% This file was created with JabRef 2.7.
% Encoding: Cp1252

@ARTICLE{Abbott1997,
  author = {Abbott, Geoffrey W. and Bloemendal, Michael and Van Stokkum, Ivo
	H. M. and Mercer, Eric A. J. and Miller, Rob T. and Sewing, Sabine
	and Wolters, Mark and Pongs, Olaf and Srai, Surjit K. S.},
  title = {Secondary structure, stability and tetramerisation of recombinant
	{KV1.1} potassium channel cytoplasmic {N}-terminal fragment},
  journal = {Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular
	Enzymology},
  year = {1997},
  volume = {1341},
  pages = {71--78},
  month = {Aug},
  day = {15},
  issue = {1},
  keywords = {Fourier transform infrared spectroscopy},
  url = {http://www.sciencedirect.com/science/article/B6T21-3TGKN3C-7/2/eb9c9b15b22407e5419bd9fa97abb357}
}

@ARTICLE{MaximeAlexandre09152007,
  author = {Alexandre, Maxime T. A. and L{\"{u}}hrs, Daniel C. and van Stokkum,
	Ivo H. M. and Hiller, Roger and Groot, Marie-Louise and Kennis, John
	T. M. and van Grondelle, Rienk},
  title = {{Triplet State Dynamics in Peridinin-Chlorophyll-a-Protein: A New
	Pathway of Photoprotection in LHCs?}},
  journal = {Biophys. J.},
  year = {2007},
  volume = {93},
  pages = {2118-2128},
  number = {6},
  abstract = {This work investigates the interaction of carotenoid and chlorophyll
	triplet states in the peridinin-chlorophyll-a-protein (PCP) of Amphidinium
	carterae using step-scan Fourier transform infrared spectroscopy.
	We identify two carotenoid triplet state lifetimes of [~]13 and [~]42
	{micro}s in the spectral region between 1800 and 1100 cm1 after excitation
	of the blue' and red' peridinin (Per) conformers and the Qy of chlorophyll-a
	(Chl-a). The fast and slow decaying triplets exhibit different spectral
	signatures in the carbonyl region. The fast component generated at
	all excitation wavelengths is from a major conformer with a lactone
	stretching mode bleach at 1745 cm1. One (1720 cm1) and two (1720
	cm1 and 1741 cm1) different Per conformers are observed for the slow
	component upon 670- and 530480-nm excitation, respectively. The above
	result implies that 3Per triplets are formed via two different pathways,
	corroborating and complementing visible triplet-singlet (T-S) spectra
	(Kleima et al., Biochemistry (2000), 39, 5184). Surprisingly, all
	difference spectra show that Per and Chl-a modes are simultaneously
	present during the 3Per decay, implying significant involvement of
	3Chl-a in the 3Per state. We suggest that this Per-Chl-a interaction
	via a delocalized triplet state lowers the 3Per energy and thus provides
	a general, photoprotection mechanism for light-harvesting antenna
	complexes. },
  doi = {10.1529/biophysj.107.106674},
  eprint = {http://www.biophysj.org/cgi/reprint/93/6/2118.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/93/6/2118}
}

@ARTICLE{BaffreauJ._jp066415+,
  author = {Baffreau, J. and Leroy-Lhez, S. and Hudhomme, P. and Groeneveld,
	M.M. and van Stokkum, I. H. M. and Williams, R.M.},
  title = {Superabsorbing Fullerenes: Spectral and Kinetic Characterization
	of Photoinduced Interactions in Perylenediimide-Fullerene-{$C_{60}$}
	Dyads},
  journal = {Journal of Physical Chemistry A},
  year = {2006},
  volume = {110},
  pages = {13123-13125},
  number = {49},
  issn = {1089-5639},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp066415+}
}

@ARTICLE{BalkowskiG._jp050404j,
  author = {Balkowski, G. and Szemik-Hojniak, A. and van Stokkum, I. H. M. and
	Zhang, H. and Buma, W.J.},
  title = {Femtosecond Excited State Studies of the Two-Center Three-Electron
	Bond Driven Twisted Internal Charge Transfer Dynamics in 1,8-Bis(dimethylamino)naphthalene},
  journal = {Journal of Physical Chemistry A},
  year = {2005},
  volume = {109},
  pages = {3535-3541},
  number = {16},
  issn = {1089-5639},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp050404j}
}

@ARTICLE{Baltuska1997,
  author = {Baltu{\v{s}}ka, A. and van Stokkum, I. H. M. and Kroon, A. and Monshouwer,
	R. and Hellingwerf, K. J. and van Grondelle, R.},
  title = {The primary events in the photoactivation of yellow protein},
  journal = {Chemical Physics Letters},
  year = {1997},
  volume = {270},
  pages = {263--266},
  month = {May},
  day = {23},
  issue = {3-4},
  url = {http://www.sciencedirect.com/science/article/B6TFN-3S9T08S-W/2/c08618cc95af10869ee68e2651bfddb0}
}

@ARTICLE{BeekmanL.M.P._jp963447w,
  author = {Beekman, L.M.P. and Frese, R.N. and Fowler, G.J.S. and Picorel, R.
	and Cogdell, R.J. and van Stokkum, I. H. M. and Hunter, C.N. and
	van Grondelle, R.},
  title = {Characterization of the Light-Harvesting Antennas of Photosynthetic
	Purple Bacteria by Stark Spectroscopy. 2. {LH2} Complexes: Influence
	of the Protein Environment},
  journal = {Journal of Physical Chemistry B},
  year = {1997},
  volume = {101},
  pages = {7293-7301},
  number = {37},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp963447w}
}

@INPROCEEDINGS{beekc,
  author = {Beekman, L.M.P. and Jones, M.R. and Van Stokkum, I. H. M. and Van
	Grondelle, R.},
  title = {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},
  booktitle = {Photosynthesis: from Light to Biosphere},
  year = {1995},
  editor = {P. Mathis},
  volume = {1},
  pages = {495-498},
  publisher = {Dordrecht, Kluwer}
}

@ARTICLE{BeekmanL.M.P._jp963445b,
  author = {Beekman, L.M.P. and Steffen, M. and van Stokkum, I. H. M. and Olsen,
	J.D. and Hunter, C.N. and Boxer, S.G. and van Grondelle, R.},
  title = {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 = {Journal of Physical Chemistry B},
  year = {1997},
  volume = {101},
  pages = {7284-7292},
  number = {37},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp963445b}
}

@ARTICLE{BeekmanL.M.P._jp953054h,
  author = {Beekman, L.M.P. and van Stokkum, I. H. M. and Monshouwer, R. and
	Rijnders, A.J. and McGlynn, P. and Visschers, R.W. and Jones, M.R.
	and van Grondelle, R.},
  title = {Primary Electron Transfer in Membrane-Bound Reaction Centers with
	Mutations at the {M210} Position},
  journal = {Journal of Physical Chemistry},
  year = {1996},
  volume = {100},
  pages = {7256-7268},
  number = {17},
  issn = {0022-3654},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp953054h}
}

@ARTICLE{BeekmanL.M.P._bi00045a012,
  author = {Beekman, L. M. P. and Visschers, R. W. and Monshouwer, R. and Heer-Dawson,
	M. and Mattioli, T. A. and McGlynn, P. and Hunter, C. N. and Robert,
	B. and van Stokkum, I. H. M.},
  title = {Time-resolved and steady-state spectroscopic analysis of membrane-bound
	reaction centers from Rhodobacter sphaeroides: Comparisons with detergent-solubilized
	complexes},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {14712-14721},
  number = {45},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi00045a012}
}

@ARTICLE{RudiBerera04042006,
  author = {Berera, Rudi and Herrero, Christian and van Stokkum, Ivo H. M. and
	Vengris, Mikas and Kodis, Gerdenis and Palacios, Rodrigo E. and van
	Amerongen, Herbert and van Grondelle, Rienk and Gust, Devens and
	Moore, Thomas A. and Moore, Ana L. and Kennis, John T. M.},
  title = {{A simple artificial light-harvesting dyad as a model for excess
	energy dissipation in oxygenic photosynthesis}},
  journal = {PNAS},
  year = {2006},
  volume = {103},
  pages = {5343-5348},
  number = {14},
  doi = {10.1073/pnas.0508530103},
  file = {5343.pdf:http\://www.pnas.org/cgi/reprint/103/14/5343.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/103/14/5343}
}

@ARTICLE{RudiBerera2006PPS,
  author = {Berera, Rudi and Moore, Gary F. and van Stokkum, Ivo H. M. and Kodis,
	Gerdenis and Liddell, Paul A. and Gervaldo, Miguel and van Grondelle,
	Rienk and Kennis, John T. M. and Gust, Devens and Moore, Thomas A.
	and Moore, Ana L. },
  title = {{Charge separation and energy transfer in a caroteno–C{$_{60}$} dyad:
	photoinduced electron transfer from the carotenoid excited states}},
  journal = {Photochem. Photobiol. Sci.},
  year = {2006},
  volume = {5},
  pages = {1142-1149}
}

@ARTICLE{BereraBJ2009,
  author = {Berera, Rudi and van Stokkum, Ivo H. M. and d{'}Haene, Sandrine and
	Kennis, John T. M. and van Grondelle, Rienk and Dekker, Jan P.},
  title = {A Mechanism of Energy Dissipation in Cyanobacteria},
  journal = {Biophysical Journal},
  year = {2009},
  volume = {96},
  pages = {2261-2267},
  number = {6},
  url = {http://www.cell.com/biophysj/abstract/S0006-3495(09)00329-4}
}

@ARTICLE{Berera2010,
  author = {Rudi Berera and Ivo H. M. van Stokkum and John T.M. Kennis and Rienk
	van Grondelle and Jan P. Dekker},
  title = {The light-harvesting function of carotenoids in the cyanobacterial
	stress-inducible {IsiA} complex},
  journal = {Chemical Physics},
  year = {2010},
  volume = {373},
  pages = {65-70},
  number = {1-2},
  abstract = {We present a spectroscopic investigation of the light-harvesting role
	of carotenoids in aggregates of the IsiA pigment-protein complex
	of the cyanobacterium Synechocystis PCC 6803. The results show that
	carotenoids in IsiA transfer energy on the sub-100 fs timescale from
	the S-2 state to chlorophyll to about the same extent as in the related
	pigment-protein complexes CP43 and CP47. Selective excitation at
	the red edge of the S-2 absorption of the carotenoids shows that
	echinenone is more efficient in energy transfer to chlorophyll (37%)
	when compared to the other carotenoid species in the system (22%).
	(C) 2010 Elsevier B. V. All rights reserved.},
  doi = {DOI: 10.1016/j.chemphys.2010.01.011},
  issn = {0301-0104},
  keywords = {Carotenoids},
  url = {http://www.sciencedirect.com/science/article/B6TFM-4Y7P71C-1/2/d6a1fdc6d96d3554c3f99f646eadca3c}
}

@ARTICLE{BereraR_jp071010q,
  author = {Berera, R. and van Stokkum, I. H. M. and Kodis, G. and Keirstead,
	A.E. and Pillai, S. and Herrero, C. and Palacios, R.E. and Vengris,
	M. and van Grondelle, R. and Gust, D. and Moore, T.A. and Moore,
	A.L. and Kennis, J.T.M.},
  title = {Energy Transfer, Excited-State Deactivation, and Exciplex Formation
	in Artificial Caroteno-Phthalocyanine Light-Harvesting Antennas},
  journal = {Journal of Physical Chemistry B},
  year = {2007},
  volume = {111},
  pages = {6868-6877},
  number = {24},
  affiliation = {Department of Biophysics, Division of Physics and Astronomy, Faculty
	of Sciences, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands,
	and Department of Chemistry and Biochemistry and the Center for the
	Study of Early Events in Photosynthesis, Arizona State University,
	Tempe, Arizona 85287-1604},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp071010q}
}

@ARTICLE{Binsl:Mullen:vanStokkum:Heringa:vanBeek:2007:JSSOBK:v18i07,
  author = {Thomas W. Binsl and Katharine M. Mullen and Ivo H. M. van Stokkum
	and Jaap Heringa and Johannes H. G. M. van Beek},
  title = {{FluxSimulator}: An {R} Package to Simulate Isotopomer Distributions
	in Metabolic Networks},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {18},
  number = {7},
  accepted = {2007-01-10},
  bibdate = {2007-01-10},
  coden = {JSSOBK},
  issn = {1548-7660},
  submitted = {2006-09-28},
  url = {http://www.jstatsoft.org/v18/i07}
}

@INCOLLECTION{ivo91,
  author = {Bloemendal, M. and Van Stokkum, I. H. M. and Van Grondelle, R.},
  title = {A new approach for the estimation of protein secondary structure
	from circular dichroism spectroscopy},
  booktitle = {Spectroscopy of biological molecules},
  publisher = {Royal Society of Chemistry, Cambridge},
  year = {1991},
  editor = {Hester, R.E. and Girling, R.B.},
  pages = {33-34}
}

@ARTICLE{Bonetti2010,
  author = {Bonetti, C. and Alexandre, M. T. A. and van Stokkum, I. H. M. and
	Hiller, R. G. and Groot, M. L. and van Grondelle, R. and Kennis,
	J. T. M.},
  title = {Identification of excited-state energy transfer and relaxation pathways
	in the peridinin-chlorophyll complex: an ultrafast mid-infrared study},
  journal = {Physical Chemistry Chemical Physics},
  year = {2010},
  volume = {12},
  pages = {9256-9266},
  number = {32},
  abstract = {The peridinin chlorophyll-a protein (PCP) is a water-soluble, trimeric
	light harvesting complex found in marine dinoflagellates that binds
	peridinin and Chl-a in an unusual stoichiometric ratio of 4 : 1.
	In this paper, the pathways of excited-state energy transfer and
	relaxation in PCP were identified by means of femtosecond visible-pump,
	mid-infrared probe spectroscopy. In addition, excited-state relaxation
	of peridinin dissolved in organic solvent (CHCl3 and MeOH) was investigated.
	For peridinin in solution, the transient IR signatures of the low-lying
	S-1 and intramolecular charge transfer (ICT) states were similar,
	in line with a previous ultrafast IR study. In PCP, excitation of
	the optically allowed S-2 state of peridinin results in ultrafast
	energy transfer to Chl-a, in competition with internal conversion
	to low-lying optically forbidden states of peridinin. After vibrational
	relaxation of the peridinin hot S-1 state in 150 fs, two separate
	low-lying peridinin singlet excited states are distinguished, assigned
	to an ICT state and to a slowly transferring, vibrationally relaxed
	S-1 state. These states exhibit different lactone bleaches, indicating
	that the ICT and S-1 states localize on distinct peridinins. Energy
	transfer from the peridinin ICT state to Chl-a constitutes the dominant
	energy transfer channel and occurs with a time constant of 2 ps.
	The peridinin S-1 state mainly decays to the ground state through
	internal conversion, in competition with slow energy transfer to
	Chl-a. The singlet excited state of Chl-a undergoes intersystem crossing
	(ISC) to the triplet state on the nanosecond timescale, followed
	by rapid triplet excitation energy transfer (TEET) from Chl-a to
	peridinin, whereby no Chl-a triplet is observed but rather a direct
	rise of the peridinin triplet. The latter contains some Chl-a features
	due to excitonic coupling of the pigments. The peridinin triplet
	state shows a lactone bleach mode at 1748 cm(-1), while that of the
	peridinin ICT state is located at 1745 cm(-1), indicating that the
	main channels of singlet and triplet energy transfer in PCP proceed
	through distinct peridinins. Our results are consistent with an energy
	transfer scheme where the ICT state mainly localizes on Per621/611
	and Per623/613, the S1 state on Per622/612 and the triplet state
	on Per624/614.}
}

@ARTICLE{biophysj.108.139246,
  author = {Cosimo Bonetti and Tilo Mathes and Ivo H. M. van Stokkum and Katharine
	M. Mullen and Marie{-}Louise Groot and Rienk van Grondelle and Peter
	Hegemann and John T.M. Kennis},
  title = {Hydrogen bond switching among flavin and amino acid side chains in
	the {BLUF} photoreceptor observed by ultrafast infrared spectroscopy},
  journal = {Biophysical Journal},
  year = {2008},
  volume = {95},
  pages = {4790-4802},
  url = {http://www.biophysj.org/cgi/content/abstract/95/10/4790}
}

@ARTICLE{cosimoB09,
  author = {Bonetti, Cosimo and Stierl, Manuela and Mathes, Tilo and van Stokkum,
	Ivo H. M. and Mullen, Katharine M. and Cohen-Stuart, Thomas A. and
	van Grondelle, Rienk and Hegemann, Peter and Kennis, John T. M.},
  title = {The Role of Key Amino Acids in the Photoactivation Pathway of the
	Synechocystis Slr1694 BLUF Domain},
  journal = {Biochemistry},
  year = {2009},
  volume = {48},
  pages = {11458-11469},
  number = {48},
  doi = {doi: 10.1021/bi901196x}
}

@ARTICLE{i96,
  author = {van Brederode, ME and Hoff, WD and van Stokkum, I. H. M. and Groot,
	ML and Hellingwerf, KJ},
  title = {Protein folding thermodynamics applied to the photocycle of photoactive
	yellow protein},
  journal = {Biophysical Journal},
  year = {1996},
  volume = {71},
  pages = {365-380}
}

@ARTICLE{vanBrederodeM.E._bi9829128,
  author = {van Brederode, M.E. and van Stokkum, I. H. M. and Katilius, E. and
	van Mourik, F. and Jones, M.R. and van Grondelle, R.},
  title = {Primary Charge Separation Routes in the {BChl:BPhe} Heterodimer Reaction
	Centers of Rhodobacter sphaeroides},
  journal = {Biochemistry},
  year = {1999},
  volume = {38},
  pages = {7545-7555},
  number = {23},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9829128}
}

@ARTICLE{vanBrederodeM.E._bi9950793,
  author = {van Brederode, M.E. and van Stokkum, I. H. M. and Katilius, E. and
	van Mourik, F. and Jones, M.R. and van Grondelle, R.},
  title = {Primary Charge Separation Routes in the {BChl:BPhe} Heterodimer Reaction
	Centers of Rhodobacter sphaeroides},
  journal = {Biochemistry},
  year = {1999},
  volume = {38},
  pages = {9556-9556},
  number = {29},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9950793}
}

@ARTICLE{MarionE.vanBrederode03021999,
  author = {van Brederode, Marion E. and van Mourik, Frank and van Stokkum, Ivo
	H. M. and Jones, Michael R. and van Grondelle, Rienk},
  title = {{Multiple pathways for ultrafast transduction of light energy in
	the photosynthetic reaction center of Rhodobacter sphaeroides}},
  journal = {PNAS},
  year = {1999},
  volume = {96},
  pages = {2054-2059},
  number = {5},
  doi = {10.1073/pnas.96.5.2054},
  file = {2054.pdf:http\://www.pnas.org/cgi/reprint/96/5/2054.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/96/5/2054}
}

@ARTICLE{photo_98,
  author = {Marion E. van Brederode and Justin P. Ridge and Ivo H. M. van Stokkum
	and Frank van Mourik and Michael R. Jones and Rienk van Grondelle},
  title = {On the efficiency of energy transfer and the different pathways of
	electron transfer in mutant reaction centers of Rhodobacter sphaeroides},
  journal = {Photosynthesis Research},
  year = {1998},
  volume = {55},
  pages = {141--146},
  number = {2},
  url = {http://www.springerlink.com/content/v702557x62725142}
}

@ARTICLE{Carroll2010,
  author = {Carroll, E. C. and Song, S. H. and Kumauchi, M. and van Stokkum,
	I. H. M. and Jailaubekov, A. and Hoff, W. D. and Larsen, D. S.},
  title = {Subpicosecond Excited-State Proton Transfer Preceding Isomerization
	During the Photorecovery of Photoactive Yellow Protein},
  journal = {Journal of Physical Chemistry Letters},
  year = {2010},
  volume = {1},
  pages = {2793-2799},
  number = {19},
  abstract = {The ultrafast excited-state dynamics underlying the receptor state
	photorecovery is resolved in the M100A mutant of the photoactive
	yellow protein (PYP) from Halorhodospira halophila. The M100A PYP
	mutant, with its distinctly slower photocycle than wt PYP, allows
	isolation of the pB signaling state for study of the photodynamics
	of the protonated chromophore cis-p-coumaric acid. Transient absorption
	signals indicate a subpicosecond excited-state proton-transfer reaction
	in the pB state that results in chromophore deprotonation prior to
	the cis-trans isomerization required in the photorecovery dynamics
	of the pG state. Two terminal photoproducts are observed, a blue-absorbing
	species presumed to be deprotonated trans-p-coumaric acid and an
	ultraviolet-ansorbing protonated photoproduct. These two photoproducts
	are hypothesized to originated from an equilibrium of open and closed
	folded forms of the signaling state, I-2 and I-2'.}
}

@ARTICLE{doi:10.1021/jp107935f,
  author = {Chen, Xiyi and Larsen, Delmar S. and Bradforth, Stephen E. and van
	Stokkum, Ivo H. M.},
  title = {Broadband Spectral Probing Revealing Ultrafast Photochemical Branching
	after Ultraviolet Excitation of the Aqueous Phenolate Anion},
  journal = {The Journal of Physical Chemistry A},
  year = {2011},
  volume = {{115}},
  pages = {{3807-3819}},
  number = {{16}},
  month = {{Apr 28}},
  doi = {10.1021/jp107935f},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp107935f},
  url = {http://pubs.acs.org/doi/abs/10.1021/jp107935f}
}

@ARTICLE{Cofino2005,
  author = {Cofino, Wim P. and van Stokkum, Ivo H. M. and van Steenwijk, Jaap
	and Wells, David E.},
  title = {A new model for the inference of population characteristics from
	experimental data using uncertainties: Part {II}. Application to
	censored datasets},
  journal = {Analytica Chimica Acta},
  year = {2005},
  volume = {533},
  pages = {31--39},
  month = {Mar},
  day = {21},
  issue = {1},
  keywords = {Censored data},
  url = {http://www.sciencedirect.com/science/article/B6TF4-4F1J8PY-5/2/29f748e8695962cdce5f8f8738329ec3}
}

