[1] A. M. Acuña, P. Van Alphen, R. Van Grondelle, and I. H. M. Van Stokkum. The phycobilisome terminal emitter transfers its energy with a rate of (20 ps)-1 to photosystem ii. Photosynthetica, 56(1):265--274, 2018. [ bib | DOI | http ]
[2] Ivo van Stokkum. Systems biophysics: Global and target analysis of light harvesting and photochemical quenching in vivo, book section 20, pages 467--482. CRC Press, Boca Raton, 2018. [ bib ]
[3] Roberta Croce, Rienk van Grondelle, Herbert van Amerongen, and Ivo van Stokkum, editors. Light Harvesting in Photosynthesis. Foundations of biochemistry and biophysics. CRC Press, Boca Raton, 2018. [ bib ]
[4] Anjali Pandit, Ivo H. M. van Stokkum, Herbert van Amerongen, and Roberta Croce. Introduction: light harvesting for photosynthesis. Photosynthesis Research, 135(1):1--2, 2018. [ bib | DOI | http ]
[5] Alonso M. Acuña, Pascal van Alphen, Filipe Branco dos Santos, Rienk van Grondelle, Klaas J. Hellingwerf, and Ivo H.M. van Stokkum. Spectrally decomposed dark-to-light transitions in a psi-deficient mutant of synechocystis sp. pcc 6803. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1859(2):57 -- 68, 2018. [ bib | DOI | http ]
[6] Hisanori Yamakawa, Ivo H. M. van Stokkum, Ulrich Heber, and Shigeru Itoh. Mechanisms of drought-induced dissipation of excitation energy in sun- and shade-adapted drought-tolerant mosses studied by fluorescence yield change and global and target analysis of fluorescence decay kinetics. Photosynthesis Research, 135(1):285--298, 2018. [ bib | DOI | http ]
[7] Alonso M. Acuña, Claire Lemaire, Rienk van Grondelle, Bruno Robert, and Ivo H. M. van Stokkum. Energy transfer and trapping in Synechococcus WH 7803. Photosynthesis Research, 135(1):115--124, 2018. [ bib | DOI | http ]
[8] Ivo H. M. van Stokkum, Michal Gwizdala, Lijin Tian, Joris J. Snellenburg, Rienk van Grondelle, Herbert van Amerongen, and Rudi Berera. A functional compartmental model of the Synechocystis PCC 6803 phycobilisome. Photosynthesis Research, 135(1):87--102, 2018. [ bib | DOI | http ]
[9] Nicoletta Liguori, Pengqi Xu, Ivo H. M. van Stokkum, Bart van Oort, Yinghong Lu, Daniel Karcher, Ralph Bock, and Roberta Croce. Different carotenoid conformations have distinct functions in light-harvesting regulation in plants. Nature Communications, 8(1):1994, 2017. [ bib | DOI | http ]
[10] Y. Hontani, M. Marazzi, K. Stehfest, T. Mathes, I. H. M. van Stokkum, M. Elstner, P. Hegemann, and J. T. M. Kennis. Reaction dynamics of the chimeric channelrhodopsin C1C2. Sci Rep, 7, 2017. [ bib | DOI ]
[11] Joris J. Snellenburg, Matthew P. Johnson, Alexander V. Ruban, Rienk van Grondelle, and Ivo H.M. van Stokkum. A four state parametric model for the kinetics of the non-photochemical quenching in Photosystem II. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1858(10):854 -- 864, 2017. [ bib | DOI | http ]
[12] Joris J. Snellenburg, Lucyna M. Wlodarczyk, Jan P. Dekker, Rienk van Grondelle, and Ivo H.M. van Stokkum. A model for the 77 K excited state dynamics in Chlamydomonas reinhardtii in state 1 and state 2. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1858(1):64--72, 2017. [ bib | DOI | http ]
[13] Ivo H. M. van Stokkum, Chanelle C. Jumper, Joris J. Snellenburg, Gregory D. Scholes, Rienk van Grondelle, and Pavel Malý. Estimation of damped oscillation associated spectra from ultrafast transient absorption spectra. The Journal of Chemical Physics, 145(17):174201, 2016. [ bib | DOI | arXiv | http ]
[14] Alonso M. Acuña, Radek Kaňa, Michal Gwizdala, Joris J. Snellenburg, Pascal van Alphen, Bart van Oort, Diana Kirilovsky, Rienk van Grondelle, and Ivo H. M. van Stokkum. A method to decompose spectral changes in Synechocystis PCC 6803 during light-induced state transitions. Photosynthesis Research, 130(1):237--249, 2016. [ bib | DOI | http ]
[15] I. H. M. van Stokkum, J. Ravensbergen, J. J. Snellenburg, R. van Grondelle, S. Pillai, T. A. Moore, D. Gust, A. L. Moore, and J. T. M. Kennis. Resolving energy and electron transfer processes in dyads with the help of global and target analysis. In Bruno Robert, editor, Artificial Photosynthesis, volume 79 of Advances in Botanical Research, pages 169 -- 192. Academic Press, 2016. [ bib | DOI ]
[16] A. M. Acuna, J. J. Snellenburg, M. Gwizdala, D. Kirilovsky, R. van Grondelle, and I. H. M. van Stokkum. Resolving the contribution of the uncoupled phycobilisomes to cyanobacterial pulse-amplitude modulated (PAM) fluorometry signals. Photosynthesis Research, 127(1):91--102, 2016. [ bib | DOI | www: ]
[17] C. Le Quiniou, B. van Oort, B. Drop, I. H. M. van Stokkum, and R. Croce. The High Efficiency of Photosystem I in the Green Alga Chlamydomonas reinhardtii Is Maintained after the Antenna Size Is Substantially Increased by the Association of Light-harvesting Complexes II. Journal of Biological Chemistry, 290(51):30587--30595, 2015. [ bib | DOI | www: ]
[18] Clotilde Le Quiniou, Lijin Tian, Bartlomiej Drop, Emilie Wientjes, Ivo H.M. van Stokkum, Bart van Oort, and Roberta Croce. PSI-LHCI of Chlamydomonas reinhardtii: Increasing the absorption cross section without losing efficiency. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1847(4-5):458 -- 467, 2015. [ bib | DOI | http ]
[19] B. van Oort, R. van Grondelle, and I. H. M. van Stokkum. A Hidden State in Light-Harvesting Complex II Revealed By Multipulse Spectroscopy. Journal of Physical Chemistry B, 119(16):5184--5193, 2015. [ bib | DOI | www: ]
[20] Jingyi Zhu, Jocelyne Vreede, Marijke Hospes, Jos Arents, John T. M. Kennis, Ivo H. M. van Stokkum, Klaas J. Hellingwerf, and Marie Louise Groot. Short hydrogen bonds and negative charge in photoactive yellow protein promote fast isomerization but not high quantum yield. The Journal of Physical Chemistry B, 119(6):2372--2383, 2015. [ bib | DOI | arXiv | www: ]
[21] Lucyna M. Wlodarczyk, Joris J. Snellenburg, Janne A. Ihalainen, Rienk van Grondelle, Ivo H.M. van Stokkum, and Jan P. Dekker. Functional rearrangement of the light-harvesting antenna upon state transitions in a green alga. Biophysical Journal, 108(2):261 -- 271, 2015. [ bib | DOI | http ]
[22] Charusheela Ramanan, Rudi Berera, Kathi Gundermann, Ivo van Stokkum, Claudia Büchel, and Rienk van Grondelle. Exploring the mechanism(s) of energy dissipation in the light harvesting complex of the photosynthetic algae cyclotella meneghiniana. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1837(9):1507 -- 1513, 2014. [ bib | DOI | http ]
[23] Tilo Mathes, Ivo H.M. van Stokkum, and John T.M. Kennis. Photoactivation mechanisms of flavin-binding photoreceptors revealed through ultrafast spectroscopy and global analysis methods. In Stefan Weber and Erik Schleicher, editors, Flavins and Flavoproteins, volume 1146 of Methods in Molecular Biology, pages 401--442. Springer New York, 2014. [ bib | DOI | http ]
[24] Ivo H.M. Stokkum and Sergey P. Laptenok. Quantitative fluorescence spectral analysis of protein denaturation. In Yves Engelborghs and Antonie J.W.G. Visser, editors, Fluorescence Spectroscopy and Microscopy, volume 1076 of Methods in Molecular Biology, pages 43--51. Humana Press, 2014. [ bib | DOI | http ]
[25] M. Maiuri, J. J. Snellenburg, I. H. M. van Stokkum, S. Pillai, K. Wong Carter, D. Gust, T. A. Moore, A. L. Moore, R. van Grondelle, G. Cerullo, and D. Polli. Ultrafast Energy Transfer and Excited State Coupling in an Artificial Photosynthetic Antenna. The Journal of Physical Chemistry B, 117(46):14183--14190, 2013. [ bib | DOI ]
[26] Petar H. Lambrev, Yuliya Miloslavina, Ivo H. M. van Stokkum, Andreas D. Stahl, Maciej Michalik, Anna Susz, Jedrzej Tworzydlo, Joanna Fiedor, Gabriella Huhn, Marie-Louise Groot, Rienk van Grondelle, Gyözö Garab, and Leszek Fiedor. Excitation energy trapping and dissipation by Ni-substituted bacteriochlorophyll a in reconstituted LH1 complexes from Rhodospirillum rubrum. The Journal of Physical Chemistry B, 117(38):11260--11271, 2013. [ bib | DOI | arXiv | http ]
[27] Ivo H.M. van Stokkum, Thibaut E. Desquilbet, Chantal D. van der Weij-de Wit, Joris J. Snellenburg, Rienk van Grondelle, Jean-Claude Thomas, Jan P. Dekker, and Bruno Robert. Energy transfer and trapping in red-chlorophyll-free Photosystem I from Synechococcus WH 7803. The Journal of Physical Chemistry B, 117(38):11176--11183, 2013. [ bib | DOI | arXiv | http ]
[28] René M. Williams, Nguyen Van Anh, and Ivo H. M. van Stokkum. Triplet formation by charge recombination in thin film blends of perylene red and pyrene: Developing a target model for the photophysics of organic photovoltaic materials. The Journal of Physical Chemistry B, 117(38):11239--11248, 2013. [ bib | DOI | arXiv | http ]
[29] John T. M. Kennis, Ivo H. M. van Stokkum, Dayna S. Peterson, Anjali Pandit, and Rebekka M. Wachter. Ultrafast proton shuttling in Psammocora Cyan Fluorescent Protein. The Journal of Physical Chemistry B, 117(38):11134--11143, 2013. [ bib | DOI | arXiv | http ]
[30] Jingyi Zhu, Laura Paparelli, Marijke Hospes, Jos Arents, John T. M. Kennis, Ivo H. M. van Stokkum, Klaas J. Hellingwerf, and Marie Louise Groot. Photoionization and electron radical recombination dynamics in Photoactive Yellow Protein investigated by ultrafast spectroscopy in the visible and near-infrared spectral region. The Journal of Physical Chemistry B, 117(38):11042--11048, 2013. [ bib | DOI | arXiv | http ]
[31] Lijin Tian, Ivo H. M. van Stokkum, Rob B. M. Koehorst, and Herbert van Amerongen. Light harvesting and blue-green light induced non-photochemical quenching in two different C-Phycocyanin mutants of Synechocystis PCC 6803. The Journal of Physical Chemistry B, 117(38):11000--11006, 2013. [ bib | DOI | arXiv | http ]
[32] R. Berera, M. Gwizdala, I. H. M. van Stokkum, D. Kirilovsky, and R. van Grondelle. Excited states of the inactive and active forms of the Orange Carotenoid Protein. Journal of Physical Chemistry B, 117(31):9121--9128, 2013. [ bib | DOI ]
[33] Joris J. Snellenburg, Jan P. Dekker, Rienk van Grondelle, and Ivo H. M. van Stokkum. Functional compartmental modeling of the photosystems in the thylakoid membrane at 77 K. The Journal of Physical Chemistry B, 117(38):11363--11371, 2013. [ bib | DOI ]
