Publications


2019

A. Japaridze, C. Gogou, J. W. J. Kerssemakers, H. M. Nguyen, C. Dekker

Direct observation of independently moving replisomes in Escherichia coli

Nature Comm, submitted

L. Restrepo-Pérez, C. Heung Wong, G. Maglia, C. Dekker, C. Joo

Label-free detection of post-translational modifications with a nanopore

Nano Lett, submitted

F. Fanalista, J.W.J. Kerssemakers, C. Dekker

FtsZ bundle formation in cell-mimicking droplets

ACS Synth. Biol., under review

K.B. Smith, M. Wehrli, A. Japaridze, S. Assenza, C. Dekker, R. Mezzenga

Interplay between confinement and drag forces determine the fate of amyloid fibrils

Phys. Rev. Lett. submitted

L. Restrepo-Pérez, G. Huang , P.R. Bohländer, N. Worp, R. Eelkema, G. Maglia, C. Joo, C. Dekker

Resolving single amino acid modifications within a peptide using a biological nanopore

ACS Nano, submitted

S. Deshpande, C. Dekker

Synthetic life on a chip

Emerging Topics in the Life Sciences, in print

S. Deshpande, S. Wunnava, D. Hueting, C. Dekker

Membrane tension-mediated growth of liposomes

Small 1902898 (2019)

E. Kim, J. Kerssemakers, I.A. Shaltiel, C.H. Haering, C. Dekker

DNA-loop extruding condensins complexes can traverse one another

Nature, under review

M. Schaich, J. Cama, K. Al Nahas, D. Sobota, K. Jahnke, S. Deshpande, C. Dekker, U.F. Keyser

An integrated microfluidic platform for quantifying drug permeation across biomimetic vesicle membranes

Molec. Pharmac. 16, 2494-2501 (2019)

A.M.O. Elbatsh, E. Kim, J.M. Eeftens, J.A. Raaijmakers, R.H. van der Weide, S. Bravo,M. Ganji, J. uit de Bos, H. Teunissen, R.H. Medema, E. de Wit, C.H. Haering, C. Dekker, B.D. Rowland

Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation

Molec. Cell, in print

S. Zhao, L. Restrepo-Pérez, M. Soskine, G. Maglia, C. Joo, Cees Dekker, A. Aksimentiev

Electro-mechanical conductance modulation of a nanopore using a removable gate

ACS Nano 13, 2398-2409 (2019)

A. Fragasso, S. Pud, C. Dekker

1/f noise in solid-state nanopores is governed by access and surface regions

Nanotechn., 27 June 2019, doi: 10.1088/1361-6528/ab2d35.

Y. Kabiri, R.B.G. Ravelli, T. Lehnert, H. Qi, A.J. Katan, N. Roest, U. Kaiser, C. Dekker, P. Peters, H. Zandbergen

Visualization of unstained DNA nanostructures with advanced in-focus transmission electron microscopy techniques

Scientific Rep. 9, 7218 (2019)

F. Fanalista, A. Birnie, R. Maan, F. Burla, K. Charles, G. Pawlik, S. Deshpande, G.H. Koenderink, M. Dogterom, C. Dekker

Shape and size control of artificial cells for bottom-up biology

ACS Nano 13, 5439-5450 (2019)

D. Verschueren, X. Shi, C. Dekker

Nano-optical tweezing of single proteins in plasmonic nanopores

Small Methods 1800465 (2019)

K. Al Nahas, J. Cama, M. Schaich, K. Hammond, S. Deshpande, C. Dekker, M.G. Ryadnov, U.F. Keyser

A Microfluidic Platform for the Characterisation of Membrane Active Antimicrobials

Lab on a chip 19, 837 (2019)

A.J. Perez, Y. Cesbron, S.L. Shaw, J.B. Villicana, H.-C.T. Tsui, M.J. Boersma, Z.A. Ye, Y. Tovpeko, C. Dekker, S. Holden, M.E. Winkler

Movement dynamics of divisome proteins and PBP2x:FtsW in cells of Streptococcus pneumoniae

PNAS, 116, 3211-3220 (2019)