@ARTICLE{Cofino2000,
  author = {Cofino, Wim P. and van Stokkum, Ivo H. M. and Wells, David E. and
	Ariese, Freek and Wegener, Jan-Willem M. and Peerboom, Renee A. L.},
  title = {A new model for the inference of population characteristics from
	experimental data using uncertainties. Application to interlaboratory
	studies},
  journal = {Chemometrics and Intelligent Laboratory Systems},
  year = {2000},
  volume = {53},
  pages = {37--55},
  month = {Nov},
  day = {13},
  issue = {1-2},
  keywords = {Population characteristics},
  url = {http://www.sciencedirect.com/science/article/B6TFP-41H9NH7-3/2/70ba5522c9ed18193d3c054836259e5a}
}

@ARTICLE{doi:10.1021/bi101565w,
  author = {Di Donato, Mariangela and Stahl, Andreas D. and van Stokkum, Ivo
	H. M. and van Grondelle, Rienk and Groot, Marie-Louise},
  title = {Cofactors Involved in Light-Driven Charge Separation in Photosystem
	{I} Identified by Subpicosecond Infrared Spectroscopy},
  journal = {Biochemistry},
  year = {2011},
  volume = {50},
  pages = {480-490},
  number = {4},
  doi = {10.1021/bi101565w},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi101565w},
  url = {http://pubs.acs.org/doi/abs/10.1021/bi101565w}
}

@ARTICLE{DiDonatoM_jp068315,
  author = {DiDonato, M. and van Grondelle, R. and van Stokkum, I. H. M. and
	Groot, M.L.},
  title = {Excitation Energy Transfer in the Photosystem {II} Core Antenna Complex
	CP43 Studied by Femtosecond Visible/Visible and Visible/Mid-Infrared
	Pump Probe Spectroscopy},
  journal = {Journal of Physical Chemistry B},
  year = {2007},
  volume = {111},
  pages = {7345-7352},
  number = {25},
  affiliation = {Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit,
	1081 HV Amsterdam, The Netherlands},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp068315+}
}

@ARTICLE{DoustA.B._jp051173j,
  author = {Doust, A.B. and van Stokkum, I. H. M. and Larsen, D.S. and Wilk,
	K.E. and Curmi, P.M.G. and van Grondelle, R. and Scholes, G.D.},
  title = {Mediation of Ultrafast Light-Harvesting by a Central Dimer in Phycoerythrin
	545 Studied by Transient Absorption and Global Analysis},
  journal = {Journal of Physical Chemistry B},
  year = {2005},
  volume = {109},
  pages = {14219-14226},
  number = {29},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp051173j}
}

@ARTICLE{FreseR.N._bi0273516,
  author = {Frese, R.N. and Germano, M. and de Weerd, F.L. and van Stokkum, I.
	H. M. and Shkuropatov, A.Ya. and Shuvalov, V.A. and van Gorkom, H.J.
	and van Grondelle, R. and Dekker, J.P.},
  title = {Electric Field Effects on the Chlorophylls, Pheophytins, and {$\beta$}-Carotenes
	in the Reaction Center of Photosystem {II}},
  journal = {Biochemistry},
  year = {2003},
  volume = {42},
  pages = {9205-9213},
  number = {30},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi0273516}
}

@INPROCEEDINGS{i98b,
  author = {Frese, RN and Gobets, B and van Stokkum, I. H. M. and van Grondelle,
	R and van Mourik, F},
  title = {Dielectric relaxation on a picosecond time-scale at 77 {K}: a fluorescence
	study on the {LH2 B800-820} complex of {R}ps. acidophila},
  booktitle = {Photosynthesis: Mechanisms and Effects},
  year = {1998},
  editor = {Garab, G},
  pages = {41-44},
  publisher = {Kluwer Academic Publishers, Dordrecht}
}

@ARTICLE{photo_05,
  author = {Raoul Frese and Uwe Oberheide and Ivo van Stokkum and Rienk van Grondelle
	and Markus Foidl and J{\"u}rgen Oelze and Herbert van Amerongen},
  title = {The organization of bacteriochlorophyll c in chlorosomes from Chloroflexus
	aurantiacus and the structural role of carotenoids and protein},
  journal = {Photosynthesis Research},
  year = {1997},
  volume = {54},
  pages = {115--126},
  issue = {2},
  url = {http://www.springerlink.com/content/l04663t5qj575152}
}

@ARTICLE{Frese2002,
  author = {Frese, Raoul N. and Palacios, Miguel A. and Azzizi, Aissa and van
	Stokkum, Ivo H. M. and Kruip, Jochen and Rogner, Matthias and Karapetyan,
	Navassard V. and Schlodder, Eberhard and van Grondelle, Rienk and
	Dekker, Jan P.},
  title = {Electric field effects on red chlorophylls, {$\beta$}-carotenes and
	{P700} in cyanobacterial Photosystem {I} complexes},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {2002},
  volume = {1554},
  pages = {180--191},
  month = {Jul},
  day = {01},
  issue = {3},
  keywords = {Synechocystis PCC 6803},
  url = {http://www.sciencedirect.com/science/article/B6T1S-4639K94-2/2/f35393c5825b6bf4795ee14986204c99}
}

@INPROCEEDINGS{m04,
  author = {M. Gauden and S. Crosson and I. H. M. van Stokkum and R.van Grondelle
	and K. Moffat and J.T.M. Kennis},
  title = {Low-temperature and time-resolved spectroscopic characterization
	of the {LOV2} domain of Avena sativa phototropin},
  booktitle = {Volume 5463 - Femtosecond Laser Applications in Biology},
  year = {2004},
  pages = {97-104},
  publisher = {Proceedings of SPIE},
  editors = {S. Avrillier and J.M. Tualle}
}

@ARTICLE{GaudenM_bi7006433,
  author = {Gauden, M. and Grinstead, J.S. and Laan, W. and van Stokkum, I. H.
	M. and Avila-Perez, M. and Toh, K.C. and Boelens, R. and Kaptein,
	R. and van Grondelle, R. and Hellingwerf, K.J. and Kennis, J.T.M.},
  title = {On the Role of Aromatic Side Chains in the Photoactivation of BLUF
	Domains},
  journal = {Biochemistry},
  year = {2007},
  volume = {46},
  pages = {7405-7415},
  number = {25},
  affiliation = {Biophysics Group, Department of Physics and Astronomy, Faculty of
	Sciences, Vrije Universiteit, De Boelelaan 1081, 1081HV Amsterdam,
	The Netherlands, Department of NMR spectroscopy, Bijvoet Center for
	Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht,
	The Netherlands, and Swammerdam Institute for Life Science, University
	of Amsterdam, Nieuwe Achtergracht 166, 1018 WY Amsterdam, The Netherlands},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi7006433}
}

@ARTICLE{MagdalenaGauden07182006,
  author = {Gauden, Magdalena and van Stokkum, Ivo H. M. and Key, Jason M. and
	L{\"{u}}hrs, Daniel Ch. and van Grondelle, Rienk and Hegemann, Peter
	and Kennis, John T. M.},
  title = {{Hydrogen-bond switching through a radical pair mechanism in a flavin-binding
	photoreceptor}},
  journal = {PNAS},
  year = {2006},
  volume = {103},
  pages = {10895-10900},
  number = {29},
  doi = {10.1073/pnas.0600720103},
  file = {10895.pdf:http\://www.pnas.org/cgi/reprint/103/29/10895.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/103/29/10895}
}

@ARTICLE{GaudenM._bi047359a,
  author = {Gauden, M. and Yeremenko, S. and Laan, W. and van Stokkum, I. H.
	M. and Ihalainen, J.A. and van Grondelle, R. and Hellingwerf, K.J.
	and Kennis, J.T.M.},
  title = {Photocycle of the Flavin-Binding Photoreceptor AppA, a Bacterial
	Transcriptional Antirepressor of Photosynthesis Genes},
  journal = {Biochemistry},
  year = {2005},
  volume = {44},
  pages = {3653-3662},
  number = {10},
  affiliation = {Department of Biophysics, Faculty of Sciences, Vrije Universiteit,
	De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Swammerdam
	Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht
	166, 1018 WY Amsterdam, The Netherlands},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi047359a}
}

@ARTICLE{Gensch2002,
  author = {Gensch, T. and Gradinaru, C. C. and van Stokkum, I. H. M. and Hendriks,
	J. and Hellingwerf, K. J. and van Grondelle, R.},
  title = {The primary photoreaction of photoactive yellow protein ({PYP}):
	anisotropy changes and excitation wavelength dependence},
  journal = {Chemical Physics Letters},
  year = {2002},
  volume = {356},
  pages = {347--354},
  month = {Apr},
  day = {22},
  issue = {3-4},
  url = {http://www.sciencedirect.com/science/article/B6TFN-45F9235-B/2/0149a895b50bb6debf89a672c79a1f18}
}

@ARTICLE{M.Germano03012004,
  author = {Germano, M. and Gradinaru, C. C. and Shkuropatov, A. Ya. and van
	Stokkum, I. H. M. and Shuvalov, V. A. and Dekker, J. P. and Grondelle,
	R. van and van Gorkom, H. J.},
  title = {{Energy and Electron Transfer in Photosystem {II} Reaction Centers
	with Modified Pheophytin Composition}},
  journal = {Biophysical Journal},
  year = {2004},
  volume = {86},
  pages = {1664-1672},
  number = {3},
  file = {1664.pdf:http\://www.biophysj.org/cgi/reprint/86/3/1664.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/86/3/1664}
}

@ARTICLE{K.Gibasiewicz03012005,
  author = {Gibasiewicz, K. and Croce, R. and Morosinotto, T. and Ihalainen,
	J. A. and van Stokkum, I. H. M. and Dekker, J. P. and Bassi, R. and
	van Grondelle, R.},
  title = {{Excitation Energy Transfer Pathways in Lhca4}},
  journal = {Biophysical Journal},
  year = {2005},
  volume = {88},
  pages = {1959-1969},
  number = {3},
  doi = {10.1529/biophysj.104.049916},
  file = {1959.pdf:http\://www.biophysj.org/cgi/reprint/88/3/1959.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/88/3/1959}
}

@ARTICLE{Giera2010106,
  author = {Wojciech Giera and V.M. Ramesh and Andrew N. Webber and Ivo van Stokkum
	and Rienk van Grondelle and Krzysztof Gibasiewicz},
  title = {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}},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {2010},
  volume = {1797},
  pages = {106 - 112},
  number = {1},
  doi = {DOI: 10.1016/j.bbabio.2009.09.006},
  issn = {0005-2728},
  keywords = {Time-resolved fluorescence},
  url = {http://www.sciencedirect.com/science/article/B6T1S-4X7GMJJ-3/2/94690520750a9e06b785410279d33c99}
}

@ARTICLE{GobetsB._jp011901c,
  author = {Gobets, B. and Kennis, J.T.M. and Ihalainen, J.A. and Brazzoli, M.
	and Croce, R. and van Stokkum, I. H. M. and Bassi, R. and Dekker,
	J.P. and van Amerongen, H. and Fleming, G.R. and van Grondelle, R.},
  title = {Excitation Energy Transfer in Dimeric Light Harvesting Complex {I}:
	A Combined Streak-Camera/Fluorescence Upconversion Study},
  journal = {Journal of Physical Chemistry B},
  year = {2001},
  volume = {105},
  pages = {10132-10139},
  number = {41},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp011901c}
}

@ARTICLE{BasGobets12012003,
  author = {Gobets, Bas and van Stokkum, Ivo H. M. and van Mourik, Frank and
	Dekker, Jan P. and van Grondelle, Rienk},
  title = {{Excitation Wavelength Dependence of the Fluorescence Kinetics in
	Photosystem I Particles from Synechocystis {PCC} 6803 and Synechococcus
	elongatus}},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {85},
  pages = {3883-3898},
  number = {6},
  file = {3883.pdf:http\://www.biophysj.org/cgi/reprint/85/6/3883.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/85/6/3883}
}

@INPROCEEDINGS{i98c,
  author = {Gobets, B and van Stokkum, I. H. M. and van Mourik, F and R{\"o}gner,
	M and Kruip, J and Dekker, JP and van Grondelle R},
  title = {Time-resolved fluorescence measurements of photosystem 1 from Synechocystis
	{PCC} 6803},
  booktitle = {Photosynthesis: Mechanisms and Effects},
  year = {1998},
  editor = {Garab, G},
  pages = {571-574},
  publisher = {Kluwer Academic Publishers, Dordrecht}
}

@ARTICLE{BasGobets07012001,
  author = {Gobets, Bas and van Stokkum, Ivo H. M. and Rogner, Matthias and Kruip,
	Jochen and Schlodder, Eberhard and Karapetyan, Navassard V. and Dekker,
	Jan P. and van Grondelle, Rienk},
  title = {{Time-Resolved Fluorescence Emission Measurements of Photosystem
	I Particles of Various Cyanobacteria: A Unified Compartmental Model}},
  journal = {Biophysical Journal},
  year = {2001},
  volume = {81},
  pages = {407-424},
  number = {1},
  file = {407.pdf:http\://www.biophysj.org/cgi/reprint/81/1/407.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/81/1/407}
}

@ARTICLE{i98a,
  author = {Gradinaru, CC and {\"O}zdemir, S and G{\"u}len, D and van Stokkum,
	I. H. M. and van Grondelle, R and van Amerongen, H},
  title = {The flow of excitation in {LHC{II}} monomers: Implications for the
	structural model of the major plant antenna},
  journal = {Biophysical Journal},
  year = {1998},
  volume = {75},
  pages = {3064-3077}
}

@INPROCEEDINGS{i98x,
  author = {Gradinaru, CC and van Stokkum, I. H. M. and van Grondelle, R and
	van Amerongen},
  title = {Ultrafast absorption changes of the LHC{II} carotenoids upon selective
	excitation of the chlorophylls},
  booktitle = {Photosynthesis: Mechanisms and Effects},
  year = {1998},
  editor = {Garab, G},
  pages = {277-281},
  publisher = {Kluwer Academic Publishers, Dordrecht}
}

@ARTICLE{GradinaruC.C._jp001752i,
  author = {Gradinaru, C.C. and van Stokkum, I. H. M. and Pascal, A.A. and van
	Grondelle, R. and van Amerongen, H.},
  title = {Identifying the Pathways of Energy Transfer between Carotenoids and
	Chlorophylls in {LHCII} and {CP29}. A Multicolor, Femtosecond Pump-Probe
	Study},
  journal = {Journal of Physical Chemistry B},
  year = {2000},
  volume = {104},
  pages = {9330-9342},
  number = {39},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp001752i}
}

@ARTICLE{ClaudiuC.Gradinaru02272001,
  author = {Gradinaru, Claudiu C. and Kennis, John T. M. and Papagiannakis, Emmanouil
	and van Stokkum, Ivo H. M. and Cogdell, Richard J. and Fleming, Graham
	R. and Niederman, Robert A. and van Grondelle, Rienk},
  title = {{An unusual pathway of excitation energy deactivation in carotenoids:
	Singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic
	antenna}},
  journal = {PNAS},
  year = {2001},
  volume = {98},
  pages = {2364-2369},
  number = {5},
  doi = {10.1073/pnas.051501298},
  file = {2364.pdf:http\://www.pnas.org/cgi/reprint/98/5/2364.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/98/5/2364}
}

@ARTICLE{Groen1996,
  author = {Groen, B. H. and Bloemendal, M. and Mulders, J. W. M. and Hadden,
	J. M. and Chapman, D. and Van Stokkum, I. H. M. and Van Grondelle,
	R.},
  title = {Spectroscopic characterization of recombinant follicle stimulating
	hormone},
  journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy},
  year = {1996},
  volume = {52},
  pages = {1331--1346},
  month = {Sep},
  issue = {10},
  keywords = {FSH},
  url = {http://www.sciencedirect.com/science/article/B6VNG-4G83X49-N/2/68a0fa60fcc70406221ed2946d55f896}
}

@ARTICLE{GrootM.L._bi034878p,
  author = {Groot, M.L. and van Wilderen, L.J.G.W. and Larsen, D.S. and van der
	Horst, M.A. and van Stokkum, I. H. M. and Hellingwerf, K.J. and van
	Grondelle, R.},
  title = {Initial Steps of Signal Generation in Photoactive Yellow Protein
	Revealed with Femtosecond Mid-Infrared Spectroscopy},
  journal = {Biochemistry},
  year = {2003},
  volume = {42},
  pages = {10054-10059},
  number = {34},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi034878p}
}

@ARTICLE{MarieLouiseGroot09132005,
  author = {Groot, Marie Louise and Pawlowicz, Natalia P. and van Wilderen, Luuk
	J. G. W. and Breton, Jacques and van Stokkum, Ivo H. M. and van Grondelle,
	Rienk},
  title = {{Initial electron donor and acceptor in isolated Photosystem {II}
	reaction centers identified with femtosecond mid-{IR} spectroscopy}},
  journal = {PNAS},
  year = {2005},
  volume = {102},
  pages = {13087-13092},
  number = {37},
  doi = {10.1073/pnas.0503483102},
  file = {13087.pdf:http\://www.pnas.org/cgi/reprint/102/37/13087.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/102/37/13087}
}

@ARTICLE{gr94,
  author = {Groot, M. L. and Peterman, E. J. G. and van Kan, P. J. M. and van
	Stokkum, I. H. M. and Dekker, JP and van Grondelle, R},
  title = {Temperature dependent triplet and fluorescence quantum yields of
	the photosystem {II} reaction center described in a thermodynamic
	model},
  journal = {Biophysical Journal},
  year = {1994},
  volume = {67},
  pages = {318-330}
}

@ARTICLE{MLGroot01011995,
  author = {Groot, M L and Peterman, E J G and van Stokkum, I H M and Dekker,
	J P and van Grondelle, R},
  title = {{Triplet and fluorescing states of the CP47 antenna complex of photosystem
	II studied as a function of temperature.}},
  journal = {Biophys. J.},
  year = {1995},
  volume = {68},
  pages = {281-290},
  number = {1},
  abstract = {Fluorescence emission and triplet-minus-singlet (T-S) absorption difference
	spectra of the CP47 core antenna complex of photosystem {II} were
	measured as a function of temperature and compared to those of chlorophyll
	a in Triton X-100. Two spectral species were found in the chlorophyll
	T-S spectra of CP47, which may arise from a difference in ligation
	of the pigments or from an additional hydrogen bond, similar to what
	has been found for Chl molecules in a variety of solvents. The T-S
	spectra show that the lowest lying state in CP47 is at approximately
	685 nm and gives rise to fluorescence at 690 nm at 4 K. The fluorescence
	quantum yield is 0.11 +/- 0.03 at 4 K, the chlorophyll triplet yield
	is 0.16 +/- 0.03. Carotenoid triplets are formed efficiently at 4
	K through triplet transfer from chlorophyll with a yield of 0.15
	+/- 0.02. The major decay channel of the lowest excited state in
	CP47 is internal conversion, with a quantum yield of about 0.58.
	Increase of the temperature results in a broadening and blue shift
	of the spectra due to the equilibration of the excitation over the
	antenna pigments. Upon increasing the temperature, a decrease of
	the fluorescence and triplet yields is observed to, at 270 K, a value
	of about 55% of the low temperature value. This decrease is significantly
	larger than of chlorophyll a in Triton X-100. Although the coupling
	to low-frequency phonon or vibration modes of the pigments is probably
	intermediate in CP47, the temperature dependence of the triplet and
	fluorescence quantum yield can be modeled using the energy gap law
	in the strong coupling limit of Englman and Jortner (1970. J. Mol.
	Phys. 18:145-164) for non-radiative decays. This yields for CP47
	an average frequency of the promoting/accepting modes of 350 cm-1
	with an activation energy of 650 cm-1 for internal conversion and
	activationless intersystem crossing to the triplet state through
	a promoting mode with a frequency of 180 cm-1. For chlorophyll a
	in Triton X-100 the average frequency of the promoting modes for
	non-radiative decay is very similar, but the activation energy (300
	cm-1) is significantly smaller. },
  eprint = {http://www.biophysj.org/cgi/reprint/68/1/281.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/68/1/281}
}

@ARTICLE{i99a,
  author = {Groot, M-L and Frese, RN and de Weerd, FL and Bromek, K and Pettersson
	{\AA} and Peterman, EJG and van Stokkum, I. H. M. and van Grondelle,
	R and Dekker, JP},
  title = {Spectroscopic properties of the {CP43} core antenna protein of photosystem
	{II}},
  journal = {Biophysical Journal},
  year = {1999},
  volume = {77},
  pages = {328-340}
}

@ARTICLE{Marie-LouiseGroot04291997,
  author = {Groot, Marie-Louise and van Mourik, Frank and Eijckelhoff, Camiel
	and van Stokkum, Ivo H. M. and Dekker, Jan P. and van Grondelle,
	Rienk},
  title = {{Charge separation in the reaction center of photosystem {II} studied
	as a function oftemperature}},
  journal = {PNAS},
  year = {1997},
  volume = {94},
  pages = {4389-4394},
  number = {9},
  doi = {10.1073/pnas.94.9.4389},
  file = {4389.pdf:http\://www.pnas.org/cgi/reprint/94/9/4389.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/94/9/4389}
}

@INPROCEEDINGS{gr1996,
  author = {Groot, M-L and van Mourik, F and van Stokkum, I. H. M. and van Grondelle,
	R.},
  title = {Quantum beats in the reaction center of photosystem {II}},
  booktitle = {Ultrafast Phenomena {X}, Springer Series in Chemical Physics},
  year = {1996},
  editor = {Barbara, PF and Fujimoto, JG and Knox, WH and Zinth, W},
  volume = {1},
  pages = {344-345},
  publisher = {Springer-Verlag, Berlin}
}

@INPROCEEDINGS{g96,
  author = {Groot, M-L and P{\aa}lsson, L-O and Pribi{\'{c}}, R and van Stokkum,
	I. H. M. and Dekker, JP and van Grondelle, R.},
  title = {Energetics and excited state dynamics of the radical pair formation
	in isolated {CP47}- reaction center complex of Photosystem {II} at
	various temperatures},
  booktitle = {Fast Elementary Processes in Chemical and Biological Systems},
  year = {1996},
  editor = {Tramer, A},
  pages = {288-292},
  publisher = {AIP Press, New York}
}