[34] J. Y. Zhu, I. H. M. van Stokkum, L. Paparelli, M. R. Jones, and M. L. Groot. Early bacteriopheophytin reduction in charge separation in reaction centers of rhodobacter sphaeroides. Biophysical Journal, 104(11):2493--2502, 2013. [ bib | DOI ]
[35] T. Mathes, I. H. M. van Stokkum, M. Stierl, and J. T. M. Kennis. Redox modulation of flavin and tyrosine determines photoinduced proton-coupled electron transfer and photoactivation of BLUF photoreceptors. Journal of Biological Chemistry, 287(38):31725--31738, 2012. [ bib | DOI ]
[36] Joris J. Snellenburg, Sergey P. Laptenok, Ralf Seger, Katharine M. Mullen, and Ivo H. M. van Stokkum. Glotaran: a Java-based Graphical User Interface for the R-package TIMP. Journal of Statistical Software, 49(3):1--22, 2012. [ bib | http ]
[37] B. van Oort, M. J. T. ter Veer, M. L. Groot, and I. H. M. van Stokkum. Excited state proton transfer in strongly enhanced GFP (sGFP2). Physical Chemistry Chemical Physics, 14(25):8852--8858, 2012. [ bib | DOI ]
[38] S. P. Laptenok, I. H. M. van Stokkum, J. W. Borst, B. van Oort, A. J. W. G. Visser, and H. van Amerongen. Disentangling picosecond events that complicate the quantitative use of the calcium sensor YC3.60. The Journal of Physical Chemistry B, 116(9):3013--3020, 2012. [ bib | DOI ]
[39] Rudi Berera, Ivo H. M. van Stokkum, Michal Gwizdala, Adjélé Wilson, Diana Kirilovsky, and Rienk van Grondelle. The photophysics of the Orange Carotenoid Protein, a light-powered molecular switch. The Journal of Physical Chemistry B, 116(8):2568--2574, 2012. [ bib | DOI ]
[40] A. Marin, I. H. M. van Stokkum, V. I. Novoderezhkin, and R. van Grondelle. Excitation-induced polarization decay in the plant light-harvesting complex LHCII. Journal of Photochemistry and Photobiology A-Chemistry, 234:91--99, 2012. [ bib ]
[41] L. J. Tian, M. Gwizdala, I. H. M. van Stokkum, R. B. M. Koehorst, D. Kirilovsky, and H. van Amerongen. Picosecond kinetics of light harvesting and photoprotective quenching in wild-type and mutant phycobilisomes isolated from the cyanobacterium synechocystis PCC 6803. Biophysical Journal, 102(7):1692--1700, 2012. [ bib ]
[42] T. Mathes, J. Y. Zhu, I. H. M. van Stokkum, M. L. Groot, P. Hegemann, and J. T. M. Kennis. Hydrogen bond switching among flavin and amino acids determines the nature of proton-coupled electron transfer in bluf photoreceptors. Journal of Physical Chemistry Letters, 3(2):203--208, 2012. [ bib ]
[43] A. D. Stahl, L. I. Crouch, M. R. Jones, I. Stokkum, R. Van Grondelle, and M. L. Groot. Role of pufx in photochemical charge separation in the RC-LH1 complex from rhodobacter sphaeroides: An ultrafast mid-ir pump-probe investigation. Journal of Physical Chemistry B, 116(1):434--444, 2012. [ bib ]
[44] O. A. Sytina, I. H. M. van Stokkum, D. J. Heyes, C. N. Hunter, and M. L. Groot. Spectroscopic characterization of the first ultrafast catalytic intermediate in protochlorophyllide oxidoreductase. Physical Chemistry Chemical Physics, 14(2):616--625, 2012. [ bib ]
[45] Xiyi Chen, Delmar S. Larsen, Stephen E. Bradforth, and Ivo H. M. van Stokkum. Broadband spectral probing revealing ultrafast photochemical branching after ultraviolet excitation of the aqueous phenolate anion. The Journal of Physical Chemistry A, 115(16):3807--3819, Apr 28 2011. [ bib | DOI | arXiv | http ]
[46] Mariangela Di Donato, Andreas D. Stahl, Ivo H. M. van Stokkum, Rienk van Grondelle, and Marie-Louise Groot. Cofactors involved in light-driven charge separation in photosystem I identified by subpicosecond infrared spectroscopy. Biochemistry, 50(4):480--490, 2011. [ bib | DOI | arXiv | http ]
[47] Sergey P. Laptenok, Nina V. Visser, Ruchira Engel, Adrie H. Westphal, Arie van Hoek, Carlo P. M. Van Mierlo, Ivo H.M. van Stokkum, Herbert van Amerongen, and Antonie J. W. G. Visser. A general approach to detect folding intermediates from steady-state and time-resolved fluorescence of single tryptophan-containing proteins. Biochemistry, 50(17):3441--3450, May 3 2011. [ bib | DOI | arXiv | http ]
[48] Alessandro Marin, Francesca Passarini, Ivo H. M. van Stokkum, Rienk van Grondelle, and Roberta Croce. Minor Complexes at Work: Light-Harvesting by Carotenoids in the Photosystem II Antenna Complexes CP24 and CP26. Biophysical Journal, 100(11):2829--2838, Jun 8 2011. [ bib | DOI ]
[49] Tilo Mathes, Ivo H. M. van Stokkum, Cosimo Bonetti, Peter Hegemann, and John T. M. Kennis. The Hydrogen-Bond Switch Reaction of the Blrb Bluf Domain of Rhodobacter sphaeroides. Journal of Physical Chemistry B, 115(24):7963--7971, Jun 23 2011. [ bib | DOI ]
[50] Elisabet Romero, Ivo H. M. van Stokkum, Jan P. Dekker, and Rienk van Grondelle. Ultrafast carotenoid band shifts correlated with Chl(z) excited states in the photosystem II reaction center: are the carotenoids involved in energy transfer? Physical Chemistry Chemical Physics, 13(13):5573--5575, 2011. [ bib | DOI ]
[51] Alisa B. Rupenyan, Jocelyne Vreede, Ivo H. M. van Stokkum, Marijke Hospes, John T. M. Kennis, Klaas J. Hellingwerf, and Marie Louise Groot. Proline 68 Enhances Photoisomerization Yield in Photoactive Yellow Protein. Journal of Physical Chemistry B, 115(20):6668--6677, May 26 2011. [ bib | DOI ]
[52] Ivo H. M. van Stokkum, Magdalena Gauden, Sean Crosson, Rienk van Grondelle, Keith Moffat, and John T. M. Kennis. The Primary Photophysics of the Avena sativa Phototropin 1 LOV2 Domain Observed with Time-resolved Emission Spectroscopy. Photochemistry and Photobiology, 87(3):534--541, May-jun 2011. [ bib | DOI ]
[53] Olga A. Sytina, Ivo H. M. van Stokkum, Rienk van Grondelle, and Marie Louise Groot. Single and multi-exciton dynamics in aqueous protochlorophyllide aggregates. The Journal of Physical Chemistry A, 115(16):3936--3946, Apr 28 2011. [ bib | DOI | arXiv | http ]
[54] K. C. Toh, Emina A. Stojkovic, Ivo H. M. van Stokkum, Keith Moffat, and John T. M. Kennis. Fluorescence quantum yield and photochemistry of bacteriophytochrome constructs. Physical Chemistry Chemical Physics, 13(25):11985--11997, 2011. [ bib | DOI ]
[55] K. C. Toh, Emina A. Stojković, Alisa B. Rupenyan, Ivo H. M. van Stokkum, Marian Salumbides, Marie-Louise Groot, Keith Moffat, and John T. M. Kennis. Primary reactions of bacteriophytochrome observed with ultrafast mid-infrared spectroscopy. The Journal of Physical Chemistry A, 115(16):3778--3786, Apr 28 2011. [ bib | DOI | arXiv | http ]
[56] Emilie Wientjes, Ivo H.M. van Stokkum, Herbert van Amerongen, and Roberta Croce. Excitation-energy transfer dynamics of higher plant photosystem I light-harvesting complexes. Biophysical Journal, 100(5):1372 -- 1380, 2011. [ bib | DOI | http ]
[57] C. D. van der Weij-de Wit, J. P. Dekker, R. van Grondelle, and I. H. M. van Stokkum. Charge Separation is Virtually Irreversible in Photosystem II Core Complexes with Oxidized Primary Quinone Acceptor. Journal of Physical Chemistry A, 115(16):3947--3956, APR 28 2011. [ bib | DOI ]
[58] Emilie Wientjes, Ivo H. M. van Stokkum, Herbert van Amerongen, and Roberta Croce. The role of the individual Lhcas in Photosystem I excitation energy trapping. Biophysical Journal, 101(3):745--754, 2011. [ bib ]
[59] A. Marin, A. B. Doust, G. D. Scholes, K. E. Wilk, P. M. G. Curmi, I. H. M. van Stokkum, and R. van Grondelle. Flow of excitation energy in the cryptophyte light-harvesting antenna phycocyanin 645. Biophysical Journal, 101(4):1004--1013, 2011. [ bib ]
[60] A. D. Stahl, M. Hospes, K. Singhal, I. van Stokkum, R. van Grondelle, M. L. Groot, and K. J. Hellingwerf. On the involvement of single-bond rotation in the primary photochemistry of photoactive yellow protein. Biophysical Journal, 101(5):1184--1192, 2011. [ bib ]
[61] L. J. Tian, I. H. M. van Stokkum, R. B. M. Koehorst, A. Jongerius, D. Kirilovsky, and H. van Amerongen. Site, rate, and mechanism of photoprotective quenching in cyanobacteria. Journal of the American Chemical Society, 133(45):18304--18311, 2011. [ bib ]
[62] M. Di Donato, Ljgw van Wilderen, I. H. M. Van Stokkum, T. C. Stuart, J. T. M. Kennis, K. J. Hellingwerf, R. van Grondelle, and M. L. Groot. Proton transfer events in gfp. Physical Chemistry Chemical Physics, 13(36):16295--16305, 2011. [ bib ]
[63] Rudi Berera, Ivo H. M. van Stokkum, John T.M. Kennis, Rienk van Grondelle, and Jan P. Dekker. The light-harvesting function of carotenoids in the cyanobacterial stress-inducible IsiA complex. Chemical Physics, 373(1-2):65--70, 2010. [ bib | DOI | http ]
[64] C. Bonetti, M. T. A. Alexandre, I. H. M. van Stokkum, R. G. Hiller, M. L. Groot, R. van Grondelle, and J. T. M. Kennis. Identification of excited-state energy transfer and relaxation pathways in the peridinin-chlorophyll complex: an ultrafast mid-infrared study. Physical Chemistry Chemical Physics, 12(32):9256--9266, 2010. [ bib ]
[65] E. C. Carroll, S. H. Song, M. Kumauchi, I. H. M. van Stokkum, A. Jailaubekov, W. D. Hoff, and D. S. Larsen. Subpicosecond excited-state proton transfer preceding isomerization during the photorecovery of photoactive yellow protein. Journal of Physical Chemistry Letters, 1(19):2793--2799, 2010. [ bib ]
[66] Wojciech Giera, V.M. Ramesh, Andrew N. Webber, Ivo van Stokkum, Rienk van Grondelle, and Krzysztof Gibasiewicz. Effect of the P700 pre-oxidation and point mutations near A0 on the reversibility of the primary charge separation in photosystem I from Chlamydomonas reinhardtii. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1797(1):106 -- 112, 2010. [ bib | DOI | http ]
[67] Joost de Klerk, Ivo H. M. van Stokkum, Anna Szemik-Hojniak, Irena Deperasinska, Cees Gooijer, Hong Zhang, Wybren-Jan Buma, and Freek Ariese. Excited state processes of 2-butylamino-6-methyl-4-nitropyridine n-oxide in nonpolar solvents. a transient absorption spectroscopy study. The Journal of Physical Chemistry A, 114(12):4045--4050, 2010. [ bib | DOI ]
[68] R. B. M. Koehorst, S. Laptenok, B. van Oort, A. van Hoek, R. B. Spruijt, I. H. M. van Stokkum, H. van Amerongen, and M. A. Hemminga. Profiling of dynamics in protein-lipid-water systems: a time-resolved fluorescence study of a model membrane protein with the label badan at specific membrane depths. European Biophysics Journal with Biophysics Letters, 39(4):647--656, 2010. [ bib ]
