Publications 2007

Dissertations 2007

Luuk J.G.W. van Wilderen
Ultrafast protein dynamics revealed by infrared spectroscopy
PhD Advisors prof. dr. R. van Grondelle and prof. dr. M.L. Groot
VU University Amsterdam, 27 June 2007, PhD Thesis

Chantal van der Weij - de Wit
Excitation energy transfer in large, intact photosynthetic systems
PhD Advisors prof. dr. R. van Grondelle and dr. J.P. Dekker
VU University Amsterdam, 29 June 2007, PhD Thesis

Rudi Berera
The role of carotenoids in natural and artificial photosynthesis
PhD Advisors prof. dr. R. van Grondelle, prof. dr. H. van Amerongen and dr. J.T.M. Kennis
VU University Amsterdam, 26 November 2007, PhD Thesis

Publications 2007

M.T.A. Alexandre, J.C. Arents, R. van Grondelle, K.J. Hellingwerf, J.T.M. Kennis
A base-catalyzed mechanism for dark state recovery in the Avena sativa phototropin-1 LOV2 domain
Biochemistry 46, 2007, p. 3129-3137

M.T.A. Alexandre, D.C. Luhrs, I.H.M. van Stokkum, R. Hiller, M.L. Groot, J.T.M. Kennis, R. van Grondelle
Triplet state dynamics in peridinin–chlorophyll a–protein: A new pathway of photo-protection in LHCs?
Biophys. J. 93, 2007, p. 2118-2128

R. Berera, I.H.M. van Stokkum, G. Kodis, A. Keirstead, S. Pillai, C. Herrero, R.E. Palacios, M. Vengris, R. van Grondelle, D. Gust, T.A. Moore, A.L. Moore, J.T.M. Kennis
Energy transfer, excited-state deactivation and exciplex formation in artificial caroteno-phthalocyanine light harvesting antennas
J. Phys. Chem. B 111, 2007, p. 6868-6877

T.W. Binsl, K.M. Mullen, I.H.M. van Stokkum, J. Heringa, J.H.G.M. van Beek
FluxSimulator: An R package to simulate isotopomer distributions in metabolic networks
J. Statistical Software 18 (7), 2007

R. Croce, A. Chojnicka, T. Morosinotto, J.A. Ihalainen, F. van Mourik, J.P. Dekker, R. Bassi, R. van Grondelle
The low-energy forms of photosystem I light-harvesting complexes: spectroscopic properties and pigment-pigment interaction characteristics
Biophys. J. 93, 2007, p. 2418-2428

M. di Donato, R. van Grondelle, I.H.M. van Stokkum, M.-L. Groot
Excitation energy transfer in the photosystem II core antenna complex CP43 studied by femtosecond visible/visible and visible/mid-infrared pump probe spectroscopy
J. Phys. Chem. B 111, 2007, p. 7345-7352

M. Gauden, J.S Grinstead, W. Laan, I.H.M. van Stokkum, M. Avila-Perez, K.C. Toh, R. Boelens, R. Kaptein, R. van Grondelle, K.J. Hellingwerf, J.T.M. Kennis
On the role of aromatic side chains in the photoactivation of BLUF domains
Biochemistry 46, 2007, p. 7405-7415

S. Georgakopoulou, G. van der Zwan, R. Bassi, R. van Grondelle, H. van Amerongen, R. Croce
Understanding the changes in the circular dichroism of light harvesting complex II upon varying its pigment composition and organization
Biochemistry 46, 2007, p. 4745-4754

M.-L. Groot, L.J.W.G. van Wilderen, M. di Donato
Time-resolved methods in biophysics. 5. Femtosecond time-resolved and dispersed infrared spectroscopy on proteins
Photochem. Photobiol. Sci. 6, 2007, p. 501-507

C. Hippius, I.H.M. van Stokkum, E. Zangrando, R.M. Williams, F. Wurthner
Excited state interactions in calix[4]arene-perylene bisimide dye conjugates: Global and target analysis of supramolecular building blocks
J. PHys. Chem. C 111, 2007, p. 13988-13996

J.A. Ihalainen, J. Bredenbeck, R. Pfister, J. Helbing, L. Chi, I.H.M. van Stokkum, G.A. Woolley, P. Hamm
Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds
Proc. Natl. Acd. Sci. USA 104, 2007, p. 5383-5388

