AMOLF Institutional Repository: AMOLF Institutional Repository

Spontaneous emission of near-infrared quantum dots controlled with photonic crystals Dissertation

B.H. Husken

May 2009
The influence of fabrication deviations on the photonic band gap of three-dimensional inverse woodpile nanostructures Article

J. Appl. Phys., 105(Article number: 93108), 1-10.

L.A. Woldering, A.P. Mosk (Allard), R.W. Tjerkstra and W.L. Vos

May 2009
Strong-field photoionization revisited Article

Nature Phys., 5(5), 335-338.

C.I. Blaga, F. Catoire, P. Colosimo, G.G. Paulus, H.G. Muller, Pierre Agostini and L.F. DiMauro

May 2009
Quantum control experiment reveals solvation-induced decoherence Article

PNAS, 106(19), 7714-7717.

P. van der Walle, M.T.W. Milder, L.K. Kuipers (Kobus) and J. Herek

May 2009
Hydrogen bond fluctuations of the hydration shell of the bromide anion Article

J. Phys. Chem. A, 113(21), 6104-6110.

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

May 2009
DNA looping provides stability and robustness to the bacteriophage λ switch Article

PNAS, 106(20), 8101-8106.

M.J. Morelli, P.R. ten Wolde (Pieter Rein) and R.J. Allen

May 2009
Waterlike thermodynamic anomalies in a repulsive-shoulder potential system Article

Phys. Rev. E, 79(Article number: 51202), 1-6.

N.V. Gribova, Y.D. Fomin, D. Frenkel and V.N. Ryzhov

May 2009
Distance-dependent proton transfer along water wires connecting acid-base pairs Article

J. Phys. Chem. A, 6599-6606.

M.J. Cox, R.L.A. Timmer (Rutger), H.J. Bakker (Huib), S. Park and N. Agmon

May 2009
Toward digital staining using imaging mass spectrometry and random forests Article

J. Proteome Res., 3558-3567.

M. Hanselmann, U. Köthe, M. Kirchner, B.Y. Renard, E.R. Amstalden van Hove, K. Glunde, R.M.A. Heeren (Ron) and F.A. Hamprecht

May 2009
Structural characterization of alpha-lactalbumin nanotubes Article

Soft Matter, 2020-2026.

J.F. Graveland-Bikker, R.I. Koning, H.K. Koerten, R.B.J. Geels, R.M.A. Heeren (Ron) and C.G. de Kruif

May 2009
Observation of spatial quantum correlations induced by multiple scattering of nonclassical light Article

Phys. Rev. Lett., 102(Article number: 193901), 1-4.

S. Smolka, A. Huck, U.L. Andersen, A. Lagendijk and P. Lodahl

May 2009
Efficiënt licht invangen met behulp van nanogestructureerde oppervlakken Article

NTvN, 176-179.

S.L. Diedenhofen, R. Algra, E.P.A.M. Bakkers (Erik) and J. Gómez Rivas (Jaime)

May 2009
Broadband sensitive pump-probe setup for ultrafast optical switching of photonic nanostructures and semiconductors Article

Rev. Sci. Instrum., 80(Article number: 73104), 1-9.

T.G. Euser, P.J. Harding and W.L. Vos

May 2009
Mutual information between input and output trajectories of biochemical networks Article

Phys. Rev. Lett., 102(Article number: 218101), 1-4.

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

May 2009
Measuring molecular reorientation at liquid surfaces with time-resolved sum-frequency spectroscopy : a theoretical framework Article

J. Phys. Chem. B, 7564-7573.

H.-K. Nienhuys and M. Bonn (Mischa)

May 2009
Structure dynamics of the proton in liquid water probed with terahertz time-domain spectroscopy Article

Phys. Rev. Lett., 102(Article number: 198303), 1-4.

K.J. Tielrooij (Klaas-Jan), R.L.A. Timmer (Rutger), H.J. Bakker (Huib) and M. Bonn (Mischa)

May 2009
Fabry-Pérot resonators for surface plasmon polaritons probed by cathodoluminescence Article

Appl. Phys. Lett., 94(Article number: 183104), 1-3.

Martin Kuttge, Ernst Jan R. Vesseur and A. Polman (Albert)

May 2009
Direct observation of type 1 fimbrial switching Article

EMBO Rep., 527-532.

