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2019

Capturing the Quenching Mechanism of Light-Harvesting Complexes of Plants by Zooming in on the Ensemble

Mascoli, V., Liguori, N., Xu, P., Roy, L. M., van Stokkum, I. H. M. & Croce, R., 14 Nov 2019, In : Chem. 5, 11, p. 2900-2912 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Quenching
Light
Lutein
Excitation energy
Energy Transfer

PH dependence, kinetics and light-harvesting regulation of nonphotochemical quenching in Chlamydomonas

Tian, L., Nawrocki, W. J., Liu, X., Polukhina, I., Van Stokkum, I. H. M. & Croce, R., 23 Apr 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 17, p. 8320-8325 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chlamydomonas
Light
Bryophyta
Chlamydomonas reinhardtii
Diatoms

Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein

Konold, P. E., Van Stokkum, I. H. M., Muzzopappa, F., Wilson, A., Groot, M. L., Kirilovsky, D. & Kennis, J. T. M., 9 Jan 2019, In : Journal of the American Chemical Society. 141, 1, p. 520-530 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Secondary Protein Structure
Carotenoids
Proteins
Structural dynamics
Hydrogen
2018

A functional compartmental model of the Synechocystis PCC 6803 phycobilisome

van Stokkum, I. H. M., Gwizdala, M., Tian, L., Snellenburg, J. J., van Grondelle, R., van Amerongen, H. & Berera, R., Mar 2018, In : Photosynthesis Research. 135, 1-3, p. 87-102 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Correction to: The phycobilisome terminal emitter transfers its energy with a rate of (20 ps)–1 to photosystem II

Acuña, A. M., van Alphen, P., van Grondelle, R. & van Stokkum, I. H. M., 28 Mar 2018, In : Photosynthetica. p. 1-1 1 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phycobilisomes
phycobilisome
Photosystem II Protein Complex
Energy Transfer
energy transfer

Development of fluorescence quenching in Chlamydomonas reinhardtii upon prolonged illumination at 77 K

Wlodarczyk, L. M., Snellenburg, J. J., Dekker, J. P. & Stokkum, I. H. M., Sep 2018, In : Photosynthesis Research. 137, 3, p. 503-513 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chlamydomonas reinhardtii
Photosystem II Protein Complex
Lighting
photosystem II
lighting

Energy transfer and trapping in Synechococcus WH 7803

Acuña, A. M., Lemaire, C., van Grondelle, R., Robert, B. & van Stokkum, I. H. M., Mar 2018, In : Photosynthesis Research. 135, 1-3, p. 115-124 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila

Mix, L. T., Carroll, E. C., Morozov, D., Pan, J., Gordon, W. R., Philip, A., Fuzell, J., Kumauchi, M., Van Stokkum, I., Groenhof, G., Hoff, W. D. & Larsen, D. S., 20 Mar 2018, In : Biochemistry. 57, 11, p. 1733-1747 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Wavelength
mannosulfan
Proteins
Fluorescence
Chromophores

Introduction: light harvesting for photosynthesis

Pandit, A., van Stokkum, I. H. M., van Amerongen, H. & Croce, R., Mar 2018, In : Photosynthesis Research. 135, 1-3, p. 1-2 2 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

Open Access
File

Light Harvesting in Photosynthesis

Croce, R. (ed.), van Grondelle, R. (ed.), van Amerongen, H. (ed.) & van Stokkum, I. (ed.), Feb 2018, Boca Rata: CRC Press. 611 p.

Research output: Book / ReportBook editingAcademic

algae
photosynthesis
energy transfer
pigments
electron transfer
Open Access
File

Spectrally decomposed dark-to-light transitions in a PSI-deficient mutant of Synechocystis sp. PCC 6803

Acuña, A. M., van Alphen, P., Branco dos Santos, F., van Grondelle, R., Hellingwerf, K. J. & van Stokkum, I. H. M., Feb 2018, In : Biochimica et Biophysica Acta - Bioenergetics. 1859, 2, p. 57-68 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Synechocystis
Fluorescence
Light
Phycobilisomes
Photosynthetic Reaction Center Complex Proteins

Spectrally decomposed dark-to-light transitions in Synechocystis sp. PCC 6803

Acuña, A. M., van Alphen, P., Branco Dos Santos, F., van Grondelle, R., Hellingwerf, K. J. & van Stokkum, I. H. M., 29 Mar 2018, In : Photosynthesis Research. p. 1-14 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synechocystis sp. PCC 6803
Synechocystis
Energy Transfer
Energy transfer
Dark Adaptation