@ARTICLE{Hadden1994,
  author = {Hadden, Jonathan M. and Bloemendal, Michael and Haris, Parvez I.
	and van Stokkum, Ivo H. M. and Chapman, Dennis and Srai, Surjit K.
	S.},
  title = {Structure and thermal stability of the extracellular fragment of
	human transferrin receptor at extracellular and endosomal {pH}},
  journal = {FEBS Letters},
  year = {1994},
  volume = {350},
  pages = {235--239},
  month = {Aug},
  day = {22},
  issue = {2-3},
  keywords = {Fourier transform infrared spectroscopy},
  url = {http://www.sciencedirect.com/science/article/B6T36-447N60H-KF/2/b701db71e778ecc07d8c756df641d0d5}
}

@ARTICLE{AndreaHaker02282003,
  author = {Haker, Andrea and Hendriks, Johnny and van Stokkum, Ivo H. M. and
	Heberle, Joachim and Hellingwerf, Klaas J. and Crielaard, Wim and
	Gensch, Thomas},
  title = {{The Two Photocycles of Photoactive Yellow Protein from Rhodobacter
	sphaeroides}},
  journal = {J. Biol. Chem.},
  year = {2003},
  volume = {278},
  pages = {8442-8451},
  number = {10},
  doi = {10.1074/jbc.M209343200},
  file = {8442.pdf:http\://www.jbc.org/cgi/reprint/278/10/8442.pdf:PDF},
  url = {http://www.jbc.org/cgi/content/abstract/278/10/8442}
}

@ARTICLE{Hendriks1999,
  author = {Hendriks, Johnny and van Stokkum, Ivo H. M. and Crielaard, Wim and
	Hellingwerf, Klaas J.},
  title = {Kinetics of and intermediates in a photocycle branching reaction
	of the photoactive yellow protein from Ectothiorhodospira halophila},
  journal = {FEBS Letters},
  year = {1999},
  volume = {458},
  pages = {252--256},
  month = {Sep},
  day = {17},
  issue = {2},
  keywords = {Transient spectroscopy},
  url = {http://www.sciencedirect.com/science/article/B6T36-3XCF7ST-17/2/0dc7786b9d3b7ff1281dec9d8fdda390}
}

@ARTICLE{JohnnyHendriks02012003,
  author = {Hendriks, Johnny and van Stokkum, Ivo H. M. and Hellingwerf, Klaas
	J.},
  title = {{Deuterium Isotope Effects in the Photocycle Transitions of the Photoactive
	Yellow Protein}},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {84},
  pages = {1180-1191},
  number = {2},
  file = {1180.pdf:http\://www.biophysj.org/cgi/reprint/84/2/1180.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/84/2/1180}
}

@ARTICLE{nat,
  author = {Derren J. Heyes and C. Neil Hunter and Ivo H. M. van Stokkum and
	Rienk van Grondelle and Marie Louise Groot},
  title = {Ultrafast enzymatic reaction dynamics in protochlorophyllide oxidoreductase},
  journal = {Nature Structural Biology},
  year = {2003},
  volume = {10},
  pages = {491 - 492}
}

@ARTICLE{HippiusC._jp711120v,
  author = {Hippius, C. and van Stokkum, I. H. M. and Gsänger, M. and Groeneveld,
	M.M. and Williams, R.M. and Würthner, F.},
  title = {Sequential {FRET} Processes in Calix[4]arene-Linked Orange-Red-Green
	Perylene Bisimide Dye Zigzag Arrays},
  journal = {Journal of Physical Chemistry C},
  year = {2008},
  volume = {112},
  pages = {2476-2486},
  number = {7},
  affiliation = {Institut für Organische Chemie and Röntgen Research Center for Complex
	Material Systems, Universität Würzburg, Am Hubland, D-97074 Würzburg,
	Germany, Molecular Photonics Group, van't Hoff Institute for Molecular
	Sciences (HIMS), Universiteit van Amsterdam, Nieuwe Achtergracht
	129, 1018 WV Amsterdam, The Netherlands, and Department of Physics
	and Astronomy, Vrije Universiteit, de Boelelaan 1081, 1081 HV Amsterdam,
	The Netherlands},
  issn = {1932-7447},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp711120v}
}

@ARTICLE{HippiusC._jp0733825,
  author = {Hippius, C. and van Stokkum, I. H. M. and Zangrando, E. and Williams,
	R.M. and Würthner, F.},
  title = {Excited State Interactions in Calix[4]arene-Perylene Bisimide Dye
	Conjugates: Global and Target Analysis of Supramolecular Building
	Blocks},
  journal = {Journal of Physical Chemistry C},
  year = {2007},
  volume = {111},
  pages = {13988-13996},
  number = {37},
  affiliation = {Universität Würzburg, Institut für Organische Chemie and Röntgen Research
	Center for Complex Material Systems, Am Hubland, D-97074 Würzburg,
	Germany, Molecular Photonics Group, van't Hoff Institute for Molecular
	Sciences (HIMS), Universiteit van Amsterdam, Nieuwe Achtergracht
	129, WS 1018 Amsterdam, The Netherlands, Department of Physics and
	Astronomy, Vrije Universiteit, de Boelelaan 1081, 1081 HV Amsterdam,
	The Netherlands, and University of Trieste, Dipartimento di Scienze
	Chimiche, Via Licio Giorgieri 1, 34127 Trieste, Italy},
  issn = {1932-7447},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0733825}
}

@ARTICLE{HippiusCatharina_jp804068b,
  author = {Hippius, Catharina and van Stokkum, Ivo H. M. and Zangrando, Ennio
	and Williams, René M. and Wykes, Michael and Beljonne, David and
	Würthner, Frank},
  title = {Ground- and Excited-State Pinched Cone Equilibria in Calix[4]arenes
	Bearing Two Perylene Bisimide Dyes},
  journal = {Journal of Physical Chemistry C},
  year = {2008},
  volume = {112},
  pages = {14626-14638},
  number = {37},
  affiliation = {Institut für Organische Chemie and Röntgen Research Center for Complex
	Material Systems, Universität Würzburg, Am Hubland, D-97074 Würzburg,
	Germany, Department of Physics and Astronomy, Vrije Universiteit,
	de Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Dipartimento
	di Scienze Chimiche, University of Trieste, Via Licio Giorgieri 1,
	34127 Trieste, Italy, Molecular Photonics Group, vant Hoff Institute
	for Molecular Sciences (HIMS), Universiteit van Amsterdam, Nieuwe
	Achtergracht 129, WS 1018 Amsterdam, The Netherlands, and Laboratory
	for Chemistry of Novel Materials, Center for Research in Molecular
	Electronics and Photonics, University of Mons-Hainaut, Place du Parc
	20, 7000 Mons, Belgium},
  issn = {1932-7447},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp804068b}
}

@ARTICLE{HoffW.D._bi980504y,
  author = {Hoff, W.D. and Xie, A. and Van Stokkum, I. H. M. and Tang, X.-j.
	and Gural, J. and Kroon, A.R. and Hellingwerf, K.J.},
  title = {Global Conformational Changes upon Receptor Stimulation in Photoactive
	Yellow Protein},
  journal = {Biochemistry},
  year = {1999},
  volume = {38},
  pages = {1009-1017},
  number = {3},
  affiliation = {Department of Biochemistry and Molecular Biology, The University of
	Chicago, Chicago, Illinois 60637, Department of Physics, Oklahoma
	State University, Stillwater, Oklahoma 74078, Faculty of Physics
	and Astronomy, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands,
	Wyeth-Ayherst Research, 401 North Middletown Road, Pearl River, New
	York 10965, and Department of Microbiology, E. C. Slater Institute,
	University of Amsterdam, 1018 WS Amsterdam, The Netherlands},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi980504y}
}

@ARTICLE{WD_Hoff10011994,
  author = {Hoff, W D and van Stokkum, I H M and van Ramesdonk, H J and van Brederode,
	M E and Brouwer, A M and Fitch, J C and Meyer, T E and van Grondelle,
	R and Hellingwerf, K J},
  title = {{Measurement and global analysis of the absorbance changes in the
	photocycle of the photoactive yellow protein from Ectothiorhodospira
	halophila.}},
  journal = {Biophys. J.},
  year = {1994},
  volume = {67},
  pages = {1691-1705},
  number = {4},
  abstract = {The photocycle of the photoactive yellow protein (PYP) from Ectothiorhodospira
	halophila was examined by time-resolved difference absorption spectroscopy
	in the wavelength range of 300-600 nm. Both time-gated spectra and
	single wavelength traces were measured. Global analysis of the data
	established that in the time domain between 5 ns and 2 s only two
	intermediates are involved in the room temperature photocycle of
	PYP, as has been proposed before (Meyer T.E., E. Yakali, M. A. Cusanovich,
	and G. Tollin. 1987. Biochemistry. 26:418-423; Meyer, T. E., G. Tollin,
	T. P. Causgrove, P. Cheng, and R. E. Blankenship. 1991. Biophys.
	J. 59:988-991). The first, red-shifted intermediate decays biexponentially
	(60% with tau = 0.25 ms and 40% with tau = 1.2 ms) to a blue-shifted
	intermediate. The last step of the photocycle is the biexponential
	(93% with tau = 0.15 s and 7% with tau = 2.0 s) recovery to the ground
	state of the protein. Reconstruction of the absolute spectra of these
	photointermediates yielded absorbance maxima of about 465 and 355
	nm for the red- and blue-shifted intermediate with an epsilon max
	at about 50% and 40% relative to the epsilon max of the ground state.
	The quantitative analysis of the photocycle in PYP described here
	paves the way to a detailed biophysical analysis of the processes
	occurring in this photoreceptor molecule. },
  eprint = {http://www.biophysj.org/cgi/reprint/67/4/1691.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/67/4/1691}
}

@ARTICLE{Hoff1997,
  author = {Hoff, Wouter D. and Van Stokkum, Ivo H. M. and Gural, Jechiam and
	Hellingwerf, Klaas J.},
  title = {Comparison of acid denaturation and light activation in the eubacterial
	blue-light receptor photoactive yellow protein},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {1997},
  volume = {1322},
  pages = {151--162},
  month = {Dec},
  day = {15},
  issue = {2-3},
  keywords = {Protein folding},
  url = {http://www.sciencedirect.com/science/article/B6T1S-3SXDX2J-7/2/2fbd53f7485d78438af3ff2ee4241fbc}
}

@ARTICLE{vanderHorst2001,
  author = {van der Horst, Michael A. and van Stokkum, Ivo H. and Crielaard,
	Wim and Hellingwerf, Klaas J.},
  title = {The role of the {N}-terminal domain of photoactive yellow protein
	in the transient partial unfolding during signalling state formation},
  journal = {FEBS Letters},
  year = {2001},
  volume = {497},
  pages = {26--30},
  month = {May},
  day = {18},
  issue = {1},
  keywords = {Photocycle kinetics},
  url = {http://www.sciencedirect.com/science/article/B6T36-43N8FNN-5/2/ea66f61cb831e7a207fe84a797239ff6}
}

@ARTICLE{vanderHorstM.A._bi050237d,
  author = {van der Horst, M.A. and van Stokkum, I. H. M. and Dencher, N.A. and
	Hellingwerf, K.J.},
  title = {Controlled Reduction of the Humidity Induces a Shortcut Recovery
	Reaction in the Photocycle of Photoactive Yellow Protein},
  journal = {Biochemistry},
  year = {2005},
  volume = {44},
  pages = {9160-9167},
  number = {25},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi050237d}
}

@ARTICLE{JanneAIhalainen03272007,
  author = {Ihalainen, Janne A. and Bredenbeck, Jens and Pfister, Rolf and Helbing,
	Jan and Chi, Lei and van Stokkum, Ivo H. M. and Woolley, G. Andrew
	and Hamm, Peter},
  title = {{Folding and unfolding of a photoswitchable peptide from picoseconds
	to microseconds}},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2007},
  volume = {104},
  pages = {5383-5388},
  number = {13},
  abstract = {Using time-resolved IR spectroscopy, we monitored the kinetics of
	folding and unfolding processes of a photoswitchable 16-residue alanine-based
	{alpha}-helical peptide on a timescale from few picoseconds to almost
	40 {micro}s and over a large temperature range (279-318 K). The folding
	and unfolding processes were triggered by an ultrafast laser pulse
	that isomerized the cross linker within a few picoseconds. The main
	folding and unfolding times (700 ns and 150 ns, respectively, at
	room temperature) are in line with previous T-jump experiments obtained
	from similar peptides. However, both processes show complex, strongly
	temperature-dependent spectral kinetics that deviate clearly from
	a single-exponential behavior. Whereas in the unfolding experiment
	the ensemble starts from a well defined folded state, the starting
	ensemble in the folding experiment is more heterogeneous, which leads
	to distinctly different kinetics of the experiments, because they
	are sensitive to different regions of the energy surface. A qualitative
	agreement with the experimental data-set can be obtained by a model
	where the unfolded states act as a hub connected to several separated
	"misfolded" states with a distribution of rates. We conclude that
	a rather large spread of rates (k1 : kn {approx} 9) is needed to
	explain the experimentally observed stretched exponential response
	with stretching factor {$\beta$} = 0.8 at 279 K. },
  doi = {10.1073/pnas.0607748104},
  eprint = {http://www.pnas.org/cgi/reprint/104/13/5383.pdf},
  url = {http://www.pnas.org/cgi/content/abstract/104/13/5383}
}

@ARTICLE{JanneA.Ihalainen10012002,
  author = {Ihalainen, Janne A. and Jensen, Poul Erik and Haldrup, Anna and van
	Stokkum, Ivo H. M. and van Grondelle, Rienk and Scheller, Henrik
	Vibe and Dekker, Jan P.},
  title = {{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}},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {83},
  pages = {2190-2201},
  number = {4},
  file = {2190.pdf:http\://www.biophysj.org/cgi/reprint/83/4/2190.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/83/4/2190}
}

@ARTICLE{Ihalainen2005,
  author = {Ihalainen, Janne A. and Klimmek, Frank and Ganeteg, Ulrika and van
	Stokkum, Ivo H. M. and van Grondelle, Rienk and Jansson, Stefan and
	Dekker, Jan P.},
  title = {Excitation energy trapping in photosystem {I} complexes depleted
	in Lhca1 and Lhca4},
  journal = {FEBS Letters},
  year = {2005},
  volume = {579},
  pages = {4787--4791},
  month = {Aug},
  day = {29},
  issue = {21},
  keywords = {Photosynthesis},
  url = {http://www.sciencedirect.com/science/article/B6T36-4GTWRWW-D/2/8dc2787303500a4bc1ec9f31cb2bbc89}
}

@ARTICLE{Ihalainen2005a,
  author = {Ihalainen, Janne A. and van Stokkum, Ivo H. M. and Gibasiewicz, Krzysztof
	and Germano, Marta and van Grondelle, Rienk and Dekker, Jan P.},
  title = {Kinetics of excitation trapping in intact Photosystem {I} of {C}hlamydomonas
	reinhardtii and {A}rabidopsis thaliana},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {2005},
  volume = {1706},
  pages = {267--275},
  month = {Feb},
  day = {17},
  issue = {3},
  keywords = {Photosystem I},
  url = {http://www.sciencedirect.com/science/article/B6T1S-4F01KGF-1/2/32a548dbbad01cb8fe2d3809138ecc59}
}

@ARTICLE{IhalainenJ.A._jp0519316,
  author = {Ihalainen, J.A. and Croce, R. and Morosinotto, T. and van Stokkum,
	I. H. M. and Bassi, R. and Dekker, J.P. and van Grondelle, R.},
  title = {Excitation Decay Pathways of Lhca Proteins: A Time-Resolved Fluorescence
	Study},
  journal = {Journal of Physical Chemistry B},
  year = {2005},
  volume = {109},
  pages = {21150-21158},
  number = {44},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0519316}
}

@ARTICLE{IhalainenJ.A._jp010921b,
  author = {Ihalainen, J.A. and Linnanto, J. and Myllyperkio, P. and van Stokkum,
	I. H. M. and Ucker, B. and Scheer, H. and Korppi-Tommola, J.E.I.},
  title = {Energy Transfer in {LH2} of Rhodospirillum Molischianum, Studied
	by Subpicosecond Spectroscopy and Configuration Interaction Exciton
	Calculations},
  journal = {Journal of Physical Chemistry B},
  year = {2001},
  volume = {105},
  pages = {9849-9856},
  number = {40},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp010921b}
}

@ARTICLE{KennisJ.T.M._bi034022k,
  author = {Kennis, J.T.M. and Crosson, S. and Gauden, M. and van Stokkum, I.
	H. M. and Moffat, K. and van Grondelle, R.},
  title = {Primary Reactions of the {LOV2} Domain of Phototropin, a Plant Blue-Light
	Photoreceptor},
  journal = {Biochemistry},
  year = {2003},
  volume = {42},
  pages = {3385-3392},
  number = {12},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi034022k}
}

@ARTICLE{kenn,
  author = {Kennis, JTM and Gobets, B and van Stokkum, I. H. M. and Dekker, JP
	and van Grondelle R and Fleming GR},
  title = {Light harvesting by chlorophylls and carotenoids in the photosystem
	{I} core complex of Synechococcus elongatus: a fluorescence upconversion
	study},
  journal = {J. Phys. Chem. B},
  year = {2001},
  volume = {105},
  pages = {4485-4494}
}

@ARTICLE{KennisJ.T.M._bi9712605,
  author = {Kennis, J.T.M. and Shkuropatov, A.Ya. and van Stokkum, I. H. M. and
	Gast, P. and Hoff, A.J. and Shuvalov, V.A. and Aartsma, T.J.},
  title = {Formation of a Long-Lived {P+BA-} State in Plant Pheophytin-Exchanged
	Reaction Centers of Rhodobacter sphaeroides {R26} at Low Temperature},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {16231-16238},
  number = {51},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9712605}
}

@ARTICLE{KennisJ.T.M._ja031840r,
  author = {Kennis, J.T.M. and van Stokkum, I. H. M. and Crosson, S. and Gauden,
	M. and Moffat, K. and van Grondelle, R.},
  title = {The {LOV2} Domain of Phototropin: A Reversible Photochromic Switch},
  journal = {Journal of the American Chemical Society},
  year = {2004},
  volume = {126},
  pages = {4512-4513},
  number = {14},
  issn = {0002-7863},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja031840r}
}

@ARTICLE{JohnT.M.Kennis12282004,
  author = {Kennis, John T. M. and Larsen, Delmar S. and van Stokkum, Ivo H.
	M. and Vengris, Mikas and van Thor, Jasper J. and van Grondelle,
	Rienk},
  title = {{Uncovering the hidden ground state of green fluorescent protein}},
  journal = {PNAS},
  year = {2004},
  volume = {101},
  pages = {17988-17993},
  number = {52},
  doi = {10.1073/pnas.0404262102},
  file = {17988.pdf:http\://www.pnas.org/cgi/reprint/101/52/17988.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/101/52/17988}
}

@ARTICLE{KleimaF.J._bi9716480,
  author = {Kleima, F.J. and Gradinaru, C.C. and Calkoen, F. and van Stokkum,
	I. H. M. and van Grondelle, R. and van Amerongen, H.},
  title = {Energy Transfer in {LHCII} Monomers at {77K} Studied by Sub-Picosecond
	Transient Absorption Spectroscopy},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {15262-15268},
  number = {49},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9716480}
}

@INPROCEEDINGS{i98y,
  author = {Kleima, FJ and Hofmann, E and Gobets, B and van Stokkum, I. H. M.
	and van Grondelle and van Amerongen, H},
  title = {Peridinin chlorophyll protein: structure and dynamics related},
  booktitle = {Photosynthesis: Mechanisms and Effects},
  year = {1998},
  editor = {Garab, G},
  pages = {441-444},
  publisher = {Kluwer Academic Publishers, Dordrecht}
}

@ARTICLE{FoskeJ.Kleima01012000,
  author = {Kleima, Foske J. and Hofmann, Eckhard and Gobets, Bas and van Stokkum,
	Ivo H. M. and van Grondelle, Rienk and Diederichs, Kay and van Amerongen,
	Herbert},
  title = {{Förster Excitation Energy Transfer in Peridinin-Chlorophyll-a-Protein}},
  journal = {Biophysical Journal},
  year = {2000},
  volume = {78},
  pages = {344-353},
  number = {1},
  file = {344.pdf:http\://www.biophysj.org/cgi/reprint/78/1/344.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/78/1/344}
}

@ARTICLE{Klerk2010,
  author = {Klerk, Joost de and van Stokkum, Ivo H. M. and Szemik-Hojniak, Anna
	and Deperasinska, Irena and Gooijer, Cees and Zhang, Hong and Buma,
	Wybren-Jan and Ariese, Freek},
  title = {Excited State Processes of 2-Butylamino-6-methyl-4-nitropyridine
	N-oxide in Nonpolar Solvents. A Transient Absorption Spectroscopy
	Study},
  journal = {The Journal of Physical Chemistry A},
  year = {2010},
  volume = {114},
  pages = {4045-4050},
  number = {12},
  doi = {doi: 10.1021/jp909468h}
}

@ARTICLE{Koehorst2010,
  author = {Koehorst, R. B. M. and Laptenok, S. and van Oort, B. and van Hoek,
	A. and Spruijt, R. B. and van Stokkum, I. H. M. and van Amerongen,
	H. and Hemminga, M. A.},
  title = {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},
  journal = {European Biophysics Journal with Biophysics Letters},
  year = {2010},
  volume = {39},
  pages = {647-656},
  number = {4},
  note = {Sp. Iss. SI},
  abstract = {Profiles of lipid-water bilayer dynamics were determined from picosecond
	time-resolved fluorescence spectra of membrane-embedded BADAN-labeled
	M13 coat protein. For this purpose, the protein was labeled at seven
	key positions. This places the label at well-defined locations from
	the water phase to the center of the hydrophobic acyl chain region
	of a phospholipid model membrane, providing us with a nanoscale ruler
	to map membranes. Analysis of the time-resolved fluorescence spectroscopic
	data provides the characteristic time constant for the twisting motion
	of the BADAN label, which is sensitive to the local flexibility of
	the protein-lipid environment. In addition, we obtain information
	about the mobility of water molecules at the membrane-water interface.
	The results provide an unprecedented nanoscale profiling of the dynamics
	and distribution of water in membrane systems. This information gives
	clear evidence that the actual barrier of membranes for ions and
	aqueous solvents is located at the region of carbonyl groups of the
	acyl chains.}
}