[69] Sergey Laptenok, Jan Willem Borst, Katharine M. Mullen, Ivo H. M. van Stokkum, Antonie J. W. G. Visser, and Herbert van Amerongen. Global analysis of Förster resonance energy transfer in live cells measured by fluorescence lifetime imaging microscopy exploiting the rise time of acceptor fluorescence. Physical Chemistry Chemical Physics, 12:7593--7602, 2010. [ bib ]
[70] Katharine M. Mullen and Ivo H. M. van Stokkum. Exponential models for time-resolved spectroscopy data. In Victor Pereyra and Godela Scherer, editors, Exponential Data Fitting and its Applications, pages 110--127. Bentham, 2010. [ bib ]
[71] Natalia P. Pawlowicz, Ivo H. M. van Stokkum, Jacques Breton, Rienk van Grondelle, and Michael R. Jones. An investigation of slow charge separation in a tyrosine M210 to tryptophan mutant of the rhodobacter sphaeroides reaction center by femtosecond mid-infrared spectroscopy. Physical Chemistry Chemical Physics, 12(11):2693--2705, 2010. [ bib | DOI ]
[72] E. Romero, I. H. M. van Stokkum, V. I. Novoderezhkin, J. P. Dekker, and R. van Grondelle. Two different charge separation pathways in photosystem II. Biochemistry, 49(20):4300--4307, 2010. [ bib ]
[73] O. A. Sytina, I. H. M. van Stokkum, D. J. Heyes, C. N. Hunter, R. van Grondelle, and M. L. Groot. Protochlorophyllide excited-state dynamics in organic solvents studied by time-resolved visible and mid-infrared spectroscopy. Journal of Physical Chemistry B, 114(12):4335--4344, 2010. [ bib ]
[74] K. C. Toh, E. A. Stojković, I. H. M. van Stokkum, K. Moffat, and J. T. M. Kennis. Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome. Proceedings of the National Academy of Sciences of the United States of America, 107(20):9170--9175, 2010. [ bib ]
[75] Peter D. Zoon, Ivo H. M. van Stokkum, Manuel Parent, Olivier Mongin, Mireille Blanchard-Desce, and Albert M. Brouwer. Fast photo-processes in triazole-based push-pull systems. Physical Chemistry Chemical Physics, 12(11):2706--2715, 2010. [ bib | DOI ]
[76] Rudi Berera, Ivo H. M. van Stokkum, Sandrine d'Haene, John T. M. Kennis, Rienk van Grondelle, and Jan P. Dekker. A mechanism of energy dissipation in cyanobacteria. Biophysical Journal, 96(6):2261--2267, 2009. [ bib | http ]
[77] Cosimo Bonetti, Manuela Stierl, Tilo Mathes, Ivo H. M. van Stokkum, Katharine M. Mullen, Thomas A. Cohen-Stuart, Rienk van Grondelle, Peter Hegemann, and John T. M. Kennis. The role of key amino acids in the photoactivation pathway of the synechocystis slr1694 bluf domain. Biochemistry, 48(48):11458--11469, 2009. [ bib | DOI ]
[78] Katharine M. Mullen and Ivo H. M. van Stokkum. The variable projection algorithm in time-resolved spectroscopy, microscopy and mass spectrometry applications. Numerical Algorithms, 51:319--340, 2009. [ bib ]
[79] Natalia P. Pawlowicz, Ivo H. M. van Stokkum, Jacques Breton, Rienk van Grondelle, and Michael R. Jones. Identification of the intermediate charge-separated state P+βL- in a leucine M214 to histidine mutant of the Rhodobacter sphaeroides reaction center using femtosecond midinfrared spectroscopy. Biophysical Journal, 96(12):4956 -- 4965, 2009. [ bib | DOI | http ]
[80] Elisabet Romero, Milena Mozzo, Ivo H. M. van Stokkum, Jan P. Dekker, Rienk van Grondelle, and Roberta Croce. The origin of the low-energy form of photosystem I light-harvesting complex Lhca4: Mixing of the lowest exciton with a charge-transfer state. Biophysical Journal, 96(5):L35 -- L37, 2009. [ bib | DOI | http ]
[81] Alisa Rupenyan, Ivo H. M. van Stokkum, Jos C. Arents, Rienk van Grondelle, Klaas J. Hellingwerf, and Marie Louise Groot. Reaction pathways of photoexcited retinal in proteorhodopsin studied by Pump-Dump-Probe spectroscopy. The Journal of Physical Chemistry B, 113(50):16251--16256, 2009. [ bib | DOI ]
[82] Andreas D. Stahl, Mariangela Di Donato, Ivo van Stokkum, Rienk van Grondelle, and Marie Louise Groot. A femtosecond visible/visible and visible/mid-infrared transient absorption study of the light harvesting complex II. Biophysical Journal, 97(12):3215 -- 3223, 2009. [ bib | DOI | http ]
[83] Ivo H. M. van Stokkum, Katharine M. Mullen, and Velitchka V. Mihaleva. Global analysis of multiple gas chromatography-mass spectrometry (GC/MS) data sets: A method for resolution of co-eluting components with comparison to MCR-ALS. Chemometrics and Intelligent Laboratory Systems, 95(2):150 -- 163, 2009. [ bib | DOI | http ]
[84] Ivo H. M. van Stokkum, Emmanouil Papagiannakis, Mikas Vengris, Jante M. Salverda, Tomás Polívka, Donatas Zigmantas, Delmar S. Larsen, Stefania S. Lampoura, Roger G. Hiller, and Rienk van Grondelle. Inter-pigment interactions in the peridinin chlorophyll protein studied by global and target analysis of time resolved absorption spectra. Chemical Physics, 357(1-3):70 -- 78, 2009. [ bib | DOI | http ]
[85] Leonas Valkunas, Ivo H. M. van Stokkum, Rudi Berera, and Rienk van Grondelle. Exciton migration and fluorescence quenching in LHCII aggregates: Target analysis using a simple nonlinear annihilation scheme. Chemical Physics, 357(1-3):17 -- 20, 2009. [ bib | DOI | http ]
[86] Nguyen Van Anh, Felix Schlosser, Michiel M. Groeneveld, Ivo H. M. van Stokkum, Frank Würthner, and René M. Williams. Photoinduced interactions in a pyrene-calix[4]arene-perylene bisimide dye system: Probing ground-state conformations with excited-state dynamics of charge separation and recombination. The Journal of Physical Chemistry C, 113(42):18358--18368, 2009. [ bib | DOI ]
[87] Luuk J. G. W. van Wilderen, Jason M. Key, Ivo H. M. van Stokkum, Rienk van Grondelle, and Marie-Louise Groot. Dynamics of Carbon Monoxide Photodissociation in Bradyrhizobium japonicum FixL Probed by Picosecond Midinfrared Spectroscopy. Journal of Physical Chemistry B, 113(11):3292--3297, 2009. [ bib ]
[88] Cosimo Bonetti, Tilo Mathes, Ivo H. M. van Stokkum, Katharine M. Mullen, Marie-Louise Groot, Rienk van Grondelle, Peter Hegemann, and John T.M. Kennis. Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy. Biophysical Journal, 95:4790--4802, 2008. [ bib | http ]
[89] C. Hippius, I. H. M. van Stokkum, M. Gsänger, M.M. Groeneveld, R.M. Williams, and F. Würthner. Sequential FRET processes in calix[4]arene-linked orange-red-green perylene bisimide dye zigzag arrays. Journal of Physical Chemistry C, 112(7):2476--2486, 2008. [ bib | http ]
[90] Catharina Hippius, Ivo H. M. van Stokkum, Ennio Zangrando, René M. Williams, Michael Wykes, David Beljonne, and Frank Würthner. Ground- and excited-state pinched cone equilibria in calix[4]arenes bearing two perylene bisimide dyes. Journal of Physical Chemistry C, 112(37):14626--14638, 2008. [ bib | http ]
[91] Natalia P. Pawlowicz, Rienk van Grondelle, Ivo H. M. van Stokkum, Jacques Breton, Michael R. Jones, and Marie Louise Groot. Identification of the First Steps in Charge Separation in Bacterial Photosynthetic Reaction Centers of Rhodobacter sphaeroides by Ultrafast Mid-Infrared Spectroscopy: Electron Transfer and Protein Dynamics. Biophys. J., 95(3):1268--1284, 2008. [ bib | DOI | arXiv | http ]
[92] Alisa Rupenyan, Ivo H. M. van Stokkum, Jos C. Arents, Rienk van Grondelle, Klaas Hellingwerf, and Marie Louise Groot. Characterization of the Primary Photochemistry of Proteorhodopsin with Femtosecond Spectroscopy. Biophys. J., 94(10):4020--4030, 2008. [ bib | DOI | arXiv | http ]
[93] I. H. M. van Stokkum, B. van Oort, F. van Mourik, B. Gobets, and H. van Amerongen. (Sub)-Picosecond Spectral Evolution of Fluorescence Studied with a Synchroscan Streak-Camera System and Target Analysis. In Thijs J. Aartsma and Jörg Matysik, editors, Biophysical Techniques in Photosynthesis, Volume II, Series Advances in Photosynthesis and Respiration, volume 26, pages 223--240. Springer, Dordrecht, 2008. [ bib | http ]
[94] Olga A. Sytina, Derren J. Heyes, C. Neil Hunter, Maxime T. Alexandre, Ivo H. M. van Stokkum, Rienk van Grondelle, and Marie-Louise Groot. Conformational changes in an ultrafast light-driven enzyme determine catalytic activity. Nature, 456(7224):1001--1004, 2008. [ bib | .html ]
[95] K. C. Toh, Ivo H. M. van Stokkum, Johnny Hendriks, Maxime T. A. Alexandre, J. C. Arents, Marcela Avila Perez, Rienk van Grondelle, Klaas J. Hellingwerf, and John T. M. Kennis. On the Signaling Mechanism and the Absence of Photoreversibility in the AppA BLUF Domain. Biophys. J., 95(1):312--321, 2008. [ bib | DOI | arXiv | http ]
[96] Chantal D. van der Weij-De Wit, Alexander B. Doust, Ivo H. M. van Stokkum, Jan P. Dekker, Krystyna E. Wilk, Paul M. G. Curmi, and Rienk van Grondelle. Phycocyanin Sensitizes both Photosystem I and Photosystem II in Cryptophyte Chroomonas CCMP270 Cells. Biophys. J., 94(6):2423--2433, 2008. [ bib | DOI | arXiv | http ]
[97] Maxime T. A. Alexandre, Daniel C. Lührs, Ivo H. M. van Stokkum, Roger Hiller, Marie-Louise Groot, John T. M. Kennis, and Rienk van Grondelle. Triplet State Dynamics in Peridinin-Chlorophyll-a-Protein: A New Pathway of Photoprotection in LHCs? Biophys. J., 93(6):2118--2128, 2007. [ bib | DOI | arXiv | http ]
[98] R. Berera, I. H. M. van Stokkum, G. Kodis, A.E. Keirstead, S. Pillai, C. Herrero, R.E. Palacios, M. Vengris, R. van Grondelle, D. Gust, T.A. Moore, A.L. Moore, and J.T.M. Kennis. Energy transfer, excited-state deactivation, and exciplex formation in artificial caroteno-phthalocyanine light-harvesting antennas. Journal of Physical Chemistry B, 111(24):6868--6877, 2007. [ bib | http ]
[99] Thomas W. Binsl, Katharine M. Mullen, Ivo H. M. van Stokkum, Jaap Heringa, and Johannes H. G. M. van Beek. FluxSimulator: An R package to simulate isotopomer distributions in metabolic networks. Journal of Statistical Software, 18(7), 2007. [ bib | http ]
[100] M. DiDonato, R. van Grondelle, I. H. M. van Stokkum, and M.L. Groot. Excitation energy transfer in the photosystem II core antenna complex cp43 studied by femtosecond visible/visible and visible/mid-infrared pump probe spectroscopy. Journal of Physical Chemistry B, 111(25):7345--7352, 2007. [ bib | http ]
[101] M. Gauden, J.S. Grinstead, W. Laan, I. H. M. van Stokkum, M. Avila-Perez, K.C. Toh, R. Boelens, R. Kaptein, R. van Grondelle, K.J. Hellingwerf, and J.T.M. Kennis. On the role of aromatic side chains in the photoactivation of bluf domains. Biochemistry, 46(25):7405--7415, 2007. [ bib | http ]