Systems biophysics: Global and target analysis of light harvesting and photochemical quenching in vivo

van Stokkum, I., Feb 2018, Light Harvesting in Photosynthesis . Croce, R., van Grondelle, R., van Amerongen, H. & van Stokkum, I. (eds.). CRC Press, Boca Rata, p. 467-482 16 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Open Access
File
Biophysics
Quenching
Photosynthesis
Photosynthetic Reaction Center Complex Proteins
Energy transfer

The phycobilisome terminal emitter transfers its energy with a rate of (20 ps)–1 to photosystem II

Acuña, A. M., Van Alphen, P., Van Grondelle, R. & Van Stokkum, I. H. M., Mar 2018, In : Photosynthetica. 56, 1, p. 265-274 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phycobilisomes
phycobilisome
Photosystem II Protein Complex
Energy Transfer
energy transfer

Vibronic Wavepackets and Energy Transfer in Cryptophyte Light-Harvesting Complexes

Jumper, C. C., Van Stokkum, I. H. M., Mirkovic, T. & Scholes, G. D., 21 Jun 2018, In : Journal of Physical Chemistry B. 122, 24, p. 6328-6340 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Energy transfer
energy transfer
Phycobiliproteins
algae
Algae
2017

A four state parametric model for the kinetics of the non-photochemical quenching in Photosystem II

Snellenburg, J. J., Johnson, M. P., Ruban, A. V., van Grondelle, R. & van Stokkum, I. H. M., Oct 2017, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1858, 10, p. 854-864

Research output: Contribution to JournalArticleAcademicpeer-review

Photosystem I Protein Complex
Chlamydomonas reinhardtii
Photosystem II Protein Complex
Excited states
Light-Harvesting Protein Complexes

Analysis of fluorescence spectra in cyanobacteria from picoseconds to minutes

Acuña Sánchez, A. M., 2017, 241 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Different carotenoid conformations have distinct functions in light-harvesting regulation in plants

Liguori, N., Xu, P., van Stokkum, I., van Oort, B., Lu, Y., Karcher, D., Bock, R. & Croce, R., 8 Dec 2017, In : Nature Communications. 8, 1, 1994.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
carotenoids
Carotenoids
Conformations
Light
Excitation energy

Modelling energy transfer and trapping in the thylakoid membrane

Snellenburg, J., 2017, 226 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Reaction dynamics of the chimeric channelrhodopsin C1C2

Hontani, Y., Marazzi, M., Stehfest, K., Mathes, T., van Stokkum, I. H. M., Elstner, M., Hegemann, P. & Kennis, J. T. M., 3 Aug 2017, In : Scientific Reports. 7, 7217.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2016

A method to decompose spectral changes in Synechocystis PCC 6803 during light-induced state transitions

Acuña, A. M., Kana, R., Gwizdala, M. S., Snellenburg, J. J., van Alphen, P., van Oort, B. F., Kirilovsky, D., van Grondelle, R. & van Stokkum, I. H. M., 2016, In : Photosynthesis Research. 130, 1-3, p. 237-249

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phycobilisomes
Synechocystis
phycobilisome
Fluorometry
Plastoquinone

Estimation of damped oscillation associated spectra from ultrafast transient absorption spectra

van Stokkum, I., Jumper, C. C., Snellenburg, J., Scholes, G. D., van Grondelle, R. & Malý, P., 2016, In : Journal of Chemical Physics. 145, 17, 174201.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Excited states
Absorption spectra
absorption spectra
oscillations
Chromophores

Resolving Energy and Electron Transfer Processes in Dyads With the Help of Global and Target Analysis

van Stokkum, I. H. M., Ravensbergen, J., Snellenburg, J. J., van Grondelle, R., Pillai, S., Moore, T. A., Gust, D., Moore, A. L. & Kennis, J. T. M., 2016, Artificial Photosynthesis. Bruno, R. (ed.). Amsterdam: Advances in Botanical Researc, Vol. 79. p. 169-192 (79).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Carotenoids
Fullerenes
Excited states
Energy transfer
Electrons

Resolving the contribution of the uncoupled phycobilisomes to cyanobacterial pulse-amplitude modulated (PAM) fluorometry signals

Acuña, A. M., Snellenburg, J. J., Gwizdala, M. S., Kirilovsky, D., van Grondelle, R. & van Stokkum, I. H. M., 2016, In : Photosynthesis Research. 127, 1, p. 91-102