S. Deshpande, F. Brandenburg, A. Lau, W.K. Spoelstra, L. Reese, S. Wunnava, M. Dogterom, C. Dekker

Spatiotemporal control of coacervate formation within liposomes

Nature Comm. 10, 1800 (2019)

F.J.H. Hol, G.M. Whitesides, C. Dekker

Bacteria in Paper, a versatile platform to study bacterial ecology

Ecology Lett., doi: 10.1111/ele.13274 (2019)

F. Wu, P. Swain, L. Kuijpers, X. Zheng, K. Felter, M. Guurink, D. Chaudhuri, B. Mulder, C. Dekker

Cell boundary confinement sets the size and position of the E. coli chromosome

Current Biology, (2019)

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L. Loeff, J. Kerssemakers, C. Joo, C. Dekker

AutoStepfinder: a fast and automated step detection method for single-molecule analysis

Nature Protocols, under review

F. Wu, A. Japaridze, X. Zheng, J.W.J. Kerssemakers, C. Dekker

Direct imaging of the circular chromosome in a live bacterium

Nature Commun. 10, 2194 (2019)

2018

X. Shi, D.V. Verschueren, C. Dekker

Active delivery of single DNA molecules into a plasmonic nanopore for label-free optical sensing

Nano Lett. 18 , 8003 (2018)

D.V. Verschueren, S. Pud, X. Shi, L. de Angelis, L. Kuipers, C. Dekker

Label-free optical detection of DNA translocations through plasmonic nanopores

ACS Nano 13, 61-70 (2019)

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W. Yang, L. Restrepo-Pérez, M. Bengtson, S.J. Heerema, A. Birnie, J. van der Torre, C. Dekker

Detection of CRISPR-dCas9 on DNA with solid-state nanopores

Nano Lett. 18, 6469-6474 (2018)

C. Dekker

How we made the carbon nanotube transistor

Nature Electr. 1, 518 (2018)

F. Fanalista, S. Deshpande, A. Lau, G. Pawlik, C. Dekker

FtsZ-induced Shape Transformation of Coacervates

Advanced Biosystems 1800136 (2018)

Y. Kabiri, A. Angelin, I. Ahmed, H. Mutlu, J. Bauer, C.M. Niemeyer, H. Zandbergen, C. Dekker

Intercalating electron dyes for TEM visualization of DNA at the single-molecule level

Chembiochem, doi: 10.1002/cbic.201800638, online Nov.30 2018

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S. Caneva, P. Gehring, V.M. García-Suárez, A. García-Fuente, D. Stefani, I.J. Olavarria-Contreras, J. Ferrer, Cees Dekker, H.S.J. van der Zant

Mechanically Controlled Quantum Interference in Graphene Break Junctions

Nature Nanotechn. 13, 1126–1131 (2018)

P. Cadinu, G. Campolo, S. Pud, J.B. Edel, C. Dekker, A.P. Ivanov

Double barrel nanopores as a new tool for controlling single-molecule transport

Nano Lett. 18 2738–2745 (2018)

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M. Ganji, I.A. Shaltiel, S. Bisht, E. Kim, A. Kalichava, C.H. Haering, C. Dekker

Real-time imaging of DNA loop extrusion by condensin

Science 360, 102-105 (2018)

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D.V. Verschueren, W. Yang, C. Dekker

Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes

Nanotechnology 29, 145302 (2018)

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S.J. Heerema, L. Vicarelli, S. Pud, R.N. Schouten, H.W. Zandbergen, C. Dekker

Probing DNA translocations with inplane current signals in a graphene nanoribbon with a nanopore

ACS Nano 12, 2623–2633 (2018)

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Y. Caspi and C. Dekker

Dividing the archaeal way: the ancient Cdv cell-division machinery

Frontiers in Microbiology 9, 174 (2018)

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S. Deshpande, K. Spoelstra, M. van Doorn, Jacob Kerssemakers, C. Dekker

Mechanical division of cell-sized liposomes

ACS Nano 12, 2560–2568 (2018)

A. Ananth, M. Genua, N. Aissaoui, L. Díaz, N.B. Eisele, S. Frey, C. Dekker, R.P. Richter, D. Görlich

Reversible Immobilization of Proteins in Sensors and Solid-state Nanopores

Small 14, 1703357 (2018)

