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Publications at LaserLaB in 2012

M. Almasian, J. Grzetic, J. van Maurik, J.D. Steill, G. Berden, S. Ingemann, W.J. Buma & J. Oomens (2012). Non-equilibrium isomer distribution of the gas-phase photoactive yellow protein chromophore.The Journal of Physical Chemistry Letters, 3(16), 2259-2263.

Bald, D. & Koul, A. (2012). Advances and strategies in discovery of new antibacterials for combating metabolically resting bacteria. Drug Discovery Today.

D. Bleger, J. Schwarz, A.M. Brouwer & S. Hecht (2012). o-Fluoroazobenzenes as Readily Synthesized Photoswitches Offering Nearly Quantitative Two-Way Isomerization with Visible Light.Journal of the American Chemical Society, 134(51), 20597-20600.

W.D.A.M. de Boer, D. Timmerman, T. Gregorkiewicz, H. Zhang, W.J. Buma, A. N. Poddubny, A.A. Prokofiev & I.N. Yassievich (2012). Self-trapped exciton state in Si nanocrystals revealed by induced absorption.Physical Review B, 85(16).

Bollen, Y.J.M., Westphal, A.H., Lindhoud, S., Berkel, W.J. van & Mierlo, C.P. van (2012). Distant residues mediate picomolar binding affinity of a protein cofactor. Nature Communications, 3, 1010.

Bruel, N., Castanie-Cornet, M.P., Cirinesi, A.M., Koningstein, G.M., Georgopoulos, C., Luirink, S. & Genevaux, P. (in press).  Hsp33 controls Elongation Factor-Tu stability and allows Escherichia coli growth in the abscence of the major DnaK and Trigger Factor chaperones. Journal of Biological Chemistry.

P. Contreras Carballada, N. Mourtzis, M. Felici, S. Bonnet, R.J.M. Nolte, R.M. Williams, L. De Cola & M.C. Feiters (2012). Variation of the Viologen Electron Relay in Cyclodextrin-Based Self-Assembled Systems for Photoinduced Hydrogen Evolution from Water.European Journal of Organic Chemistry.

Daleke, M.H., Woude, A.D. van der, Parret, A.H., Ummels, R., Groot, A.M., Watson, D., Piersma, S.R., Jimenez, C.R., Luirink, S., Bitter, W. & Houben, E.N. (2012). Specific chaperones for the type VII protein. Journal of Biological Chemistry, 287(38), 31939-31947.

S.R. Domingos, M.R. Panman, B.H. Bakker, F. Hartl, W.J. Buma & S. Woutersen (2012). Amplifying vibrational circular dichroism by manipulation of the electronic manifold.Chemical Communications, 48(3), 353-355.

S.R. Domingos, P.S. Pereira Silva, W.J. Buma, M.H. Garcia, N. C. Lopes, J. A. Paixao, M. R. Silva & S. Woutersen (2012). Amplification of the linear and nonlinear optical response of a chiral molecular crystal.Journal of Chemical Physics, 136(13).

D.D. Günbaş & A.M. Brouwer (2012). Degenerate molecular shuttles with flexible and rigid spacers.The Journal of organic chemistry, 77(13), 5724-5735.

Harvey, C.E., Petterson, I.E.I., Weckhuysen, B.M., Gooijer, C., Ariese, F. & Mank, A.J.G. (2012). Looking Inside Catalyst Extrudates with Time-Resolved Surface-Enhanced Raman Spectroscopy (TR-SERS). Applied Spectroscopy, 66(10), 1179-1185.

Hollund, H.I., Ariese, F., Fernandes, R., Jans, M.M.E. & Kars, H. (2012). Testing an alternative high-throughput tool for investigating bone diagenesis: FTIR in attenuated total reflection (ATR) mode. Archaeometry, 2012.

Houben, E.N., Bestebroer, J., Ummels, R., Wilson, L., Piersma, S.R., Jimenez, C.R., Ottenhoff, TH, Luirink, S. & Bitter, W. (2012). Composition of the type VII secretion system membrane complex. Molecular Microbiology, 86, 472-484.

A. Jacquart, R.M. Williams, A.M. Brouwer & E. Ishow (2012). Decoupling fluorescence and photochromism in bifunctional azo derivatives for bulk emissive structures.Chemistry - A European Journal, 18(12), 3706-3720.

Jin, B., Wang, G.X., Millo, D., Hildebrandt, P. & Xia, X.A. (2012). Electric-field controle of the pH-dependent redox process of cytochrome c immobilized on gold electrode. Journal of Physical Chemistry C.  Nanomaterials and Interfaces, 116, 13038-13044.

Jong, W.S.P., Soprova, Z., Punder, K. de, Hagen-Jongman, C.M. ten, Wagner, S., Gier, J.W. de, Andersen, P., Wel, N.N. van der & Luirink, S. (2012). A structurally informed autotransporter platform for efficient heterologous protein secretion and display. Microbial Cell Factories, 11(85).

Kozuch, J., Steinem, C., Hildebrandt, P. & Millo, D. (2012). Combined electrochemistry and surface-enhanced infrared absorption spectroscopy of gramicidin A incorporated into tethered bilayer lipid membranes. Angewandte Chemie International Edition in English, 51, 8114-8117.

T. Kumpulainen & A.M. Brouwer (2012). Excited-state proton transfer and ion pair formation in a Cinchona organocatalyst.Physical Chemistry Chemical Physics, 14(37), 13019-13026.[go to publisher's site]

Lammers, I., Lhiaubet-Vallet, V., Jimenez, M.C., Ariese, F., Miranda, M.A. & Gooijer, C. (2012). Stereoselective Binding of Flurbiprofen Enantiomers and their Methyl Esters to Human Serum Albumin Studied by Time-Resolved Phosphorescence. Chirality, 24(10), 840-846.

Lehmann, C.S., Ram, N.B. & Janssen, M.H.M. (2012). Velocity map photoelectron-photoion coincidence imaging on a single detector. Review of Scientific Instruments, 83(9).

Luirink, S., Yu, Z., Wagner, S. & Gier, J.W. de (2012). Biogenesis of inner membrane proteins in Escherichia coli. Biochimica et Biophysica Acta. Bioenergetics, 2012(6), 965-976.

