AMOLF Institutional Repository: AMOLF Institutional Repository

A novel workflow control system for Fourier transform ion cyclotron resonance mass spectrometry allows for unique on-the-fly data-dependent decisions Article

Rapid Commun. Mass Spectrom., 1245-1256.

I.M. Taban Barbu, Y.E.M. van der Burgt, M.C. Duursma, Z. Takáts, M. Seynen (Marco), M. Konijnenburg, A.J.M. Vijftigschild, I. Attema and R.M.A. Heeren (Ron)

January 2008
Characterizing the functional dynamics of zinc phthalocyanine from femtoseconds to nanoseconds Article

J. Photochem. Photobiol., A, 99-105.

J. Savolainen (Janne), D. van der Linden, N. Dijkhuizen and J. Herek

January 2008
Chance and necessity in chromosomal gene distributions Article

Trends Genet., 216-219.

R. Hermsen (Rutger), P.R. ten Wolde (Pieter Rein) and S. Teichmann

January 2008
Scaling strong-field interactions towards the classical limit Article

Nature Phys., 386-389.

P. Colosimo, G. Doumy, C.I. Blaga, J. Wheeler, C. Hauri, F. Catoire, J. Tate, R. Chirla, A.M. March, G.G. Paulus, et al. L.F. DiMauro

January 2008
Attosecond electron dynamics Article

Annu. Rev. Phys. Chem., 463-492.

M.F. Kling and M.J.J. Vrakking

January 2008
Reaction coordinates for the flipping of genetic switches Article

Biophys. J., 3413-3423.

M.J. Morelli, S. Tanase-Nicola, R.J. Allen and P.R. ten Wolde (Pieter Rein)

January 2008
Parallel proton transfer pathways in aqueous acid-base reactions Article

J. Chem. Phys., 128(Article number: 174501), 1-10.

M.J. Cox and H.J. Bakker (Huib)

January 2008
Periodicity enclosed in boundaries : local density of states in photonic clusters Article

Opt. Express, 16(10), 6974-6984.

V. Prosentsov and A. Lagendijk

January 2008
Clustering versus percolation in the assembly of colloids coated with long DNA Article

Langmuir, 5118-5123.

N. Geerts, T. Schmatko and E. Eiser

January 2008
Structural properties of opals grown with vertical controlled drying Article

Langmuir, 4670-4675.

A. Hartsuiker and W.L. Vos

January 2008
Full characterization of anisotropic diffuse light Article

Opt. Express, 16(10), 7435-7446.

P.M. Johnson, S. Faez (Sanli) and A. Lagendijk

January 2008
Fabrication of three-dimensional nanostructures by focused ion beam milling Article

J. Vac. Sci. Technol. B, 973-977.

R.W. Tjerkstra, F.B. Segerink, J.J. Kelly and W.L. Vos

January 2008
Numerical studies of nucleation pathways of ordered and disordered phases Dissertation

C. Valeriani

November 2007
The physics of cellulose biosynthesis: polymerization and self-organization, from plants to bacteria Dissertation

Theory of Biomolecular Matter

F. Diotallevi

October 2007
Fluctuations in genetic networks: a computational study Dissertation

Biochemical Networks

M.J. Morelli

October 2007
Plasmonkettingen : nanoschaal antennes Article

NTvN, 73(10), 346-348.

A.F. Koenderink (Femius), R. de Waele and A. Polman (Albert)

October 2007
Slow guided surface plasmons at telecom frequencies Article

Nature Photon., 573-576.

M. Sandtke and L.K. Kuipers (Kobus)

October 2007
Surface plasmon polariton propagation in straight and tailored waveguides Dissertation

M. Sandtke

June 2007
On the concept of imaging nanoscale vector fields Article

Nature Photon.