[102] C. Hippius, I. H. M. van Stokkum, E. Zangrando, R.M. Williams, and F. Würthner. Excited state interactions in calix[4]arene-perylene bisimide dye conjugates: Global and target analysis of supramolecular building blocks. Journal of Physical Chemistry C, 111(37):13988--13996, 2007. [ bib | http ]
[103] Janne A. Ihalainen, Jens Bredenbeck, Rolf Pfister, Jan Helbing, Lei Chi, Ivo H. M. van Stokkum, G. Andrew Woolley, and Peter Hamm. Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds. Proceedings of the National Academy of Sciences, 104(13):5383--5388, 2007. [ bib | DOI | arXiv | http ]
[104] Sergey Laptenok, Katharine M. Mullen, Jan Willem Borst, Ivo H. M. van Stokkum, Vladimir V. Apanasovich, and Antonie J. W. G. Visser. Fluorescence lifetime imaging microscopy (FLIM) data analysis with TIMP. Journal of Statistical Software, 18(8), 2007. [ bib | http ]
[105] Katharine M. Mullen and Ivo H. M. van Stokkum. An introduction to the special volume “Spectroscopy and Chemometrics in R”. Journal of Statistical Software, 18(1), 2007. [ bib | http ]
[106] Katharine M. Mullen and Ivo H. M. van Stokkum. TIMP: an R package for modeling multi-way spectroscopic measurements. Journal of Statistical Software, 18(3), 2007. [ bib | http ]
[107] Katharine M. Mullen, Mikas Vengris, and Ivo H. M. van Stokkum. Algorithms for separable nonlinear least squares with application to modelling time-resolved spectra. Journal of Global Optimization, 38:201--213, 2007. [ bib ]
[108] N. P. Pawlowicz, M.-L. Groot, I. H. M. van Stokkum, J. Breton, and R. van Grondelle. Charge Separation and Energy Transfer in the Photosystem II Core Complex Studied by Femtosecond Midinfrared Spectroscopy. Biophys. J., 93(8):2732--2742, 2007. [ bib | DOI | arXiv | http ]
[109] I. Petkova, M.S. Mudadu, A. Singh, R.P. Thummel, I. H. M. van Stokkum, W.J. Buma, and J. Waluk. Structure and photophysics of 2-(2'-pyridyl)benzindoles: The role of intermolecular hydrogen bonds. Journal of Physical Chemistry A, 111(45):11400--11409, 2007. [ bib | http ]
[110] Alexander V. Ruban, Rudi Berera, Cristian Ilioaia, Ivo H. M. van Stokkum, John T. M. Kennis, Andrew A. Pascal, Herbert van Amerongen, Bruno Robert, Peter Horton, and Rienk van Grondelle. Identification of a mechanism of photoprotective energy dissipation in higher plants. Nature, 450(7169):575--578, 2007. [ bib | .html ]
[111] Victor Arni D. P. Sicam, Joris J. Snellenburg, Rob G. L. Van Der Heijde, and Ivo H. M. Van Stokkum. Pseudo Forward Ray-Tracing: A New Method for Surface Validation in Cornea Topography. Optometry & Vision Science, 84(9):E915--E923, 2007. [ bib | http | Abstract ]
[112] J. Baffreau, S. Leroy-Lhez, P. Hudhomme, M.M. Groeneveld, I. H. M. van Stokkum, and R.M. Williams. Superabsorbing fullerenes: Spectral and kinetic characterization of photoinduced interactions in perylenediimide-fullerene-C60 dyads. Journal of Physical Chemistry A, 110(49):13123--13125, 2006. [ bib | http ]
[113] Rudi Berera, Christian Herrero, Ivo H. M. van Stokkum, Mikas Vengris, Gerdenis Kodis, Rodrigo E. Palacios, Herbert van Amerongen, Rienk van Grondelle, Devens Gust, Thomas A. Moore, Ana L. Moore, and John T. M. Kennis. A simple artificial light-harvesting dyad as a model for excess energy dissipation in oxygenic photosynthesis. PNAS, 103(14):5343--5348, 2006. [ bib | DOI | http ]
[114] Rudi Berera, Gary F. Moore, Ivo H. M. van Stokkum, Gerdenis Kodis, Paul A. Liddell, Miguel Gervaldo, Rienk van Grondelle, John T. M. Kennis, Devens Gust, Thomas A. Moore, and Ana L. Moore. Charge separation and energy transfer in a caroteno-C60 dyad: photoinduced electron transfer from the carotenoid excited states. Photochem. Photobiol. Sci., 5:1142--1149, 2006. [ bib ]
[115] Magdalena Gauden, Ivo H. M. van Stokkum, Jason M. Key, Daniel Ch. Lührs, Rienk van Grondelle, Peter Hegemann, and John T. M. Kennis. Hydrogen-bond switching through a radical pair mechanism in a flavin-binding photoreceptor. PNAS, 103(29):10895--10900, 2006. [ bib | DOI | http ]
[116] Miguel A. Palacios, Joerg Standfuss, Mikas Vengris, , Bart F. van Oort, Ivo H. M. van Stokkum, Werner Kühlbrandt, Herbert van Amerongen, and Rienk van Grondelle. A comparison of the three isoforms of the light-harvesting complex II using transient absorption and time-resolved fluorescence measurements. Photosynthesis Research, 88(3):269--285, 2006. [ bib | http ]
[117] E. Papagiannakis, I. H. M. van Stokkum, M. Vengris, R.J. Cogdell, R. van Grondelle, and D.S. Larsen. Excited-state dynamics of carotenoids in light-harvesting complexes. 1. exploring the relationship between the S1 and S* states. Journal of Physical Chemistry B, 110(11):5727--5736, 2006. [ bib | http ]
[118] E. Papagiannakis, M. Vengris, D.S. Larsen, I. H. M. van Stokkum, R.G. Hiller, and R. van Grondelle. Use of ultrafast dispersed pump-dump-probe and pump-repump-probe spectroscopies to explore the light-induced dynamics of peridinin in solution. Journal of Physical Chemistry B, 110(1):512--521, 2006. [ bib | http ]
[119] Raul Perez-Ruiz, Michiel Groeneveld, Ivo H. M. van Stokkum, Rosa Tormos, René M. Williams, and Miguel A. Miranda. Fast transient absorption spectroscopy of the early events in photoexcited chiral benzophenone-naphthalene dyads. Chemical Physics Letters, 429:276--281, Sep 2006. [ bib | http ]
[120] T. Polívka, I. H. M. van Stokkum, D. Zigmantas, R. van Grondelle, V. Sundström, and R.G. Hiller. Energy transfer in the major intrinsic light-harvesting complex from Amphidinium carterae. Biochemistry, 45(28):8516--8526, 2006. [ bib | http ]
[121] Ivo H. M. van Stokkum and Henri E. Bal. A problem solving environment for interactive modelling of multiway data. Concurrency and computation: practice and experience, 18:263--269, 2006. [ bib ]
[122] I. H. M. van Stokkum, B. Gobets, T. Gensch, F. van Mourik, K. J. Hellingwerf, R. van Grondelle, and J. T. M. Kennis. Symposium-in-print: Green fluorescent protein and homologs. (sub)-picosecond spectral evolution of fluorescence in photoactive proteins studied with a synchroscan streak camera system. Photochemistry and Photobiology, 82:380--388, 2006. [ bib ]
[123] C.D. van der Weij-DeWit, A.B. Doust, I. H. M. van Stokkum, J.P. Dekker, K.E. Wilk, P.M.G. Curmi, G.D. Scholes, and R. van Grondelle. How energy funnels from the phycoerythrin antenna complex to photosystem I and photosystem II in cryptophyte rhodomonas CS24 cells. Journal of Physical Chemistry B, 110(49):25066--25073, 2006. [ bib | http ]
[124] L. J. G. W. van Wilderen, M. A. van der Horst, I. H. M. van Stokkum, K. J. Hellingwerf, R. van Grondelle, and M. L. Groot. Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein. PNAS, 103(41):15050--15055, 2006. [ bib | DOI | http ]
[125] Sergey Yeremenko, Ivo H. M. van Stokkum, Keith Moffat, and Klaas J. Hellingwerf. Influence of the Crystalline State on Photoinduced Dynamics of Photoactive Yellow Protein Studied by Ultraviolet-Visible Transient Absorption Spectroscopy. Biophysical Journal, 90(11):4224--4235, 2006. [ bib | DOI | http ]
[126] Katharine M. Mullen, Mikas Vengris, and Ivo H. M. van Stokkum. Separable nonlinear models for time-resolved spectra. In I. García, L. G. Casado, E.M.T. Hendrix, and B. Tóth, editors, Proceedings of the International Workshop on Global Optimization, pages 183--188, September 2005. [ bib ]
[127] G. Balkowski, A. Szemik-Hojniak, I. H. M. van Stokkum, H. Zhang, and W.J. Buma. Femtosecond excited state studies of the two-center three-electron bond driven twisted internal charge transfer dynamics in 1,8-bis(dimethylamino)naphthalene. Journal of Physical Chemistry A, 109(16):3535--3541, 2005. [ bib | http ]
[128] Wim P. Cofino, Ivo H. M. van Stokkum, Jaap van Steenwijk, and David E. Wells. A new model for the inference of population characteristics from experimental data using uncertainties: Part II. application to censored datasets. Analytica Chimica Acta, 533:31--39, Mar 2005. [ bib | http ]
[129] A.B. Doust, I. H. M. van Stokkum, D.S. Larsen, K.E. Wilk, P.M.G. Curmi, R. van Grondelle, and G.D. Scholes. Mediation of ultrafast light-harvesting by a central dimer in phycoerythrin 545 studied by transient absorption and global analysis. Journal of Physical Chemistry B, 109(29):14219--14226, 2005. [ bib | http ]
[130] M. Gauden, S. Yeremenko, W. Laan, I. H. M. van Stokkum, J.A. Ihalainen, R. van Grondelle, K.J. Hellingwerf, and J.T.M. Kennis. Photocycle of the flavin-binding photoreceptor appa, a bacterial transcriptional antirepressor of photosynthesis genes. Biochemistry, 44(10):3653--3662, 2005. [ bib | http ]
[131] K. Gibasiewicz, R. Croce, T. Morosinotto, J. A. Ihalainen, I. H. M. van Stokkum, J. P. Dekker, R. Bassi, and R. van Grondelle. Excitation Energy Transfer Pathways in Lhca4. Biophysical Journal, 88(3):1959--1969, 2005. [ bib | DOI | http ]
[132] Marie Louise Groot, Natalia P. Pawlowicz, Luuk J. G. W. van Wilderen, Jacques Breton, Ivo H. M. van Stokkum, and Rienk van Grondelle. Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy. PNAS, 102(37):13087--13092, 2005. [ bib | DOI | http ]
[133] M.A. van der Horst, I. H. M. van Stokkum, N.A. Dencher, and K.J. Hellingwerf. Controlled reduction of the humidity induces a shortcut recovery reaction in the photocycle of photoactive yellow protein. Biochemistry, 44(25):9160--9167, 2005. [ bib | http ]
[134] Janne A. Ihalainen, Frank Klimmek, Ulrika Ganeteg, Ivo H. M. van Stokkum, Rienk van Grondelle, Stefan Jansson, and Jan P. Dekker. Excitation energy trapping in photosystem I complexes depleted in Lhca1 and Lhca4. FEBS Letters, 579:4787--4791, Aug 2005. [ bib | http ]
[135] Janne A. Ihalainen, Ivo H. M. van Stokkum, Krzysztof Gibasiewicz, Marta Germano, Rienk van Grondelle, and Jan P. Dekker. Kinetics of excitation trapping in intact photosystem I of Chlamydomonas reinhardtii and Arabidopsis thaliana. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1706:267--275, Feb 2005. [ bib | http ]
[136] J.A. Ihalainen, R. Croce, T. Morosinotto, I. H. M. van Stokkum, R. Bassi, J.P. Dekker, and R. van Grondelle. Excitation decay pathways of Lhca proteins: A time-resolved fluorescence study. Journal of Physical Chemistry B, 109(44):21150--21158, 2005. [ bib | http ]