@ARTICLE{RemcoKort07012005,
  author = {Kort, Remco and O'Brien, Andrea C. and van Stokkum, Ivo H. M. and
	Oomes, Suus J. C. M. and Crielaard, Wim and Hellingwerf, Klaas J.
	and Brul, Stanley},
  title = {{Assessment of Heat Resistance of Bacterial Spores from Food Product
	Isolates by Fluorescence Monitoring of Dipicolinic Acid Release}},
  journal = {Applied and Environmental Microbiology},
  year = {2005},
  volume = {71},
  pages = {3556-3564},
  number = {7},
  file = {3556.pdf:http\://aem.asm.org/cgi/reprint/71/7/3556.pdf:PDF},
  url = {http://aem.asm.org/cgi/content/abstract/71/7/3556}
}

@ARTICLE{BrentP.Krueger06012001,
  author = {Krueger, Brent P. and Lampoura, Stefania S. and van Stokkum, Ivo
	H. M. and Papagiannakis, Emmanouil and Salverda, Jante M. and Gradinaru,
	Claudiu C. and Rutkauskas, Danielis and Hiller, Roger G. and van
	Grondelle, Rienk},
  title = {{Energy Transfer in the Peridinin Chlorophyll-a Protein of Amphidinium
	carterae Studied by Polarized Transient Absorption and Target Analysis}},
  journal = {Biophys. J.},
  year = {2001},
  volume = {80},
  pages = {2843-2855},
  number = {6},
  file = {2843.pdf:http\://www.biophysj.org/cgi/reprint/80/6/2843.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/80/6/2843}
}

@ARTICLE{wout_2003,
  author = {Wouter Laan and Michael A. van der Horst and Ivo H. van Stokkum and
	Klaas J. Hellingwerf},
  title = {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},
  journal = {Photochemistry and Photobiology},
  year = {2003},
  volume = {78},
  pages = {290-297},
  number = {3},
  file = {PhotochemPhotobiol2003_78_290Laan.pdf:http\://www.nat.vu.nl/~ivo/pub/2003/PhotochemPhotobiol2003_78_290Laan.pdf:PDF}
}

@ARTICLE{LampouraS.S._jp0021289,
  author = {Lampoura, S.S. and van Grondelle, R. and van Stokkum, I. H. M. and
	Cogdell, R.J. and Wiersma, D.A. and Duppen, K.},
  title = {Exciton Dynamics in {LH1} and {LH2} of Rhodopseudomonas Acidophila
	and Rhodobium Marinum Probed with Accumulated Photon Echo and Pump-Probe
	Measurements},
  journal = {Journal of Physical Chemistry B},
  year = {2000},
  volume = {104},
  pages = {12072-12078},
  number = {50},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0021289}
}

@ARTICLE{la,
  author = {Lampoura, S.S. and B.P. Krueger and I. H. M. van Stokkum and J.M.
	Salverda and C.C. Gradinaru and D. Rutkauskas and R.G. Hiller and
	R. van Grondelle},
  title = {Energy transfer in the peridinin chlorophyll: a protein of Amphidinium
	carterae studied by polarized transient absorption Measurements},
  journal = {Int. J. Mod. Phys. B},
  year = {2001},
  volume = {15},
  pages = {3849-3852}
}

@ARTICLE{laptenok2010,
  author = {Sergey Laptenok and Jan Willem Borst and Katharine M. Mullen and
	Ivo H. M. van Stokkum and Antonie J. W. G. Visser and Herbert van
	Amerongen},
  title = {Global analysis of {F}örster resonance energy transfer in live cells
	measured by fluorescence lifetime imaging microscopy exploiting the
	rise time of acceptor fluorescence},
  journal = {Physical Chemistry Chemical Physics},
  year = {2010},
  volume = {12},
  pages = {7593–7602}
}

@ARTICLE{laptenok,
  author = {Sergey Laptenok and Katharine M. Mullen and Jan Willem Borst and
	Ivo H. M. van Stokkum and Vladimir V. Apanasovich and Antonie J.
	W. G. Visser},
  title = {Fluorescence Lifetime Imaging Microscopy ({FLIM}) data analysis with
	\pkg{TIMP}},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {18},
  number = {8},
  url = {http://www.jstatsoft.org/v18/i08/}
}

@ARTICLE{doi:10.1021/bi101965d,
  author = {Laptenok, Sergey P. and Visser, Nina V. and Engel, Ruchira and Westphal,
	Adrie H. and van Hoek, Arie and Van Mierlo, Carlo P. M. and van Stokkum,
	Ivo H.M. and van Amerongen, Herbert and Visser, Antonie J. W. G.},
  title = {A General Approach to Detect Folding Intermediates from Steady-State
	and Time-Resolved Fluorescence of Single Tryptophan-Containing Proteins},
  journal = {Biochemistry},
  year = {2011},
  volume = {{50}},
  pages = {{3441-3450}},
  number = {{17}},
  month = {{May 3}},
  doi = {10.1021/bi101965d},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi101965d},
  url = {http://pubs.acs.org/doi/abs/10.1021/bi101965d}
}

@ARTICLE{Larsen2003c,
  author = {Larsen, Delmar S. and Papagiannakis, Emmanouil and van Stokkum, Ivo
	H. M. and Vengris, Mikas and Kennis, John T. M. and van Grondelle,
	Rienk},
  title = {Excited state dynamics of {$\beta$}-carotene explored with dispersed
	multi-pulse transient absorption},
  journal = {Chemical Physics Letters},
  year = {2003},
  volume = {381},
  pages = {733--742},
  month = {Nov},
  day = {21},
  issue = {5-6},
  url = {http://www.sciencedirect.com/science/article/B6TFN-49XPV3C-4/2/17ec647f103b82d63a809bd92e29e372}
}

@ARTICLE{DelmarS.Larsen09012004,
  author = {Larsen, Delmar S. and van Stokkum, Ivo H. M. and Vengris, Mikas and
	van der Horst, Michael A. and de Weerd, Frank L. and Hellingwerf,
	Klaas J. and van Grondelle, Rienk},
  title = {{Incoherent Manipulation of the Photoactive Yellow Protein Photocycle
	with Dispersed Pump-Dump-Probe Spectroscopy}},
  journal = {Biophysical Journal},
  year = {2004},
  volume = {87},
  pages = {1858-1872},
  number = {3},
  doi = {10.1529/biophysj.104.043794},
  file = {1858.pdf:http\://www.biophysj.org/cgi/reprint/87/3/1858.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/87/3/1858}
}

@ARTICLE{Larsen2003b,
  author = {Larsen, Delmar S. and Vengris, Mikas and van Stokkum, Ivo H. M. and
	van der Horst, Michael A. and Cordfunke, Robert A. and Hellingwerf,
	Klaas J. and van Grondelle, Rienk},
  title = {Initial photo-induced dynamics of the photoactive yellow protein
	chromophore in solution},
  journal = {Chemical Physics Letters},
  year = {2003},
  volume = {369},
  pages = {563--569},
  month = {Feb},
  day = {28},
  issue = {5-6},
  url = {http://www.sciencedirect.com/science/article/B6TFN-47T2P87-2/2/b697a1f805ce6672a0932c6ead538958}
}

@ARTICLE{DelmarS.Larsen04012004,
  author = {Larsen, Delmar S. and Vengris, Mikas and van Stokkum, Ivo H. M. and
	van der Horst, Michael A. and de Weerd, Frank L. and Hellingwerf,
	Klaas J. and van Grondelle, Rienk},
  title = {{Photoisomerization and Photoionization of the Photoactive Yellow
	Protein Chromophore in Solution}},
  journal = {Biophysical Journal},
  year = {2004},
  volume = {86},
  pages = {2538-2550},
  number = {4},
  file = {2538.pdf:http\://www.biophysj.org/cgi/reprint/86/4/2538.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/86/4/2538}
}

@ARTICLE{LarsenO.F.A._jp021756i,
  author = {Larsen, O.F.A. and van Stokkum, I. H. M. and Pandit, A. and van Grondelle,
	R. and van Amerongen, H.},
  title = {Ultrafast Polarized Fluorescence Measurements on Tryptophan and a
	Tryptophan-Containing Peptide},
  journal = {Journal of Physical Chemistry B},
  year = {2003},
  volume = {107},
  pages = {3080-3085},
  number = {13},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp021756i}
}

@ARTICLE{OlafF.A.Larsen08012001,
  author = {Larsen, Olaf F. A. and van Stokkum, Ivo H. M. and Gobets, Bas and
	van Grondelle, Rienk and van Amerongen, Herbert},
  title = {{Probing the Structure and Dynamics of a DNA Hairpin by Ultrafast
	Quenching and Fluorescence Depolarization}},
  journal = {Biophysical Journal},
  year = {2001},
  volume = {81},
  pages = {1115-1126},
  number = {2},
  file = {1115.pdf:http\://www.biophysj.org/cgi/reprint/81/2/1115.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/81/2/1115}
}

@ARTICLE{Larsen2003a,
  author = {Larsen, Olaf F. A. and van Stokkum, Ivo H. M. and Groot, Marie-Louise
	and Kennis, John T. M. and van Grondelle, Rienk and van Amerongen,
	Herbert},
  title = {Electronic states in 2-aminopurine revealed by ultrafast transient
	absorption and target analysis},
  journal = {Chemical Physics Letters},
  year = {2003},
  volume = {371},
  pages = {157--163},
  month = {Mar},
  day = {28},
  issue = {1-2},
  url = {http://www.sciencedirect.com/science/article/B6TFN-483BWY0-2/2/137488826d0dae4caad04cd5e855cde1}
}

@ARTICLE{olaf_04,
  author = {Olaf F. A. Larsen and Ivo H. M. van Stokkum and Frank L. de Weerd
	and Mikas Vengris and Charuvila T. Aravindakumar and Rienk van Grondelle
	and Nicholas E. Geacintov and Herbert van Amerongen},
  title = {Ultrafast transient-absorption and steady-state fluorescence measurements
	on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted
	{DNA} duplexes},
  journal = {Physical Chemistry Chemical Physics},
  year = {2004},
  volume = {6},
  pages = {154 - 160}
}

@ARTICLE{LauteslagerX.Y._jp983595h,
  author = {Lauteslager, X.Y. and van Stokkum, I. H. M. and van Ramesdonk, H.J.
	and Brouwer, A.M. and Verhoeven, J.W.},
  title = {Conformational Dynamics of Semiflexibly Bridged Donor-Acceptor Systems
	Studied with a Streak Camera and Spectrotemporal Parametrization
	of Fluorescence},
  journal = {Journal of Physical Chemistry A},
  year = {1999},
  volume = {103},
  pages = {653-659},
  number = {6},
  issn = {1089-5639},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp983595h}
}

@ARTICLE{i01s,
  author = {Xavier Y. Lauteslager and Ivo H. M. van Stokkum and H. John van Ramesdonk
	and Dick Bebelaar and Jan Fraanje and Kees Goubitz and Henk Schenk
	and Albert M. Brouwer and Jan W. Verhoeven},
  title = {Conformational Dynamics of Charge-Transfer States in Donor-Bridge-Acceptor
	Systems},
  journal = {European Journal of Organic Chemistry},
  year = {2001},
  volume = {16},
  pages = {3105-3118}
}

@ARTICLE{ISI:000291571100033,
  author = {Marin, Alessandro and Passarini, Francesca and van Stokkum, Ivo H.
	M. and van Grondelle, Rienk and Croce, Roberta},
  title = {{Minor Complexes at Work: Light-Harvesting by Carotenoids in the
	Photosystem II Antenna Complexes CP24 and CP26}},
  journal = {Biophysical Journal},
  year = {2011},
  volume = {{100}},
  pages = {{2829-2838}},
  number = {{11}},
  month = {{Jun 8}},
  address = {{600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA}},
  affiliation = {{Croce, R (Reprint Author), Univ Groningen, Dept Biophys Chem, Groningen
	Biomol Sci \& Biotechnol Inst, Groningen, Netherlands. Passarini,
	F; Croce, R, Univ Groningen, Dept Biophys Chem, Groningen Biomol
	Sci \& Biotechnol Inst, Groningen, Netherlands. Marin, A; van Stokkum,
	IHM; van Grondelle, R, Vrije Univ Amsterdam, Fac Sci, Amsterdam,
	Netherlands.}},
  author-email = {{r.croce@vu.nl}},
  doc-delivery-number = {{776WQ}},
  doi = {{10.1016/j.bpj.2011.04.029}},
  funding-acknowledgement = {{Netherlands Organization for Scientific Research-Chemical Sciences;
	Earth and Life Science (ALW)}},
  funding-text = {{This work was supported by the Netherlands Organization for Scientific
	Research-Chemical Sciences through a TOP grant to R.v.G. and Earth
	and Life Science (ALW) through a Vidi grant to R.C.}},
  issn = {{0006-3495}},
  journal-iso = {{Biophys. J.}},
  keywords-plus = {{FEMTOSECOND TRANSIENT ABSORPTION; CHLOROPHYLL ENERGY-TRANSFER; HIGHER-PLANTS;
	BINDING-SITES; GREEN PLANTS; EXCITED-STATE; S-1 STATE; FUNCTIONAL
	ARCHITECTURE; TRANSFER PATHWAYS; LOW-TEMPERATURE}},
  language = {{English}},
  number-of-cited-references = {{63}},
  publisher = {{CELL PRESS}},
  subject-category = {{Biophysics}},
  times-cited = {{0}},
  type = {{Article}},
  unique-id = {{ISI:000291571100033}}
}

@ARTICLE{ISI000291709500028,
  author = {Mathes, Tilo and van Stokkum, Ivo H. M. and Bonetti, Cosimo and Hegemann,
	Peter and Kennis, John T. M.},
  title = {{The Hydrogen-Bond Switch Reaction of the Blrb Bluf Domain of Rhodobacter
	sphaeroides}},
  journal = {Journal of Physical Chemistry B},
  year = {2011},
  volume = {{115}},
  pages = {{7963-7971}},
  number = {{24}},
  month = {{Jun 23}},
  address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
  affiliation = {{Mathes, T (Reprint Author), Humboldt Univ, Inst Biol Expt Biophys,
	Invalidenstr 42, D-10115 Berlin, Germany. Mathes, T; Hegemann, P,
	Humboldt Univ, Inst Biol Expt Biophys, D-10115 Berlin, Germany. van
	Stokkum, IHM; Bonetti, C; Kennis, JTM, Vrije Univ Amsterdam, Fac
	Sci, Dept Phys \& Astron, Biophys Grp, NL-1081 HV Amsterdam, Netherlands.}},
  author-email = {{tilo.mathes.1@biologie.hu-berlin.de}},
  doi = {{10.1021/jp201296m}},
  issn = {{1520-6106}},
  keywords-plus = {{ULTRAFAST INFRARED-SPECTROSCOPY; FLAVIN-BINDING PHOTORECEPTOR; MEDIATED
	SIGNAL-TRANSDUCTION; LIGHT PHOTORECEPTOR; ENERGY-TRANSFER; ADENINE-DINUCLEOTIDE;
	ELECTRONIC-STRUCTURE; CRYSTAL-STRUCTURES; ESCHERICHIA-COLI; AQUEOUS-SOLUTION}},
  language = {{English}},
  publisher = {{AMER CHEMICAL SOC}},
  subject-category = {{Chemistry}},
  type = {{Article}}
}

@INPROCEEDINGS{bred,
  author = {Van Brederode ME and van Stokkum I. H. M. and Jones MR, Van Grondelle
	R},
  title = {Wavelength and temperature dependence of the {P+QA} recombination
	reaction in the {M210W} reaction centre only mutant of Rhodobacter
	sphaeroides},
  booktitle = {Photosynthesis: from Light to Biosphere},
  year = {1995},
  editor = {P. Mathis},
  volume = {1},
  pages = {907-910},
  publisher = {Dordrecht, Kluwer}
}

@INCOLLECTION{ivo88a,
  author = {Melssen, W.J. and Van Stokkum, I. H. M.},
  title = {Selectivity for interaural time-difference and amplitude-modulation
	frequency in the auditory midbrain of the grassfrog},
  booktitle = {Basic Issues in Hearing},
  publisher = {Academic Press, London},
  year = {1988},
  editor = {H. Duifhuis and J.W. Horst and H.P. Wit},
  pages = {279-284}
}

@ARTICLE{Melssen1990,
  author = {Melssen, Willem J. and Epping, Willem J. M. and van Stokkum, Ivo
	H. M.},
  title = {Sensitivity for interaural time and intensity difference of auditory
	midbrain neurons in the grassfrog},
  journal = {Hearing Research},
  year = {1990},
  volume = {47},
  pages = {235--256},
  month = {Aug},
  day = {15},
  issue = {3},
  keywords = {Amplitude modulation},
  url = {http://www.sciencedirect.com/science/article/B6T73-485GF8D-B9/2/ada19ef668b1f657dc28e80f594f8ac5}
}

@INCOLLECTION{pereyra2010,
  author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
  title = {Exponential models for time-resolved spectroscopy data},
  booktitle = {Exponential Data Fitting and its Applications},
  publisher = {Bentham},
  year = {2010},
  editor = {Victor Pereyra and Godela Scherer},
  pages = {110–127}
}

@ARTICLE{numalg,
  author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
  title = {The variable projection algorithm in time-resolved spectroscopy,
	microscopy and mass spectrometry applications},
  journal = {Numerical Algorithms},
  year = {2009},
  volume = {51},
  pages = {319-340},
  issue = {3}
}

@ARTICLE{intro,
  author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
  title = {An Introduction to the Special Volume ``{S}pectroscopy and {C}hemometrics
	in {R}''},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {18},
  number = {1},
  url = {http://www.jstatsoft.org/v18/i01/}
}

@ARTICLE{TIMP,
  author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
  title = {{TIMP}: an {R} package for modeling multi-way spectroscopic measurements},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {18},
  number = {3},
  url = {http://www.jstatsoft.org/v18/i03/}
}

@INPROCEEDINGS{go05,
  author = {Katharine M. Mullen and Mikas Vengris and Ivo H. M. van Stokkum},
  title = {Separable nonlinear models for time-resolved spectra},
  booktitle = {Proceedings of the International Workshop on Global Optimization},
  year = {2005},
  editor = {I. Garc\'{i}a and L. G. Casado and E.M.T. Hendrix and B. T\'{o}th},
  pages = {183-188},
  month = {September},
  author1_email = {kate@nat.vu.nl},
  author2_email = {ivo@nat.vu.nl}
}

@ARTICLE{jgo,
  author = {Katharine M. Mullen and Mikas Vengris and Ivo H. M. van Stokkum},
  title = {Algorithms for Separable Nonlinear Least Squares with Application
	to Modelling Time-resolved Spectra},
  journal = {Journal of Global Optimization},
  year = {2007},
  volume = {38},
  pages = {201-213}
}

@ARTICLE{iv01,
  author = {Naus, H. and van Stokkum, I. H. M. and Ubachs, W and Hogervorst,
	W.},
  title = {Quantitative analysis of decay transients applied to a multi-mode
	pulsed cavity ring-down experiment},
  journal = {Applied Optics},
  year = {2001},
  volume = {40},
  pages = {4416-4426}
}

@ARTICLE{Palacios2003,
  author = {Palacios, Miguel A. and Frese, Raoul N. and Gradinaru, Claudiu C.
	and van Stokkum, I. H. M. and Premvardhan, Lavanya L. and Horton,
	Peter and Ruban, Alexander V. and van Grondelle, Rienk and van Amerongen,
	Herbert},
  title = {Stark spectroscopy of the light-harvesting complex {II} in different
	oligomerisation states},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {2003},
  volume = {1605},
  pages = {83--95},
  month = {Aug},
  day = {18},
  issue = {1-3},
  keywords = {LHCII},
  url = {http://www.sciencedirect.com/science/article/B6T1S-490H910-1/2/0ee0ab00e8580fc343a19b188392c30d}
}

@ARTICLE{photo_2006,
  author = {Miguel A. Palacios and Joerg Standfuss and Mikas Vengris and and
	Bart F. van Oort and Ivo H. M. van Stokkum and Werner K{\"{u}}hlbrandt
	and Herbert van Amerongen and Rienk van Grondelle},
  title = {A comparison of the three isoforms of the light-harvesting complex
	{II} using transient absorption and time-resolved fluorescence measurements},
  journal = {Photosynthesis Research},
  year = {2006},
  volume = {88},
  pages = {269--285},
  number = {3},
  url = {http://www.springerlink.com/content/yp125x44j1r28688}
}

@ARTICLE{PanditA._jp021757a,
  author = {Pandit, A. and Larsen, O.F.A. and van Stokkum, I. H. M. and van Grondelle,
	R. and Kraayenhof, R. and van Amerongen, H.},
  title = {Ultrafast Polarized Fluorescence Measurements on Monomeric and Self-Associated
	Melittin},
  journal = {Journal of Physical Chemistry B},
  year = {2003},
  volume = {107},
  pages = {3086-3090},
  number = {13},
  affiliation = {Department of Structural Biology, Faculty of Earth and Life Sciences,
	Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam,
	The Netherlands, Division of Physics and Astronomy, Faculty of Sciences,
	Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam,
	The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology
	and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp021757a}
}

@ARTICLE{PanditA._bi0269005,
  author = {Pandit, A. and Ma, H. and van Stokkum, I. H. M. and Gruebele, M.
	and van Grondelle, R.},
  title = {Time-Resolved Dissociation of the Light-Harvesting 1 Complex of Rhodospirillum
	rubrum, Studied by Infrared Laser Temperature Jump},
  journal = {Biochemistry},
  year = {2002},
  volume = {41},
  pages = {15115-15120},
  number = {51},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi0269005}
}

@ARTICLE{photo_2003,
  author = {Anjali Pandit and Ivo H. M. van Stokkum and Sofia Georgakopoulou
	and Gert van der Zwan and Rienk van Grondelle},
  title = {Investigations of intermediates appearing in the reassociation of
	the light-harvesting 1 complex of Rhodospirillum rubrum},
  journal = {Photosynthesis Research},
  year = {2003},
  volume = {75},
  pages = {235--248},
  number = {3},
  url = {http://www.springerlink.com/content/gl27263k40g62490}
}