Millo, D. (2012). Spectroelectrochemical analysis of electroactive microbial biofilms. Biochemical Society Transactions, 40, 1284-1290.

V.A. Nguyen & R.M. Williams (2012). Bis-semiquinone (bi-radical) formation by photoinduced proton coupled electron transfer in covalently linked catechol-quinone systems: Aviram's hemiquinones revisited.Photochemical & Photobiological Sciences, 11(6), 957-961.

M.R. Panman, P. Bodis, D.J. Shaw, B.H. Bakker, A.C. Newton, E.R. Kay, D.A. Leigh, W.J. Buma, A.M. Brouwer & S. Woutersen (2012). Time-resolved vibrational spectroscopy of a molecular shuttle.Physical Chemistry Chemical Physics, 14(6), 1865-1875.

M. Plugge, V. Alain-Rizzo, P. Audebert & A.M. Brouwer (2012). Excited state dynamics of 3,6-diaryl-1,2,4,5-tetrazines: experimental and theoretical studies.Journal of Photochemistry and Photobiology A-Chemistry, 234, 12-20.

T.N. Raja, A.M. Brouwer, T. Nabuurs & R. Tennebroek (2012). A fluorescence approach to investigate repartitioning of coalescing agents in acrylic polymer emulsions.Colloid and polymer science, 290(6), 541-552.

Sauri, A., Hagen-Jongman, C.M. ten, Ulsen, J.P. van & Luirink, S. (2012). Estimating the size of the active translocation pore of an autotransporter. Journal of Molecular Biology, 2012(3), 335-345.

Schkolnik, G., Utesch, T., Salewski, J., Tenger, K., Millo, D., Kranich, A., Zebger, I., Schulz, C., Zimanyi, L., Rakhely, G., Mroginski, M.A. & Hildebrandt, P. (2012). Mapping local electric fields in proteins at biomimetic interfaces. Chemical Commununications, 48, 70-72.

Schkolnik, G., Salewski, J., Millo, D., Zebger, I., Franzen, S. & Hildebrandt, P. (2012). Vibrational Stark effect of the electric-field reporter 4-mercaptobenzonitrile as a tool for investigating electrostatics at electrode/SAM/solution interfaces. International Journal of Molecular Sciences, 13, 7466-7482.

Sezer, M., Millo, D., Weidinger, I.M., Zebger, I. & Hildebrandt, P. (2012). Analyzing the catalytic processes of immobilized redox enzymes by vibrational spectroscopies. IUBMB Life, 64, 7466-7482.

Shanmugham, A., Bakayan, A., Völler, P., Grosveld, J., Lill, H. & Bollen, Y.J. (2012). The hydrophobic core of twin-arginine signal sequences orchestrates specific binding to Tat-pathway related chaperones. PLoS ONE, 7, e34159.

Tardioli, S., Lammers, I., Hooijschuur, J.H., Ariese, F., Zwan, G. van der & Gooijer, C. (2012). Complementary Fluorescence and Phosphorescence Study of the Interaction of Brompheniramine with Human Serum Albumin. Journal of Physical Chemistry B, 116(24), 7033-7039.

Utesch, T., Millo, D., Castro, M., Hildebrandt, P., Zebger, I. & Mroginski, M.A. (2012). Effect of the protonation degree of a self-assembled monolayer on the immobilization dynamics of a [NiFe] hydrogenase. Langmuir.

Braaf, B., Vermeer, K.A., Vienola, K.V. & Boer, J.F. de (2012). Angiography of the retina and the choroid with phase-resolved OCT using interval-optimized backstitched B-scans. Optics Express, 20(20), 20516-20534.

Cuper, N.J., Graaff, J.C. de, Hartman, B.J., Verdaasdonk, R. & Kalkman, C.J. (2012). Difficult arterial cannulation in children: is a near-infrared vascular imaging system the answer? British Journal of Anaesthesia, 109(3), 420-426.

Cuper, N.J., Graaff, J.C. de, van Dijk, A.T.H., Verdaasdonk, R., van der Werff, D.B.M. & Kalkman, C.J. (2012). Predictive factors for difficult intravenous cannulation in pediatric patients at a tertiary pediatric hospital. Pediatric Anesthesia, 22(3), 223-229.

Gemert, M.J.C. van, Geld, C.W. van der, Bruijninckx, C.M.A., Verdaasdonk, R. & Neumann, H.A.M. (2012). Comment to Vuylsteke ME and Mordon SR. Endovenous Laser Ablation: A Review of Mechanisms of Action. Ann Vasc Surg 2012;26:424-33. Annals of Vascular Surgery, 26(6), 881-883.

Groot, M. de, Evans, C.L. & Boer, J.F. de (2012). Self-interference fluorescence microscopy: three dimensional fluorescence imaging without depth scanning. Optics Express, 20(14), 15253-15262.

Heuveling, D.A., Visser, G.W.M., Groot, M. de, Boer, J.F. de, Salumbides - Baclayon, M., Roos, W.H., Wuite, G.J.L., Leemans, C.R., Bree, R. de & Dongen, G.A.M.S. van (2012). Nanocolloidal albumin-IRDye 800CW: a near-infrared fluorescent tracer with optimal retention in the sentinel lymph node. European Journal of Nuclear Medicine and Molecular Imaging, 39(7), 1161-1168.

Islam, M.S., Oliveira, M.C., Wang, Y., Henry, F.P., Randolph, M.A., Park, B. H. & Boer, J.F. de (2012). Extracting structural features of rat sciatic nerve using polarization-sensitive spectral domain optical coherence tomography. Journal of Biomedical Optics, 17(5).

Li, J.A., Groot, M. de, Helderman, F., Mo, J., Daniels, J.M.A., Grünberg, K., Sutedja, G.T. & Boer, J.F. de (2012). High speed miniature motorized endoscopic probe for optical frequency domain imaging. Optics Express, 20(22), 24132-24138.

Munck, J.C. de, Houdt, P.J. van, Verdaasdonk, R. & Ossenblok, P.P.W. (2012). A semi-automatic method to determine electrode positions and labels from gel artifacts in EEG/fMRI-studies. Neuroimage, 59(1), 399-403.