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phycobilisomes
phycobilisome
Fluorometry
fluorometry
autotrophs
2015

A Hidden State in Light-Harvesting Complex II Revealed By Multipulse Spectroscopy

van Oort, B. F., van Grondelle, R. & van Stokkum, I. H. M., 2015, In : Journal of Physical Chemistry B. 119, 16, p. 5184-5193

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
quenching
Spectroscopy
Quenching
luminous intensity
High intensity light

Functional rearrangement of the light-harvesting antenna upon state transitions in a green alga

Wlodarczyk, L. M., Snellenburg, J. J., Ihalainen, J. A., van Grondelle, R., van Stokkum, I. H. M. & Dekker, J. P., 2015, In : Biophysical Journal. 108, 2, p. 261-271 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chlorophyta
Photosystem II Protein Complex
Photosystem I Protein Complex
Light
Energy Transfer

PSI-LHCI of Chlamydomonas reinhardtii: Increasing the absorption cross section without losing efficiency

Le Quiniou, C. L., Tian, L., Drop, B. A., Wientjes, I. E., van Stokkum, I. H. M., van Oort, B. F. & Croce, R., 2015, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1847, 4-5, p. 458-467

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Photosystem I Protein Complex
Chlamydomonas reinhardtii
Chlorophyll
Algae
Photosynthetic membranes

Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield

Zhu, J., Vreede, J., Hospes, M., Arents, J., Kennis, J. T. M., van Stokkum, I. H. M., Hellingwerf, K. J. & Groot, M. L., 2015, In : Journal of Physical Chemistry B. 119, 6, p. 2372-2383

Research output: Contribution to JournalArticleAcademicpeer-review

Quantum yield
Chromophores
Isomerization
chromophores
isomerization
Photosystem I Protein Complex
Chlamydomonas reinhardtii
Chlorophyta
Algae
Excitation energy
2014

Exploring the mechanism(s) of energy dissipation in the light harvesting complex of the photosynthetic algae Cyclotella meneghiniana

Ramanan, C., Berera, R., Gundermann, K., van Stokkum, I. H. M., Buchel, C. & van Grondelle, R., 2014, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 2014, 9, p. 1507-1513

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Photosynthetic Reaction Center Complex Proteins
Algae
Energy dissipation
Light
Diatoms
Spectrum Analysis
Light Signal Transduction
Photochemistry
Proteins
Flavin-Adenine Dinucleotide

Quantitative Fluorescence Spectral Analysis of Protein Denaturation

van Stokkum, I. H. M. & Laptenok, S., 2014, In : Methods in Molecular Biology. 2014, p. 43-51

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Protein Denaturation
Thermodynamics
Fluorescence
2013

Closed Reaction Centers of PS1 Still Can Perform the First Steps of Charge Separation. A Mid IR Pump Probe Study with fs Resolution

Stahl, A. D., Di Donato, M., van Stokkum, I. H. M., van Grondelle, R. & Groot, M. L., 2013, Photosynthesis Research for Food, Fuel and the Future. Springer Berlin Heidelberg, p. 127-130

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Early Bacteriopheophytin Reduction in Charge Separation in Reaction Centers of Rhodobacter sphaeroides

Zhu, J., van Stokkum, I. H. M., Paparelli, L., Jones, M. R. & Groot, M. L., 2013, In : Biophysical Journal. 104, 11, p. 2493-2502

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bacteriochlorophylls
Rhodobacter sphaeroides
Tetrapyrroles
Electrons
Energy Transfer

Energy Transfer and Trapping in Red-Chlorophyll-Free Photosystem I from Synechococcus WH 7803

van Stokkum, I. H. M., Desquilbet, T. E., van der Weij-de Wit, C. D., Snellenburg, J. J., van Grondelle, R., Thomas, J-C., Dekker, J. P. & Robert, B. H., 2013, In : Journal of Physical Chemistry B. 117, 38, p. 11176-11183 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Photosystem I Protein Complex
chlorophylls
Chlorophyll
Energy transfer
energy transfer

Excited States of the Inactive and Active Forms of the Orange Carotenoid Protein

Berera, R., Gwizdala, M. S., van Stokkum, I. H. M., Kirilovsky, D. & van Grondelle, R., 2013, In : Journal of Physical Chemistry B. 117, p. 9121-9128