A.M. Adiciptaningrum, I.C. Blomfield and S.J. Tans (Sander)

May 2009
Nanowire plasmon excitation by adiabatic mode transformation Article

Phys. Rev. Lett., 102(Article number: 203904), 1-4.

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

May 2009
Differential affinity and catalytic activity of CheZ in E. coli chemotaxis Article

PLoS Comput. Biol., 5(Article number: 1000378), 1-13.

S.B. van Albada and P.R. ten Wolde (Pieter Rein)

May 2009
Sample preparation issues for tissue imaging by imaging MS Article

Proteomics, 2622-2633.

B. Kükrer-Kaletas, I.M. van der Wiel, J. Stauber, L. Dekker, C. Güzel, Theo M. Luider and R.M.A. Heeren (Ron)

May 2009
Rheological characterization of the nucleus pulposus: implications for functional replacement Article

J. Orthop. Res., 27(5), 620-626.

J.L. Bron, G.H. Koenderink (Gijsje), V. Everts and T.H. Smit

May 2009
Lyomesophases of C3-symmetrical bipyridine-based discs in alkanes: an X-ray diffraction study Article

Langmuir, 25(15), 8794-8801.

R. Martín-Rapún, D. Byelov (Dimitry), A.R.A. Palmans, W.H. de Jeu and E.W. Meijer

April 2009
Imaging of chemical and physical state of individual cellular lipid droplets using multiplex CARS microscopy Article

J. Raman Spectrosc., 40, SI(7), 763-769.

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

April 2009
Ion-ing out the details Article

Nature Chem., 24-25.

H.J. Bakker (Huib)

April 2009
Crystallization-induced order in polystyrene-poly(ethylene oxide) metallo-supramolecular diblock copolymer Article

Polymer, 2149-2153.

M. Al-Hussein and W.H. de Jeu

April 2009
Observation of photoactive yellow protein anchored to a modified Au(111) surface by scanning tunneling microscopy Article

Chem. Phys. Lett., 113-117.

I.I. Rzeznicka, G.W.H. Wurpel, M. Bonn (Mischa), M.A. van der Horst, K.J. Hellingwerf, S. Matsunaga, T. Yamada and M. Kawai

April 2009
Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei Article

Nucleic Acids Res., 3558-3568.

S. de Nooijer, J. Wellink, B.M. Mulder (Bela) and T. Bisseling

April 2009
Accurate calculation of the local density of optical states in inverse-opal photonic crystals Article

J. Opt. Soc. Am. B, 987-997.

I.S. Nikolaev, W.L. Vos and A.F. Koenderink (Femius)

April 2009
Shaping the fluorescent emission by lattice resonances in plasmonic crystals of nanoantennas Article

Phys. Rev. Lett., 102(Article number: 146807), 1-4.

G. Vecchi, V. Giannini and J. Gómez Rivas (Jaime)

April 2009
Force generation by microtubule bundles Article

Biophys. Rev. Lett., 33-43.

J. Husson, L. Laan (Liedewij) and A.M. Dogterom (Marileen)

April 2009
Manipulation of the local density of photonic states to elucidate fluorescent protein emission rates Article

Phys. Chem. Chem. Phys., 2525-2531.

Y. Cesa, C. Blum, Johanna M. van den Broek, A.P. Mosk (Allard), W.L. Vos and V. Subramaniam (Vinod)

April 2009
Identification of competing ultrafast all-optical switching mechanisms in Si woodpile photonic crystals Article

J. Opt. Soc. Am. B, 610-619.

P.J. Harding, T.G. Euser and W.L. Vos

April 2009
Impulsive orientation and alignment of quantum-state-selected NO molecules Article

Nature Phys., 289-293.

O. Ghafur, A. Rouzée, A. Gijsbertsen (Arjan), W. Siu, S. Stolte and M.J.J. Vrakking

April 2009
Destabilization of the hydrogen-bond structure of water by the osmolyte trimethylamine-N-oxide Article

J. Phys. Chem. B, 4038-4044.

Y.L.A. Rezus (Yves) and H.J. Bakker (Huib)

April 2009
Cathodoluminescence plasmon microscopy Dissertation

Photonic Materials

Martin Kuttge

March 2009
Feature visualization on large scale imaging mass spectrometry data Dissertation

A. Broersen

March 2009
Homogeneous bubble nucleation driven by local hot spots: a molecular dynamics study Article

J. Phys. Chem. B, 113(12), 3776-3784.

Z.-J. Wang, C. Valeriani and D. Frenkel

March 2009
A velocity map imaging detector with an integrated gas injection system Article

Rev. Sci. Instrum., 80(3, Article number: 33110), 1-6.