Sheehy, C.K., Yang, Q., Arathorn, D.W., Teeruveedhula, P., Boer, J.F. de & Roorda, A.J. (2012). High-speed, image-based eye tracking with a scanning laser ophthalmoscope. Biomedical Optics Express, 3(10), 2611-2622.

Wu, H., Boer, J.F. de & Chen, T.C. (2012). Diagnostic Capability of Spectral-Domain Optical Coherence Tomography for Glaucoma. American Journal of Ophthalmology, 153(5), 815-826.

van der Schoot, J., Vermeer, K.A., Boer, J.F. de & Lemij, H.G. (2012). The Effect of Glaucoma on the Optical Attenuation Coefficient of the Retinal Nerve Fiber Layer in Spectral Domain Optical Coherence Tomography Images. Investigative Ophthalmology and Visual Science, 53(4), 2424-2430.

Berera, R., Stokkum, I.H.M. van, Gwizdala, M.S., Wilson, A., Kirilovsky, D. & Grondelle, R. van (2012). The photophysics of the Orange Carotenoid Protein, a light-powered molecular switch. Journal of Physical Chemistry B, 116, 2568-2574.

Laptenok, S., Stokkum, I.H.M. van, Borst, J.W., Oort, B. van, Visser, A.J.W.G. & Amerongen, H. van (2012). Disentangling picosecond events that complicate the quantitative use of the calcium sensor YC3.60. Journal of Physical Chemistry B, 116(9), 3013-3020.

Marin, A. (2012, april 18). Energy transport pathways in photosynthetic antennas. VU Vrije Universiteit. Prom./coprom.: prof. dr. R. van Grondelle.

Marin, A., Stokkum, I.H.M. van, Novoderezhkin, V.I. & Grondelle, R. van (2012). Excitation-induced polarization decay in the plant light-harvesting complex LHCII. Journal of Photochemistry and Photobiology A. Chemistry, 234, 91-99.

Mathes, T., Zhu, J., van Stokkum, I.H.M., Groot, M.L., Hegemann, P. & Kennis, J.T.M. (2012). Hydrogen Bond Switching among Flavin and Amino Acids Determines the Nature of Proton-Coupled Electron Transfer in BLUF Photoreceptors. Journal of Physical Chemistry Letters, 3(2), 203-208.

Mathes, T., Zhu, J., Stokkum, I.H.M. van, Groot, M.L., Hegemann, P. & Kennis, J.T.M. (2012). Hydrogen Bond Switching among Flavin and Amino Acids Determines the Nature of Proton-Coupled Electron Transfer in BLUF Photoreceptors. Journal of Physical Chemistry Letters, 3, 203-208.

Mathes, T., Stokkum, I.H.M. van, Stierl, M. & Kennis, J.T.M. (2012). Redox modulation of flavin and tyrosine determines photoinduced proton-coupled electron transfer and photoactivation of BLUF photoreceptors. Journal of Biological Chemistry, 287, 31725-31738.

Oort, B.F. van, Veer, M.J.T. ter, Groot, M.L. & Stokkum, I.H.M. van (2012). Excited state proton transfer in strongly enhanced GFP (sGFP2). Physical Chemistry Chemical Physics - PCCP, 14(25), 8852-8858.

Romero Mesa, E., Diner, B.A., Nixon, P.J., Coleman, W.J., Dekker, J.P. & Grondelle, R. van (2012). Mixed exciton–charge-transfer states in photosystem II: Stark spectroscopy on site–directed mutants. Biophysical Journal, 103(2), 185-194.

Snellenburg, J.J., Laptenok, S., Seger, R., Mullen, K.M. & Stokkum, I.H.M. van (2012). Glotaran: A Java-Based Graphical User Interface for the R Package TIMP. Journal of Statistical Software, 49(3), 1-22.

Stahl, A.D., Crouch, L.I., Jones, M.R., van Stokkum, I.H.M., Grondelle, R. van & Groot, M.L. (2012). Role of PufX in Photochemical Charge Separation in the RC-LH1 Complex from Rhodobacter sphaeroides: An Ultrafast Mid-IR Pump-Probe Investigation. Journal of Physical Chemistry B, 116(1), 434-444.

Zhu, J., Mathes, T., Stahl, A.D., Kennis, J.T.M. & Groot, M.L. (2012). Ultrafast mid-infrared spectroscopy by chirped pulse upconversion in 1800-1000cm(-1) region. Optics Express, 20(10), 10562-10571.

Berera, R., Stokkum, I.H.M. van, Gwizdala, M.S., Wilson, A., Kirilovsky, D. & Grondelle, R. van (2012). The photophysics of the Orange Carotenoid Protein, a light-powered molecular switch. Journal of Physical Chemistry B, 116, 2568-2574.

Laptenok, S., Stokkum, I.H.M. van, Borst, J.W., Oort, B. van, Visser, A.J.W.G. & Amerongen, H. van (2012). Disentangling picosecond events that complicate the quantitative use of the calcium sensor YC3.60. Journal of Physical Chemistry B, 116(9), 3013-3020.

Marin, A. (2012, april 18). Energy transport pathways in photosynthetic antennas. VU Vrije Universiteit. Prom./coprom.: prof. dr. R. van Grondelle.

Marin, A., Stokkum, I.H.M. van, Novoderezhkin, V.I. & Grondelle, R. van (2012). Excitation-induced polarization decay in the plant light-harvesting complex LHCII. Journal of Photochemistry and Photobiology A. Chemistry, 234, 91-99.

Mathes, T., Zhu, J., van Stokkum, I.H.M., Groot, M.L., Hegemann, P. & Kennis, J.T.M. (2012). Hydrogen Bond Switching among Flavin and Amino Acids Determines the Nature of Proton-Coupled Electron Transfer in BLUF Photoreceptors. Journal of Physical Chemistry Letters, 3(2), 203-208.