@ARTICLE{pan,
  author = {Pandit, A and Visschers, RW and van Stokkum, I. H. M. and Kraayenhof,
	R and van Grondelle, R},
  title = {Oligomerization of light-harvesting {I} antenna peptides of Rhodospirillum
	rubrum},
  journal = {Biochemistry},
  year = {2001},
  volume = {40},
  pages = {12913-12924}
}

@ARTICLE{PapagiannakisE._jp027174i,
  author = {Papagiannakis, E. and Das, S.K. and Gall, A. and van Stokkum, I.
	H. M. and Robert, B. and van Grondelle, R. and Frank, H.A. and Kennis,
	J.T.M.},
  title = {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 = {Journal of Physical Chemistry B},
  year = {2003},
  volume = {107},
  pages = {5642-5649},
  number = {23},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp027174i}
}

@ARTICLE{EmmanouilPapagiannakis04302002,
  author = {Papagiannakis, Emmanouil and Kennis, John T. M. and van Stokkum,
	Ivo H. M. and Cogdell, Richard J. and van Grondelle, Rienk},
  title = {{An alternative carotenoid-to-bacteriochlorophyll energy transfer
	pathway in photosynthetic light harvesting}},
  journal = {PNAS},
  year = {2002},
  volume = {99},
  pages = {6017-6022},
  number = {9},
  doi = {10.1073/pnas.092626599},
  file = {6017.pdf:http\://www.pnas.org/cgi/reprint/99/9/6017.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/99/9/6017}
}

@ARTICLE{PapagiannakisE._bi047977r,
  author = {Papagiannakis, E. and Larsen, D.S. and van Stokkum, I. H. M. and
	Vengris, M. and Hiller, R.G. and van Grondelle, R.},
  title = {Resolving the Excited State Equilibrium of Peridinin in Solution},
  journal = {Biochemistry},
  year = {2004},
  volume = {43},
  pages = {15303-15309},
  number = {49},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi047977r}
}

@INCOLLECTION{bookpulse1,
  author = {Emmanouil Papagiannakis and Delmar Larsen and Mikas Vengris and Ivo
	van Stokkum and Rienk van Grondelle},
  title = {Multi-Pulse Transient Absorption and Carotenoid Excited-State Dynamics:
	{$\beta$}-Carotene},
  booktitle = {Ultrafast Phenomena XIV},
  year = {2005},
  pages = {592--594},
  url = {http://www.springerlink.com/content/m1506825m25288u7}
}

@ARTICLE{photo1_05,
  author = {Emmanouil Papagiannakis and Ivo H. M. van Stokkum and Holger Fey
	and Claudia B{\"{u}}chel and Rienk van Grondelle},
  title = {Spectroscopic Characterization of the Excitation Energy Transfer
	in the Fucoxanthin-Chlorophyll Protein of Diatoms},
  journal = {Photosynthesis Research},
  year = {2005},
  volume = {86},
  pages = {241--250},
  issue = {1},
  url = {http://www.springerlink.com/content/t25612216t0xp288}
}

@ARTICLE{PapagiannakisE._jp034931j,
  author = {Papagiannakis, E. and van Stokkum, I. H. M. and van Grondelle, R.
	and Niederman, R.A. and Zigmantas, D. and Sundstrom, V. and Polivka,
	T.},
  title = {A Near-Infrared Transient Absorption Study of the Excited-State Dynamics
	of the Carotenoid Spirilloxanthin in Solution and in the LH1 Complex
	of {R}hodospirillum rubrum},
  journal = {Journal of Physical Chemistry B},
  year = {2003},
  volume = {107},
  pages = {11216-11223},
  number = {40},
  affiliation = {Department of Chemical Physics, Lund University, P.O. Box 124, 22100
	Lund, Sweden},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp034931j}
}

@ARTICLE{PapagiannakisE._jp054633h,
  author = {Papagiannakis, E. and van Stokkum, I. H. M. and Vengris, M. and Cogdell,
	R.J. and van Grondelle, R. and Larsen, D.S.},
  title = {Excited-State Dynamics of Carotenoids in Light-Harvesting Complexes.
	1. Exploring the Relationship between the S{$_1$} and S* States},
  journal = {Journal of Physical Chemistry B},
  year = {2006},
  volume = {110},
  pages = {5727-5736},
  number = {11},
  affiliation = {Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081,
	1081 HV Amsterdam, The Netherlands, Institute of Biomedical & Life
	Sciences, University of Glasgow, Glasgow, United Kingdom, Department
	of Chemistry, University of California, Davis, One Shields Avenue,
	Davis, California 95616, and Faculty of Physics, Vilnius University,
	Sauletekio Avenue 9, Block 3, Vilnius, Lithuania},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp054633h}
}

@ARTICLE{PapagiannakisE._jp053094d,
  author = {Papagiannakis, E. and Vengris, M. and Larsen, D.S. and van Stokkum,
	I. H. M. and Hiller, R.G. and van Grondelle, R.},
  title = {Use of Ultrafast Dispersed Pump-Dump-Probe and Pump-Repump-Probe
	Spectroscopies to Explore the Light-Induced Dynamics of Peridinin
	in Solution},
  journal = {Journal of Physical Chemistry B},
  year = {2006},
  volume = {110},
  pages = {512-521},
  number = {1},
  affiliation = {Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit,
	De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands, and School
	of Biological Sciences, Macquarie University, NSW 2109, Australia},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp053094d}
}

@ARTICLE{NataliaP.Pawlowicz08012008,
  author = {Pawlowicz, Natalia P. and van Grondelle, Rienk and van Stokkum, Ivo
	H. M. and Breton, Jacques and Jones, Michael R. and Groot, Marie
	Louise},
  title = {{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}},
  journal = {Biophys. J.},
  year = {2008},
  volume = {95},
  pages = {1268-1284},
  number = {3},
  abstract = {Time-resolved visible pump/mid-infrared (mid-IR) probe spectroscopy
	in the region between 1600 and 1800 cm-1 was used to investigate
	electron transfer, radical pair relaxation, and protein relaxation
	at room temperature in the Rhodobacter sphaeroides reaction center
	(RC). Wild-type RCs both with and without the quinone electron acceptor
	QA, were excited at 600 nm (nonselective excitation), 800 nm (direct
	excitation of the monomeric bacteriochlorophyll (BChl) cofactors),
	and 860 nm (direct excitation of the dimer of primary donor (P) BChls
	(PL/PM)). The region between 1600 and 1800 cm-1 encompasses absorption
	changes associated with carbonyl (C=O) stretch vibrational modes
	of the cofactors and protein. After photoexcitation of the RC the
	primary electron donor P excited singlet state (P*) decayed on a
	timescale of 3.7 ps to the state [IMG]f1.gif" ALT="Formula" BORDER="0">
	(where BL is the accessory BChl electron acceptor). This is the first
	report of the mid-IR absorption spectrum of [IMG]f2.gif" ALT="Formula"
	BORDER="0"> the difference spectrum indicates that the 9-keto C=O
	stretch of BL is located around 1670-1680 cm-1. After subsequent
	electron transfer to the bacteriopheophytin HL in [~]1 ps, the state
	[IMG]f3.gif" ALT="Formula" BORDER="0"> was formed. A sequential analysis
	and simultaneous target analysis of the data showed a relaxation
	of the [IMG]f3.gif" ALT="Formula" BORDER="0"> radical pair on the
	[~]20 ps timescale, accompanied by a change in the relative ratio
	of the [IMG]f4.gif" ALT="Formula" BORDER="0"> and [IMG]f5.gif" ALT="Formula"
	BORDER="0"> bands and by a minor change in the band amplitude at
	1640 cm-1 that may be tentatively ascribed to the response of an
	amide C=O to the radical pair formation. We conclude that the drop
	in free energy associated with the relaxation of [IMG]f3.gif" ALT="Formula"
	BORDER="0"> is due to an increased localization of the electron hole
	on the PL half of the dimer and a further consequence is a reduction
	in the electrical field causing the Stark shift of one or more amide
	C=O oscillators. },
  doi = {10.1529/biophysj.108.130880},
  eprint = {http://www.biophysj.org/cgi/reprint/95/3/1268.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/95/3/1268}
}

@ARTICLE{Pawlowicz10152007,
  author = {Pawlowicz, N. P. and Groot, M.-L. and van Stokkum, I. H. M. and Breton,
	J. and van Grondelle, R.},
  title = {{Charge Separation and Energy Transfer in the Photosystem II Core
	Complex Studied by Femtosecond Midinfrared Spectroscopy}},
  journal = {Biophys. J.},
  year = {2007},
  volume = {93},
  pages = {2732-2742},
  number = {8},
  abstract = {The core of photosystem II (PSII) of green plants contains the reaction
	center (RC) proteins D1D2-cytb559 and two core antennas CP43 and
	CP47. We have used time-resolved visible pump/midinfrared probe spectroscopy
	in the region between 1600 and 1800 cm1 to study the energy transfer
	and charge separation events within PSII cores. The absorption difference
	spectra in the region of the keto and ester chlorophyll modes show
	spectral evolution with time constants of 3 ps, 27 ps, 200 ps, and
	2 ns. Comparison of infrared (IR) difference spectra obtained for
	the isolated antennas CP43 and CP47 and the D1D2-RC with those measured
	for the PSII core allowed us to identify the features specific for
	each of the PSII core components. From the presence of the CP43 and
	CP47 specific features in the spectra up to time delays of 2030 ps,
	we conclude that the main part of the energy transfer from the antennas
	to the RC occurs on this timescale. Direct excitation of the pigments
	in the RC evolution associated difference spectra to radical pair
	formation of [IMG]f1.gif" ALT="Formula" BORDER="0"> on the same timescale
	as multi-excitation annihilation and excited state equilibration
	within the antennas CP43 and CP47, which occur within [~]13 ps. The
	formation of the earlier radical pair [IMG]f2.gif" ALT="Formula"
	BORDER="0"> as identified in isolated D1D2 complexes with time-resolved
	mid-IR spectroscopy is not observed in the current data, probably
	because of its relatively low concentration. Relaxation of the state
	[IMG]f3.gif" ALT="Formula" BORDER="0"> caused by a drop in free energy,
	occurs in 200 ps in closed cores. We conclude that the kinetic model
	proposed earlier for the energy and electron transfer dynamics within
	the D1D2-RC, plus two slowly energy-transferring antennas C43 and
	CP47 explain the complex excited state and charge separation dynamics
	in the PSII core very well. We further show that the time-resolved
	IR-difference spectrum of [IMG]f1.gif" ALT="Formula" BORDER="0">
	as observed in PSII cores is virtually identical to that observed
	in the isolated D1D2-RC complex of PSII, demonstrating that the local
	structure of the primary reactants has remained intact in the isolated
	D1D2 complex. },
  doi = {10.1529/biophysj.107.105452},
  eprint = {http://www.biophysj.org/cgi/reprint/93/8/2732.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/93/8/2732}
}

@ARTICLE{Pawlowicz2010,
  author = {Natalia P. Pawlowicz and Ivo H. M. van Stokkum and Jacques Breton
	and Rienk van Grondelle and Michael R. Jones},
  title = {An investigation of slow charge separation in a Tyrosine {M210} to
	Tryptophan mutant of the Rhodobacter sphaeroides reaction center
	by femtosecond mid-infrared spectroscopy},
  journal = {Physical Chemistry Chemical Physics},
  year = {2010},
  volume = {12},
  pages = {2693-2705},
  number = {11},
  doi = {DOI: 10.1039/b905934b}
}

@ARTICLE{Pawlowicz20094956,
  author = {Natalia P. Pawlowicz and Ivo H. M. van Stokkum and Jacques Breton
	and Rienk van Grondelle and Michael R. Jones},
  title = {Identification of the Intermediate Charge-Separated State {P+{$\beta$}L-}
	in a Leucine {M214} to Histidine Mutant of the {R}hodobacter sphaeroides
	Reaction Center Using Femtosecond Midinfrared Spectroscopy},
  journal = {Biophysical Journal},
  year = {2009},
  volume = {96},
  pages = {4956 - 4965},
  number = {12},
  doi = {DOI: 10.1016/j.bpj.2009.03.031},
  issn = {0006-3495},
  url = {http://www.sciencedirect.com/science/article/B94RW-4WGVKGW-P/2/44157f270cf54de3077e7e0129440975}
}

@ARTICLE{Perez-Ruiz2006,
  author = {Perez-Ruiz, Raul and Groeneveld, Michiel and van Stokkum, Ivo H.
	M. and Tormos, Rosa and Williams, Ren{\'{e}} M. and Miranda, Miguel
	A.},
  title = {Fast transient absorption spectroscopy of the early events in photoexcited
	chiral benzophenone-naphthalene dyads},
  journal = {Chemical Physics Letters},
  year = {2006},
  volume = {429},
  pages = {276--281},
  month = {Sep},
  day = {29},
  issue = {1-3},
  url = {http://www.sciencedirect.com/science/article/B6TFN-4KJ6KN8-1/2/f108ed120c75e1d5f32acffc0f7abbdf}
}

@ARTICLE{Peterman1997,
  author = {Peterman, Erwin J. G. and Monshouwer, Ren{\'{e}} and van Stokkum,
	Ivo H. M. and van Grondelle, Rienk and van Amerongen, Herbert},
  title = {Ultrafast singlet excitation transfer from carotenoids to chlorophylls
	via different pathways in light-harvesting complex {II} of higher
	plants},
  journal = {Chemical Physics Letters},
  year = {1997},
  volume = {264},
  pages = {279--284},
  month = {Jan},
  day = {10},
  issue = {3-4},
  url = {http://www.sciencedirect.com/science/article/B6TFN-3S9D8N3-1F/2/8859fbd9f7516a5533aa289d926f4a57}
}

@ARTICLE{PetkovaI._jp0735841,
  author = {Petkova, I. and Mudadu, M.S. and Singh, A. and Thummel, R.P. and
	van Stokkum, I. H. M. and Buma, W.J. and Waluk, J.},
  title = {Structure and Photophysics of 2-(2'-Pyridyl)benzindoles: The Role
	of Intermolecular Hydrogen Bonds},
  journal = {Journal of Physical Chemistry A},
  year = {2007},
  volume = {111},
  pages = {11400-11409},
  number = {45},
  affiliation = {Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka
	44/52, 01-224 Warsaw, Poland, Institute of Organic Chemistry, Bulgarian
	Academy of Sciences, Akad. G. Bontchev bl. IX, Sofia 1113, Bulgaria,
	Van't Hoff Institute for Molecular Sciences, University of Amsterdam,
	Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, Department
	of Chemistry, University of Houston, Houston, Texas, 77204-5003,
	and Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081
	HV Amsterdam, The Netherlands},
  issn = {1089-5639},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0735841}
}

@ARTICLE{PetushkovV.N._jp034266e,
  author = {Valentin N. Petushkov and Ivo H. M. van Stokkum and Bas Gobets and
	Frank van Mourik and John Lee and Rienk van Grondelle and Antonie
	J.W.G. Visser},
  title = {Ultrafast Fluorescence Relaxation Spectroscopy of 6,7-Dimethyl-(8-ribityl)-lumazine
	and Riboflavin, Free and Bound to Antenna Proteins from Bioluminescent
	Bacteria},
  journal = {Journal of Physical Chemistry B},
  year = {2003},
  volume = {107},
  pages = {10934-10939},
  number = {39},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp034266e}
}

@ARTICLE{PolivkaT_bi060265b,
  author = {Pol{\'{i}}vka, T. and van Stokkum, I. H. M. and Zigmantas, D. and
	van Grondelle, R. and Sundstr{\"{o}}m, V. and Hiller, R.G.},
  title = {Energy Transfer in the Major Intrinsic Light-Harvesting Complex from
	{{\it Amphidinium carterae}}},
  journal = {Biochemistry},
  year = {2006},
  volume = {45},
  pages = {8516-8526},
  number = {28},
  affiliation = {Institute of Physical Biology, University of South Bohemia, Czech
	Republic, Institute of Plant Molecular Biology, Czech Academy of
	Sciences, Czech Republic, Department of Chemical Physics, Lund University,
	Sweden, Department of Physics and Astronomy, Vrije Universiteit,
	Amsterdam, The Netherlands, Department of Chemistry, University of
	California, Berkeley, California, Physical Biosciences Division,
	Lawrence Berkeley National Laboratory, Berkeley, California 94720,
	and Department of Biological Sciences, Macquarie University, NSW
	2109, Australia},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi060265b}
}

@ARTICLE{pri93,
  author = {Pribi{\'{c}}, R. and Van Stokkum, I. H. M. and Chapman, D. and Haris,
	P.I. and Bloemendal, M.},
  title = {Protein secondary structure from Fourier Transform Infrared and/or
	Circular Dichroism spectra},
  journal = {Analytical Biochemistry},
  year = {1993},
  volume = {214},
  pages = {366-378}
}

@INPROCEEDINGS{pr94,
  author = {Pribi{\'{c}}, R. and Van Stokkum, I. H. M. and Van den Bos, A.},
  title = {Inference regions of nonlinear parameters in global analysis},
  booktitle = {Proceedings {SYSID} 1994, 10th {IFAC} Symposium on System Identification},
  year = {1994},
  editor = {Blanke, M. and S{\"o}derstr{\"o}m, T.},
  pages = {2423-2428},
  publisher = {Danish Automation Society, Copenhagen}
}

@ARTICLE{Romero2009L35,
  author = {Elisabet Romero and Milena Mozzo and Ivo H. M. van Stokkum and Jan
	P. Dekker and Rienk van Grondelle and Roberta Croce},
  title = {The Origin of the Low-Energy Form of Photosystem {I} Light{-}Harvesting
	Complex Lhca4: Mixing of the Lowest Exciton with a Charge{-}Transfer
	State},
  journal = {Biophysical Journal},
  year = {2009},
  volume = {96},
  pages = {L35 - L37},
  number = {5},
  doi = {DOI: 10.1016/j.bpj.2008.11.043},
  issn = {0006-3495},
  url = {http://www.sciencedirect.com/science/article/B94RW-4VRPN44-1/2/d4374b92f183d213568b0fee8c25e7ad}
}

@ARTICLE{ISI:000288447100008,
  author = {Romero, Elisabet and van Stokkum, Ivo H. M. and Dekker, Jan P. and
	van Grondelle, Rienk},
  title = {{Ultrafast carotenoid band shifts correlated with Chl(z) excited
	states in the photosystem II reaction center: are the carotenoids
	involved in energy transfer?}},
  journal = {Physical Chemistry Chemical Physics},
  year = {2011},
  volume = {{13}},
  pages = {{5573-5575}},
  number = {{13}},
  abstract = {{We show a correlation between the electronic excitation of the peripheral
	chlorophylls (Chls(Z)) of the photosystem II reaction center and
	a shift of the S(2) absorption bands of beta-carotene, and suggest
	that the carotenoids may enhance the excitation energy transfer rate
	from these chlorophylls to the central cofactors.}},
  address = {{THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF,
	CAMBS, ENGLAND}},
  affiliation = {{Romero, E (Reprint Author), Vrije Univ Amsterdam, Fac Sci, Dept Phys
	\& Astron, De Boelelaan 1081, NL-1081 HV Amsterdam, Netherlands.
	Romero, E Romero, E; van Stokkum, IHM; Dekker, JP; van Grondelle,
	R, Vrije Univ Amsterdam, Fac Sci, Dept Phys \& Astron, NL-1081 HV
	Amsterdam, Netherlands.}},
  doc-delivery-number = {{735VB}},
  doi = {{10.1039/c0cp02896g}},
  funding-acknowledgement = {{Marie Curie Research Training Network INTRO2 of the E.U.\{{[}\}MRTN
	- CT - 505069]; Netherlands Organization for Scientific Research
	(NWO)}},
  funding-text = {{This work was supported by the Marie Curie Research Training Network
	INTRO2 (MRTN - CT - 505069) (E. R.) of the E.U. and by The Netherlands
	Organization for Scientific Research (NWO).}},
  issn = {{1463-9076}},
  journal-iso = {{Phys. Chem. Chem. Phys.}},
  keywords-plus = {{PRIMARY ELECTRON-DONOR; CHARGE SEPARATION; FLUORESCENCE; SPECTROSCOPY;
	ARRANGEMENT; RESOLUTION; DYNAMICS; SPECTRA; LIGHT; LH2}},
  language = {{English}},
  number-of-cited-references = {{21}},
  publisher = {{ROYAL SOC CHEMISTRY}},
  subject-category = {{Chemistry; Physics}},
  times-cited = {{1}},
  type = {{Article}},
  unique-id = {{ISI:000288447100008}}
}

@ARTICLE{Romero2010,
  author = {Romero, E. and van Stokkum, I. H. M. and Novoderezhkin, V. I. and
	Dekker, J. P. and van Grondelle, R.},
  title = {Two Different Charge Separation Pathways in Photosystem {II}},
  journal = {Biochemistry},
  year = {2010},
  volume = {49},
  pages = {4300-4307},
  number = {20},
  abstract = {Charge separation is an essential step in the conversion of solar
	energy into chemical energy in photosynthesis. To investigate this
	process, we performed transient absorption experiments at 77 K with
	various excitation conditions on the isolated Photosystem II reaction
	center preparations from spinach. The results have been analyzed
	by global and target analysis and demonstrate that at least two different
	excited states, (Chl(D1)Phe(D1))* and (P(D1)P(D2)Chl(D1))*, give
	rise to two different pathways for ultrafast charge separation. We
	propose that the disorder produced by slow protein motions causes
	energetic differentiation among reaction center complexes, leading
	to different charge separation pathways. Because of the low temperature,
	two excitation energy trap states are also present, generating charge-separated
	states on long time scales. We conclude that these slow trap states
	are the same as the excited states that lead to ultrafast charge
	separation, indicating that at 77 K charge separation can be either
	activation-less and last or activated and slow.}
}

@ARTICLE{vanRotterdam2002,
  author = {van Rotterdam, Bart J. and Crielaard, Wim and van Stokkum, Ivo H.
	M. and Hellingwerf, Klaas J. and Westerhoff, Hans V.},
  title = {Simplicity in complexity: the photosynthetic reaction center performs
	as a simple 0.2 {V} battery},
  journal = {FEBS Letters},
  year = {2002},
  volume = {510},
  pages = {105--107},
  month = {Jan},
  day = {02},
  issue = {1-2},
  keywords = {Photosynthesis},
  url = {http://www.sciencedirect.com/science/article/B6T36-44KWT43-1/2/c245f3b0071c42271e5a0db0da98a34c}
}