[137] Remco Kort, Andrea C. O'Brien, Ivo H. M. van Stokkum, Suus J. C. M. Oomes, Wim Crielaard, Klaas J. Hellingwerf, and Stanley Brul. Assessment of Heat Resistance of Bacterial Spores from Food Product Isolates by Fluorescence Monitoring of Dipicolinic Acid Release. Applied and Environmental Microbiology, 71(7):3556--3564, 2005. [ bib | http ]
[138] Emmanouil Papagiannakis, Delmar Larsen, Mikas Vengris, Ivo van Stokkum, and Rienk van Grondelle. Multi-pulse transient absorption and carotenoid excited-state dynamics: β-carotene. In Ultrafast Phenomena XIV, pages 592--594. 2005. [ bib | http ]
[139] Emmanouil Papagiannakis, Ivo H. M. van Stokkum, Holger Fey, Claudia Büchel, and Rienk van Grondelle. Spectroscopic characterization of the excitation energy transfer in the fucoxanthin-chlorophyll protein of diatoms. Photosynthesis Research, 86:241--250, 2005. [ bib | http ]
[140] A. Sautter, B.K. Kaletas, D.G. Schmid, R. Dobrawa, M. Zimine, G. Jung, I. H. M. van Stokkum, L. DeCola, R.M. Williams, and F. Würthner. Ultrafast energy-electron transfer cascade in a multichromophoric light-harvesting molecular square. Journal of the American Chemical Society, 127(18):6719--6729, 2005. [ bib | http ]
[141] Ivo H. M. van Stokkum. Global and target analysis of time-resolved spectra, lecture notes for the troisième cycle de la physique en suisse romande. Technical report, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands, 2005. [ bib | .pdf ]
[142] Mikas Vengris, Ivo van Stokkum, Xiang He, Alasdair Bell, Peter Tonge, Rienk van Grondelle, and Delmar Larsen. Ultrafast excited and ground-state isomerization dynamics of the green fluorescent protein chromophore in solution. In Ultrafast Phenomena XIV, pages 610--612. 2005. [ bib | http ]
[143] M. Gauden, S. Crosson, I. H. M. van Stokkum, R.van Grondelle, K. Moffat, and J.T.M. Kennis. Low-temperature and time-resolved spectroscopic characterization of the LOV2 domain of avena sativa phototropin. In Volume 5463 - Femtosecond Laser Applications in Biology, pages 97--104. Proceedings of SPIE, 2004. [ bib ]
[144] M. Germano, C. C. Gradinaru, A. Ya. Shkuropatov, I. H. M. van Stokkum, V. A. Shuvalov, J. P. Dekker, R. van Grondelle, and H. J. van Gorkom. Energy and Electron Transfer in Photosystem II Reaction Centers with Modified Pheophytin Composition. Biophysical Journal, 86(3):1664--1672, 2004. [ bib | http ]
[145] J.T.M. Kennis, I. H. M. van Stokkum, S. Crosson, M. Gauden, K. Moffat, and R. van Grondelle. The LOV2 domain of phototropin: A reversible photochromic switch. Journal of the American Chemical Society, 126(14):4512--4513, 2004. [ bib | http ]
[146] John T. M. Kennis, Delmar S. Larsen, Ivo H. M. van Stokkum, Mikas Vengris, Jasper J. van Thor, and Rienk van Grondelle. Uncovering the hidden ground state of green fluorescent protein. PNAS, 101(52):17988--17993, 2004. [ bib | DOI | http ]
[147] Delmar S. Larsen, Ivo H. M. van Stokkum, Mikas Vengris, Michael A. van der Horst, Frank L. de Weerd, Klaas J. Hellingwerf, and Rienk van Grondelle. Incoherent Manipulation of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy. Biophysical Journal, 87(3):1858--1872, 2004. [ bib | DOI | http ]
[148] Delmar S. Larsen, Mikas Vengris, Ivo H. M. van Stokkum, Michael A. van der Horst, Frank L. de Weerd, Klaas J. Hellingwerf, and Rienk van Grondelle. Photoisomerization and Photoionization of the Photoactive Yellow Protein Chromophore in Solution. Biophysical Journal, 86(4):2538--2550, 2004. [ bib | http ]
[149] Olaf F. A. Larsen, Ivo H. M. van Stokkum, Frank L. de Weerd, Mikas Vengris, Charuvila T. Aravindakumar, Rienk van Grondelle, Nicholas E. Geacintov, and Herbert van Amerongen. Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA duplexes. Physical Chemistry Chemical Physics, 6:154 -- 160, 2004. [ bib ]
[150] E. Papagiannakis, D.S. Larsen, I. H. M. van Stokkum, M. Vengris, R.G. Hiller, and R. van Grondelle. Resolving the excited state equilibrium of peridinin in solution. Biochemistry, 43(49):15303--15309, 2004. [ bib | http ]
[151] Ivo H. M. van Stokkum, Delmar S. Larsen, and Rienk van Grondelle. Global and target analysis of time-resolved spectra. Biochimica et Biophysica Acta, 1657:82--104, and erratum, 1658, 262, 2004. [ bib ]
[152] Ivo H. M. van Stokkum, Delmar S. Larsen, and Rienk van Grondelle. Erratum to ”Global and target analysis of time-resolved spectra” [Biochimica et Biophysica Acta 1658/2-3 (2004) 82-104]. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1658:262--262, Oct 2004. [ bib | http ]
[153] Ivo H. M. van Stokkum, Delmar S. Larsen, and Rienk van Grondelle. Global and target analysis of time-resolved spectra. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1657:82--104, Jul 2004. [ bib | http ]
[154] Frank Van Mourik, Marie-Louise Groot, Rienk Van Grondelle, Jan P. Dekker, and Ivo H. M. Van Stokkum. Global and target analysis of fluorescence measurements on photosystem 2 reaction centers upon red excitation . Physical Chemistry Chemical Physics, 6:4820 -- 4824, 2004. [ bib ]
[155] Mikas Vengris, Michael A. van der Horst, Goran Zgrablic, Ivo H. M. van Stokkum, Stefan Haacke, Majed Chergui, Klaas J. Hellingwerf, Rienk van Grondelle, and Delmar S. Larsen. Contrasting the Excited-State Dynamics of the Photoactive Yellow Protein Chromophore: Protein versus Solvent Environments. Biophysical Journal, 87(3):1848--1857, 2004. [ bib | DOI | http ]
[156] M. Vengris, I. H. M. van Stokkum, X. He, A.F. Bell, P.J. Tonge, R. van Grondelle, and D.S. Larsen. Ultrafast excited and ground-state dynamics of the green fluorescent protein chromophore in solution. Journal of Physical Chemistry A, 108(21):4587--4598, 2004. [ bib | http ]
[157] R.N. Frese, M. Germano, F.L. de Weerd, I. H. M. van Stokkum, A.Ya. Shkuropatov, V.A. Shuvalov, H.J. van Gorkom, R. van Grondelle, and J.P. Dekker. Electric field effects on the chlorophylls, pheophytins, and β-carotenes in the reaction center of photosystem II. Biochemistry, 42(30):9205--9213, 2003. [ bib | http ]
[158] Bas Gobets, Ivo H. M. van Stokkum, Frank van Mourik, Jan P. Dekker, and Rienk van Grondelle. Excitation Wavelength Dependence of the Fluorescence Kinetics in Photosystem I Particles from Synechocystis PCC 6803 and Synechococcus elongatus. Biophysical Journal, 85(6):3883--3898, 2003. [ bib | http ]
[159] M.L. Groot, L.J.G.W. van Wilderen, D.S. Larsen, M.A. van der Horst, I. H. M. van Stokkum, K.J. Hellingwerf, and R. van Grondelle. Initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy. Biochemistry, 42(34):10054--10059, 2003. [ bib | http ]
[160] Andrea Haker, Johnny Hendriks, Ivo H. M. van Stokkum, Joachim Heberle, Klaas J. Hellingwerf, Wim Crielaard, and Thomas Gensch. The Two Photocycles of Photoactive Yellow Protein from Rhodobacter sphaeroides. J. Biol. Chem., 278(10):8442--8451, 2003. [ bib | DOI | http ]
[161] Johnny Hendriks, Ivo H. M. van Stokkum, and Klaas J. Hellingwerf. Deuterium Isotope Effects in the Photocycle Transitions of the Photoactive Yellow Protein. Biophysical Journal, 84(2):1180--1191, 2003. [ bib | http ]
[162] Derren J. Heyes, C. Neil Hunter, Ivo H. M. van Stokkum, Rienk van Grondelle, and Marie Louise Groot. Ultrafast enzymatic reaction dynamics in protochlorophyllide oxidoreductase. Nature Structural Biology, 10:491 -- 492, 2003. [ bib ]
[163] J.T.M. Kennis, S. Crosson, M. Gauden, I. H. M. van Stokkum, K. Moffat, and R. van Grondelle. Primary reactions of the LOV2 domain of phototropin, a plant blue-light photoreceptor. Biochemistry, 42(12):3385--3392, 2003. [ bib | http ]
[164] Wouter Laan, Michael A. van der Horst, Ivo H. van Stokkum, and Klaas J. Hellingwerf. Initial characterization of the primary photochemistry of appa, a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from rhodobacter sphaeroides: A key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine. Photochemistry and Photobiology, 78(3):290--297, 2003. [ bib ]
[165] Delmar S. Larsen, Emmanouil Papagiannakis, Ivo H. M. van Stokkum, Mikas Vengris, John T. M. Kennis, and Rienk van Grondelle. Excited state dynamics of β-carotene explored with dispersed multi-pulse transient absorption. Chemical Physics Letters, 381:733--742, Nov 2003. [ bib | http ]
[166] Delmar S. Larsen, Mikas Vengris, Ivo H. M. van Stokkum, Michael A. van der Horst, Robert A. Cordfunke, Klaas J. Hellingwerf, and Rienk van Grondelle. Initial photo-induced dynamics of the photoactive yellow protein chromophore in solution. Chemical Physics Letters, 369:563--569, Feb 2003. [ bib | http ]
[167] O.F.A. Larsen, I. H. M. van Stokkum, A. Pandit, R. van Grondelle, and H. van Amerongen. Ultrafast polarized fluorescence measurements on tryptophan and a tryptophan-containing peptide. Journal of Physical Chemistry B, 107(13):3080--3085, 2003. [ bib | http ]
[168] Olaf F. A. Larsen, Ivo H. M. van Stokkum, Marie-Louise Groot, John T. M. Kennis, Rienk van Grondelle, and Herbert van Amerongen. Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis. Chemical Physics Letters, 371:157--163, Mar 2003. [ bib | http ]
[169] Miguel A. Palacios, Raoul N. Frese, Claudiu C. Gradinaru, I. H. M. van Stokkum, Lavanya L. Premvardhan, Peter Horton, Alexander V. Ruban, Rienk van Grondelle, and Herbert van Amerongen. Stark spectroscopy of the light-harvesting complex II in different oligomerisation states. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1605:83--95, Aug 2003. [ bib | http ]
[170] A. Pandit, O.F.A. Larsen, I. H. M. van Stokkum, R. van Grondelle, R. Kraayenhof, and H. van Amerongen. Ultrafast polarized fluorescence measurements on monomeric and self-associated melittin. Journal of Physical Chemistry B, 107(13):3086--3090, 2003. [ bib | http ]
[171] Anjali Pandit, Ivo H. M. van Stokkum, Sofia Georgakopoulou, Gert van der Zwan, and Rienk van Grondelle. Investigations of intermediates appearing in the reassociation of the light-harvesting 1 complex of rhodospirillum rubrum. Photosynthesis Research, 75(3):235--248, 2003. [ bib | http ]
[172] E. Papagiannakis, S.K. Das, A. Gall, I. H. M. van Stokkum, B. Robert, R. van Grondelle, H.A. Frank, and J.T.M. Kennis. Light harvesting by carotenoids incorporated into the B850 light-harvesting complex from rhodobacteris phaeroides R-26.1: Excited-state relaxation, ultrafast triplet formation, and energy transfer to bacteriochlorophyll. Journal of Physical Chemistry B, 107(23):5642--5649, 2003. [ bib | http ]