H. Gersen, L. Novotny, L.K. Kuipers (Kobus) and N.F. van Hulst

May 2007
Controlling plasmon-enhanced luminescence Dissertation

Photonic Materials

H. Mertens

April 2007
Experiments on scattering lasers from Mie to random Dissertation

K.L. van der Molen

April 2007
Biomolecular imaging mass spectrometry: mapping molecular distributions in cells and tissue sections Dissertation

A.F.M. Altelaar

March 2007
Structural and conformational aspects of gas phase peptides probed by electron capture dissociation Dissertation

R. Mihalca

March 2007
Ultrafast optical switching of photonic crystals Dissertation

T.G. Euser

March 2007
Scattering lasers: an exploration of the smallest lasers possible Dissertation

T. Savels

February 2007
Identification of leptomeningeal metastasis-related proteins in cerebrospinal fluid of patients with breast cancer by a combination of MALDI-TOF, MALDI-FTICR and nanoLC-FTICR MS Article

Proteomics, 7(3), 474-481.

A. Roempp, L. Dekker, I.M. Taban Barbu, G. Jenster, W. Boogerd, H. Bonfrer, B. Spengler, R.M.A. Heeren (Ron), Peter Sillevis Smitt and Theo M. Luider

February 2007
On the scalability of evolution strategies in the optimization of dynamic molecular alignment In Proceedings

O.M. Shir, M.J.J. Vrakking and Th. Bäck

January 2007
Ultrafast electron dynamics Book Chapter

M.J.J. Vrakking

January 2007
Gaining Insights into Laser Pulse Shaping by Evolution Strategies In Proceedings

O.M. Shir, J.N. Kok and Th. Bäck

January 2007
How cellulose synthase density in the plasma membrane may dictate cell wall texture Book Chapter

A.M.C. Emons (Anne Mie), M. Akkerman, M. Ebskamp, J.H.N. Schel and B.M. Mulder (Bela)

January 2007
Membrane nanotubes Book Chapter

I. Derényi, G. Koster, M.M. van Duijn, A. Czövek, A.M. Dogterom (Marileen) and J. Prost

January 2007
Conceptual designs in laser pulse shaping obtained by niching in evolution strategies In Proceedings

O.M. Shir, M. Emmerich, Th. Bäck and M.J.J. Vrakking

January 2007
A comparative study of extractable lipids in the sherds and surface residual crusts of ceramic vessels from neolithic and roman iron age settlements in the Netherlands Book Chapter

T.F.M. Oudemans (Tania) and J.J. Boon

January 2007
Multiplex coherent anti-Stokes Raman scattering microscopy on lipid droplets in HeLa cells In Proceedings

H.A. Rinia, K.N.J. Burger, M. Bonn (Mischa) and M. Müller (Michiel)

January 2007
Metal soap degradation of oil paintings : aggregates, increased transparency and efflorescence In Proceedings

P. Noble and J.J. Boon

January 2007
Lead soap effluorescence in a 19th C painting : appearance, nature and sources of materials In Proceedings

K. Keune, K. Kirsch and J.J. Boon

January 2007
Chemical processes in aged oil paints affecting metal soap migration and aggregation In Proceedings

J.J. Boon, F.G. Hoogland and K. Keune

January 2007
Imaging TOF-SIMS and NanoSIMS studies of Barite-Celestite particles in grounds from paintings by Van Gogh In Proceedings

Beatrice Marino, J.J. Boon, E. Hendriks, F. Horréard and F. Hillion

January 2007
Opaque to transparent : insights on Bloom, Haze, Protrusions and "Ground Staining" from the Hudson River School and the church archive In Proceedings

J. Zucker and J.J. Boon

January 2007
Ultrafast all-optical switching of 3D photonic band gap crystals In Proceedings

T.G. Euser, Hong Wei, J. Kalkman, Y. Jun, M. Guina, S. Suomalainen, A. Polman (Albert), D.J. Norris and W.L. Vos

January 2007
Microtubule forces and organization Book Chapter

A.M. Dogterom (Marileen), J. Husson, L. Laan (Liedewij), E.L. Munteanu and C. Tischer

January 2007
SEM studies of cross sectional cuts of biomineralized tissues from Gallus and Coturnix eggshells using an Argon ion millin CP-system In Proceedings