O. Ghafur, W. Siu, P. Johnsson, M.F. Kling, M. Drescher and M.J.J. Vrakking

March 2009
Mammalian end binding proteins control persistent microtubule growth Article

J. Cell Biol., 184(5), 691-706.

Y. Komarova, C.O. de Groot, I. Grigoriev (Ilya), S. Montenegro Gouveia, E.L. Munteanu, J.M. Schober, S. Honnappa, R.M. Buey, C.C. Hoogenraad (Casper), A.M. Dogterom (Marileen), et al. A. Akhmanova (Anna)

March 2009
Local density of states, spectrum, and far-field interference of surface plasmon polaritons probed by cathodoluminescence Article

Phys. Rev. B, 79(Article number: 113405), 1-4.

Martin Kuttge, Ernst Jan R. Vesseur, A.F. Koenderink (Femius), H.J. Lezec, H.A. Atwater (Harry), F.J. García de Abajo (Javier) and A. Polman (Albert)

March 2009
TeraHertz dielectric relaxation of biological water confined in model membranes made of lyotropic phopholipids Article

Mol. Cryst. Liq. Cryst., 108-117.

D. Paparo, K.J. Tielrooij (Klaas-Jan), H.J. Bakker (Huib) and M. Bonn (Mischa)

March 2009
Efficient generation of propagating plasmons by electron beams Article

Nano Lett., 1176-1181.

W. Cai, R. Sainidou, J. Xu, A. Polman (Albert) and F.J. García de Abajo (Javier)

March 2009
Determining absolute molecular orientation at interfaces : a phase retrieval approach for sum frequency generation spectroscopy Article

J. Phys. Chem. C, 6100-6106.

M. Sovago, E.M. Vartiainen and M. Bonn (Mischa)

March 2009
Broad-band omnidirectional antireflection coatings based on semiconductor nanorods Article

Adv. Mater., 973-978.

S.L. Diedenhofen, G. Vecchi, R. Algra, A. Hartsuiker, O.L. Muskens, G.W.G. Immink, E.P.A.M. Bakkers (Erik), W.L. Vos and J. Gómez Rivas (Jaime)

March 2009
Geometrical frustration : a study of 4d hard spheres Article

Phys. Rev. E, 79(Article number: 30201), 1-4.

J.A. van Meel, D. Frenkel and P. Charbonneau

March 2009
Reorientation of HDO in liquid H2O at different temperatures: Comparison of first and second order correlation functions Article

Chem. Phys. Lett., 71-74.

K.J. Tielrooij (Klaas-Jan), C. Petersen, Y.L.A. Rezus (Yves) and H.J. Bakker (Huib)

March 2009
Nitromatrix provides improved LC-MALDI signals and more protein identifications Article

Proteomics, 1662-1671.

P. Kouvonen, L.A. McDonnell, R.M.A. Heeren (Ron) and G.L. Corthals

March 2009
Force- and kinesin-8-dependent effects in the spatial regulation of fission yeast microtubule dynamics Article

Mol. Syst. Biol., 5(Article number: 250), 1-10.

C. Tischer, D. Brunner and A.M. Dogterom (Marileen)

March 2009
Electrical excitation of surface plasmon polaritons Dissertation

Photonic Materials

R.V.A. van Loon

February 2009
Hydrogen bonding strength of interfacial water determined with surface sum-frequency generation Article

Chem. Phys. Lett., 7-12.

M. Sovago, R.K. Campen, H.J. Bakker (Huib) and M. Bonn (Mischa)

February 2009
On-chip green silica upconversion microlaser Article

Opt. Lett., 482-484.

T. Lu, L. Yang (Le), R.V.A. van Loon, A. Polman (Albert) and K.J. Vahala

February 2009
Large photonic strength of highly tunable resonant nanowire materials Article

Nano Lett., 930-934.