[173] E. Papagiannakis, I. H. M. van Stokkum, R. van Grondelle, R.A. Niederman, D. Zigmantas, V. Sundstrom, and T. Polivka. A near-infrared transient absorption study of the excited-state dynamics of the carotenoid spirilloxanthin in solution and in the lh1 complex of Rhodospirillum rubrum. Journal of Physical Chemistry B, 107(40):11216--11223, 2003. [ bib | http ]
[174] Valentin N. Petushkov, Ivo H. M. van Stokkum, Bas Gobets, Frank van Mourik, John Lee, Rienk van Grondelle, and Antonie J.W.G. Visser. Ultrafast fluorescence relaxation spectroscopy of 6,7-dimethyl-(8-ribityl)-lumazine and riboflavin, free and bound to antenna proteins from bioluminescent bacteria. Journal of Physical Chemistry B, 107(39):10934--10939, 2003. [ bib | http ]
[175] Markus Wendling, Frank van Mourik, Ivo H. M. van Stokkum, Jante M. Salverda, Hartmut Michel, and Rienk van Grondelle. Low-Intensity Pump-Probe Measurements on the B800 Band of Rhodospirillum molischianum. Biophysical Journal, 84(1):440--449, 2003. [ bib | http ]
[176] Raoul N. Frese, Miguel A. Palacios, Aissa Azzizi, Ivo H. M. van Stokkum, Jochen Kruip, Matthias Rogner, Navassard V. Karapetyan, Eberhard Schlodder, Rienk van Grondelle, and Jan P. Dekker. Electric field effects on red chlorophylls, β-carotenes and P700 in cyanobacterial photosystem I complexes. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1554:180--191, Jul 2002. [ bib | http ]
[177] T. Gensch, C. C. Gradinaru, I. H. M. van Stokkum, J. Hendriks, K. J. Hellingwerf, and R. van Grondelle. The primary photoreaction of photoactive yellow protein (PYP): anisotropy changes and excitation wavelength dependence. Chemical Physics Letters, 356:347--354, Apr 2002. [ bib | http ]
[178] Janne A. Ihalainen, Poul Erik Jensen, Anna Haldrup, Ivo H. M. van Stokkum, Rienk van Grondelle, Henrik Vibe Scheller, and Jan P. Dekker. Pigment Organization and Energy Transfer Dynamics in Isolated Photosystem I (PSI) Complexes from Arabidopsis thaliana Depleted of the PSI-G, PSI-K, PSI-L, or PSI-N Subunit. Biophysical Journal, 83(4):2190--2201, 2002. [ bib | http ]
[179] A. Pandit, H. Ma, I. H. M. van Stokkum, M. Gruebele, and R. van Grondelle. Time-resolved dissociation of the light-harvesting 1 complex of rhodospirillum rubrum, studied by infrared laser temperature jump. Biochemistry, 41(51):15115--15120, 2002. [ bib | http ]
[180] Emmanouil Papagiannakis, John T. M. Kennis, Ivo H. M. van Stokkum, Richard J. Cogdell, and Rienk van Grondelle. An alternative carotenoid-to-bacteriochlorophyll energy transfer pathway in photosynthetic light harvesting. PNAS, 99(9):6017--6022, 2002. [ bib | DOI | http ]
[181] Bart J. van Rotterdam, Wim Crielaard, Ivo H. M. van Stokkum, Klaas J. Hellingwerf, and Hans V. Westerhoff. Simplicity in complexity: the photosynthetic reaction center performs as a simple 0.2 V battery. FEBS Letters, 510:105--107, Jan 2002. [ bib | http ]
[182] I. H. M. van Stokkum and RH Lozier. Target analysis of the bacteriorhodopsin photocycle using a spectrotemporal model. J. Phys. Chem. B, 106:3477--3485, 2002. [ bib ]
[183] Cornelis A. van Walree, Veronica E. M. Kaats-Richters, Leonardus W. Jenneskens, René M. Williams, and Ivo H. M. van Stokkum. Intramolecular excimer and exciplex emission of 1,4-dipyrenyl substituted cyclohexasilane. Chemical Physics Letters, 355:65--70, Mar 2002. [ bib | http ]
[184] Frank L. de Weerd, Ivo H. M. van Stokkum, Herbert van Amerongen, Jan P. Dekker, and Rienk van Grondelle. Pathways for Energy Transfer in the Core Light-Harvesting Complexes CP43 and CP47 of Photosystem II. Biophysical Journal, 82(3):1586--1597, 2002. [ bib | http ]
[185] Frank L. de Weerd, Ivo H. M. van Stokkum, and Rienk van Grondelle. Subpicosecond dynamics in the excited state absorption of all-trans-β-carotene. Chemical Physics Letters, 354:38--43, Mar 2002. [ bib | http ]
[186] Michael A. van der Horst, Ivo H. van Stokkum, Wim Crielaard, and Klaas J. Hellingwerf. The role of the N-terminal domain of photoactive yellow protein in the transient partial unfolding during signalling state formation. FEBS Letters, 497:26--30, May 2001. [ bib | http ]
[187] B. Gobets, J.T.M. Kennis, J.A. Ihalainen, M. Brazzoli, R. Croce, I. H. M. van Stokkum, R. Bassi, J.P. Dekker, H. van Amerongen, G.R. Fleming, and R. van Grondelle. Excitation energy transfer in dimeric light harvesting complex I: A combined streak-camera/fluorescence upconversion study. Journal of Physical Chemistry B, 105(41):10132--10139, 2001. [ bib | http ]
[188] Bas Gobets, Ivo H. M. van Stokkum, Matthias Rogner, Jochen Kruip, Eberhard Schlodder, Navassard V. Karapetyan, Jan P. Dekker, and Rienk van Grondelle. Time-Resolved Fluorescence Emission Measurements of Photosystem I Particles of Various Cyanobacteria: A Unified Compartmental Model. Biophysical Journal, 81(1):407--424, 2001. [ bib | http ]
[189] Claudiu C. Gradinaru, John T. M. Kennis, Emmanouil Papagiannakis, Ivo H. M. van Stokkum, Richard J. Cogdell, Graham R. Fleming, Robert A. Niederman, and Rienk van Grondelle. An unusual pathway of excitation energy deactivation in carotenoids: Singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic antenna. PNAS, 98(5):2364--2369, 2001. [ bib | DOI | http ]
[190] J.A. Ihalainen, J. Linnanto, P. Myllyperkio, I. H. M. van Stokkum, B. Ucker, H. Scheer, and J.E.I. Korppi-Tommola. Energy transfer in LH2 of rhodospirillum molischianum, studied by subpicosecond spectroscopy and configuration interaction exciton calculations. Journal of Physical Chemistry B, 105(40):9849--9856, 2001. [ bib | http ]
[191] JTM Kennis, B Gobets, I. H. M. van Stokkum, JP Dekker, van Grondelle R, and Fleming GR. Light harvesting by chlorophylls and carotenoids in the photosystem I core complex of synechococcus elongatus: a fluorescence upconversion study. J. Phys. Chem. B, 105:4485--4494, 2001. [ bib ]
[192] Brent P. Krueger, Stefania S. Lampoura, Ivo H. M. van Stokkum, Emmanouil Papagiannakis, Jante M. Salverda, Claudiu C. Gradinaru, Danielis Rutkauskas, Roger G. Hiller, and Rienk van Grondelle. Energy Transfer in the Peridinin Chlorophyll-a Protein of Amphidinium carterae Studied by Polarized Transient Absorption and Target Analysis. Biophys. J., 80(6):2843--2855, 2001. [ bib | http ]
[193] S.S. Lampoura, B.P. Krueger, I. H. M. van Stokkum, J.M. Salverda, C.C. Gradinaru, D. Rutkauskas, R.G. Hiller, and R. van Grondelle. Energy transfer in the peridinin chlorophyll: a protein of amphidinium carterae studied by polarized transient absorption measurements. Int. J. Mod. Phys. B, 15:3849--3852, 2001. [ bib ]
[194] Olaf F. A. Larsen, Ivo H. M. van Stokkum, Bas Gobets, Rienk van Grondelle, and Herbert van Amerongen. Probing the Structure and Dynamics of a DNA Hairpin by Ultrafast Quenching and Fluorescence Depolarization. Biophysical Journal, 81(2):1115--1126, 2001. [ bib | http ]
[195] Xavier Y. Lauteslager, Ivo H. M. van Stokkum, H. John van Ramesdonk, Dick Bebelaar, Jan Fraanje, Kees Goubitz, Henk Schenk, Albert M. Brouwer, and Jan W. Verhoeven. Conformational dynamics of charge-transfer states in donor-bridge-acceptor systems. European Journal of Organic Chemistry, 16:3105--3118, 2001. [ bib ]
[196] H. Naus, I. H. M. van Stokkum, W Ubachs, and W. Hogervorst. Quantitative analysis of decay transients applied to a multi-mode pulsed cavity ring-down experiment. Applied Optics, 40:4416--4426, 2001. [ bib ]
[197] A Pandit, RW Visschers, I. H. M. van Stokkum, R Kraayenhof, and R van Grondelle. Oligomerization of light-harvesting I antenna peptides of rhodospirillum rubrum. Biochemistry, 40:12913--12924, 2001. [ bib ]
[198] Petra A.W. Van Den Berg, Scott B. Mulrooney, Bas Gobets, Ivo H. M. Van Stokkum, Arie Van Hoek, JR. Williams, Charles H., and Antonie J.W.G. Visser. Exploring the conformational equilibrium of E. coli thioredoxin reductase: Characterization of two catalytically important states by ultrafast flavin fluorescence spectroscopy. Protein Sci, 10(10):2037--2049, 2001. [ bib | DOI | http ]
[199] G.W.H. Wurpel, A.M. Brouwer, I. H. M. van Stokkum, A. Farran, and D.A. Leigh. Enhanced hydrogen bonding induced by optical excitation: Unexpected subnanosecond photoinduced dynamics in a peptide-based [2]rotaxane. Journal of the American Chemical Society, 123(45):11327--11328, 2001. [ bib | http ]
[200] M.M. Yatskou, R.B.M. Koehorst, A. van Hoek, H. Donker, T.J. Schaafsma, B. Gobets, I. van Stokkum, and R. van Grondelle. Spectroscopic properties of a self-assembled zinc porphyrin tetramer II. time-resolved fluorescence spectroscopy. Journal of Physical Chemistry A, 105(51):11432--11440, 2001. [ bib | http ]
[201] Wim P. Cofino, Ivo H. M. van Stokkum, David E. Wells, Freek Ariese, Jan-Willem M. Wegener, and Renee A. L. Peerboom. A new model for the inference of population characteristics from experimental data using uncertainties. application to interlaboratory studies. Chemometrics and Intelligent Laboratory Systems, 53:37--55, Nov 2000. [ bib | http ]
[202] C.C. Gradinaru, I. H. M. van Stokkum, A.A. Pascal, R. van Grondelle, and H. van Amerongen. Identifying the pathways of energy transfer between carotenoids and chlorophylls in LHCII and CP29. a multicolor, femtosecond pump-probe study. Journal of Physical Chemistry B, 104(39):9330--9342, 2000. [ bib | http ]
[203] Foske J. Kleima, Eckhard Hofmann, Bas Gobets, Ivo H. M. van Stokkum, Rienk van Grondelle, Kay Diederichs, and Herbert van Amerongen. Förster Excitation Energy Transfer in Peridinin-Chlorophyll-a-Protein. Biophysical Journal, 78(1):344--353, 2000. [ bib | http ]
[204] S.S. Lampoura, R. van Grondelle, I. H. M. van Stokkum, R.J. Cogdell, D.A. Wiersma, and K. Duppen. Exciton dynamics in LH1 and LH2 of rhodopseudomonas acidophila and rhodobium marinum probed with accumulated photon echo and pump-probe measurements. Journal of Physical Chemistry B, 104(50):12072--12078, 2000. [ bib | http ]
[205] M.E. van Brederode, I. H. M. van Stokkum, E. Katilius, F. van Mourik, M.R. Jones, and R. van Grondelle. Primary charge separation routes in the BChl:BPhe heterodimer reaction centers of rhodobacter sphaeroides. Biochemistry, 38(23):7545--7555, 1999. [ bib | http ]