@ARTICLE{ruban2007,
  author = {Ruban, Alexander V. and Berera, Rudi and Ilioaia, Cristian and van
	Stokkum, Ivo H. M. and Kennis, John T. M. and Pascal, Andrew A. and
	van Amerongen, Herbert and Robert, Bruno and Horton, Peter and van
	Grondelle, Rienk},
  title = {Identification of a mechanism of photoprotective energy dissipation
	in higher plants},
  journal = {Nature},
  year = {2007},
  volume = {450},
  pages = {575-578},
  number = {7169},
  url = {http://www.nature.com/nature/journal/v450/n7169/abs/nature06262.html}
}

@ARTICLE{AlisaRupenyan05152008,
  author = {Rupenyan, Alisa and van Stokkum, Ivo H. M. and Arents, Jos C. and
	van Grondelle, Rienk and Hellingwerf, Klaas and Groot, Marie Louise},
  title = {{Characterization of the Primary Photochemistry of Proteorhodopsin
	with Femtosecond Spectroscopy}},
  journal = {Biophys. J.},
  year = {2008},
  volume = {94},
  pages = {4020-4030},
  number = {10},
  abstract = {Proteorhodopsin is an ion-translocating member of the microbial rhodopsin
	family. Light absorption by its retinal chromophore initiates a photocycle,
	driven by trans/cis isomerization, leading to transmembrane translocation
	of a proton toward the extracellular side of the cytoplasmic membrane.
	Here we report a study on the photoisomerization dynamics of the
	retinal chromophore of proteorhodopsin, using femtosecond time-resolved
	spectroscopy, by probing in the visible- and in the midinfrared spectral
	regions. Experiments were performed both at pH 9.5 (a physiologically
	relevant pH value in which the primary proton acceptor of the protonated
	Schiff base, Asp97, is deprotonated) and at pH 6.5 (with Asp97 protonated).
	Simultaneous analysis of the data sets recorded in the two spectral
	regions and at both pH values reveals a multiexponential excited
	state decay, with time constants of [~]0.2 ps, [~]2 ps, and [~]20
	ps. From the difference spectra associated with these dynamics, we
	conclude that there are two chromophore-isomerizaton pathways that
	lead to the K-state: one with an effective rate of [~](2 ps)-1 and
	the other with a rate of [~](20 ps)-1. At high pH, both pathways
	are equally effective, with an estimated quantum yield for K-formation
	of [~]0.7. At pH 6.5, the slower pathway is less productive, which
	results in an isomerization quantum yield of 0.5. We further observe
	an ultrafast response of residue Asp227, which forms part of the
	counterion complex, corresponding to a strengthening of its hydrogen
	bond with the Schiff base on K-state formation; and a feature that
	develops on the 0.2 ps and 2 ps timescale and probably reflects a
	response of an amide {II} band in reaction to the isomerization process.
	},
  doi = {10.1529/biophysj.107.121376},
  eprint = {http://www.biophysj.org/cgi/reprint/94/10/4020.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/94/10/4020}
}

@ARTICLE{alisaJPCB09,
  author = {Rupenyan, Alisa and van Stokkum, Ivo H. M. and Arents, Jos C. and
	van Grondelle, Rienk and Hellingwerf, Klaas J. and Groot, Marie Louise},
  title = {Reaction Pathways of Photoexcited Retinal in Proteorhodopsin Studied
	by {Pump-Dump-Probe} Spectroscopy},
  journal = {The Journal of Physical Chemistry B},
  year = {2009},
  volume = {113},
  pages = {16251-16256},
  number = {50},
  doi = {doi: 10.1021/jp9065289}
}

@ARTICLE{ISI:000290652100031,
  author = {Rupenyan, Alisa B. and Vreede, Jocelyne and van Stokkum, Ivo H. M.
	and Hospes, Marijke and Kennis, John T. M. and Hellingwerf, Klaas
	J. and Groot, Marie Louise},
  title = {{Proline 68 Enhances Photoisomerization Yield in Photoactive Yellow
	Protein}},
  journal = {Journal of Physical Chemistry B},
  year = {2011},
  volume = {{115}},
  pages = {{6668-6677}},
  number = {{20}},
  month = {{May 26}},
  address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
  affiliation = {{Rupenyan, AB (Reprint Author), Swiss Fed Inst Technol, Lab Phys Chem,
	Wolfgang Pauli Str 10, CH-8093 Zurich, Switzerland. Vreede, J, Univ
	Amsterdam, Vant Hoff Inst Mol Sci, NL-1010 WV Amsterdam, Netherlands.
	Hospes, M; Hellingwerf, KJ, Univ Amsterdam, Swammerdam Inst Life
	Sci, Lab Microbiol, NL-1010 WV Amsterdam, Netherlands. Rupenyan,
	AB; van Stokkum, IHM; Kennis, JTM; Hellingwerf, KJ; Groot, ML, Vrije
	Univ Amsterdam, Fac Sci, Dept Phys \& Astron, NL-1081 HV Amsterdam,
	Netherlands.}},
  author-email = {{a.b.rupenyan@uva.nl}},
  doc-delivery-number = {{764SE}},
  doi = {{10.1021/jp112113s}},
  funding-acknowledgement = {{Netherlands Organization for Scientific Research; Human Frontier
	Science Program}},
  funding-text = {{This research was supported by The Netherlands Organization for Scientific
	Research and the Human Frontier Science Program. J.V. thanks Gerrit
	Groenhof at the Max Planck Institute for Biophysical Chemistry, Goettingen,
	Germany, for kindly providing the force field parameters of the chromophore.
	A.B.R. thanks Jos Thieme from VU University Amsterdam for technical
	support.}},
  issn = {{1520-6106}},
  journal-iso = {{J. Phys. Chem. B}},
  keywords-plus = {{TRANSIENT ABSORPTION-SPECTROSCOPY; ECTOTHIORHODOSPIRA-HALOPHILA;
	PHOTOCYCLE; DYNAMICS; CHROMOPHORE; FLUORESCENCE; MUTANTS; WATER;
	ISOMERIZATION; INTERMEDIATE}},
  language = {{English}},
  number-of-cited-references = {{50}},
  publisher = {{AMER CHEMICAL SOC}},
  subject-category = {{Chemistry}},
  times-cited = {{0}},
  type = {{Article}},
  unique-id = {{ISI:000290652100031}}
}

@INPROCEEDINGS{i98z,
  author = {Salverda, JM and van Mourik, F and van Stokkum, I. H. M. and Wendling,
	M and van Grondelle, R},
  title = {Polarized and colored photon echo measurements on the {LH2} antenna
	of {R}ps. acidophila and {R}s. molischianum},
  booktitle = {Photosynthesis: Mechanisms and Effects},
  year = {1998},
  editor = {Garab, G},
  pages = {45-48},
  publisher = {Kluwer Academic Publishers, Dordrecht}
}

@ARTICLE{SautterA._ja0448216,
  author = {Sautter, A. and Kaletas, B.K. and Schmid, D.G. and Dobrawa, R. and
	Zimine, M. and Jung, G. and van Stokkum, I. H. M. and DeCola, L.
	and Williams, R.M. and Würthner, F.},
  title = {Ultrafast Energy-Electron Transfer Cascade in a Multichromophoric
	Light-Harvesting Molecular Square},
  journal = {Journal of the American Chemical Society},
  year = {2005},
  volume = {127},
  pages = {6719-6729},
  number = {18},
  issn = {0002-7863},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja0448216}
}

@ARTICLE{SchererT._j100092a025,
  author = {Scherer, T. and van Stokkum, I. H. M. and Brouwer, A. M. and Verhoeven,
	J. W.},
  title = {Excited-State Conformational Dynamics of Flexibly and Semirigidly
	Bridged Electron Donor-Acceptor Systems in Solution. Influence of
	Temperature and Solvent Viscosity},
  journal = {Journal of Physical Chemistry},
  year = {1994},
  volume = {98},
  pages = {10539-10549},
  number = {41},
  issn = {0022-3654},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/j100092a025}
}

@ARTICLE{jorispub1,
  author = {Sicam, Victor Arni D. P. and Snellenburg, Joris J. and Van Der Heijde,
	Rob G. L. and Van Stokkum, Ivo H. M.},
  title = {{Pseudo Forward Ray-Tracing: A New Method for Surface Validation
	in Cornea Topography}},
  journal = {Optometry \& Vision Science},
  year = {2007},
  volume = {84},
  pages = {E915-E923},
  number = {9},
  abstract = {http://www.optvissci.com/pt/re/ovs/abstract.00006324-200709000-00020.htm},
  copyright = {http://copyrighttoolbox.surf.nl/copyrighttoolbox/authors/sample-wording/educational-use/provisions/},
  file = {sicam-snellenburg.pdf:http\://www.nat.vu.nl/~jsnel/paper/sicam-snellenburg.pdf:PDF},
  url = {http://meta.wkhealth.com/pt/pt-core/template-journal/lwwgateway/media/landingpage.htm?an=00006324-200709000-00020}
}

@ARTICLE{Stahl20093215,
  author = {Andreas D. Stahl and Mariangela Di Donato and Ivo van Stokkum and
	Rienk van Grondelle and Marie Louise Groot},
  title = {A Femtosecond Visible/Visible and Visible/Mid-Infrared Transient
	Absorption Study of the Light Harvesting Complex {II}},
  journal = {Biophysical Journal},
  year = {2009},
  volume = {97},
  pages = {3215 - 3223},
  number = {12},
  doi = {DOI: 10.1016/j.bpj.2009.09.037},
  issn = {0006-3495},
  url = {http://www.sciencedirect.com/science/article/B94RW-4XX39TB-N/2/823955b52a75d6e56afb34b3c37cb395}
}

@TECHREPORT{lecture,
  author = {Ivo H. M. van Stokkum},
  title = {Global and Target Analysis of Time-resolved Spectra, Lecture notes
	for the Troisi{\`{e}}me Cycle de la Physique en Suisse Romande},
  institution = {Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit,
	Amsterdam, The Netherlands},
  year = {2005},
  url = {http://www.nat.vu.nl/~ivo/pub/2005/lecturenotes3cycle.pdf}
}

@INPROCEEDINGS{i99,
  author = {van Stokkum, I. H. M.},
  title = {Added value of singles in {3D PET}},
  booktitle = {Proceedings of the 1999 International meeting on fully three-dimensional
	image reconstruction in radiology and nuclear medicine},
  year = {1999},
  pages = {115-118}
}

@ARTICLE{ieee1x,
  author = {van Stokkum, I. H. M.},
  title = {Parameter Precision in Global Analysis of Time Resolved Spectra},
  journal = {IEEE Transactions on Instrumentation and Measurement},
  year = {1997},
  volume = {46},
  pages = {764-768},
  number = {4}
}

@INPROCEEDINGS{ieee2x,
  author = {van Stokkum, I. H. M.},
  title = {Parameter Precision in Global Analysis of Time Resolved Spectra},
  booktitle = {Quality Measurements: The Indispensable Bridge between Theory and
	Reality},
  year = {1996},
  volume = {1},
  pages = {168-173},
  organization = {IEEE Instrumentation and Measurement Technology Conference}
}

@ARTICLE{vanStokkum1990b,
  author = {van Stokkum, Ivo H. M.},
  title = {Modelling the response of auditory midbrain neurons in the grassfrog
	to temporally structured monaural stimuli},
  journal = {Hearing Research},
  year = {1990},
  volume = {43},
  pages = {231--250},
  month = {Jan},
  issue = {2-3},
  keywords = {Anuran},
  url = {http://www.sciencedirect.com/science/article/B6T73-4CF5W2R-G/2/0bb61683a06f2e5ca035405c6d0e92c1}
}

@PHDTHESIS{thesisivo,
  author = {van Stokkum, I. H. M.},
  title = {Analysis of auditory brainstem neurons in the grassfrog},
  school = {Catholic University of Nijmegen},
  year = {1989}
}

@ARTICLE{vanStokkum1987,
  author = {van Stokkum, Ivo H. M.},
  title = {Sensitivity of neurons in the dorsal medullary nucleus of the grassfrog
	to spectral and temporal characteristics of sound},
  journal = {Hearing Research},
  year = {1987},
  volume = {29},
  pages = {223--235},
  issue = {2-3},
  keywords = {Amplitude modulation},
  url = {http://www.sciencedirect.com/science/article/B6T73-485GM6P-S7/2/382f5f3bd1189b5e9242b6ecbad822db}
}

@ARTICLE{pse_short,
  author = {Ivo H. M. van Stokkum and Henri E. Bal},
  title = {A Problem Solving Environment for interactive modelling of multiway
	data},
  journal = {Concurrency and computation: practice and experience},
  year = {2006},
  volume = {18},
  pages = {263-269}
}

@ARTICLE{vanStokkumI.H.M._bi9707943,
  author = {van Stokkum, I. H. M. and Beekman, L.M.P. and Jones, M.R. and van
	Brederode, M.E. and van Grondelle, R.},
  title = {Primary Electron Transfer Kinetics in Membrane-Bound Rhodobacter
	sphaeroides Reaction Centers: A Global and Target Analysis},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {11360-11368},
  number = {38},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9707943}
}

@ARTICLE{ivo93,
  author = {van Stokkum, I. H. M. and Brouwer, A.M. and Van Ramesdonk, H.J. and
	Scherer, T.},
  title = {Multiresponse parameter estimation and compartmental analysis of
	time resolved fluorescence spectra: Application to conformational
	dynamics of charge-separated species in solution},
  journal = {Proc. Kon. Ned. Akad. v. Wetensch},
  year = {1993},
  volume = {96},
  pages = {43-68}
}

@ARTICLE{ivo88b,
  author = {van Stokkum, I. H. M. and Epping, W.J.M.},
  title = {Responses of auditory brainstem neurons in the grassfrog to clicks},
  journal = {Acta Biologica Hungarica},
  year = {1988},
  volume = {29},
  pages = {291-304}
}

@ARTICLE{ISI:000289774200005,
  author = {van Stokkum, Ivo H. M. and Gauden, Magdalena and Crosson, Sean and
	van Grondelle, Rienk and Moffat, Keith and Kennis, John T. M.},
  title = {{The Primary Photophysics of the Avena sativa Phototropin 1 LOV2
	Domain Observed with Time-resolved Emission Spectroscopy}},
  journal = {Photochemistry and Photobiology},
  year = {2011},
  volume = {{87}},
  pages = {{534-541}},
  number = {{3}},
  month = {{May-jun}},
  abstract = {{The phototropins are blue-light receptors that base their light-dependent
	action on the reversible formation of a covalent bond between a flavin
	mononucleotide (FMN) cofactor and a conserved cysteine in light,
	oxygen or voltage (LOV) domains. The primary reactions of the Avena
	sativa phototropin 1 LOV2 domain were investigated by means of time-resolved
	and low-temperature fluorescence spectroscopy. Synchroscan streak
	camera experiments revealed a fluorescence lifetime of 2.2 ns in
	LOV2. A weak long-lived component with emission intensity from 600
	to 650 nm was assigned to phosphorescence from the reactive FMN triplet
	state. This observation allowed determination of the LOV2 triplet
	state energy level at physiological temperature at 16600 cm(-1).
	FMN dissolved in aqueous solution showed pH-dependent fluorescence
	lifetimes of 2.7 ns at pH 2 and 3.9-4.1 ns at pH 3-8. Here, too,
	a weak phosphorescence band was observed. The fluorescence quantum
	yield of LOV2 increased from 0.13 to 0.41 upon cooling the sample
	from 293 to 77 K. A pronounced phosphorescence emission around 600
	nm was observed in the LOV2 domain between 77 and 120 K in the steady-state
	emission.}},
  address = {{COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}},
  affiliation = {{Kennis, JTM (Reprint Author), Vrije Univ Amsterdam, Fac Sci, Dept
	Phys \& Astron, Amsterdam, Netherlands. van Stokkum, IHM; Gauden,
	M; van Grondelle, R; Kennis, JTM, Vrije Univ Amsterdam, Fac Sci,
	Dept Phys \& Astron, Amsterdam, Netherlands. Crosson, S; Moffat,
	K, Univ Chicago, Dept Biochem \& Mol Biol, Chicago, IL 60637 USA.
	Moffat, K, Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA.}},
  author-email = {{j.t.m.kennis@vu.nl}},
  doc-delivery-number = {{753LD}},
  doi = {{10.1111/j.1751-1097.2011.00903.x}},
  funding-acknowledgement = {{Chemical Sciences Council of the Netherlands Foundation for Scientific
	Research (NWO-CW); Earth and Life Sciences Council of the Netherlands
	Foundation for Scientific Research (NWO-ALW); Foundation of Fundamental
	Research on Matter (FOM); NIH\{{[}\}GM 36452]; NSF}},
  funding-text = {{The construct of oat phot1 LOV2 was generously provided by Kevin
	Gardner of University of Texas and Southwestern Medical Center, Dallas.
	M.G. was supported by the Chemical Sciences Council of the Netherlands
	Foundation for Scientific Research (NWO-CW). J.T.M.K. was supported
	by the Earth and Life Sciences Council of the Netherlands Foundation
	for Scientific Research (NWO-ALW) via a VIDI grant, and through the
	Foundation of Fundamental Research on Matter (FOM). K.M. was supported
	through NIH grant GM 36452, S.C. was supported through an NSF Predoctoral
	Fellowship.}},
  issn = {{0031-8655}},
  journal-iso = {{Photochem. Photobiol.}},
  keywords-plus = {{BLUE-LIGHT RECEPTOR; ALGA CHLAMYDOMONAS-REINHARDTII; FLAVIN-BINDING
	PHOTORECEPTOR; J-ALPHA HELIX; STRUCTURAL-CHANGES; SIGNALING MECHANISM;
	RHODOBACTER-SPHAEROIDES; HISTIDINE KINASES; PHOT-LOV1 DOMAIN; AQUEOUS-SOLUTION}},
  language = {{English}},
  number-of-cited-references = {{90}},
  publisher = {{WILEY-BLACKWELL}},
  subject-category = {{Biochemistry \& Molecular Biology; Biophysics}},
  times-cited = {{0}},
  type = {{Article}},
  unique-id = {{ISI:000289774200005}}
}

@ARTICLE{vanStokkum1989,
  author = {van Stokkum, Ivo H. M. and Gielen, C. C. A. M.},
  title = {A model for the peripheral auditory nervous system of the grassfrog},
  journal = {Hearing Research},
  year = {1989},
  volume = {41},
  pages = {71--85},
  month = {Aug},
  issue = {1},
  keywords = {Anuran},
  url = {http://www.sciencedirect.com/science/article/B6T73-485H319-X/2/74482d7e19e3233e617f40a8fa5d65f2}
}

@ARTICLE{i_2006,
  author = {I. H. M. van Stokkum and B. Gobets and T. Gensch and F. van Mourik
	and K. J. Hellingwerf and R. van Grondelle and J. T. M. Kennis},
  title = {Symposium-in-Print: Green Fluorescent Protein and Homologs. (Sub)-Picosecond
	Spectral Evolution of Fluorescence in Photoactive Proteins Studied
	with a Synchroscan Streak Camera System},
  journal = {Photochemistry and Photobiology},
  year = {2006},
  volume = {82},
  pages = {380-388},
  file = {PhotochemPhotobiol82_380_388.pdf:http\://www.nat.vu.nl/~ivo/pub/2006/PhotochemPhotobiol82_380_388.pdf:PDF}
}

@ARTICLE{vanStokkum1995,
  author = {van Stokkum, I. H. M. and van der Graaf, W. A. and Lenstra, D.},
  title = {Weighted fit of optical spectra},
  journal = {Optics Communications},
  year = {1995},
  volume = {121},
  pages = {103--108},
  month = {Dec},
  day = {01},
  issue = {4-6},
  url = {http://www.sciencedirect.com/science/article/B6TVF-3XY2PXG-3/2/8594545ebf321bb087dc365196c77820}
}

@ARTICLE{i95,
  author = {van Stokkum, I. H. M. and Lambrou, G.N. and Van den Berg, T.J.T.P.},
  title = {Hemodynamic parameter estimation from ocular fluorescein angiograms},
  journal = {Graefe's Archive for Clinical and Experimental Ophthalmology},
  year = {1995},
  volume = {233},
  pages = {123-130}
}

@ARTICLE{pse_long,
  author = {Ivo H. M. van Stokkum and Delmar S. Larsen and Rienk van Grondelle},
  title = {Global and Target Analysis of Time-resolved Spectra},
  journal = {Biochimica et Biophysica Acta},
  year = {2004},
  volume = {1657},
  pages = {82-104, and erratum, {{\bf 1658}}, 262}
}

@ARTICLE{vanStokkum2004a,
  author = {van Stokkum, Ivo H. M. and Larsen, Delmar S. and van Grondelle, Rienk},
  title = {Erratum to ''{G}lobal and target analysis of time-resolved spectra''
	[{Biochimica et Biophysica Acta} 1658/2-3 (2004) 82-104]},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {2004},
  volume = {1658},
  pages = {262--262},
  month = {Oct},
  day = {04},
  issue = {3},
  url = {http://www.sciencedirect.com/science/article/B6T1S-4D5P0FB-1/2/6dd0f74e3ce7f0159dd7dfacf7d6c0c7}
}

@ARTICLE{vanStokkum2004b,
  author = {van Stokkum, Ivo H. M. and Larsen, Delmar S. and van Grondelle, Rienk},
  title = {Global and target analysis of time-resolved spectra},
  journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
  year = {2004},
  volume = {1657},
  pages = {82--104},
  month = {Jul},
  day = {09},
  issue = {2-3},
  keywords = {Global analysis},
  url = {http://www.sciencedirect.com/science/article/B6T1S-4CK7MW0-3/2/ccec4c719e748c44b43c827df76e0b45}
}

@ARTICLE{vanStokkumI.H.M._bi00033a024,
  author = {van Stokkum, I. H. M. and Linsdell, H. and Hadden, J. M. and Haris,
	P. I. and Chapman, D. and Bloemendal, M.},
  title = {Temperature-Induced Changes in Protein Structures Studied by Fourier
	Transform Infrared Spectroscopy and Global Analysis},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {10508-10518},
  number = {33},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi00033a024}
}