Research output: Contribution to JournalArticleAcademicpeer-review

carotenoids
Carotenoids
Excited states
proteins
Proteins
membranes
Membranes
Photosynthetic Reaction Center Complex Proteins
Fluorescence spectroscopy
Energy transfer

Light Harvesting and Blue-Green Light Induced Non-Photochemical Quenching in Two Different C-Phycocyanin Mutants of Synechocystis PCC 6803

Tian, L., van Stokkum, I. H. M., Koehorst, R. B. M. & van Amerongen, H., 2013, In : Journal of Physical Chemistry B. 117, p. 11000-11006

Research output: Contribution to JournalArticleAcademicpeer-review

Phycocyanin
Methyl Green
Quenching
quenching
Excitation energy

Photoionization and Electron Radical Recombination Dynamics in Photoactive Yellow Protein Investigated by Ultrafast Spectroscopy in the Visible and Near-Infrared Spectral Region

Zhu, J., Hospes, M., Arents, J., Kennis, J. T. M., van Stokkum, I. H. M., Hellingwerf, K. J. & Groot, M. L., 2013, In : Journal of Physical Chemistry B. 117, 38, p. 11042-11048

Research output: Contribution to JournalArticleAcademicpeer-review

Photoionization
Chromophores
photoionization
Electron absorption
Spectroscopy
Perylene
Pyrene
pyrenes
Absorption spectroscopy
Excited states

Ultrafast Energy Transfer and Excited State Coupling in an Artificial Photosynthetic Antenna

Maiuri, M., Snellenburg, J. J., van Stokkum, I. H. M., Pillai, S., Carter, K. W., Gust, D., Moore, T. A., Moore, A. L. & van Grondelle, R., 2013, In : Journal of Physical Chemistry B. 117, 46, p. 14183-14190

Research output: Contribution to JournalArticleAcademicpeer-review

Excited states
Energy transfer
antennas
energy transfer
Antennas

Ultrafast geminate electron-radical recombination dynamics in photoactive yellow protein

Zhu, J., Paparelli, L., Arents, J., Hellingwerf, K. J., Kennis, J. T. M., van Stokkum, I. H. M. & Groot, M. L., 2013, XVIIIth International Conference on Ultrafast Phenomena. EDP Sciences, p. 07010

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Ultrafast Proton Shuttling in Psammocora Cyan Fluorescent Protein

Kennis, J. T. M., van Stokkum, I. H. M., Peterson, D. S., Pandit, A. & Wachter, R. M., 2013, In : Journal of Physical Chemistry B. 117, p. 11134-11143

Research output: Contribution to JournalArticleAcademicpeer-review

Chromophores
Protons
chromophores
Proton transfer
proteins
2012

Disentangling picosecond events that complicate the quantitative use of the calcium sensor YC3.60

Laptenok, S., van Stokkum, I. H. M., Borst, J. W., van Oort, B. F., Visser, A. J. W. G. & van Amerongen, H., 2012, In : Journal of Physical Chemistry B. 116, 9, p. 3013-3020 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Energy transfer
calcium
Calcium
energy transfer
proteins

Excitation-induced polarization decay in the plant light-harvesting complex LHCII

Marin, A., van Stokkum, I. H. M., Novoderezhkin, V. I. & van Grondelle, R., 2012, In : Journal of Photochemistry and Photobiology A. Chemistry. 234, p. 91-99

Research output: Contribution to JournalArticleAcademicpeer-review

chlorophylls
Chlorophyll
antennas
Polarization
Antennas

Excited state proton transfer in strongly enhanced GFP (sGFP2)

van Oort, B. F., ter Veer, M. J. T., Groot, M. L. & van Stokkum, I. H. M., 2012, In : Physical Chemistry Chemical Physics - PCCP. 14, 25, p. 8852-8858

Research output: Contribution to JournalArticleAcademicpeer-review

Proton transfer
Green Fluorescent Proteins
Excited states
Chromophores
Light absorption

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. 1-22

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Graphical User Interface
Graphical user interfaces
Java
User interfaces
User Interface

Hydrogen Bond Switching among Flavin and Amino Acids Determines the Nature of Proton-Coupled Electron Transfer in BLUF Photoreceptors

Mathes, T., Zhu, J., van Stokkum, I. H. M., Groot, M. L., Hegemann, P. & Kennis, J. T. M., 2012, In : Journal of Physical Chemistry Letters. 3, 2, p. 203-208

Research output: Contribution to JournalArticleAcademicpeer-review

photoreceptors
amino acids
Protons
Amino acids
Hydrogen bonds