Mathes, T., Zhu, J., Stokkum, I.H.M. van, Groot, M.L., Hegemann, P. & Kennis, J.T.M. (2012). Hydrogen Bond Switching among Flavin and Amino Acids Determines the Nature of Proton-Coupled Electron Transfer in BLUF Photoreceptors. Journal of Physical Chemistry Letters, 3, 203-208.

Mathes, T., Stokkum, I.H.M. van, Stierl, M. & Kennis, J.T.M. (2012). Redox modulation of flavin and tyrosine determines photoinduced proton-coupled electron transfer and photoactivation of BLUF photoreceptors. Journal of Biological Chemistry, 287, 31725-31738.

Oort, B.F. van, Veer, M.J.T. ter, Groot, M.L. & Stokkum, I.H.M. van (2012). Excited state proton transfer in strongly enhanced GFP (sGFP2). Physical Chemistry Chemical Physics - PCCP, 14(25), 8852-8858.

Romero Mesa, E., Diner, B.A., Nixon, P.J., Coleman, W.J., Dekker, J.P. & Grondelle, R. van (2012). Mixed exciton–charge-transfer states in photosystem II: Stark spectroscopy on site–directed mutants. Biophysical Journal, 103(2), 185-194.

Snellenburg, J.J., Laptenok, S., Seger, R., Mullen, K.M. & Stokkum, I.H.M. van (2012). Glotaran: A Java-Based Graphical User Interface for the R Package TIMP. Journal of Statistical Software, 49(3), 1-22.

Stahl, A.D., Crouch, L.I., Jones, M.R., van Stokkum, I.H.M., Grondelle, R. van & Groot, M.L. (2012). Role of PufX in Photochemical Charge Separation in the RC-LH1 Complex from Rhodobacter sphaeroides: An Ultrafast Mid-IR Pump-Probe Investigation. Journal of Physical Chemistry B, 116(1), 434-444.

Zhu, J., Mathes, T., Stahl, A.D., Kennis, J.T.M. & Groot, M.L. (2012). Ultrafast mid-infrared spectroscopy by chirped pulse upconversion in 1800-1000cm(-1) region. Optics Express, 20(10), 10562-10571.

Akca BI, Nguyen VD, Kalkman J, Ismail N, Sengo G, Sun F, Driessen A, van Leeuwen TG, Pollnau M, Worhoff K, de Ridder RM, Toward Spectral-Domain Optical Coherence Tomography on a Chip. IEEE J SEL TOP QUANT 2012;18 (3):1223-1233

Barwari K, de Bruin DM, Faber DJ, van Leeuwen TG, de la Rosette JJ, Laguna MP, Differentiation between normal renal tissue and renal tumours using functional optical coherence tomography: a phase I in vivo human study. BJU INT 2012;110 (8 Part B):E415-E420 [PubMed]

Bosschaart N. Quantitative and localized spectroscopy for non-invasive bilirubinometry in neonates. s.l.: s.n.; 2012. 108p. ISBN 9789461820655 [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Leeuwen AGJM; copromotor(s): Aalders MCG)

Bosschaart N, Aalders MCG, van Leeuwen TG, Faber DJ, Spectral domain detection in low-coherence spectroscopy. BIOMED OPT EXPRESS 2012;3 (9):2263-2272 [PubMed]

Bosschaart N, Kok JH, Newsum AM, Ouweneel DM, Mentink R, van Leeuwen TG, Aalders MCG, Limitations and opportunities of transcutaneous bilirubin measurements. PEDIATRICS 2012;129 (4):689-694 [PubMed]

Bremmer RH, de Bruin KG, van Gemert MJC, van Leeuwen TG, Aalders MCG, Forensic quest for age determination of bloodstains. FORENSIC SCI INT 2012;216 (1-3):1-11 [PubMed]

Cernohorsky P, de Bruin DM, van Herk M, Bras J, Faber DJ, Strackee SD, van Leeuwen TG, In-situ imaging of articular cartilage of the first carpometacarpal joint using co-registered optical coherence tomography and computed tomography. J BIOMED OPT 2012;17 (6):060501 [PubMed]

de Kinkelder R. Optical diagnostic techniques in ophthalmology. s.l.: s.n.; 2012. 127p. ISBN 9789462031692 [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Leeuwen AGJM; copromotor(s): Verbraak FD, Faber DJ)

de Kinkelder R, de Bruin DM, Verbraak FD, van Leeuwen TG, Faber DJ, Comparison of retinal nerve fiber layer thickness measurements by spectral-domain optical coherence tomography systems using a phantom eye model. J BIOPHOTONICS 2012;ahead of print [PubMed]

de Kinkelder R, van Leeuwen TG, Verbraak FD, Detection of early-stage age related macular degeneration with a compact rarebit test. BRIT J OPHTHALMOL 2012;96 (10):1354-1355 [PubMed]

Edelman GJ, Gaston E, van Leeuwen TG, Cullen PJ, Aalders MCG, Hyperspectral imaging for non-contact analysis of forensic traces. FORENSIC SCI INT 2012;223 (1-3):28-39 [PubMed]

Edelman G, Manti V, van Ruth SM, van Leeuwen T, Aalders M, Identification and age estimation of blood stains on colored backgrounds by near infrared spectroscopy. FORENSIC SCI INT 2012;220 (1-3):239-244 [PubMed]

Edelman G, van Leeuwen TG, Aalders MCG, Hyperspectral imaging for the age estimation of blood stains at the crime scene. FORENSIC SCI INT 2012;223 (1-3):72-77 [PubMed]

Grootendorst DJ, Jose J, Fratila RM, Visscher M, Velders A, ten Haken B, van Leeuwen TG, Steenbergen W, Manohar S, Ruers TJM, Evaluation of a superparamagnetic iron oxide nanoparticle (Endorem) as a photoacoustic contrast agent for nodal enhancement. CONTRAST MEDIA MOL I 2012;--:--

Grootendorst DJ, Jose J, Wouters MW, van Boven H, van der Hage J, van Leeuwen TG, Steenbergen W, Manohar S, Ruers TJM, First experiences of photoacoustic imaging for detection of melanoma metastases in resected human lymph nodes. LASER SURG MED 2012;44 (7):541-549 [PubMed]