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S. Deshpande and C. Dekker

On chip microfluidic production of cell-sized liposomes

Nature Protocols 13 856–874 (2018)

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P. Ketterer, A.N. Ananth, D. Laman Trip, A. Mishra, E. Bertosin, M. Ganji, J. van der Torre, P. Onck, H. Dietz, C. Dekker

DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

Nature Comm. 9, 902 (2018)

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S.H. Kim, M. Ganji, J. van der Torre, E. Abbondanzieri, C. Dekker

DNA sequence encodes the position of DNA supercoils

eLife 7:e36557 (2018)

L. Restrepo-Pérez, C. Joo, C. Dekker

Paving the Way to Single-Molecule Protein Sequencing

Nature Nanotechn. 13, 786–796 (2018)

A.N. Ananth, A. Mishra, S. Frey, A. Dwarakasing, R. Versloot, E. Van der Giessen, D. Gorlich, P. Onck, C. Dekker

Spatial structure of disordered proteins dictates conductance and selectivity in Nuclear Pore Complex mimics

eLife, 7, e31510 (2018)

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2017

X. Shi, D. Verschueren, S. Pud, C. Dekker

Integrating sub-3nm plasmonic gaops into solid-state nanopores

Small 1703307 (2017)

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K. Spoelstra, S. Deshpande, C. Dekker

Tailoring the appearance: what will synthetic cells look like?

Current Opinions in Biotechnology 51, 47 (2018)

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J.M. Eeftens and C. Dekker

Catching DNA with hoops – biophysical approaches to clarify the mechanism of SMC proteins

Nature Struct. Molec. Biol. 24, 1012 (2017)

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J.M. Eeftens, S. Bisht, J. Kerssemakers, C.H. Haering, C. Dekker

Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism

EMBO J. e201797596 (2017)

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M. Neklyudova, A. Erdamar, L. Vicarelli, S.J. Heerema, T. Rehfeldt, G. Pandraud, Z. Kolahdouz, C. Dekker, H.W. Zandbergen

Through-membrane electron-beam lithography for ultrathin membrane applications

Appl. Phys. Lett. 111, 063105 (2017)

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T. Terakawa, S. Bisht, J.M. Eeftens, C. Dekker, C.H. Haering, E.C. Greene

The condensin complex is a mechanochemical motor that translocates along DNA

Science, eaan6516 (2017)

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S. Deshpande, A. Birnie, C. Dekker

On-chip density-based purification of liposomes

Biomicrofluidics, 11, 034106 (2017)

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Y. Kabiri, A.N. Ananth, J. van der Torre, A. Katan, J.-Y. Hong, S. Malladi, J. Kong, H. Zandbergen, C. Dekker

Distortion of DNA origami on graphene imaged with advanced TEM techniques

Small 1700876 (2017)

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R. Vlijm, S. H. Kim, P. de Zwart, Y. Dalal, C. Dekker

The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes

Nanoscale, 9, 1862 – 1870 (2017)

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J. Wiktor, M. van der Does, L. Buller, D.J. Sherratt, C. Dekker

Direct observation of end resection by RecBCD during double-stranded DNA break repair in vivo

Nucl. Acid Res., 46, 1821 (2018)

L. Restrepo-Pérez, S. John, A. Aksimentiev, C. Joo, C. Dekker

SDS-Assisted Protein Transport Through Solid-State Nanopores

Nanoscale 9, 11685 (2017)

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A.W. Bisson-Filho, Y.-P. Hsu, G.R. Squyres, E. Kuru, F. Wu, C. Jukes, C. Dekker, S. Holden, M.S. VanNieuwenhze, Y.V. Brun, E.C. Garner

Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division

Science 355, 739-743 (2017)

D.R. Burnham, B. Nijholt, I. De Vlaminck, J. Quan, T. Yusufzai, C. Dekker

Annealing helicase HARP closes RPA-stabilised DNA bubbles non-processively

Nucl. Acid Res. 45, 4687-4695 (2017)

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Y. Nechemia-Arbely, D. Fachinetti, K. H. Miga, N. Sekulic, G. Soni, A. Karwei Wong, A. Young Lee, K. Nguyen, C. Dekker, B. Ren, B. E. Black, D. W. Cleveland

Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points

J Cell Biol., 216, 607 (2017)