J.J. Boon, J. van der Horst (Jerre) and S. Asahina

January 2007
Mass spectrometry of modern paints In Proceedings

J.J. Boon, F.G. Hoogland and J. van der Horst (Jerre)

January 2007
Parametric visualization of high resolution correlated multi-spectral features using PCA In Proceedings

A. Broersen, R. van Liere and R.M.A. Heeren (Ron)

January 2007
Imaging of peptides in the rat brain using MALDI-FTICR mass spectrometry Article

J. Am. Soc. Mass Spectrom., 145-151.

I.M. Taban Barbu, A.F.M. Altelaar, Y.E.M. van der Burgt, L.A. McDonnell, R.M.A. Heeren (Ron), J. Fuchser and G. Baykut

January 2007
Flatband slow light in photonic crystals featuring spatial pulse compression and terahertz bandwidth Article

Opt. Express, 15(1), 219-226.

M.D. Settle, R.J.P. Engelen, M. Salib, A. Michaeli, L.K. Kuipers (Kobus) and T.F. Krauss

January 2007
Scaling of wave-packet dynamics in an intense midinfrared field Article

Phys. Rev. Lett., 98(Article number: 13901), 1-4.

J. Tate, T. Auguste, H.G. Muller, P. Salières, Pierre Agostini and L.F. DiMauro

January 2007
λ/4 resonance of an optical monopole antenna probed by single molecule fluorescence Article

Nano Lett., 28-33.

T.H. Taminiau, F.B. Segerink, L.K. Kuipers (Kobus) and N.F. van Hulst

January 2007
Morphology of a highly asymmetric double crystallizable PCL-b-PEO block copolymer Article

J. Chem. Phys., 126(Article number: 24904), 1-7.

L.-B. Li, F. Meng, Z. Zhong, D. Byelov (Dimitry), W.H. de Jeu and J. Feijen

January 2007
Analysis of the propagation of terahertz surface plasmon polaritons on semicondutor groove gratings Article

J. Appl. Phys., 101(Article number: 23707), 1-6.

Martin Kuttge, H. Kurz, J. Gómez Rivas (Jaime), J.A Sánchez-Gil and P. Haring Bolivar

January 2007
Statistical analysis of time-resolved emission from ensembles of semiconductor quantum dots: interpretation of exponential decay models Article

Phys. Rev. B, 75(Article number: 35329), 1-8.

A.F. van Driel, I.S. Nikolaev, P. Vergeer, P. Lodahl, Daniël A. Vanmaekelbergh and W.L. Vos

January 2007
Shear-induced smectic order in isotactic polypropylene reviseted Article

Macromolecules, 288-289.

D. Byelov (Dimitry), P. Panine and W.H. de Jeu

January 2007
Empirical fitness landscapes reveal accessible evolutionary paths Article

Nature, 383-386.

F.J. Poelwijk (Frank), D.J. Kiviet, D.M. Weinreich and S.J. Tans (Sander)

January 2007
Parallel processing of large datasets from nanoLC-FTICR-MS measurements Article

J. Am. Soc. Mass Spectrom., 152-161.

Y.E.M. van der Burgt, I.M. Taban Barbu, M. Konijnenburg, M. Biskup, M.C. Duursma, R.M.A. Heeren (Ron), A. Roempp, R.V. van Nieuwpoort and H.E. Bal

January 2007
Imaging mass spectrometry imaging Article

Int. J. Mass Spectrom., 260(2-3)

R.M.A. Heeren (Ron) and J.V. Sweedler

January 2007
Extended data analysis strategies for high resolution imaging MS: New methods to deal with extremely large image hyperspectral datasets Article

Int. J. Mass Spectrom., 222-236.

L.A. Klerk, A. Broersen, I.W. Fletcher, R. van Liere and R.M.A. Heeren (Ron)

January 2007
Microtubule organization in three-dimensional confined geometries: evaluating the role of elasticity through a combined in vitro and modeling approach Article

Biophys. J., 1046-1057.