[206] M.E. van Brederode, I. H. M. van Stokkum, E. Katilius, F. van Mourik, M.R. Jones, and R. van Grondelle. Primary charge separation routes in the BChl:BPhe heterodimer reaction centers of rhodobacter sphaeroides. Biochemistry, 38(29):9556--9556, 1999. [ bib | http ]
[207] Marion E. van Brederode, Frank van Mourik, Ivo H. M. van Stokkum, Michael R. Jones, and Rienk van Grondelle. Multiple pathways for ultrafast transduction of light energy in the photosynthetic reaction center of Rhodobacter sphaeroides. PNAS, 96(5):2054--2059, 1999. [ bib | DOI | http ]
[208] M-L Groot, RN Frese, FL de Weerd, K Bromek, Pettersson Å, EJG Peterman, I. H. M. van Stokkum, R van Grondelle, and JP Dekker. Spectroscopic properties of the CP43 core antenna protein of photosystem II. Biophysical Journal, 77:328--340, 1999. [ bib ]
[209] Johnny Hendriks, Ivo H. M. van Stokkum, Wim Crielaard, and Klaas J. Hellingwerf. Kinetics of and intermediates in a photocycle branching reaction of the photoactive yellow protein from ectothiorhodospira halophila. FEBS Letters, 458:252--256, Sep 1999. [ bib | http ]
[210] W.D. Hoff, A. Xie, I. H. M. Van Stokkum, X.-j. Tang, J. Gural, A.R. Kroon, and K.J. Hellingwerf. Global conformational changes upon receptor stimulation in photoactive yellow protein. Biochemistry, 38(3):1009--1017, 1999. [ bib | http ]
[211] X.Y. Lauteslager, I. H. M. van Stokkum, H.J. van Ramesdonk, A.M. Brouwer, and J.W. Verhoeven. Conformational dynamics of semiflexibly bridged donor-acceptor systems studied with a streak camera and spectrotemporal parametrization of fluorescence. Journal of Physical Chemistry A, 103(6):653--659, 1999. [ bib | http ]
[212] I. H. M. van Stokkum. Added value of singles in 3D PET. In Proceedings of the 1999 International meeting on fully three-dimensional image reconstruction in radiology and nuclear medicine, pages 115--118, 1999. [ bib ]
[213] Marion E. van Brederode, Justin P. Ridge, Ivo H. M. van Stokkum, Frank van Mourik, Michael R. Jones, and Rienk van Grondelle. On the efficiency of energy transfer and the different pathways of electron transfer in mutant reaction centers of rhodobacter sphaeroides. Photosynthesis Research, 55(2):141--146, 1998. [ bib | http ]
[214] RN Frese, B Gobets, I. H. M. van Stokkum, R van Grondelle, and F van Mourik. Dielectric relaxation on a picosecond time-scale at 77 K: a fluorescence study on the LH2 B800-820 complex of Rps. acidophila. In G Garab, editor, Photosynthesis: Mechanisms and Effects, pages 41--44. Kluwer Academic Publishers, Dordrecht, 1998. [ bib ]
[215] B Gobets, I. H. M. van Stokkum, F van Mourik, M Rögner, J Kruip, JP Dekker, and van Grondelle R. Time-resolved fluorescence measurements of photosystem 1 from synechocystis PCC 6803. In G Garab, editor, Photosynthesis: Mechanisms and Effects, pages 571--574. Kluwer Academic Publishers, Dordrecht, 1998. [ bib ]
[216] CC Gradinaru, S Özdemir, D Gülen, I. H. M. van Stokkum, R van Grondelle, and H van Amerongen. The flow of excitation in LHCII monomers: Implications for the structural model of the major plant antenna. Biophysical Journal, 75:3064--3077, 1998. [ bib ]
[217] CC Gradinaru, I. H. M. van Stokkum, R van Grondelle, and van Amerongen. Ultrafast absorption changes of the lhcII carotenoids upon selective excitation of the chlorophylls. In G Garab, editor, Photosynthesis: Mechanisms and Effects, pages 277--281. Kluwer Academic Publishers, Dordrecht, 1998. [ bib ]
[218] FJ Kleima, E Hofmann, B Gobets, I. H. M. van Stokkum, van Grondelle, and H van Amerongen. Peridinin chlorophyll protein: structure and dynamics related. In G Garab, editor, Photosynthesis: Mechanisms and Effects, pages 441--444. Kluwer Academic Publishers, Dordrecht, 1998. [ bib ]
[219] JM Salverda, F van Mourik, I. H. M. van Stokkum, M Wendling, and R van Grondelle. Polarized and colored photon echo measurements on the LH2 antenna of Rps. acidophila and Rs. molischianum. In G Garab, editor, Photosynthesis: Mechanisms and Effects, pages 45--48. Kluwer Academic Publishers, Dordrecht, 1998. [ bib ]
[220] M Wendling, F van Mourik, I. H. M. van Stokkum, JM Salverda, H Michel, and R van Grondelle. Low-intensity pump-probe measurements on the B800 band of rhodospirillim molischianum. In G Garab, editor, Photosynthesis: Mechanisms and Effects, pages 49--52. Kluwer Academic Publishers, Dordrecht, 1998. [ bib ]
[221] A. Baltuška, I. H. M. van Stokkum, A. Kroon, R. Monshouwer, K. J. Hellingwerf, and R. van Grondelle. The primary events in the photoactivation of yellow protein. Chemical Physics Letters, 270:263--266, May 1997. [ bib | http ]
[222] Geoffrey W. Abbott, Michael Bloemendal, Ivo H. M. Van Stokkum, Eric A. J. Mercer, Rob T. Miller, Sabine Sewing, Mark Wolters, Olaf Pongs, and Surjit K. S. Srai. Secondary structure, stability and tetramerisation of recombinant KV1.1 potassium channel cytoplasmic N-terminal fragment. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1341:71--78, Aug 1997. [ bib | http ]
[223] L.M.P. Beekman, R.N. Frese, G.J.S. Fowler, R. Picorel, R.J. Cogdell, I. H. M. van Stokkum, C.N. Hunter, and R. van Grondelle. Characterization of the light-harvesting antennas of photosynthetic purple bacteria by stark spectroscopy. 2. LH2 complexes: Influence of the protein environment. Journal of Physical Chemistry B, 101(37):7293--7301, 1997. [ bib | http ]
[224] L.M.P. Beekman, M. Steffen, I. H. M. van Stokkum, J.D. Olsen, C.N. Hunter, S.G. Boxer, and R. van Grondelle. Characterization of the light-harvesting antennas of photosynthetic purple bacteria by stark spectroscopy. 1. lh1 antenna complex and the b820 subunit from rhodospirillum rubrum. Journal of Physical Chemistry B, 101(37):7284--7292, 1997. [ bib | http ]
[225] Raoul Frese, Uwe Oberheide, Ivo van Stokkum, Rienk van Grondelle, Markus Foidl, Jürgen Oelze, and Herbert van Amerongen. The organization of bacteriochlorophyll c in chlorosomes from chloroflexus aurantiacus and the structural role of carotenoids and protein. Photosynthesis Research, 54:115--126, 1997. [ bib | http ]
[226] Marie-Louise Groot, Frank van Mourik, Camiel Eijckelhoff, Ivo H. M. van Stokkum, Jan P. Dekker, and Rienk van Grondelle. Charge separation in the reaction center of photosystem II studied as a function oftemperature. PNAS, 94(9):4389--4394, 1997. [ bib | DOI | http ]
[227] Wouter D. Hoff, Ivo H. M. Van Stokkum, Jechiam Gural, and Klaas J. Hellingwerf. Comparison of acid denaturation and light activation in the eubacterial blue-light receptor photoactive yellow protein. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1322:151--162, Dec 1997. [ bib | http ]
[228] J.T.M. Kennis, A.Ya. Shkuropatov, I. H. M. van Stokkum, P. Gast, A.J. Hoff, V.A. Shuvalov, and T.J. Aartsma. Formation of a long-lived P+BA- state in plant pheophytin-exchanged reaction centers of rhodobacter sphaeroides R26 at low temperature. Biochemistry, 36(51):16231--16238, 1997. [ bib | http ]
[229] F.J. Kleima, C.C. Gradinaru, F. Calkoen, I. H. M. van Stokkum, R. van Grondelle, and H. van Amerongen. Energy transfer in LHCII monomers at 77K studied by sub-picosecond transient absorption spectroscopy. Biochemistry, 36(49):15262--15268, 1997. [ bib | http ]
[230] Erwin J. G. Peterman, René Monshouwer, Ivo H. M. van Stokkum, Rienk van Grondelle, and Herbert van Amerongen. Ultrafast singlet excitation transfer from carotenoids to chlorophylls via different pathways in light-harvesting complex II of higher plants. Chemical Physics Letters, 264:279--284, Jan 1997. [ bib | http ]
[231] I. H. M. van Stokkum. Parameter precision in global analysis of time resolved spectra. IEEE Transactions on Instrumentation and Measurement, 46(4):764--768, 1997. [ bib ]
[232] I. H. M. van Stokkum, L.M.P. Beekman, M.R. Jones, M.E. van Brederode, and R. van Grondelle. Primary electron transfer kinetics in membrane-bound rhodobacter sphaeroides reaction centers: A global and target analysis. Biochemistry, 36(38):11360--11368, 1997. [ bib | http ]
[233] M.E. Van Brederode, M.R. Jones, F. Van Mourik, I. H. M. Van Stokkum, and R. Van Grondelle. A new pathway for transmembrane electron transfer in photosynthetic reaction centers of rhodobacter sphaeroides not involving the excited special pair. Biochemistry, 36(23):6855--6861, 1997. [ bib | http ]
[234] F.M. Vos, G.L. van der Heijde, H.J.W. Spoelder, I. H. M. van Stokkum, and F.C.A. Groen. A new instrument to measure the shape of the cornea based on pseudorandom color coding. IEEE Transactions on Instrumentation and Measurement, 46(4):794 -- 797, 1997. [ bib ]
[235] L.M.P. Beekman, I. H. M. van Stokkum, R. Monshouwer, A.J. Rijnders, P. McGlynn, R.W. Visschers, M.R. Jones, and R. van Grondelle. Primary electron transfer in membrane-bound reaction centers with mutations at the M210 position. Journal of Physical Chemistry, 100(17):7256--7268, 1996. [ bib | http ]
[236] ME van Brederode, WD Hoff, I. H. M. van Stokkum, ML Groot, and KJ Hellingwerf. Protein folding thermodynamics applied to the photocycle of photoactive yellow protein. Biophysical Journal, 71:365--380, 1996. [ bib ]
[237] B. H. Groen, M. Bloemendal, J. W. M. Mulders, J. M. Hadden, D. Chapman, I. H. M. Van Stokkum, and R. Van Grondelle. Spectroscopic characterization of recombinant follicle stimulating hormone. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 52:1331--1346, Sep 1996. [ bib | http ]
[238] M-L Groot, F van Mourik, I. H. M. van Stokkum, and R. van Grondelle. Quantum beats in the reaction center of photosystem II. In PF Barbara, JG Fujimoto, WH Knox, and W Zinth, editors, Ultrafast Phenomena X, Springer Series in Chemical Physics, volume 1, pages 344--345. Springer-Verlag, Berlin, 1996. [ bib ]
[239] M-L Groot, L-O Pålsson, R Pribić, I. H. M. van Stokkum, JP Dekker, and R. van Grondelle. Energetics and excited state dynamics of the radical pair formation in isolated CP47- reaction center complex of photosystem II at various temperatures. In A Tramer, editor, Fast Elementary Processes in Chemical and Biological Systems, pages 288--292. AIP Press, New York, 1996. [ bib ]
[240] I. H. M. van Stokkum. Parameter precision in global analysis of time resolved spectra. In Quality Measurements: The Indispensable Bridge between Theory and Reality, volume 1, pages 168--173. IEEE Instrumentation and Measurement Technology Conference, 1996. [ bib ]