2016

F. Wu, C. Dekker

Nanofabricated structures and microfluidic devices for bacteria: from techniques to biology

Chem. Soc. Rev. 45 268-280 (2016)

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F. Wu, J. Halatek, M Reiter, E. Kingma, E. Frey, C. Dekker

Multistability and dynamic transitions of intracellular Min protein patterns

Molecular Systems Biology 12 837 (2016)

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S.J. Heerema and C. Dekker

Graphene nanodevices for DNA sequencing

Nature Nanotechn. 11 127–136 (2016)

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J. Wiktor, C. Lesterlin, D. J. Sherratt, C. Dekker

CRISPR-mediated control of the bacterial initiation of replication

Nucleic Acids Research 44 3801-10 (2016)

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S. Deshpande, Y. Caspi, A. Meijering, C. Dekker

Octanol-assisted liposome assembly: A robust method to produce liposomes on chip

Nature Commun. 7 10447 (2016)

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C. Plesa, D. Verschueren, J.W. Ruitenberg, M.J. Witteveen, M.P. Jonsson, A.Y. Grosberg, Y. Rabin, C. Dekker

Direct observation of DNA knots using solid state nanopores

Nature Nanotechn. 11 1093–1097 (2016)

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F.J.H. Hol, O. Rotem, E. Jurkevitch, C. Dekker, D.A. Koster

Predator-prey dynamics in micro-scale patchy landscapes

Proc. Roy. Soc. B 283, 20152154 (2016)

S. McGinn et al

New Technologies for DNA analysis

New Biotechnology 33 311 (2016)

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M. Ganji, S. H. Kim, J. van der Torre, E. Abbondanzieri, C. Dekker

Intercalation-based single-molecule fluorescence assay to study DNA supercoil dynamics

Nano Lett. 16 4699 (2016)

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S.H. Kim, R. Vlijm, J. van der Torre, Y. Dalal, C. Dekker

CENP-A and H3 nucleosomes display a similar stability to force-mediated disassembly

Plos One 11 e0165078 (2016)

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S. Pud, S.-H. Chao, M. Belkin, D. Verschueren, T. Huijben, C. van Engelenburg, Cees Dekker, A.. Aksimentiev

Mechanical Trapping of DNA in a Double-Nanopore System

Nano Lett. 16, 8021 (2016) PDF

J.M. Eeftens, A.J. Katan, M. Kschonsak, M. Hassler, L. de Wilde, E.M. Dief, C. Haering, C. Dekker

Condensin Smc2–Smc4 dimers are flexible and dynamic

Cell Reports 14 1813-8 (2016)

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2015

S. Pud, D. Verschueren, N. Vukovic, C. Plesa, M.P. Jonsson,C. Dekker

Self-aligned plasmonic nanopores by optically controlled dielectric breakdown

Nano Lett. 15, 7112-7 (2015) PDF

F. Wu, B.G.C. van Schie, J. E. Keymer, C. Dekker

Symmetry and scale orient Min protein patterns in shaped bacterial sculptures

Nature Nanotechn. 10, 719–726 (2015) PDF SI videos News and Views On The Cover

C. Plesa, N. van Loo,C. Dekker

DNA nanopore translocation in glutamate solutions

Nanoscale 7 13605-13609 (2015)

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J. Eeftens, J. van der Torre, D.R. Burnham, C. Dekker

Copper-free click chemistry for attachment of biomolecules in magnetic tweezers

BMC Biophys. 8 9 (2015)

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F.J.H. Hol, B. Hubert, C. Dekker, J.E. Keymer

Density dependent adaptive resistance allows swimming bacteria to colonize an antibiotic gradient

Int. Soc. Microb. Ecol. J. 10, 30 (2015) Advance Online Publication

F. J.H. Hol, P. Galajda, R.G. Woolthuis, C. Dekker, J.E. Keymer

The idiosyncrasy of spatial structure in bacterial competition

BMC research notes, 8, 245 (2015)

A.C. Ferrari et al

Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems

Nanoscale 7 4598-4810 (2015)

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R. Vlijm, M. Lee, J. Lipfert, A. Lusser, C. Dekker, N.H. Dekker

Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes

Cell Reports 10 216 – 225 (2015)