Hartsuiker L, Petersen W, Rayavarapu RG, Lenferink A, Poot AA, Terstappen LWMM, van Leeuwen TG, Manohar S, Otto C, Raman and Fluorescence Spectral Imaging of Live Breast Cancer Cells Incubated with PEGylated Gold Nanorods. APPL SPECTROSC 2012;66 (1):66-74

Hassell MECJ, Grundeken MJ, de Bruin DM, van de Hoef TP , van Leeuwen TG, Henriques JPS, Piek JJ, Wykrzykowska JJ, Successful treatment of a long tapered lesion with two overlapping ABSORB® bioresorbable vascular scaffolds of different diameters: Evaluation by three-dimensional optical coherence tomography. INT J CARDIOL 2012;ahead of print [PubMed]

Heijblom M, Meijer LM, van Leeuwen TG, Steenbergen W, Manohar S, Monte Carlo simulations shed light on Bathsheba's suspect breast. J BIOPHOTONICS 2012;ahead of print [PubMed]

Heijblom M, Piras D, Xia W, van Hespen JCG, Klaase JM, van den Engh FM, van Leeuwen TG, Steenbergen W, Manohar S, Visualizing breast cancer using the Twente photoacoustic mammoscope: what do we learn from twelve new patient measurements?. OPT EXPRESS 2012;20 (11):11582-11597 [PubMed]

Jose J. Prospects of Passive Element Enriched Photoacoustic Computed Tomography (PER-PACT). Enschede: s.n.; 2012. 159p. ISBN 978-90 365 3347 8 Proefschrift Twente University, MIRA Inst.for biomed technol & techn medicine, Faculty of Science. (Promotor(s): van Leeuwen AGJM; copromotor(s): Manohar S)

Jose J, Willemink RGH, Steenbergen W, Slump CH, van Leeuwen TG, Manohar S, Speed-of-sound compensated photoacoustic tomography for accurate imaging. MED PHYS 2012;39 (12):7262-7271 [PubMed]

Kalkman J, Bykov AV, Streekstra GJ, van Leeuwen TG, Multiple scattering effects in Doppler optical coherence tomography of flowing blood. PHYS MED BIOL 2012;57 (7):1907-1917 [PubMed]

Kodach VM. Development of functional near-infrared optical coherence tomography. s.l.: s.n.; 2012. 114p. ISBN 9789461820815 [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Leeuwen AGJM; copromotor(s): Kalkman J, Faber DJ)

Leproux A. Breast lesion detection using diffuse optical imaging. s.l.: s.n.; 2012. 143p. [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Leeuwen AGJM, Tromberg BJ; copromotor(s): van der Voort M, Cerussi AE)

Nguyen VD, Weiss N, Beeker W, Hoekman M, Leinse A, Heideman RG, van Leeuwen TG, Kalkman J, Integrated-optics-based swept-source optical coherence tomography. OPT LETT 2012;37 (23):4820-4822 [PubMed]

Stam B. Three dimensional modeling of bruise evolution for improved age determination. s.l.: s.n.; 2012. 139p. [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Leeuwen AGJM, van Gemert MJC; copromotor(s): Aalders MCG)

Stam B, van Gemert MJC, van Leeuwen TG, Aalders MCG, How the blood pool properties at onset affect the temporal behavior of simulated bruises. MED BIOL ENG COMPUT 2012;50 (2):165-171 [PubMed]

van der Pol E, van Gemert MJC, Sturk A, Nieuwland R, van Leeuwen TG, Single vs. swarm detection of microparticles and exosomes by flow cytometry. J THROMB HAEMOST 2012;10 (5):919-930 [PubMed]

Weiss N, van Leeuwen TG, Kalkman J, Doppler-based lateral motion tracking for optical coherence tomography. OPT LETT 2012;37 (12):2220-2222 [PubMed]

Wessels R, de Bruin DM, Faber DJ, van Boven HH, Vincent AD, van Leeuwen TG, van Beurden M, Ruersa TJM, Optical coherence tomography in vulvar intraepithelial neoplasia. J BIOMED OPT 2012;17 (11):116022 [PubMed]

Broedersz, C.P., Sheinman, M. & MacKintosh, F.C. (2012). Filament-Length-Controlled Elasticity in 3D Fiber Networks. Physical Review Letters, 108(6).

Engel, M.F.M., Akker, C. van den, Schleeger, M., Veliko, K.P., Koenderink, G.H. & Bonn, M. (2012). The Polyphenol EGCG Inhibits Amyloid Formation Less Efficiently at Phospholipid Interfaces than in Bulk Solution. The Journal of the American Chemical Society, 134(36), 14781-14788.

Farge, G.A., Laurens, N., Broekmans, O.D., Wildenberg, S.M.J.L., Dekker, L.C.M., Gaspari, M., Gustafsson, C. M., Peterman, E.J.G., Falkenberg, M. & Wuite, G.J.L. (2012). Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A. Nature Communications, 3(1013).

Gentry, B.S., van der Meulen, S., Noguera, P., Alonso-Latorre, B., Plastino, J. & Koenderink, G.H. (2012). Multiple actin binding domains of Ena/VASP proteins determine actin network stiffening. European Biophysics Journal, 41(11), 979-990.

Gomez-Marin, A., Partoune, N., Stephens, G.J. & Louis, M. (2012). Automated Tracking of Animal Posture and Movement during Exploration and Sensory Orientation Behaviors. PLoS ONE, 7(8).

Groot, M. de, Evans, C.L. & Boer, J.F. de (2012). Self-interference fluorescence microscopy: three dimensional fluorescence imaging without depth scanning. Optics Express, 20(14), 15253-15262.

Heuveling, D.A., Visser, G.W.M., Groot, M. de, Boer, J.F. de, Salumbides - Baclayon, M., Roos, W.H., Wuite, G.J.L., Leemans, C.R., Bree, R. de & Dongen, G.A.M.S. van (2012). Nanocolloidal albumin-IRDye 800CW: a near-infrared fluorescent tracer with optimal retention in the sentinel lymph node. European Journal of Nuclear Medicine and Molecular Imaging, 39(7), 1161-1168.