M. Cosentino Lagomarsino (Marco), C. Tanase, J.W. Vos (Jan), A.M.C. Emons (Anne Mie), B.M. Mulder (Bela) and A.M. Dogterom (Marileen)

January 2007
High-resolution MALDI imaging mass spectrometry allows localization of peptide distributions at cellular length scales in pituitary tissue sections Article

Int. J. Mass Spectrom., 203-211.

A.F.M. Altelaar, I.M. Taban Barbu, L.A. McDonnell, Peter D.E.M. Verhaert, R.P.J. de Lange, R.A.H. Adan, W.J. Mooi, R.M.A. Heeren (Ron) and S.R. Piersma

January 2007
Identifying biomolecular origins of solid organic residues preserved in Iron Age Pottery using DTMS and MVA Article

J. Archaeol. Sci., 173-193.

T.F.M. Oudemans (Tania), G.B. Eijkel (Gert) and J.J. Boon

January 2007
Enhanced nonlinear optical effects with a tapered plasmonic waveguide Article

Nano Lett., 334-337.

E. Verhagen (Ewold), L.K. Kuipers (Kobus) and A. Polman (Albert)

January 2007
Monte Carlo study of substrate-induced folding and refolding of lattice proteins Article

Biophys. J., 1150-1156.

I. Coluzza and D. Frenkel

January 2007
Quantitative CARS spectroscopy using the maximum entropy method: the main lipid phase transition Article

ChemPhysChem, 279-287.

H.A. Rinia, M. Bonn (Mischa), M. Müller (Michiel) and E.M. Vartiainen

January 2007
Direct measurement of force generation by actin filament polymerization using an optical trap Article

PNAS, 2181-2186.

M.J. Footer, J.W.J. Kerssemakers, J.A. Theriot and A.M. Dogterom (Marileen)

January 2007
Frequency selection of supercontinuum ultrashort pulses using a Fresnel zone plate Article

Opt. Commun., 336-339.

A. Gürtler, J.J. Gilijamse, A. Wetzels, L.D. Noordam, E. Sali and M. Bellini

January 2007
A laboratory simulation of the carbonization of sunflower achenes and seeds Article

J. Anal. Appl. Pyrolysis, 316-327.

F. Braadbaart, P.J. Wright, J. van der Horst (Jerre) and J.J. Boon

January 2007
Programmable nanolithography with plasmon nanoparticle arrays Article

Nano Lett., 745-749.

A.F. Koenderink (Femius), J.V. Hernández, F. Robicheaux, L.D. Noordam and A. Polman (Albert)

January 2007
Interfacial wetting in the 4-state Potts model: a cluster approach Article

Physica A, 537-545.

C.E. Paraskevaidis, C. Papatriantafillou and B.M. Mulder (Bela)

January 2007
Strongly nonexponential time-resolved fluorescence of quantum-dot ensembles in three-dimensional photonic crystals Article

Phys. Rev. B, 75(Article number: 115302), 1-5.

I.S. Nikolaev, P. Lodahl, A.F. van Driel, A.F. Koenderink (Femius) and W.L. Vos

January 2007
Ultrafast vibrational energy transfer between surface and bulk water at the air-water interface Article

Phys. Rev. Lett., 98(Article number: 98302), 1-4.

M. Smits, A. Ghosh, M. Sterrer, M. Müller (Michiel) and M. Bonn (Mischa)

January 2007
Specific peptides identified by mass spectrometry in placental tissue from pregnancies complicated by early onset preeclampsia attained by laser capture dissection Article

Proteomics - Clin. Appl., 325-335.

C.J.M. de Groot, C. Güzel, R.P.M. Steegers-Theunissen, M.P.M. de Maat (Moniek), P. Derkx, E.-M. Roes, R.M.A. Heeren (Ron), Theo M. Luider and Eric A.P. Steegers

January 2007
Gain narrowing in few-atom systems Article

Phys. Rev. Lett., 98(Article number: 103601), 1-4.