@ARTICLE{target,
  author = {van Stokkum, I. H. M. and Lozier, RH},
  title = {Target analysis of the bacteriorhodopsin photocycle using a spectrotemporal
	model},
  journal = {J. Phys. Chem. B},
  year = {2002},
  volume = {106},
  pages = {3477-3485}
}

@ARTICLE{vanStokkum1991,
  author = {van Stokkum, Ivo H. M. and Melssen, Willem J.},
  title = {Measuring and modelling the response of auditory midbrain neurons
	in the grassfrog to temporally structured binaural stimuli},
  journal = {Hearing Research},
  year = {1991},
  volume = {52},
  pages = {113--132},
  month = {Mar},
  issue = {1},
  keywords = {Anuran},
  url = {http://www.sciencedirect.com/science/article/B6T73-485H32M-1C/2/43f2844a196d6d0aee11be1f7bec9ce6}
}

@INPROCEEDINGS{beekb,
  author = {van Stokkum, I. H. M. and F. van Mourik and M.-L. Groot and R. van
	Grondelle},
  title = {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},
  booktitle = {Photosynthesis: from Light to Biosphere},
  year = {1995},
  editor = {P. Mathis},
  volume = {1},
  pages = {887-890},
  publisher = {Dordrecht, Kluwer}
}

@ARTICLE{vanStokkum2009150,
  author = {Ivo H. M. van Stokkum and Katharine M. Mullen and Velitchka V. Mihaleva},
  title = {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},
  journal = {Chemometrics and Intelligent Laboratory Systems},
  year = {2009},
  volume = {95},
  pages = {150 - 163},
  number = {2},
  doi = {DOI: 10.1016/j.chemolab.2008.10.004},
  issn = {0169-7439},
  keywords = {Multivariate curve resolution alternating least squares},
  url = {http://www.sciencedirect.com/science/article/B6TFP-4TT9G9Y-2/2/023c3de71d2471d96ef8e1b4c377ff36}
}

@INCOLLECTION{streakreview,
  author = {I. H. M. van Stokkum and B. van Oort and F. van Mourik and B. Gobets
	and H. van Amerongen},
  title = {{(Sub)-Picosecond Spectral Evolution of Fluorescence Studied with
	a Synchroscan Streak-Camera System and Target Analysis}},
  booktitle = {{Biophysical Techniques in Photosynthesis, Volume {II}, Series Advances
	in Photosynthesis and Respiration}},
  publisher = {Springer, Dordrecht},
  year = {2008},
  editor = {Aartsma, Thijs J. and Matysik, J{\"{o}}rg},
  volume = {26},
  pages = {223-240},
  isbn = {978-1-4020-8249-8},
  url = {http://www.springer.com/west/home/new+%26+forthcoming+titles+%28default%29?SGWID=4-40356-22-173795609-0}
}

@ARTICLE{vanStokkum200970,
  author = {Ivo H. M. van Stokkum and Emmanouil Papagiannakis and Mikas Vengris
	and Jante M. Salverda and Tom{\'{a}}s Pol{\'{i}}vka and Donatas Zigmantas
	and Delmar S. Larsen and Stefania S. Lampoura and Roger G. Hiller
	and Rienk van Grondelle},
  title = {Inter-pigment interactions in the peridinin chlorophyll protein studied
	by global and target analysis of time resolved absorption spectra},
  journal = {Chemical Physics},
  year = {2009},
  volume = {357},
  pages = {70 - 78},
  number = {1-3},
  note = {Excited State Dynamics in Light Harvesting Materials},
  doi = {DOI: 10.1016/j.chemphys.2008.10.005},
  issn = {0301-0104},
  keywords = {Peridinin chlorophyll protein},
  url = {http://www.sciencedirect.com/science/article/B6TFM-4TP49RS-1/2/547d9b815d70999da20a291a2b76c3dc}
}

@ARTICLE{vanStokkumI.H.M._j100054a021,
  author = {van Stokkum, I. H. M. and Scherer, T. and Brouwer, A. M. and Verhoeven,
	J. W.},
  title = {Conformational dynamics of flexibly and semirigidly bridged electron
	donor-acceptor systems as revealed by spectrotemporal parametrization
	of fluorescence},
  journal = {Journal of Physical Chemistry},
  year = {1994},
  volume = {98},
  pages = {852-866},
  number = {3},
  issn = {0022-3654},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/j100054a021}
}

@ARTICLE{vanStokkum1990a,
  author = {van Stokkum, Ivo H. M. and Spoelder, Hans J. W. and Bloemendal, Michael
	and van Grondelle, Rienk and Groen, Frans C. A.},
  title = {Estimation of protein secondary structure and error analysis from
	circular dichroism spectra},
  journal = {Analytical Biochemistry},
  year = {1990},
  volume = {191},
  pages = {110--118},
  month = {Nov},
  day = {15},
  issue = {1},
  url = {http://www.sciencedirect.com/science/article/B6W9V-4F031H9-7X/2/c5ac776796f63ea06b6bf35705f49643}
}

@ARTICLE{sytina2008,
  author = {Sytina, Olga A. and Heyes, Derren J. and Hunter, C. Neil and Alexandre,
	Maxime T. and van Stokkum, Ivo H. M. and van Grondelle, Rienk and
	Groot, Marie{-}Louise},
  title = {Conformational changes in an ultrafast light-driven enzyme determine
	catalytic activity},
  journal = {Nature},
  year = {2008},
  volume = {456},
  pages = {1001-1004},
  number = {7224},
  url = {http://www.nature.com/nature/journal/v456/n7224/abs/nature07354.html}
}

@ARTICLE{doi:10.1021/jp108317u,
  author = {Sytina, Olga A. and van Stokkum, Ivo H. M. and van Grondelle, Rienk
	and Groot, Marie Louise},
  title = {Single and Multi-Exciton Dynamics in Aqueous Protochlorophyllide
	Aggregates},
  journal = {The Journal of Physical Chemistry A},
  year = {2011},
  volume = {{115}},
  pages = {{3936-3946}},
  number = {{16}},
  month = {{Apr 28}},
  doi = {10.1021/jp108317u},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp108317u},
  url = {http://pubs.acs.org/doi/abs/10.1021/jp108317u}
}

@ARTICLE{Sytina2010,
  author = {Sytina, O. A. and van Stokkum, I. H. M. and Heyes, D. J. and Hunter,
	C. N. and van Grondelle, R. and Groot, M. L.},
  title = {Protochlorophyllide Excited-State Dynamics in Organic Solvents Studied
	by Time-Resolved Visible and Mid-Infrared Spectroscopy},
  journal = {Journal of Physical Chemistry B},
  year = {2010},
  volume = {114},
  pages = {4335-4344},
  number = {12},
  abstract = {Protochlorophyllide (PChlide) is a precursor in the biosynthesis of
	chlorophyll. Complexed with NADPH to the enzyme protochlorophyllide
	oxidoreductase (POR), it is reduced to chlorophyllide, a process
	that Occurs via a set of spectroscopically distinct intermediate
	states and is initiated from the excited state of PChlide. To obtain
	a better understanding of these catalytic events, we characterized
	the excited state dynamics of PChlide in the solvents tetrahydrofuran
	(THF), methanol, and Tris/Triton buffer using ultrafast transient
	absorption in the visible and mid-infrared spectral regions and time-resolved
	fluorescence emission experiments. For comparison, we present time-resolved
	transient absorption measurements of chlorophyll a in THE From the
	combined analysis of these experiments, we derive that during the
	2-3 ns excited state lifetime an extensive multiphasic quenching
	of the emission occurs due to solvation of the excited state, which
	is in agreement with the previously proposed internal charge transfer
	(ICT) character of the S I state (Zhao, G. J.; Han, K. L. Biophys.
	J. 2008, 94, 38). The solvation process in methanol occurs in conjunction
	with a strengthening of a hydrogen bond to the Pchlide keto carbonyl
	group. We demonstrate that the internal conversion from the S2 to
	S1 excited states is remarkably slow and stretches out on to the
	700 fs time scale, causing a rise of blue-shifted signals in the
	transient absorption and a gain of emission in the time-resolved
	fluorescence. A triplet state is populated oil the nanosecond time
	scale with a maximal yield of similar to 23%. The consequences of
	these observations for the catalytic pathway and the role of the
	triplet and ICT state in activation of the enzyme are discussed.}
}

@ARTICLE{ISI:000291656900023,
  author = {Toh, K. C. and Stojkovic, Emina A. and van Stokkum, Ivo H. M. and
	Moffat, Keith and Kennis, John T. M.},
  title = {{Fluorescence quantum yield and photochemistry of bacteriophytochrome
	constructs}},
  journal = {Physical Chemistry Chemical Physics},
  year = {2011},
  volume = {{13}},
  pages = {{11985-11997}},
  number = {{25}},
  abstract = {{Bacteriophytochromes (Bphs) are red-light photoreceptor proteins
	with a photosensory core that consists of three distinct domains,
	PAS, GAF and PHY, and covalently binds biliverdin (BV) to a conserved
	cysteine in the PAS domain. In a recent development, PAS-GAF variants
	were engineered for use as a near-infrared fluorescent marker in
	mammalian tissues (Tsien and co-workers, Science, 2009, 324, 804-807).
	Here, we report the fluorescence quantum yield and photochemistry
	of two highly-related Bphs from Rps. palustris, RpBphP2 (P2) and
	RpBphP3 (P3) with distinct photoconversion and fluorescence properties.
	We applied ultrafast spectroscopy to wild type P3 and P2 PAS-GAF
	proteins and their P3 D216A, Y272F and P2 D202A PAS-GAF-PHY mutant
	proteins. In these mutants hydrogen-bond interactions between a conserved
	aspartate (Asp) which connects the BV chromophore with the PHY domains
	are disrupted. The excited-state lifetime of the truncated P3 and
	P2 PAS-GAF proteins was significantly longer than in their PAS-GAF-PHY
	counterparts that constitute the full photosensory core. Mutation
	of the conserved Asp to Ala in the PAS-GAF-PHY protein had a similar
	but larger effect. The fluorescence quantum yields of the P3 D216A
	and Y272F mutants were 0.066, higher than that of wild type P3 (0.043)
	and similar to the engineered Bph of Tsien and co-workers. We conclude
	that elimination of a key hydrogen-bond interaction between Asp and
	a conserved Arg in the PHY domain is responsible for the excited-state
	lifetime increase in all Bph variants studied here. H/D exchange
	resulted in a 1.4-1.7 fold increase of excited-state lifetime. The
	results support a reaction model in which deactivation of the BV
	chromophore proceeds via excited-state proton transfer from the BV
	pyrrole nitrogens to the backbone of the conserved Asp or to a bound
	water. This work may aid in rational structure-and mechanism-based
	conversion of constructs based on P3 and other BPhs into efficient
	near-IR, deep tissue, fluorescent markers.}},
  address = {{THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF,
	CAMBS, ENGLAND}},
  affiliation = {{Kennis, JTM (Reprint Author), Vrije Univ Amsterdam, Dept Phys \&
	Astron, Biophys Sect, De Boelelaan 1081, NL-1081 HV Amsterdam, Netherlands.
	Toh, KC; van Stokkum, IHM; Kennis, JTM, Vrije Univ Amsterdam, Dept
	Phys \& Astron, Biophys Sect, NL-1081 HV Amsterdam, Netherlands.
	Stojkovic, EA; Moffat, K, Univ Chicago, Dept Biochem \& Mol Biol,
	Chicago, IL 60637 USA. Moffat, K, Univ Chicago, Inst Biophys Dynam,
	Chicago, IL 60637 USA.}},
  author-email = {{j.t.m.kennis@vu.nl}},
  doc-delivery-number = {{777WX}},
  doi = {{10.1039/c1cp00050k}},
  funding-acknowledgement = {{Earth and Life Sciences Council of the Netherlands Foundation for
	Scientific Research (NWO-ALW); NIH\{{[}\}GM036452]}},
  funding-text = {{K.C.T. and J.T.M.K. were supported by the Earth and Life Sciences
	Council of the Netherlands Foundation for Scientific Research (NWO-ALW)
	through a VIDI grant to J.T.M.K. E.A.S and K.M. were supported by
	NIH grant GM036452 to K.M.}},
  issn = {{1463-9076}},
  journal-iso = {{Phys. Chem. Chem. Phys.}},
  keywords-plus = {{CYANOBACTERIAL PHYTOCHROME CPH1; CHROMOPHORE-BINDING DOMAIN; TIME-RESOLVED
	SPECTROSCOPY; EXCITED-STATE DYNAMICS; ENERGY-TRANSFER; CRYSTAL-STRUCTURE;
	RESONANCE RAMAN; GROUND-STATE; AGROBACTERIUM-TUMEFACIENS; MIDINFRARED
	SPECTROSCOPY}},
  language = {{English}},
  number-of-cited-references = {{79}},
  publisher = {{ROYAL SOC CHEMISTRY}},
  subject-category = {{Chemistry; Physics}},
  times-cited = {{0}},
  type = {{Article}},
  unique-id = {{ISI:000291656900023}}
}

@ARTICLE{doi:10.1021/jp106891x,
  author = {Toh, K. C. and Stojkovi{\'{c}}, Emina A. and Rupenyan, Alisa B. and
	van Stokkum, Ivo H. M. and Salumbides, Marian and Groot, Marie-Louise
	and Moffat, Keith and Kennis, John T. M.},
  title = {Primary Reactions of Bacteriophytochrome Observed with Ultrafast
	Mid-Infrared Spectroscopy},
  journal = {The Journal of Physical Chemistry A},
  year = {2011},
  volume = {{115}},
  pages = {{3778-3786}},
  number = {{16}},
  month = {{Apr 28}},
  doi = {10.1021/jp106891x},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp106891x},
  url = {http://pubs.acs.org/doi/abs/10.1021/jp106891x}
}

@ARTICLE{Toh2010,
  author = {Toh, K. C. and Stojkovi{\'{c}}, E. A. and van Stokkum, I. H. M. and
	Moffat, K. and Kennis, J. T. M.},
  title = {Proton-transfer and hydrogen-bond interactions determine fluorescence
	quantum yield and photochemical efficiency of bacteriophytochrome},
  journal = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {2010},
  volume = {107},
  pages = {9170-9175},
  number = {20},
  abstract = {Phytochromes are red-light photoreceptor proteins that regulate a
	variety of responses and cellular processes in plants, bacteria,
	and fungi. Thephytochromelight activation mechanism involves isomerization
	around the C15=C16 double bond of an open-chain tetrapyrrole chromophore,
	resulting in a flip of its D-ring. In an important new development,
	bacteriophytochrome (Bph) has been engineered for use as a fluorescent
	marker in mammalian tissues. Here we report that an unusual Bph,
	RpBphP3 from Rhodopseudomonas palustris, denoted P3, is fluorescent.
	This Bph modulates synthesis of light-harvesting complex in combination
	with a second Bph exhibiting classical photochemistry, RpBphP2, denoted
	P2. We identify the factors that determine the fluorescence and isomerization
	quantum yields through the application of ultrafast spectroscopy
	to wild-type and mutants of P2 and P3. The excited-state lifetime
	of the biliverdin chromophore in P3 was significantly longer at 330-500
	ps than in P2 and other classical phytochromes and accompanied by
	a significantly reduced isomerization quantum yield. H/D exchange
	reduces the rate of decay from the excited state of biliverdin by
	a factor of 1.4 and increases the isomerization quantum yield. Comparison
	of the properties of the P2 and P3 variants shows that the quantum
	yields of fluorescence and isomerization are determined by excited-state
	deprotonation of biliverdin at the pyrrole rings, in competition
	with hydrogen-bond rupture between the D-ring and the apoprotein.
	This work provides a basis for structure-based conversion of Bph
	into an efficient near-IR fluorescent marker.}
}

@ARTICLE{K.C.Toh07012008,
  author = {Toh, K. C. and van Stokkum, Ivo H. M. and Hendriks, Johnny and Alexandre,
	Maxime T. A. and Arents, J. C. and Perez, Marcela Avila and van Grondelle,
	Rienk and Hellingwerf, Klaas J. and Kennis, John T. M.},
  title = {{On the Signaling Mechanism and the Absence of Photoreversibility
	in the AppA BLUF Domain}},
  journal = {Biophys. J.},
  year = {2008},
  volume = {95},
  pages = {312-321},
  number = {1},
  abstract = {The flavoprotein AppA from Rhodobacter sphaeroides contains an N-terminal,
	FAD-binding BLUF photoreceptor domain. Upon illumination, the AppA
	BLUF domain forms a signaling state that is characterized by red-shifted
	absorbance by 10 nm, a state known as AppARED. We have applied ultrafast
	spectroscopy on the photoaccumulated AppARED state to investigate
	the photoreversible properties of the AppA BLUF domain. On light
	absorption by AppARED, the FAD singlet excited state FADRED* decays
	monoexponentially in 7 ps to form the neutral semiquinone radical
	FADH*, which subsequently decays to the original AppARED molecular
	ground state in 60 ps. Thus, FADRED* is deactivated rapidly via electron
	and proton transfer, probably from the conserved tyrosine Tyr-21
	to FAD, followed by radical-pair recombination. We conclude that,
	in contrast to many other photoreceptors, the AppA BLUF domain is
	not photoreversible and does not enter alternative reaction pathways
	upon absorption of a second photon. To explain these properties,
	we propose that a molecular configuration is formed upon excitation
	of AppARED that corresponds to a forward reaction intermediate previously
	identified for the dark-state BLUF photoreaction. Upon excitation
	of AppARED, the BLUF domain therefore enters its forward reaction
	coordinate, readily re-forming the AppARED ground state and suppressing
	reverse or side reactions. The monoexponential decay of FAD* indicates
	that the FAD-binding pocket in AppARED is significantly more rigid
	than in dark-state AppA. Steady-state fluorescence experiments on
	wild-type, W104F, and W64F mutant BLUF domains show tryptophan fluorescence
	maxima that correspond with a buried conformation of Trp-104 in dark
	and light states. We conclude that Trp-104 does not become exposed
	to solvent during the BLUF photocycle. },
  doi = {10.1529/biophysj.107.117788},
  eprint = {http://www.biophysj.org/cgi/reprint/95/1/312.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/95/1/312}
}

@ARTICLE{Valkunas200917,
  author = {Leonas Valkunas and Ivo H. M. van Stokkum and Rudi Berera and Rienk
	van Grondelle},
  title = {Exciton migration and fluorescence quenching in {LHCII} aggregates:
	Target analysis using a simple nonlinear annihilation scheme},
  journal = {Chemical Physics},
  year = {2009},
  volume = {357},
  pages = {17 - 20},
  number = {1-3},
  note = {Excited State Dynamics in Light Harvesting Materials},
  doi = {DOI: 10.1016/j.chemphys.2008.07.025},
  issn = {0301-0104},
  keywords = {Non{-}photochemical quenching},
  url = {http://www.sciencedirect.com/science/article/B6TFM-4T7XGVW-1/2/b8bf22a5db39eab19c2be203d614d719}
}

@ARTICLE{vananh2009,
  author = {Van Anh, Nguyen and Schlosser, Felix and Groeneveld, Michiel M. and
	van Stokkum, Ivo H. M. and Würthner, Frank and Williams, René M.},
  title = {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},
  journal = {The Journal of Physical Chemistry C},
  year = {2009},
  volume = {113},
  pages = {18358-18368},
  number = {42},
  doi = {doi: 10.1021/jp9055279}
}

@INPROCEEDINGS{bed96,
  author = {Van Brederode, ME and Beekman, LMP and Kuciauskas, D and Jones, MR
	and van Stokkum, I. H. M. and van Grondelle, R},
  title = {Characteristics of the electron transfer reactions in the {M210W}
	reaction centre only mutant of Rhodobacter sphaeroides},
  booktitle = {The Reaction Center of Photosynthetic Bacteria: Structure and Dynamics},
  year = {1996},
  editor = {Michel-Beyerle, ME},
  pages = {225-237},
  publisher = {Springer-Verlag, Berlin}
}

@ARTICLE{VanBrederodeM.E._bi9703756,
  author = {Van Brederode, M.E. and Jones, M.R. and Van Mourik, F. and Van Stokkum,
	I. H. M. and Van Grondelle, R.},
  title = {A New Pathway for Transmembrane Electron Transfer in Photosynthetic
	Reaction Centers of Rhodobacter sphaeroides Not Involving the Excited
	Special Pair},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {6855-6861},
  number = {23},
  issn = {0006-2960},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9703756}
}

@ARTICLE{PetraA.W.VanDenBerg10012001,
  author = {Van Den Berg, Petra A.W. and Mulrooney, Scott B. and Gobets, Bas
	and Van Stokkum, Ivo H. M. and Van Hoek, Arie and Williams, Charles
	H., JR. and Visser, Antonie J.W.G.},
  title = {{Exploring the conformational equilibrium of E. coli thioredoxin
	reductase: Characterization of two catalytically important states
	by ultrafast flavin fluorescence spectroscopy}},
  journal = {Protein Sci},
  year = {2001},
  volume = {10},
  pages = {2037-2049},
  number = {10},
  doi = {10.1110/ps.06701},
  file = {2037.pdf:http\://www.proteinscience.org/cgi/reprint/10/10/2037.pdf:PDF},
  url = {http://www.proteinscience.org/cgi/content/abstract/10/10/2037}
}

@ARTICLE{gen95,
  author = {Van Haeringen, B and de Lange, F. and van Stokkum, I. H. M. and Srai,
	SKS and Evans, RW and van Grondelle, R. and Bloemendal, M},
  title = {Dynamic structure of human serum transferrin from transient electric
	birefringence},
  journal = {Proteins, Structure, Function, and Genetics},
  year = {1995},
  volume = {23},
  pages = {233-240}
}

@INCOLLECTION{ivo92a,
  author = {Van Kan, P.J.M. and Groot, M.L. and Van Stokkum, I. H. M. and Kwa,
	S.L.S. and Van Grondelle, R. and Dekker, J.P.},
  title = {Chlorophyll triplet states in the {CP47} core antenna protein of
	photosystem {II}},
  booktitle = {Research in Photosynthesis},
  publisher = {Kluwer Academic Publishers,Dordrecht},
  year = {1992},
  editor = {N. Murata},
  volume = {1},
  pages = {271-274}
}