Klug, W. S., Roos, W.H. & Wuite, G.J.L. (2012). Unlocking Internal Prestress from Protein Nanoshells. Physical Review Letters, 109(168104).

Laurens, N. (2012, maart 29). A biophysical exploration of proteins and their substrates. VU Vrije Universiteit. Prom./coprom.: prof. dr. ir. G.J.L. Wuite.

Laurens, N., Driessen, R.P.C., Heller, I., Vorselen, D., Noom, M.C., Hol, F.J.H., White, M.F., Dame, R.T. & Wuite, G.J.L. (in press).  Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA. Nature Communications, 3.

Laurens, N., Rusling, D.A., Pernstich, C., Brouwer, I., Halford, S.E. & Wuite, G.J.L. (2012). DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics. Nucleic Acids Research, 40(11), 4988-4997.

Li, J.A., Groot, M. de, Helderman, F., Mo, J., Daniels, J.M.A., Grünberg, K., Sutedja, G.T. & Boer, J.F. de (2012). High speed miniature motorized endoscopic probe for optical frequency domain imaging. Optics Express, 20(22), 24132-24138.

Likitlersuang, J., Stephens, G.J., Palanski, K. & Ryu, W.S.C. (2012). C. elegans Tracking and Behavioral Measurement. Journal of Visualized Experiments, 69.

MacKintosh, F.C. (2012). Active diffusion: The erratic dance of chromosomal loci. Proceedings of the National Academy of Sciences of the United States of America, 109(19), 7138-7139.

Ronde, W.H. de (2012, februari 07). Multiplexing Biochemical Signals. VU Vrije Universiteit. Prom./coprom.: prof. dr. P.R. ten Wolde.

Roos, W.H., Gertsman, I., May, E.R., Brooks, C.L., Johnson, J.E. & Wuite, G.J.L. (2012). Mechanics of bacteriophage maturation. Proceedings of the National Academy of Sciences of the United States of America, 109(7), 2342-2347.

Rusling, D.A., Laurens, N., Pernstich, C., Brouwer, I., Wuite, G.J.L. & Halford, S.E. (2012). DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations. Nucleic Acids Research, 40(11), 4977-4987.

Sheinman, M., Broedersz, C.P. & MacKintosh, F.C. (2012). Actively Stressed Marginal Networks. Physical Review Letters, 109(23).

Sheinman, M., Benichou, O., Kafri, Y. & Voituriez, R. (2012). Classes of fast and specific search mechanisms for proteins on DNA. Reports on Progress in Physics, 75(2), 026601.

Sheinman, M. & Kafri, Y. (2012). How does the DNA sequence affect the Hill curve of transcriptional response? Physical Biology, 9(5).

Sheinman, M., Broedersz, C.P. & MacKintosh, F.C. (2012). Nonlinear effective-medium theory of disordered spring networks. Physical Review E, 85(2).

Snijder, J., Ivanovska, I.L., Salumbides - Baclayon, M., Roos, W.H. & Wuite, G.J.L. (2012). Probing the impact of loading rate on the mechanical properties of viral nanoparticles. Micron, 43(12), 1343-1350.

Stuhrmann, B., Soares e Silva, M., Depken, S.M., MacKintosh, F.C. & Koenderink, G.H. (2012). Nonequilibrium fluctuations of a remodeling in vitro cytoskeleton. Physical Review E, 86(2).

Bagdonaite, J., Murphy, M.T., Kaper, L. & Ubachs, W.M.G. (2012). Constraint on a variation of the proton-to-electron mass ratio from H-2 absorption towards quasar Q2348-011. Monthly Notices of the Royal Astronomical Society, 421(1), 419-425.

Barmes, I., Witte, S.M. & Eikema, K.S.E. (2012). Doppler-Free Two-Photon Direct Frequency Comb Spectroscopy With Coherent Control. In CLEO: Science and Innovations, OSA Technical Digest (pp. CF1C.6). Optical Society of America.

Barmes, I., Witte, S.M. & Eikema, K.S.E. (2013). Spatial and Spectral Coherent Control over Direct Frequency Comb Excitation. In Proceedings of the XVIIIth International Conference on Ultrafast Phenomena. EPJ Web of Conferences.

Benko, C., Ruehl, A., Martin, M.J., Eikema, K.S.E., Fermann, M.E., Hartl, I. & Ye, J. (2012). Full phase stabilization of a Yb:fiber femtosecond frequency comb via high-bandwidth transducers. Optics Letters, 37(12), 2196-2198.

Borbely, J. S., Rooij, R. van, Knoop, S. & Vassen, W. (2012). Magnetic-field-dependent trap loss of ultracold metastable helium. Physical Review A, 85(2).

Butz, A., Galli, A., Hasekamp, O., Landgraf, J., Tol, P.J.J. & Aben, E.A.A. (2012). TROPOMI aboard Sentinel-5 Precursor: Prospective performance of CH4 retrievals for aerosol and cirrus loaded atmospheres. Remote Sensing of Environment, 120(SI), 267-276.

Chavan, D.C., Watering, T.C. van de, Gruca, G.L., Rector, J.H., Heeck, K., Slaman, M.J. & Iannuzzi, D. (2012). Ferrule-top nanoindenter: An optomechanical fiber sensor for nanoindentation. Review of Scientific Instruments, 83(115110).

Cipullo, A., Gruca, G.L., Heeck, K., De Filippis, F., Iannuzzi, D., Minardo, A. & Zeni, L. (2012). Numerical study of a ferrule-top cantilever optical fiber sensor for wind-tunnel applications and comparison with experimental results. Sensors and Actuators A-Physical, 178, 17-25.

Cipullo, A., Gruca, G.L., Heeck, K., De Filippis, F., Iannuzzi, D., Minardo, A. & Zeni, L. (2012). Velocity measurements of low speed air ows by ferrule-top cantilever optical ber sensor. Sensors and Actuators A-Physical, 17.

Dickenson, G.D., Salumbides, E.J., Niu, M., Jungen, C., Ross, S.C. & Ubachs, W.M.G. (2012). Precision spectroscopy of high rotational states in H-2 investigated by Doppler-free two-photon laser spectroscopy in the EF (1)Sigma(+)(g)-X (1)Sigma(+)(g) system. Physical Review A, 86(3).