T. Savels, A.P. Mosk (Allard) and A. Lagendijk

January 2007
Carrier multiplication and its reduction by photodoping in colloidal InAs quantum dots Article

J. Phys. Chem. C, 4146-4152.

J.J.H. Pijpers, E. Hendry, M.T.W. Milder, R. Fanciulli, J. Savolainen (Janne), J. Herek, Daniël A. Vanmaekelbergh, S. Ruhman, D. Mocatta, D. Oron, et al. A. Aharoni, M. Bonn (Mischa)

January 2007
Confined space and effective interactions of multiple self-avoiding chains Article

Phys. Rev. Lett., 98(Article number: 128303), 1-4.

S. Jun (Suckjoon), A. Arnold and B.-Y. Ha

January 2007
Lattice-based Monte Carlo method for telechelic chain molecules Article

Phys. Rev. E, 75(Article number: 36708), 1-6.

B. Bozorgui and D. Frenkel

January 2007
Ultrafast dynamics of water in cationic micelles Article

J. Chem. Phys., 126(Article number: 124507), 1-10.

A.M. Dokter, S. Woutersen (Sander) and H.J. Bakker (Huib)

January 2007
Direct measurement of phase coexistence in DPPC/cholesterol vesicles using Raman spectroscopy Article

Chem. Phys. Lipids, 76-84.

M.J.L. de Lange, M. Bonn (Mischa) and M. Müller (Michiel)

January 2007
Disulfide bond cleavages observed in SORI-CID of three nonapeptides complexed with divalent transition-metal cations Article

J. Mass Spectrom., 450-458.

R. Mihalca, Y.E.M. van der Burgt, A.J.R. Heck (Albert) and R.M.A. Heeren (Ron)

January 2007
The cellulose synthase complex: a polymerization driven supramolecular motor Article

Biophys. J., 2666-2673.

F. Diotallevi and B.M. Mulder (Bela)

January 2007
Simple off-lattice model to study the folding and aggregation of peptides Article

Mol. Phys., 375-385.

N. Combe and D. Frenkel

January 2007
Spatial extent of random laser modes Article

Phys. Rev. Lett., 98(Article number: 143901), 1-4.

K.L. van der Molen, R.W. Tjerkstra, A.P. Mosk (Allard) and A. Lagendijk

January 2007
Attosecond real-time observation of electron tunnelling in atoms Article

Nature, 627-632.

M. Uiberacker, T. Uphues, M. Schultze, A.J. Verhoef, V.S. Yakovlev, M.F. Kling, J. Rauschenberger, N.M. Kabachnik, H. Schröder, M. Lezius, et al. K.L. Kompa, S. Hendel, F. Krausz (Ferenc)

January 2007
Water as a molecular hinge in amide-like structures Article

J. Chem. Phys., 126(Article number: 154507), 1-10.

R.L.A. Timmer (Rutger) and H.J. Bakker (Huib)

January 2007
Fundamental limits to position determination by concentration gradients Article

PLoS Comput. Biol., 3(4, Article number: 78), 763-771.

F. Tostevin (Filipe), P.R. ten Wolde (Pieter Rein) and M. Howard

January 2007
An allosteric model of circadian KaiC phosphorylation Article

PNAS, 7420-7425.

J.S. van Zon (Jeroen), D.K. Lubensky (David), P.R.H. Altena and P.R. ten Wolde (Pieter Rein)

January 2007
Low-noise rotating sample holder for ultrafast transient spectroscopy at cryogenic temperatures Article

Rev. Sci. Instrum., 78(Article number: 53102), 1-5.

R. Fanciulli, J. Cerjak (Iliya) and J. Herek

January 2007
Imaging mass spectrometry at cellular length scales Article

Nature Protoc., 1185-1196.

A.F.M. Altelaar, S.L. Luxembourg (Stefan), L.A. McDonnell, S.R. Piersma and R.M.A. Heeren (Ron)

January 2007
Singularity of the dyadic Green's function for heterogeneous dielectrics Article

Phys. Rev. E, 75(Article number: 56601), 1-5.