@INPROCEEDINGS{beeka,
  author = {Van Kan, P.J.M. and Van Stokkum, I. H. M. and Styring, S.},
  title = {Time-resolved {EPR} spectroscopy of the triplet state of the primary
	electron donor {P680} in {PS {II}}},
  booktitle = {Photosynthesis: from Light to Biosphere},
  year = {1995},
  editor = {P. Mathis},
  volume = {1},
  pages = {543-546},
  publisher = {Dordrecht, Kluwer}
}

@INCOLLECTION{ivo92b,
  author = {Van Mourik, F. and Corten, E.P.M. and Van Stokkum, I. H. M. and Visschers,
	R.W. and Loach, P.A. and Kraayenhof, R. and Van Grondelle, R.},
  title = {Self assembly of the {LH-1} antenna of Rhodospirillum rubrum, a time-resolved
	study of the aggregation of the {B820} subunit form},
  booktitle = {Research in Photosynthesis},
  publisher = {Kluwer Academic Publishers,Dordrecht},
  year = {1992},
  editor = {N. Murata},
  volume = {1},
  pages = {101-104}
}

@ARTICLE{VanMourik2004,
  author = {Van Mourik, Frank and Groot, Marie-Louise and Van Grondelle, Rienk
	and Dekker, Jan P. and Van Stokkum, Ivo H. M.},
  title = {{Global and target analysis of fluorescence measurements on photosystem
	2 reaction centers upon red excitation }},
  journal = {Physical Chemistry Chemical Physics},
  year = {2004},
  volume = {6},
  pages = {4820 - 4824}
}

@ARTICLE{ivo86,
  author = {Van Stokkum, I. H. M. and Johannesma, P.I.M. and Eggermont, J.J.},
  title = {Representation of time-dependent correlation and recurrence-time
	functions: A new method to analyse non-stationary point-processes},
  journal = {Biological Cybernetics},
  year = {1986},
  volume = {55},
  pages = {17-24}
}

@ARTICLE{MikasVengris09012004,
  author = {Vengris, Mikas and van der Horst, Michael A. and Zgrablic, Goran
	and van Stokkum, Ivo H. M. and Haacke, Stefan and Chergui, Majed
	and Hellingwerf, Klaas J. and van Grondelle, Rienk and Larsen, Delmar
	S.},
  title = {{Contrasting the Excited-State Dynamics of the Photoactive Yellow
	Protein Chromophore: Protein versus Solvent Environments}},
  journal = {Biophysical Journal},
  year = {2004},
  volume = {87},
  pages = {1848-1857},
  number = {3},
  doi = {10.1529/biophysj.104.043224},
  file = {1848.pdf:http\://www.biophysj.org/cgi/reprint/87/3/1848.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/87/3/1848}
}

@INCOLLECTION{bookpulse,
  author = {Mikas Vengris and Ivo van Stokkum and Xiang He and Alasdair Bell
	and Peter Tonge and Rienk van Grondelle and Delmar Larsen},
  title = {Ultrafast excited and ground-state isomerization dynamics of the
	Green Fluorescent Protein chromophore in solution},
  booktitle = {Ultrafast Phenomena XIV},
  year = {2005},
  pages = {610-612},
  url = {http://www.springerlink.com/content/m6u40244600kuj81}
}

@ARTICLE{VengrisM._jp037902h,
  author = {Vengris, M. and van Stokkum, I. H. M. and He, X. and Bell, A.F. and
	Tonge, P.J. and van Grondelle, R. and Larsen, D.S.},
  title = {Ultrafast Excited and Ground-State Dynamics of the Green Fluorescent
	Protein Chromophore in Solution},
  journal = {Journal of Physical Chemistry A},
  year = {2004},
  volume = {108},
  pages = {4587-4598},
  number = {21},
  issn = {1089-5639},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp037902h}
}

@ARTICLE{HMVisser09011995,
  author = {Visser, HM and Somsen, OJG and van Mourik, F and Lin, S and van Stokkum,
	I. H. M. and van Grondelle, R},
  title = {{Direct observation of sub-picosecond equilibration of excitation
	energy in the light-harvesting antenna of Rhodospirillum rubrum}},
  journal = {Biophys. J.},
  year = {1995},
  volume = {69},
  pages = {1083-1099},
  number = {3},
  file = {1083.pdf:http\://www.biophysj.org/cgi/reprint/69/3/1083.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/69/3/1083}
}

@ARTICLE{VisserH.Matthieu_j100041a055,
  author = {Visser, H. Matthieu and Groot, Marie-Louise and van Mourik, Frank
	and van Stokkum, Ivo H. M. and Dekker, Jan P. and van Grondelle,
	Rienk},
  title = {Subpicosecond Transient Absorption Difference Spectroscopy on the
	Reaction Center of Photosystem {II}: Radical Pair Formation at 77
	{K}},
  journal = {Journal of Physical Chemistry},
  year = {1995},
  volume = {99},
  pages = {15304-15309},
  number = {41},
  issn = {0022-3654},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/j100041a055}
}

@ARTICLE{Visser1996,
  author = {Visser, H. M. and Kleima, F. J. and van Stokkum, I. H. M. and van
	Grondelle, R. and van Amerongen, H.},
  title = {Probing the many energy-transfer processes in the photosynthetic
	light-harvesting complex {II} at 77 {K} using energy-selective sub-picosecond
	transient absorption spectroscopy},
  journal = {Chemical Physics},
  year = {1996},
  volume = {210},
  pages = {297--312},
  month = {Oct},
  day = {01},
  issue = {1-2},
  url = {http://www.sciencedirect.com/science/article/B6TFM-3VB3S3T-S/2/ed5bbd5a910c358d091db41dfb33e456}
}

@ARTICLE{ieee1,
  author = {Vos, F.M. and van der Heijde, G.L. and Spoelder, H.J.W. and van Stokkum,
	I. H. M. and Groen, F.C.A.},
  title = {A new instrument to measure the shape of the cornea based on pseudorandom
	color coding},
  journal = {IEEE Transactions on Instrumentation and Measurement},
  year = {1997},
  volume = {46},
  pages = {794 - 797},
  number = {4}
}

@INPROCEEDINGS{ieee2,
  author = {Vos, F.M. and van der Heijde, G.L. and Spoelder, H.J.W. and van Stokkum,
	I. H. M. and Groen, F.C.A.},
  title = {A new PRBA-based instrument to measure the shape of the cornea},
  booktitle = {Quality Measurements: The Indispensable Bridge between Theory and
	Reality},
  year = {1996},
  volume = {1},
  pages = {416 - 421},
  organization = {IEEE Instrumentation and Measurement Technology Conference}
}

@ARTICLE{vanWalree2002,
  author = {van Walree, Cornelis A. and Kaats-Richters, Veronica E. M. and Jenneskens,
	Leonardus W. and Williams, Ren{\'{e}} M. and van Stokkum, Ivo H.
	M.},
  title = {Intramolecular excimer and exciplex emission of 1,4-dipyrenyl substituted
	cyclohexasilane},
  journal = {Chemical Physics Letters},
  year = {2002},
  volume = {355},
  pages = {65--70},
  month = {Mar},
  day = {25},
  issue = {1-2},
  url = {http://www.sciencedirect.com/science/article/B6TFN-457D1TP-5/2/91d224654917d6b1195f8afbfcca05a8}
}

@ARTICLE{FrankL.deWeerd03012002,
  author = {de Weerd, Frank L. and van Stokkum, Ivo H. M. and van Amerongen,
	Herbert and Dekker, Jan P. and van Grondelle, Rienk},
  title = {{Pathways for Energy Transfer in the Core Light-Harvesting Complexes
	CP43 and CP47 of Photosystem {II}}},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {82},
  pages = {1586-1597},
  number = {3},
  file = {1586.pdf:http\://www.biophysj.org/cgi/reprint/82/3/1586.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/82/3/1586}
}

@ARTICLE{deWeerd2002,
  author = {de Weerd, Frank L. and van Stokkum, Ivo H. M. and van Grondelle,
	Rienk},
  title = {Subpicosecond dynamics in the excited state absorption of all-trans-{$\beta$}-Carotene},
  journal = {Chemical Physics Letters},
  year = {2002},
  volume = {354},
  pages = {38--43},
  month = {Mar},
  day = {05},
  issue = {1-2},
  url = {http://www.sciencedirect.com/science/article/B6TFN-45B55WW-1/2/eb0879bc26e075d0db2c1d3149c851b1}
}

@ARTICLE{ChantalDvanderWeijDeWit03152008,
  author = {van der Weij-De Wit, Chantal D. and Doust, Alexander B. and van Stokkum,
	Ivo H. M. and Dekker, Jan P. and Wilk, Krystyna E. and Curmi, Paul
	M. G. and van Grondelle, Rienk},
  title = {{Phycocyanin Sensitizes both Photosystem I and Photosystem {II} in
	Cryptophyte Chroomonas CCMP270 Cells}},
  journal = {Biophys. J.},
  year = {2008},
  volume = {94},
  pages = {2423-2433},
  number = {6},
  abstract = {This article presents an investigation of the energy migration dynamics
	in intact cells of the unicellular photosynthetic cryptophyte Chroomonas
	CCMP270 by steady-state and time-resolved fluorescence measurements.
	By kinetic modeling of the fluorescence data on chlorophyll and phycocyanin
	645 excitation (at 400 and 582 nm respectively), it has been possible
	to show the excited state energy distribution in the photosynthetic
	antenna of this alga. Excitation energy from phycocyanin 645 is distributed
	nearly equally between photosystem I and photosystem {II} with very
	high efficiency on a 100-ps timescale. The excitation energy trapping
	times for both photosystem I ([~]30 ps) and photosystem I (200 and
	[~]540 ps) correspond well to those obtained from experiments on
	isolated photosystems. The results are compared with previous results
	for another cryptophyte species, Rhodomonas CS24, and suggest a similar
	membrane organization for the cryptophytes with the phycobiliproteins
	tightly packed in the thylakoid lumen around the periphery of the
	photosystems. },
  doi = {10.1529/biophysj.107.113993},
  eprint = {http://www.biophysj.org/cgi/reprint/94/6/2423.pdf},
  url = {http://www.biophysj.org/cgi/content/abstract/94/6/2423}
}

@ARTICLE{vanderWeij-DeWitC.D._jp061546w,
  author = {van der Weij{-}DeWit, C.D. and Doust, A.B. and van Stokkum, I. H. M.
	and Dekker, J.P. and Wilk, K.E. and Curmi, P.M.G. and Scholes, G.D.
	and van Grondelle, R.},
  title = {How Energy Funnels from the Phycoerythrin Antenna Complex to Photosystem
	{I} and Photosystem {II} in Cryptophyte Rhodomonas CS24 Cells},
  journal = {Journal of Physical Chemistry B},
  year = {2006},
  volume = {110},
  pages = {25066-25073},
  number = {49},
  issn = {1520-6106},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp061546w}
}

@INPROCEEDINGS{i98q,
  author = {Wendling, M and van Mourik, F and van Stokkum, I. H. M. and Salverda,
	JM and Michel, H and van Grondelle, R},
  title = {Low-intensity pump-probe measurements on the {B800} band of Rhodospirillim
	molischianum},
  booktitle = {Photosynthesis: Mechanisms and Effects},
  year = {1998},
  editor = {Garab, G},
  pages = {49-52},
  publisher = {Kluwer Academic Publishers, Dordrecht}
}

@ARTICLE{MarkusWendling01012003,
  author = {Wendling, Markus and Mourik, Frank van and van Stokkum, Ivo H. M.
	and Salverda, Jante M. and Michel, Hartmut and Grondelle, Rienk van},
  title = {{Low-Intensity Pump-Probe Measurements on the {B800} Band of Rhodospirillum
	molischianum}},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {84},
  pages = {440-449},
  number = {1},
  file = {440.pdf:http\://www.biophysj.org/cgi/reprint/84/1/440.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/84/1/440}
}

@ARTICLE{Wientjes20111372,
  author = {Emilie Wientjes and Ivo H.M. van Stokkum and Herbert van Amerongen
	and Roberta Croce},
  title = {Excitation-Energy Transfer Dynamics of Higher Plant Photosystem {I}
	Light-Harvesting Complexes},
  journal = {Biophysical Journal},
  year = {2011},
  volume = {100},
  pages = {1372 - 1380},
  number = {5},
  doi = {DOI: 10.1016/j.bpj.2011.01.030},
  issn = {0006-3495},
  url = {http://www.sciencedirect.com/science/article/B94RW-528YMC8-2/2/95612d92a10fbf4c3fa51698310b4052}
}

@ARTICLE{L.J.G.W.vanWilderen10102006,
  author = {van Wilderen, L. J. G. W. and van der Horst, M. A. and van Stokkum,
	I. H. M. and Hellingwerf, K. J. and van Grondelle, R. and Groot,
	M. L.},
  title = {{Ultrafast infrared spectroscopy reveals a key step for successful
	entry into the photocycle for photoactive yellow protein}},
  journal = {PNAS},
  year = {2006},
  volume = {103},
  pages = {15050-15055},
  number = {41},
  doi = {10.1073/pnas.0603476103},
  file = {15050.pdf:http\://www.pnas.org/cgi/reprint/103/41/15050.pdf:PDF},
  url = {http://www.pnas.org/cgi/content/abstract/103/41/15050}
}

@ARTICLE{vanWilderenJPCB2009,
  author = {van Wilderen, Luuk J. G. W. and Key, Jason M. and van Stokkum, Ivo
	H. M. and van Grondelle, Rienk and Groot, Marie{-}Louise},
  title = {{Dynamics of Carbon Monoxide Photodissociation in {B}radyrhizobium
	japonicum {FixL} Probed by Picosecond Midinfrared Spectroscopy}},
  journal = {{Journal of Physical Chemistry B}},
  year = {2009},
  volume = {{113}},
  pages = {{3292-3297}},
  number = {{11}}
}

@ARTICLE{WurpelG.W.H._ja015919c,
  author = {Wurpel, G.W.H. and Brouwer, A.M. and van Stokkum, I. H. M. and Farran,
	A. and Leigh, D.A.},
  title = {Enhanced Hydrogen Bonding Induced by Optical Excitation: Unexpected
	Subnanosecond Photoinduced Dynamics in a Peptide-Based [2]Rotaxane},
  journal = {Journal of the American Chemical Society},
  year = {2001},
  volume = {123},
  pages = {11327-11328},
  number = {45},
  issn = {0002-7863},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja015919c}
}

@ARTICLE{YatskouM.M._jp010411h,
  author = {Yatskou, M.M. and Koehorst, R.B.M. and van Hoek, A. and Donker, H.
	and Schaafsma, T.J. and Gobets, B. and van Stokkum, I. and van Grondelle,
	R.},
  title = {Spectroscopic Properties of a Self-Assembled Zinc Porphyrin Tetramer
	{II.} Time-Resolved Fluorescence Spectroscopy},
  journal = {Journal of Physical Chemistry A},
  year = {2001},
  volume = {105},
  pages = {11432-11440},
  number = {51},
  issn = {1089-5639},
  url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp010411h}
}

@ARTICLE{SergeyYeremenko06012006,
  author = {Yeremenko, Sergey and van Stokkum, Ivo H. M. and Moffat, Keith and
	Hellingwerf, Klaas J.},
  title = {{Influence of the Crystalline State on Photoinduced Dynamics of Photoactive
	Yellow Protein Studied by Ultraviolet-Visible Transient Absorption
	Spectroscopy}},
  journal = {Biophysical Journal},
  year = {2006},
  volume = {90},
  pages = {4224-4235},
  number = {11},
  doi = {10.1529/biophysj.105.074765},
  file = {4224.pdf:http\://www.biophysj.org/cgi/reprint/90/11/4224.pdf:PDF},
  url = {http://www.biophysj.org/cgi/content/abstract/90/11/4224}
}

@ARTICLE{Zoon2010,
  author = {Peter D. Zoon and Ivo H. M. van Stokkum and Manuel Parent and Olivier
	Mongin and Mireille Blanchard-Desce and Albert M. Brouwer},
  title = {Fast photo-processes in triazole-based push–pull systems},
  journal = {Physical Chemistry Chemical Physics},
  year = {2010},
  volume = {12},
  pages = {2706-2715},
  number = {11},
  doi = {DOI: 10.1039/b921322h}
}


@article{ ISI:000289697500032,
Author = {van der Weij-de Wit, C. D. and Dekker, J. P. and van Grondelle, R. and
   van Stokkum, I. H. M.},
Title = {{Charge Separation is Virtually Irreversible in Photosystem II Core
   Complexes with Oxidized Primary Quinone Acceptor}},
Journal = {{Journal of Physical Chemistry A}},
Year = {2011},
Volume = {{115}},
Number = {{16}},
Pages = {{3947-3956}},
Month = {{APR 28}},
Abstract = {{X-ray structures of the Photosystem II (PSII) core revealed relatively
   large interpigment distances between the CP43 and CP47 antenna compleyes
   and the reaction center (RC) with respect to the interpigment distances
   in a single unit. This finding questions the possibility of fast energy
   equilibration among the antenna and the RC, which has been the basic
   explanation for the measured PSII fluorescence kinetics for more than
   two decades. In this study, we present time-resolved fluorescence
   measurements obtained with a streak-camera setup on PSH core complexes
   from Thermosynechococcus elongatus at room temperature (RT) and at 77 K.
   Kinetic modeling of the RT data obtained with oxidized quinone acceptor
   Q(A) reveals that the kinetics are best described by fast primary charge
   separation at a time scale of 1.5 ps and slow energy transfer from the
   antenna into the RC, which results in an energy equilibration time
   between the antenna and the RC of about 44 ps. This model is consistent
   with structure-based computations. Primary radical pair formation was
   found to be a virtually irreversible process. Energy equilibration
   within the CP43 and CP47 complexes is shown to occur at a time scale of
   8 ps. Kinetic modeling of the 77K data reveals similar energy transfer
   time scales in the antenna units and among the antenna and the RC as at
   RT, respectively, 7 and 37 ps. We conclude that the energy transfer from
   the CP43/CP47 antenna to; the RC is the dominant factor in the total
   charge separation kinetics in intact PSII cores.}},
Publisher = {{AMER CHEMICAL SOC}},
Address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
Type = {{Article}},
Language = {{English}},
Affiliation = {{van Grondelle, R (Reprint Author), Vrije Univ Amsterdam, Fac Sci, Dept Phys \& Astron, De Boelelaan 1081, NL-1081 HV Amsterdam, Netherlands.
   van der Weij-de Wit, CD; Dekker, JP; van Grondelle, R; van Stokkum, IHM, Vrije Univ Amsterdam, Fac Sci, Dept Phys \& Astron, NL-1081 HV Amsterdam, Netherlands.}},
DOI = {{10.1021/jp1083746}},
ISSN = {{1089-5639}},
Keywords-Plus = {{EXCITATION-ENERGY TRANSFER; REACTION CENTERS; ELECTRON-TRANSFER;
   CRYSTAL-STRUCTURE; FLUORESCENCE SPECTROSCOPY; PICOSECOND FLUORESCENCE;
   LOW-TEMPERATURE; TARGET ANALYSIS; KINETICS; CP47}},
Funding-Acknowledgement = {{Netherlands Organization of Scientific Research (NWO) via the foundation
   of Earth and Life Sciences (ALW); Foundation for Fundamental Research on
   Matter (FOM)}},
Funding-Text = {{We thank Eberhard Schlodder (Technische Universitat Berlin) for kindly
   providing the samples and for useful discussions. Marloes Groot is
   thanked for critical reading of the text. This research is supported by
   The Netherlands Organization of Scientific Research (NWO) via the
   foundation of Earth and Life Sciences (ALW) and the Foundation for
   Fundamental Research on Matter (FOM).}},
Number-of-Cited-References = {{48}},
Times-Cited = {{0}},
Journal-ISO = {{J. Phys. Chem. A}},
Doc-Delivery-Number = {{752NB}},
Unique-ID = {{ISI:000289697500032}},
}

@article{ 2011Emilie,
   author = {Wientjes, Emilie and van Stokkum, Ivo H. M. and van Amerongen, Herbert and Croce, Roberta},
   title = {The Role of the Individual Lhcas in Photosystem I Excitation Energy Trapping},
   journal = {Biophysical Journal},
   volume = {101},
   number = {3},
   pages = {745-754},
   year = {2011}
}

@article{ 2011AmarinBJ,
author = {Marin, A. and Doust, A. B. and Scholes, G. D. and Wilk, K. E. and Curmi, P. M. G. and van Stokkum, I. H. M. and van Grondelle, R.},
   title = {Flow of Excitation Energy in the Cryptophyte Light-Harvesting Antenna Phycocyanin 645},
   journal = {Biophysical Journal},
   volume = {101},
   number = {4},
   pages = {1004-1013},
    year = {2011}
}

@article{ 2011AndyBJ,
author = {Stahl, A. D. and Hospes, M. and Singhal, K. and van Stokkum, I. and van Grondelle, R. and Groot, M. L. and Hellingwerf, K. J.},
   title = {On the Involvement of Single-Bond Rotation in the Primary Photochemistry of Photoactive Yellow Protein},
   journal = {Biophysical Journal},
   volume = {101},
   number = {5},
   pages = {1184-1192},
   year = {2011}
}
@article{ 2011LijinJACS,
   author = {Tian, L. J. and van Stokkum, I. H. M. and Koehorst, R. B. M. and Jongerius, A. and Kirilovsky, D. and van Amerongen, H.},
   title = {Site, Rate, and Mechanism of Photoprotective Quenching in Cyanobacteria},
   journal = {Journal of the American Chemical Society},
   volume = {133},
   number = {45},
   pages = {18304-18311},
   year = {2011}
}

@article{ 2011DidoPCCP,
author = {Di Donato, M. and van Wilderen, Ljgw and Van Stokkum, I. H. M. and Stuart, T. C. and Kennis, J. T. M. and Hellingwerf, K. J. and van Grondelle, R. and Groot, M. L.},
   title = {Proton transfer events in GFP},
   journal = {Physical Chemistry Chemical Physics},
   volume = {13},
   number = {36},
   pages = {16295-16305},
   year = {2011}
}