Dickenson, G.D. & Ubachs, W.M.G. (2012). The D-1 Pi(u) state of HD and the mass scaling relation of its predissociation widths. Journal of Physics B. Atomic, Molecular and Optical Physics, 45(14).

Fischer, D.G., Dijk, T. van, Visser, T.D. & Wolf, E. (2012). Coherence effects in Mie scattering. Journal of the Optical Society of America. A: Optics, image science, and vision., 29(1), 78-84.

Galli, A., Butz, A., Scheepmaker, R.A., Hasekamp, O., Landgraf, J., Tol, P.J.J., Wunch, D., Deutscher, N.M., Toon, G.C., Wennberg, P.O., Griffith, D.W.T. & Aben, E.A.A. (2012). CH4, CO, and H2O spectroscopy for the Sentinel-5 Precursor mission: an assessment with the Total Carbon Column Observing Network measurements. Atmospheric Measurement, 5(6), 1387-1398.

Gan, C. H., Gu, Y.L., Visser, T.D. & Gbur, G.J. (2012). Coherence Converting Plasmonic Hole Arrays. Plasmonics, 7, 313-322.

Gruca, G.L., Chavan, D.C., Cipullo, A., Babaei Gavan, K., De Filippis, F., Minardo, A., Rector, J.H., Heeck, K., Zeni, L. & Iannuzzi, D. (2012). Development of fiber optic ferrule-top cantilevers for sensing and beam-steering applications. Proceedings of SPIE, 84390E.

Gruca, G.L., Chavan, D.C., Watering, T.C. van de, Rector, J.H. & Iannuzzi, D. (2012). Ferrule-top cantilevers for measurements in harsh environments. SPIE Newsroom.

Gu, Z.Y., Vieitez, M.O., Duijn, E.J. van & Ubachs, W.M.G. (2012). A Rayleigh-Brillouin scattering spectrometer for ultraviolet wavelengths. Review of Scientific Instruments, 83(5).

Haddad, M.A., Zhao, D., Linnartz, H.V.J. & Ubachs, W.M.G. (2012). Spin-orbit Splitting and Lifetime Broadening in the A(2)Delta Electronic State of l-C5H. Chinese Journal of Chemical Physics, 25(2), 129-134.

Hooghiemstra, P.B., Krol, M.C., Bergamaschi, P., Laat, A.T.J. de, Werf, G.R. van der, Novelli, P.C., Deeter, M.N., Aben, E.A.A. & Rockmann, T. (2012). Comparing optimized CO emission estimates using MOPITT or NOAA surface network observations. Journal of Geophysical Research, 117(D06309).

Hooghiemstra, P.B., Krol, M.C., Leeuwen, T.T. van, Werf, G.R. van der, Novelli, P.C., Deeter, M.N., Aben, E.A.A. & Rockmann, T. (2012). Interannual variability of carbon monoxide emission estimates over South America from 2006 to 2010. Journal of Geophysical Research, 117.

Ilyushin, V.V., Jansen, P., Kozlov, M.G., Levshakov, S.G., Kleiner, I, Ubachs, W.M.G. & Bethlem, H.L. (2012). Sensitivity to a possible variation of the proton-to-electron mass ratio torsion-wagging-rotation transitions in methylamine CH3NH2. Physical Review A, 85(3).

Knoop, S., Borbely, J. S., Rooij, R. van & Vassen, W. (2012). Nonexponential one-body loss in a Bose-Einstein condensate. Physical Review A, 85(2).

Knoop, S., Borbely, J., Vassen, W. & Kokkelmans, S.J.J.M.F. (2012). Universal three-body parameter in ultracold 4He*. Physical Review A, 6(86).

Knoop, S., Borbely, J. S., Vassen, W. & Kokkelmans, S.J.J.M.F. (2012). Universal three-body parameter in ultracold 4He*. Physical Review A, 86(6).

Koelemeij, J.C.J., Noom, D.W.E., Jong, D. de, Haddad, M.A. & Ubachs, W.M.G. (2012). Observation of the v '=8 <- v=0 vibrational overtone in cold trapped HD+. Applied Physics B. Lasers and Optics, 107(4), 1075-1085.

Laat, A.T.J. de, Dijkstra, R., Schrijver, H., Nedelec, P. & Aben, E.A.A. (2012). Validation of six years of SCIAMACHY carbon monoxide observations using MOZAIC CO profile measurements. Atmospheric Measurement, 5(9), 2133-2142.

Laat, A.T.J. de, Dijkstra, R., Schrijver, H., Nedelec, P. & Aben, E.A.A. (2012). Validation of six years of SCIAMACHY carbon monoxide observations using MOZAIC CO profile measurements (vol 5, pg 2133, 2012). Atmospheric Measurement, 5(10), 2431-2431.

Lange, A. de, Dickenson, G.D., Salumbides, E.J., Ubachs, W.M.G., Oliveira, N. de, Joyeux, D. & Nahon, L. (2012). VUV Fourier-transform absorption study of the Lyman and Werner bands in D-2. Journal of Chemical Physics, 136(23).

Meerakker, S.Y.T. van de, Bethlem, H.L., Vanhaecke, N. & Meijer, G. (2012). Manipulation and Control of Molecular Beams. Chemical Reviews, 112(9), 4828-4878.

Morgenweg, J. & Eikema, K.S.E. (2012). A 1.8 mJ, picosecond Nd:YVO4 bounce amplifier pump front-end system for high-accuracy XUV-frequency comb spectroscopy. Laser Physics Letters, 9(11), 781-785.

Morgenweg, J. & Eikema, K.S.E. (2012). Tailored pulse sequences from an 880 nm pumped Nd:YVO4 bounce amplifier. Optics Letters, 37(2), 208-210.

Nijs, A.J. de & Bethlem, H.L. (2012). On deflection fields, weak-focusing and strong-focusing storage rings for polar molecules. Physical Chemistry Chemical Physics - PCCP, 13, 19052-19058.