C.-A. Guérin, B. Gralak and A. Tip

January 2007
Highly efficient ultrafast energy transfer into molecules at surface step sites Article

J. Phys. Chem. C, 6149-6153.

E.H.G. Backus (Ellen), M. Forsblom, M. Persson and M. Bonn (Mischa)

January 2007
THz dielectric relaxation of ionic liquid:water mixtures Article

Chem. Phys. Lett., 60-64.

M. Koeberg, C. Wu, D. Kim and M. Bonn (Mischa)

January 2007
Short XUV pulses to characterize field-free molecular alignment Article

J. Mod. Opt., 953-966.

F. Lépine, M.F. Kling, Y.F. Ni (Yongfeng), J.I. Khan, O. Ghafur, Tatiana Marchenko, E. Gustafsson, P. Johnsson, K. Varju, T. Remetter, et al. M.J.J. Vrakking

January 2007
Heterovibrational interactions, cooperative hydrogen bonding, and vibrational energy relaxation pathways in a rotaxane Article

J. Phys. Chem. C, 6798-6804.

P. Bodis, R.L.A. Timmer (Rutger), S. Yeremenko, W.J. Buma, J.S. Hannam, D.A. Leigh and S. Woutersen (Sander)

January 2007
Morphological change during crystallization of thin amorphous solid water films on Ru(0001) Article

J. Chem. Phys., 126(Article number: 181103), 1-5.

T. Kondo, H.S. Kato, M. Bonn (Mischa) and M. Kawai

January 2007
Focused ion beam scan routine, dwell time and dose optimizations for submicrometre period planar photonic crystal components and stamps in silicon Article

Nanotechnology, 18(Article number: 195305), 1-11.

W.C.L. Hopman, F. Ay, W. Hu, V.J. Gadgil, L.K. Kuipers (Kobus), M. Pollnau and R.M. de Ridder

January 2007
Gas-solid coexistence of adhesive spheres Article

J. Chem. Phys., 126(Article number: 196101), 1-2.

P. Charbonneau and D. Frenkel

January 2007
Simultaneous ultrafast probing of intramolecular vibrations and photoinduced charge carriers in rubrene using broadband time-domain THz spectroscopy Article

Phys. Rev. B, 75(Article number: 195216), 1-5.

M. Koeberg, E. Hendry, J.M. Schins, H.A. van Laarhoven, C.F.J. Flipse, K. Reimann, M. Woerner, T. Elsaesser and M. Bonn (Mischa)

January 2007
Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry Article

Rev. Sci. Instrum., 78(Article number: 53716), 1-10.

I. Klinkert, L.A. McDonnell, S.L. Luxembourg (Stefan), A.F.M. Altelaar, E.R. Amstalden van Hove, S.R. Piersma and R.M.A. Heeren (Ron)

January 2007
Ultrafast evolution of photonic eigenstates in k-space Article

Nature Phys., 401-405.

R.J.P. Engelen, Y. Sugimoto, H. Gersen, N. Ikeda, K. Asakawa and L.K. Kuipers (Kobus)

January 2007
Fabrication of magnetic atom chips based on FePt Article

J. Magn. Magn. Mater., 192-197.

Y.T. Xing, I. Barb, R. Gerritsma, R.J.C. Spreeuw, H. Luigjes, Q.F. Xiao, C. Rétif and J.B. Goedkoop

January 2007
A finite-cluster phase in λ-DNA-coated colloids Article

Soft Matter, 703-706.

T. Schmatko, B. Bozorgui, N. Geerts, D. Frenkel, E. Eiser and W.C.K. Poon

January 2007
Ultrafast optical switching of the THz transmission through metallic subwavelength hole arrays Article

Phys. Rev. B, 75(Article number: 235305), 1-5.

E. Hendry, M.J. Lockyear, J. Gómez Rivas (Jaime), L.K. Kuipers (Kobus) and M. Bonn (Mischa)

January 2007

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