P.E. Jensen, R. Bassi, E.J. Boekema, J.P. Dekker, S. Jansson, D. Leister, C. Robinson, H.V. Scheller
Structure, function and regulation of plant photosystem I
Biochim. Biophys. Acta 1767, 2007, p. 335-352

J.T.M. Kennis, S. Crosson
A bacterial pathogen sees the light
Science 317, 2007, p. 1041-1042 (Perspective)

J.T.M. Kennis, M.L. Groot
Ultrafast spectroscopy of biological photoreceptors
Curr. Op. Struct. Biol. 17, 2007, p. 623-630

S. Lapentok, K.M. Mullen, J.W. Borst, I.H.M. van Stokkum, V.V. Apanasovich, A.W.J.G. Visser
Fluorescence Lifetime Imaging Microscopy (FLIM) data analysis with TIMP
J. Statistical Software 18 (8), 2007

K.M. Mullen, I.H.M. van Stokkum
An introduction to the special volume "Spectroscopy and Chemometrics in R"
J. Statistical Software 18 (1), 2007

K.M. Mullen, I.H.M. van Stokkum
TIMP: An R package for modeling multi-way spectroscopic measurements
J. Statistical Software 18 (3), 2007

K.M. Mullen, M. Vengris, I.H.M. van Stokkum
Algorithms for separable nonlinear least squares with application to modelling time-resolved spectra
J. Global Optimization 38, 2007, p. 201-213

V.I. Novoderezhkin, J.P. Dekker, R. van Grondelle
Mixing of exciton and charge-transfer states in Photosystem II reaction centers: modeling of Stark spectra with modified Redfield theory
Biophys. J. 93, 2007, p. 1293-1311

V.I. Novoderezhkin, D. Rutkauskas, R. van Grondelle
Multistate conformational model of a single LH2 complex: Quantitative picture of time-dependent spectral fluctuations
Chem. Phys. 341, 2007, p. 45-56

N.P. Pawlowicz, M.-L. Groot, I.H.M. van Stokkum, J. Breton, R. van Grondelle
Charge separation and energy transfer in the Photosystem II core complex studied by femtosecond mid-infrared spectroscopy
Biophys. J. 93, 2007, p. 2732-2742

I. Petkova, M.S. Mudadu, A. Singh, R.P. Thummel, I.H.M. van Stokkum, W.J. Buma, J. Waluk
Structure and photophysics of 2-(2'-pyridyl)benzindoles: The role of intermolecular hydrogen bonds
J. Phys. Chem. A 111, 2007, p. 11400-11409

I. Renge, R. van Grondelle, J.P. Dekker
Pigment spectra and intermolecular interaction potentials in glasses and proteins
Biophys. J. 93, 2007, 2491-2503

A.V. Ruban, R. Berera, C. Ilioaia, I.H.M. van Stokkum, J.T.M. Kennis, A.A. Pascal, H. van Amerongen, B. Robert, P. Horton, R. van Grondelle
Identification of a mechanism of photoprotective energy dissipation in higher plants
Nature 450, 2007, p. 575-579

V.A.D.P. Sicam, J.J. Snellenburg, R.G.L. van der Heijde, I.H.M. van Stokkum
Pseudo forward ray-tracing: A new method for surface validation in cornea topography
Optometry and Vision Research 84, 2007, p. 915-923

L. Valkunas, J. Janusonis, D. Rutkauskas, R. van Grondelle
Protein dynamics revealed in the excitonic spectra of single LH2 complexes
J. Lumin. 127, 2007, p. 269-275

C.D. van der Weij – de Wit, J.A. Ihalainen, R. van Grondelle, J.P. Dekker
Excitation energy transfer in native and unstacked thylakoid membranes studied by low temperature and ultrafast fluorescence spectroscopy
Photosynth. Res. 93, 2007, p. 173-182

C.D. van der Weij – de Wit, J.A. Ihalainen, E. van de Vijver, S. D'Haene, H.C.P. Matthijs, R. van Grondelle, J.P. Dekker
Fluorescence quenching of IsiA in the early stage of iron-deficiency and at cryogenic temperatures
Biochim. Biophys. Acta 1767, 2007, p. 1393-1400