O.L. Muskens, S.L. Diedenhofen, B.C. Kaas, R. Algra, E.P.A.M. Bakkers (Erik), J. Gómez Rivas (Jaime) and A. Lagendijk

February 2009
Force spectroscopy of a single artificial biomolecule bond : The Kramers' high-barrier limit holds close to the critical force Article

J. Chem. Phys., 130(Article number: 51103), 1-4.

J. Husson, A.M. Dogterom (Marileen) and F. Pincet

February 2009
Strong luminescence quantum-efficiency enhancement near prolate metal nanoparticles: Dipolar versus higher-order modes Article

J. Appl. Phys., 105(Article number: 44302), 1-8.

H. Mertens and A. Polman (Albert)

February 2009
Phase variation of type 1 fimbriae : a single cell investigation Dissertation

Biophysics

A.M. Adiciptaningrum

January 2009
Light trapping for solar cells using localised surface plasmons in self-assembled AG nanoparticles In Proceedings

F.J. Beck, S. Mokkapati, A. Polman (Albert) and K.R. Catchpole (Kylie)

January 2009
Optical and magnetic properties of hexagonal arrays of subwavelength holes in optically thin cobalt films Article

Nano Lett., 9(1), 1-6.

G. Ctistis (Georgios), E. Papaioannou, P. Patoka, J. Gutek, P. Fumagalli and M. Giersig

January 2009
Tracking light pulses with near-field microscopy Book Chapter

R.J.P. Engelen and L.K. Kuipers (Kobus)

January 2009
Residue analysis : summary Book Chapter

J.J. Boon, T.F.M. Oudemans (Tania), J. van der Horst (Jerre) and A.E. Kerkhoff

January 2009
Analysis of archaeological residues on pottery Book Chapter

J.J. Boon, T.F.M. Oudemans (Tania), J. van der Horst (Jerre) and A.E. Kerkhoff

January 2009
Water as a molecular hinge in amide-like structures In Proceedings

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

January 2009
Immobilized water molecules in hydrophobic solvation In Proceedings

Y.L.A. Rezus (Yves) and H.J. Bakker (Huib)

January 2009
Ultrafast dynamics of water in ionic micelles In Proceedings

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

January 2009
Seagram mural paintings from the viewpoint of preservation and restoration Book Chapter

L. Carlyle, J.J. Boon, M. Bustin and P. Smithen

January 2009
Proton conduction in aqueous acid-base reactions In Proceedings

M.J. Cox, B.J. Siwick and H.J. Bakker (Huib)

January 2009
Tissue analysis with high resolution imaging mass spectrometry Book Chapter

A.F.M. Altelaar and R.M.A. Heeren (Ron)

January 2009
Modeling tip growth : pushing ahead Book Chapter

M.N. de Keijzer, A.M.C. Emons (Anne Mie) and B.M. Mulder (Bela)

January 2009
Electron capture dissociation of peptide hormone changes upon opening of the tocin ring and complexation with transition metal cations Article

Rapid Commun. Mass Spectrom., 31-38.

Y.E.M. van der Burgt, M. Palmblad, H.C. Dalebout, R.M.A. Heeren (Ron) and A.M. Deelder

January 2009
Size-dependent oscillator strength and quantum efficiency of CdSe quantum dots controlled via the local density of states Article

Phys. Rev. B, 79(Article number: 45301), 1-9.

M.D. Leistikow, J. Johansen, S. Kettelarij, P. Lodahl and W.L. Vos

January 2009
Influence of ions on aqueous acid-base reactions Article

ChemPhysChem, 236-244.

M.J. Cox, B.J. Siwick and H.J. Bakker (Huib)

January 2009
Effect of confinement on proton-transfer reactions in water nanopools Article

ChemPhysChem, 245-251.

K.J. Tielrooij (Klaas-Jan), M.J. Cox and H.J. Bakker (Huib)

January 2009
Subwavelength structure of the evanescent field of an optical Bloch wave Article

Phys. Rev. Lett., 102(Article number: 23902), 1-4.

R.J.P. Engelen, D. Mori, T. Baba and L.K. Kuipers (Kobus)

January 2009
Coherent anti-Stokes Raman scattering microscopy for quantitative characterization of mixing and flow in microfluidics Article

Opt. Lett., 211-213.