[241] ME Van Brederode, LMP Beekman, D Kuciauskas, MR Jones, I. H. M. van Stokkum, and R van Grondelle. Characteristics of the electron transfer reactions in the M210W reaction centre only mutant of rhodobacter sphaeroides. In ME Michel-Beyerle, editor, The Reaction Center of Photosynthetic Bacteria: Structure and Dynamics, pages 225--237. Springer-Verlag, Berlin, 1996. [ bib ]
[242] H. M. Visser, F. J. Kleima, I. H. M. van Stokkum, R. van Grondelle, and H. van Amerongen. Probing the many energy-transfer processes in the photosynthetic light-harvesting complex II at 77 K using energy-selective sub-picosecond transient absorption spectroscopy. Chemical Physics, 210:297--312, Oct 1996. [ bib | http ]
[243] F.M. Vos, G.L. van der Heijde, H.J.W. Spoelder, I. H. M. van Stokkum, and F.C.A. Groen. A new prba-based instrument to measure the shape of the cornea. In Quality Measurements: The Indispensable Bridge between Theory and Reality, volume 1, pages 416 -- 421. IEEE Instrumentation and Measurement Technology Conference, 1996. [ bib ]
[244] L.M.P. Beekman, M.R. Jones, I. H. M. Van Stokkum, and R. Van Grondelle. Wavelength dependence of the stimulated emission decay of membrane bound Rb. sphaeroides reaction centers and observation of a BChl-a anion involved in electron transfer. In P. Mathis, editor, Photosynthesis: from Light to Biosphere, volume 1, pages 495--498. Dordrecht, Kluwer, 1995. [ bib ]
[245] L. M. P. Beekman, R. W. Visschers, R. Monshouwer, M. Heer-Dawson, T. A. Mattioli, P. McGlynn, C. N. Hunter, B. Robert, and I. H. M. van Stokkum. Time-resolved and steady-state spectroscopic analysis of membrane-bound reaction centers from rhodobacter sphaeroides: Comparisons with detergent-solubilized complexes. Biochemistry, 34(45):14712--14721, 1995. [ bib | http ]
[246] M L Groot, E J G Peterman, I H M van Stokkum, J P Dekker, and R van Grondelle. Triplet and fluorescing states of the CP47 antenna complex of photosystem II studied as a function of temperature. Biophys. J., 68(1):281--290, 1995. [ bib | arXiv | http ]
[247] Van Brederode ME, van Stokkum I. H. M., and Van Grondelle R Jones MR. Wavelength and temperature dependence of the P+QA recombination reaction in the M210W reaction centre only mutant of rhodobacter sphaeroides. In P. Mathis, editor, Photosynthesis: from Light to Biosphere, volume 1, pages 907--910. Dordrecht, Kluwer, 1995. [ bib ]
[248] I. H. M. van Stokkum, W. A. van der Graaf, and D. Lenstra. Weighted fit of optical spectra. Optics Communications, 121:103--108, Dec 1995. [ bib | http ]
[249] I. H. M. van Stokkum, G.N. Lambrou, and T.J.T.P. Van den Berg. Hemodynamic parameter estimation from ocular fluorescein angiograms. Graefe's Archive for Clinical and Experimental Ophthalmology, 233:123--130, 1995. [ bib ]
[250] I. H. M. van Stokkum, H. Linsdell, J. M. Hadden, P. I. Haris, D. Chapman, and M. Bloemendal. Temperature-induced changes in protein structures studied by fourier transform infrared spectroscopy and global analysis. Biochemistry, 34(33):10508--10518, 1995. [ bib | http ]
[251] I. H. M. van Stokkum, F. van Mourik, M.-L. Groot, and R. van Grondelle. Low-intensity fluorescence spectra from the photosystem II reaction centre measured using a picosecond synchroscan streak camera. effects of sample degradation on the observed lifetimes. In P. Mathis, editor, Photosynthesis: from Light to Biosphere, volume 1, pages 887--890. Dordrecht, Kluwer, 1995. [ bib ]
[252] B Van Haeringen, F. de Lange, I. H. M. van Stokkum, SKS Srai, RW Evans, R. van Grondelle, and M Bloemendal. Dynamic structure of human serum transferrin from transient electric birefringence. Proteins, Structure, Function, and Genetics, 23:233--240, 1995. [ bib ]
[253] P.J.M. Van Kan, I. H. M. Van Stokkum, and S. Styring. Time-resolved EPR spectroscopy of the triplet state of the primary electron donor P680 in PS II. In P. Mathis, editor, Photosynthesis: from Light to Biosphere, volume 1, pages 543--546. Dordrecht, Kluwer, 1995. [ bib ]
[254] HM Visser, OJG Somsen, F van Mourik, S Lin, I. H. M. van Stokkum, and R van Grondelle. Direct observation of sub-picosecond equilibration of excitation energy in the light-harvesting antenna of Rhodospirillum rubrum. Biophys. J., 69(3):1083--1099, 1995. [ bib | http ]
[255] H. Matthieu Visser, Marie-Louise Groot, Frank van Mourik, Ivo H. M. van Stokkum, Jan P. Dekker, and Rienk van Grondelle. Subpicosecond transient absorption difference spectroscopy on the reaction center of photosystem II: Radical pair formation at 77 K. Journal of Physical Chemistry, 99(41):15304--15309, 1995. [ bib | http ]
[256] M. L. Groot, E. J. G. Peterman, P. J. M. van Kan, I. H. M. van Stokkum, JP Dekker, and R van Grondelle. Temperature dependent triplet and fluorescence quantum yields of the photosystem II reaction center described in a thermodynamic model. Biophysical Journal, 67:318--330, 1994. [ bib ]
[257] Jonathan M. Hadden, Michael Bloemendal, Parvez I. Haris, Ivo H. M. van Stokkum, Dennis Chapman, and Surjit K. S. Srai. Structure and thermal stability of the extracellular fragment of human transferrin receptor at extracellular and endosomal pH. FEBS Letters, 350:235--239, Aug 1994. [ bib | http ]
[258] W D Hoff, I H M van Stokkum, H J van Ramesdonk, M E van Brederode, A M Brouwer, J C Fitch, T E Meyer, R van Grondelle, and K J Hellingwerf. Measurement and global analysis of the absorbance changes in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila. Biophys. J., 67(4):1691--1705, 1994. [ bib | arXiv | http ]
[259] R. Pribić, I. H. M. Van Stokkum, and A. Van den Bos. Inference regions of nonlinear parameters in global analysis. In M. Blanke and T. Söderström, editors, Proceedings SYSID 1994, 10th IFAC Symposium on System Identification, pages 2423--2428. Danish Automation Society, Copenhagen, 1994. [ bib ]
[260] T. Scherer, I. H. M. van Stokkum, A. M. Brouwer, and J. W. Verhoeven. Excited-state conformational dynamics of flexibly and semirigidly bridged electron donor-acceptor systems in solution. influence of temperature and solvent viscosity. Journal of Physical Chemistry, 98(41):10539--10549, 1994. [ bib | http ]
[261] I. H. M. van Stokkum, T. Scherer, A. M. Brouwer, and J. W. Verhoeven. Conformational dynamics of flexibly and semirigidly bridged electron donor-acceptor systems as revealed by spectrotemporal parametrization of fluorescence. Journal of Physical Chemistry, 98(3):852--866, 1994. [ bib | http ]
[262] R. Pribić, I. H. M. Van Stokkum, D. Chapman, P.I. Haris, and M. Bloemendal. Protein secondary structure from fourier transform infrared and/or circular dichroism spectra. Analytical Biochemistry, 214:366--378, 1993. [ bib ]
[263] I. H. M. van Stokkum, A.M. Brouwer, H.J. Van Ramesdonk, and T. Scherer. Multiresponse parameter estimation and compartmental analysis of time resolved fluorescence spectra: Application to conformational dynamics of charge-separated species in solution. Proc. Kon. Ned. Akad. v. Wetensch, 96:43--68, 1993. [ bib ]
[264] P.J.M. Van Kan, M.L. Groot, I. H. M. Van Stokkum, S.L.S. Kwa, R. Van Grondelle, and J.P. Dekker. Chlorophyll triplet states in the CP47 core antenna protein of photosystem II. In N. Murata, editor, Research in Photosynthesis, volume 1, pages 271--274. Kluwer Academic Publishers,Dordrecht, 1992. [ bib ]
[265] F. Van Mourik, E.P.M. Corten, I. H. M. Van Stokkum, R.W. Visschers, P.A. Loach, R. Kraayenhof, and R. Van Grondelle. Self assembly of the LH-1 antenna of rhodospirillum rubrum, a time-resolved study of the aggregation of the B820 subunit form. In N. Murata, editor, Research in Photosynthesis, volume 1, pages 101--104. Kluwer Academic Publishers,Dordrecht, 1992. [ bib ]
[266] M. Bloemendal, I. H. M. Van Stokkum, and R. Van Grondelle. A new approach for the estimation of protein secondary structure from circular dichroism spectroscopy. In R.E. Hester and R.B. Girling, editors, Spectroscopy of biological molecules, pages 33--34. Royal Society of Chemistry, Cambridge, 1991. [ bib ]
[267] Ivo H. M. van Stokkum and Willem J. Melssen. Measuring and modelling the response of auditory midbrain neurons in the grassfrog to temporally structured binaural stimuli. Hearing Research, 52:113--132, Mar 1991. [ bib | http ]
[268] Willem J. Melssen, Willem J. M. Epping, and Ivo H. M. van Stokkum. Sensitivity for interaural time and intensity difference of auditory midbrain neurons in the grassfrog. Hearing Research, 47:235--256, Aug 1990. [ bib | http ]
[269] Ivo H. M. van Stokkum. Modelling the response of auditory midbrain neurons in the grassfrog to temporally structured monaural stimuli. Hearing Research, 43:231--250, Jan 1990. [ bib | http ]
[270] Ivo H. M. van Stokkum, Hans J. W. Spoelder, Michael Bloemendal, Rienk van Grondelle, and Frans C. A. Groen. Estimation of protein secondary structure and error analysis from circular dichroism spectra. Analytical Biochemistry, 191:110--118, Nov 1990. [ bib | http ]
[271] I. H. M. van Stokkum. Analysis of auditory brainstem neurons in the grassfrog. PhD thesis, Catholic University of Nijmegen, 1989. [ bib ]
[272] Ivo H. M. van Stokkum and C. C. A. M. Gielen. A model for the peripheral auditory nervous system of the grassfrog. Hearing Research, 41:71--85, Aug 1989. [ bib | http ]
[273] W.J. Melssen and I. H. M. Van Stokkum. Selectivity for interaural time-difference and amplitude-modulation frequency in the auditory midbrain of the grassfrog. In H. Duifhuis, J.W. Horst, and H.P. Wit, editors, Basic Issues in Hearing, pages 279--284. Academic Press, London, 1988. [ bib ]
[274] I. H. M. van Stokkum and W.J.M. Epping. Responses of auditory brainstem neurons in the grassfrog to clicks. Acta Biologica Hungarica, 29:291--304, 1988. [ bib ]
[275] Ivo H. M. van Stokkum. Sensitivity of neurons in the dorsal medullary nucleus of the grassfrog to spectral and temporal characteristics of sound. Hearing Research, 29:223--235, 1987. [ bib | http ]
[276] I. H. M. Van Stokkum, P.I.M. Johannesma, and J.J. Eggermont. Representation of time-dependent correlation and recurrence-time functions: A new method to analyse non-stationary point-processes. Biological Cybernetics, 55:17--24, 1986. [ bib ]

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