivo van Stokkum | Biophysics of Photosynthesis section | Department of Physics and Astronomy
Research
Systems Biophysics of photosynthesis
The aim of Systems biophysics is to develop compartmental, spectral, and thermodynamic models that describe complex photosynthetic systems. Such models are based upon measured time-resolved absorption and emission spectra, which are two-dimensional data sets. Global and target analysis methods and software have been developed to identify the model and estimate the biophysical parameters that describe all data.
Teaching
Bachelor courses
- 2SBI Toegepaste Informatica voor SBI
- 3SBI Modelleren voor SBI
- 2MNW Practicum Natuurkunde en Informatica, module Programmeren in Mathematica
- 3MNW Project Systeemmodelleren
Master courses
- BMTP Ph&A: From Physics to Physiology
- Ph&A Photosynthesis and Energy
- BMTP Ph&A: Parameter Estimation Applied to Medical & Biological Science
Ancillary activities
No ancillary activities
Ancillary activities are updated daily
Keywords
- Q Science
- Biophyiscs of photosynthesis
- System biophysics of photosynthesis
- Target analysis of time-resolved fulorescenve spectra
- fluorescence spectra analysis
- Global and target analysis
- Complex photosynthetic systems
- Time-resolved adsorption spectra
- Time resolved emission spectra
- Pyglotaran
- Modeling Multiway spectroscopic measurements
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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SDG 6 Clean Water and Sanitation -
SDG 7 Affordable and Clean Energy
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Global and target analysis of time-resolved spectra
van Stokkum, I. H. M., Larsen, D. S. & van Grondelle, R., 2004, In: Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1657, 2-3, p. 82-104Research output: Contribution to Journal › Article › Academic › peer-review
Open Access -
TIMP: An R package for modeling multi-way spectroscopic measurements
Mullen, K. M. & van Stokkum, I. H. M., 2007, In: Journal of Statistical Software. 18, 3Research output: Contribution to Journal › Article › Academic › peer-review
Open AccessFile476 Downloads (Pure) -
Glotaran: A Java-Based Graphical User Interface for the R Package TIMP
Snellenburg, J. J., Laptenok, S., Seger, R., Mullen, K. M. & van Stokkum, I. H. M., 2012, In: Journal of Statistical Software. 49, 3, p. 1-22Research output: Contribution to Journal › Article › Academic › peer-review
Open AccessFile866 Downloads (Pure) -
Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra
van Stokkum, I. H. M., Weißenborn, J., Weigand, S. & Snellenburg, J. J., Oct 2023, In: Photochemical and Photobiological Sciences. 22, 10, p. 2413-2431 19 p.Research output: Contribution to Journal › Article › Academic › peer-review
Open Access -
Multistep 11-cis to All-trans Retinal Photoisomerization in Bestrhodopsin, an Unusual Microbial Rhodopsin
Broser, M., Kaziannis, S., van Stokkum, I. H. M., Mukherjee, A., Dostal, J., Busse, W., Munhoven, A., Bernardo, C., Hegemann, P., Kloz, M. & Kennis, J. T. M., 23 Jul 2025, In: Journal of the American Chemical Society. 147, 29, p. 25571-25583 13 p.Research output: Contribution to Journal › Article › Academic › peer-review
Open Access
Courses
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Parameter Estimation Applied to Medical and Biological Sciences
van Stokkum, I. 1/09/26 → 31/08/27
Course
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Projects
- 1 Finished
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BSC - Cluster 2.4 Thylakoid membrane
Snellenburg, J. (Project Researcher) & van Stokkum, I. (Principal Investigator)
1/07/10 → 1/09/16
Project: Research
Datasets
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Supplementary Information (SI) to the pyglotaran release paper
van Stokkum, I. (Creator), Weissenborn, J. (Contributor), Weigand, S. (Contributor) & Snellenburg, J. (Owner), Zenodo, 28 Jul 2023
DOI: 10.5281/zenodo.7658982, https://zenodo.org/record/7658983 and one more link, https://github.com/glotaran/pyglotaran-release-paper-supplementary-information/tree/accepted-for-publication (show fewer)
Dataset / Software: Dataset
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CCDC 154407: Experimental Crystal Structure Determination
Goubitz, K. (Contributor), Schenk, H. (Contributor), Brouwer, A. M. (Contributor), Lauteslager, X. Y. (Contributor), Bebelaar, D. (Contributor), Fraanje, J. (Contributor), Verhoeven, J. W. (Contributor), Van John Ramesdonk, J. R. H. (Contributor) & Van Stokkum, I. H. M. (Contributor), The Cambridge Structural Database, 1 Jan 2001
DOI: 10.5517/cc55nwv, https://doi.org/10.5517%2Fcc55nwv
Dataset / Software: Dataset
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pyglotaran: a Python library for global and target analysis
Weißenborn, J. (Creator), Snellenburg, J. (Creator), Weigand, S. (Contributor) & Stokkum, I. H. M. V. (Supervisor), Zenodo, 25 Aug 2024
DOI: 10.5281/zenodo.4534043, https://zenodo.org/records/13371565
Dataset / Software: Software
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CCDC 687096: Experimental Crystal Structure Determination
Hippius, C. (Contributor), Van Stokkum, I. H. M. (Contributor), Zangrando, E. (Contributor), Williams, R. M. (Contributor), Wykes, M. (Contributor), Beljonne, D. (Contributor) & Wurthner, F. (Contributor), Unknown, 18 Sept 2008
DOI: 10.5517/ccr1zd4, http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccr1zd4&sid=DataCite
Dataset / Software: Dataset