D. Schafer (Dawn), M. Müller (Michiel), M. Bonn (Mischa), D.W.M. Marr, J. van Maarseveen (Jan) and J.A. Squier (Jeff)

January 2009
Method to deterministically study photonic nanostructures in different experimental instruments Article

J. Microsc., 18-23.

B.H. Husken, L.A. Woldering, C. Blum and W.L. Vos

January 2009
Observation of polarization singularities at the nanoscale Article

Phys. Rev. Lett., 102(Article number: 33902), 1-4.

M. Burresi, R.J.P. Engelen, A. Opheij, D. van Oosten, D. Mori, T. Baba and L.K. Kuipers (Kobus)

January 2009
Structure and dynamics of interfacial water in model lung surfactants Article

Faraday Discuss., 145-159.

A. Ghosh, R.K. Campen, M. Sovago and M. Bonn (Mischa)

January 2009
Experimental observation of second-harmonic generation and diffusion inside random media Article

J. Opt. Soc. Am. B, 235-243.

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

January 2009
Method for broadband spectroscopy of light transport through opaque scattering media Article

Opt. Lett., 395-397.

O.L. Muskens and A. Lagendijk

January 2009
Photoswitchable sexithiophene-based molecular wires Article

Org. Lett., 721-724.

J. Areephong, J.H. Hurenkamp, M.T.W. Milder, A. Meetsma, J. Herek, W.R. Browne and B.L. Feringa

January 2009
Perspectives for imaging mass spectrometry in the proteomics landscape Article

Proteomics, 819-834.

L. MacAleese (Luke), J. Stauber and R.M.A. Heeren (Ron)

January 2009
Frequency dependence of the molecular reorientation of liquid water Book Chapter

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

January 2009
Computational methods to study strongly-binding polymer-colloid systems Dissertation

B. Bozorgui

December 2008
Force generation in dividing E. coli cells : a handles-on approach using optical tweezers Dissertation

G.S. Verhoeven

December 2008
Plasmonic solar cells Article

Opt. Express, 16(26), 21793-21800.

K.R. Catchpole (Kylie) and A. Polman (Albert)

December 2008
Concise representation of mass spectrometry images by probabilistic latent semantic analysis Article

Anal. Chem., 80(24), 9649-9658.

M. Hanselmann, M. Kirchner, B.Y. Renard, E.R. Amstalden van Hove, K. Glunde, R.M.A. Heeren (Ron) and F.A. Hamprecht

November 2008
Atoms and clusters in strong laser fields Dissertation

Tatiana Marchenko

October 2008
Transcription regulation and genome organization Dissertation

Biochemical Networks

R. Hermsen (Rutger)

October 2008
Multiple scattering of waves in anisotropic random media Dissertation

B.C. Kaas

September 2008
A computational study of E. coli chemotaxis Dissertation

Biochemical Networks

S.B. van Albada

September 2008
Fabrication of photonic crystals and nanocavities Dissertation

L.A. Woldering

September 2008
Near-field visualization of strongly confined surface plasmon polaritons in metal-insulator-metal waveguides Article

Nano Lett., 2925-2929.

E. Verhagen (Ewold), J.A. Dionne (Jennifer), L.K. Kuipers (Kobus), H.A. Atwater (Harry) and A. Polman (Albert)

September 2008
Low-frequency atomic stabilization and dichotomy in superintense laser fields : Full Floquet results Article

Phys. Rev. A, 78(Article number: 33405), 1-11.

M. Stroe, I. Simbotin and M. Gavrila (Mihai)

September 2008
Low-frequency atomic stabilization and dichotomy in superintense laser fields from the high-intensity high-frequency Floquet theory Article

Phys. Rev. A, 78(3, Article number: 33404), 1-12.

M. Gavrila (Mihai), I. Simbotin and M. Stroe

September 2008
Niching in derandomized evolution strategies and its applications in quantum control: a journey from organic diversity to conceptual quantum desings Dissertation

O.M. Shir

June 2008
Dynamics and regulation at the tip: a high resolution view on microtubule assembly Dissertation

E.L. Munteanu

June 2008
Ultrafast investigations of slow light in photonic crystal structures Dissertation

R.J.P. Engelen

June 2008
Photonic crystals modified by optically resonant systems Dissertation

P.J. Harding

June 2008
Fitness landscapes of gene regulation in variable environments Dissertation

Biophysics

F.J. Poelwijk (Frank)

May 2008
Coherent control of biomolecules Dissertation

J. Savolainen (Janne)

May 2008

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