Nijs, A.J. de, Ubachs, W.M.G. & Bethlem, H.L. (2012). Sensitivity of rotational transitions in CH and CD to a possible variation of fundamental constants. Physical Review A, 86(3).

Pang, X.Y., Fischer, D.G. & Visser, T.D. (2012). Generalized Gouy phase for focused partially coherent light and its implications for interferometry. Journal of the Optical Society of America. A: Optics, image science, and vision., 29(6), 989-993.

Pinkert, T.J., Salumbides, E.J., Tahvili, M.S., Ubachs, W.M.G., Bente, E.A.J.M. & Eikema, K.S.E. (2012). Frequency comb generation by CW laser injection into a quantum-dot mode-locked laser. Optics Express, 20(19), 21357-21371.

Quintero Perez, M., Jansen, P. & Bethlem, H.L. (2012). Velocity map imaging of a slow beam of ammonia molecules inside a quadrupole guide. Physical Chemistry Chemical Physics - PCCP, 14(27), 9630-9635.

Raghunathan, S.B., Schouten, H.F. & Visser, T.D. (2012). Correlation singularities in partially coherent electromagnetic beams. Optics Letters, 37(20), 4179-4181.

Raghunathan, S.B., Gan, C. H., Dijk, T. van, Kim, B.E., Schouten, H.F., Ubachs, W.M.G., Lalanne, P. & Visser, T.D. (2012). Plasmon switching: Observation of dynamic surface plasmon steering by selective mode excitation in a sub-wavelength slit. Optics Express, 20(14), 15326-15335.

Rooij, R. van (2012, juni 08). Frequency Metrology in Quantum Degenerate Helium. VU Vrije Universiteit. Prom./coprom.: prof. dr. W.M.G. Ubachs & dr. W. Vassen.

Ruehl, A., Gambetta, A., Hartl, I., Fermann, M.E., Eikema, K.S.E. & Marangoni, M. (2012). Widely-tunable mid-infrared frequency comb source based on difference frequency generation. Optics Letters, 37(12), 2232-2234.

Salumbides, E.J., Niu, M., Bagdonaite, J., Oliveira, N. de, Joyeux, D., Nahon, L. & Ubachs, W.M.G. (2012). CO A-X system for constraining cosmological drift of the proton-electron mass ratio. Physical Review A, 86(2).

Schenato, L., Palmieri, L., Gruca, G.L., Iannuzzi, D., Marcato, G., Pasuto, A. & Galtarossa, A. (2012). Fiber opticsensors for precursory acoustic signals detection in rockfall events. Journal of the European Optical Society. Rapid Publications, 7.

Schepers, D., Guerlet, S., Butz, A., Landgraf, J., Frankenberg, C., Hasekamp, O., Blavier, J.-F., Deutscher, N.M., Griffith, D.W.T., Hase, F., Kyro, E., Morino, I., Scherlock, V., Sussmann, R. & Aben, E.A.A. (2012). Methane retrievals from Greenhouse Gases Observing Satellite (GOSAT) shortwave infrared measurements: Performance comparison of proxy and physics retrieval algorithms. Journal of Geophysical Research, 117.

Tilstra, L.G., Graaf, M. de, Aben, E.A.A. & Stammes, P. (2012). In-flight degradation correction of SCIAMACHY UV reflectances and Absorbing Aerosol Index. Journal of Geophysical Research, 117.

Vassen, W., Cohen-Tannoudji, C., Leduc, M., Boiron, D., Westbrook, C.I., Truscott, A., Baldwin, K., Birkl, G., Cancio, P. & Trippenbach, M. (2012). Cold and trapped metastable noble gases. Reviews of Modern Physics, 84(1), 175-210.

Vassen, W., Knoop, S., Borbely, J. S. & Kokkelmans, S.J.J.M.F. (2012). Universal three-body parameter in ultracold 4He*. Physical Review A, 86.

Veefkind, J.P., Aben, E.A.A., McMullan, K., Forster, H., Vries, J. de, Otter, G., Claas, J., Eskes, H.J., Haan, J.F. de, Kleipool, Q., Weele, M. van, Hasekamp, O., Hoogeveen, R., Landgraf, J., Snel, R., Tol, P.J.J., Ingmann, P., Voors, R., Kruizinga, B., Vink, R. & Visser, H. (2012). TROPOMI on the ESA Sentinel-5 Precursor: A GMES mission for global observations of the atmospheric composition for climate, air quality and ozone layer applications. Remote Sensing of Environment, 120(SI), 70-83.

Vidot, J., Landgraf, J., Hasekamp, O.P., Butz, A., Galli, A., Tol, P.J.J. & Aben, E.A.A. (2012). Carbon monoxide from shortwave infrared reflectance measurements: A new retrieval approach for clear sky and partially cloudy atmospheres. Remote Sensing of Environment, 120(SI), 255-266.

Weber, A.C.J., Pizzirusso, A., Muccioli, L., Zannoni, C., Meerts, W.L., Lange, C.A. de & Burnell, E.E. (2012). Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics. Journal of Chemical Physics, 136(17).

Witte, S.M., Hickstein, D.D., Ranitovic, P., Tong, X.-M., Huismans, Y., Arpin, P., Zhou, X., Keister, K.E., Hogle, C.W., Zhang, B., Ding, C., Johnsson, P., Toshima, N., Vrakking, M.J.J., Murnane, M.M. & Kapteyn, H.C. (2012). Direct Visualization of Laser-Driven Electron Multiple Scattering and Tunneling Distance in Strong-Field Ionization. Physical Review Letters, 109, 073004.

Witte, S.M. & Eikema, K.S.E. (2012). Ultrafast Optical Parametric Chirped-Pulse Amplification. IEEE Journal of Selected Topics in Quantum Electronics, 18(1), 296-307.

Witte, S.M., Tenner, V.T., Noom, D.W.E. & Eikema, K.S.E. (2013). Coherent Lensless imaging with Ultra-Broadband Light Sources. In Proceedings of the XVIIIth International Conference on Ultrafast Phenomena.

Zhao, D., Linnartz, H.V.J. & Ubachs, W.M.G. (2012). The electronic spectrum of the Cs-C11H3 radical. Journal of Chemical Physics, 2012(136).

 

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