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M. Belkin, S.-H. Chao, M. Jonsson, C. Dekker, A. Aksimentiev

Plasmonic nanopores for trapping, controlling displacement, and sequencing of DNA

ACS Nano9 10598–10611 (2015)

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F. Wu, E. van Rijn, B.G.C. van Schie, J.E. Keymer, C. Dekker

Multicolor imaging of the bacterial nucleoid and cell division proteins with blue, orange, and near-infrared fluorescent proteins

Frontiers Microbiol. 6 607 (2015)

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L. Vicarelli, S.J. Heerema, C. Dekker, H.W. Zandbergen

Controlling defects in graphene for optimizing the electrical properties of graphene nanodevices

ACS Nano 4 3428 (2015)

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R. Vlijm, A. Mashaghi, S. Bernard, M. Modesti, C. Dekker

Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence,

Nanoscale 7 3205-3216 (2015)

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M. Muthukumar, C. Plesa, C. Dekker

Single-molecule sensing with nanopores

Physics Today 68, 40 (2015) Physics Today On The Cover

S.J. Heerema, G.F. Schneider, M. Rozemuller, L. Vicarelli, H. W. Zandbergen and C. Dekker

1/f noise in graphene nanopores

Nanotechn. 26 074001 (2015)

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C. Plesa, C. Dekker

Data analysis methods for solid-state nanopores

Nanotechn. 26 084003 (2015)

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R. Vlijm, M. Lee, O. Ordu, A. Boltengagen, A. Lusser, N.H. Dekker, C. Dekker

Comparing the assembly and handedness dynamics of (H3.3-H4)2 tetrasomes to canonical tetrasomes

Plos One 10 e0141267 (2015)

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C. Plesa, J.W. Ruitenberg, M.J. Witteveen, C. Dekker

Detection of individual proteins bound along DNA using solid state nanopores

Nano Lett. 15 3153–3158 (2015)

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Y. Li, F. Nicoli, C. Chen, L. Lagae, G. Groeseneken, T. Stakenborg, C. Dekker, P. Van Dorpe, M.P. Jonsson

Photoresistance Switching of Plasmonic Nanopores

Nano Lett. 15 776–782 (2015)

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C. Plesa, N. van Loo, P. Ketterer, H. Dietz, C. Dekker

Velocity of DNA during translocation through a solid state nanopore

Nano Lett. 15 732–737 (2015)

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T.R. Blosser, L. Loeff, E.R. Westra, M. Vlot, T. Künne, M. Sobota, C. Buyzerd, C. Dekker, S.J.J. Brouns, C. Joo

Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex

Molec. Cell 58 60–70 (2015)

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2014

F.J.H. Hol and C. Dekker

Zooming in to see the bigger picture: using nanofabrication to study bacteria

Science 346 1251821 (2014)

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F. Nicoli, D. Verschueren, C. Dekker, M. P. Jonsson

DNA Translocation through Solid-State Plasmonic Nanopores

Nano Lett. 14, 6917–6925 (2014)

D.R. Burnham, I. De Vlaminck, T. Henighan, C. Dekker

Skewed Brownian fluctuations in single-molecule magnetic tweezers

Plos One 9 e108271 (2014)

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J.W.J. Kerssemakers, T.R. Blosser, C. Dekker

A simple self-calibrating method to measure the height of fluorescent molecules and beads with nanometer resolution

Nano Lett. 14 4469 (2014)

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A.J. Katan, R. Vlijm, A. Lusser, C. Dekker

Dynamics of nucleosomal structures measured by high-speed Atomic Force Microscopy

Small 8 976–984 (2014)

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Y. Caspi and C. Dekker

Divided we stand: splitting synthetic cells for their proliferation

Systems and Synthetic Biology 8 249-269 (2014)

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FJH Hol, MJ Voges, C Dekker, JE Keymer

Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community

BMC Biology 12:70 (2014)

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A. Mashaghi and C. Dekker

Systems and synthetic biology approaches to cell division

Systems and Synthetic Biology 8 173–178 (2014)

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2013

M.T.J. van Loenhout, I. De Vlaminck, B. Flebus, J.F. den Blanken, L. Zweiffel, K.M. Hooning, J.W.J. Kerssemakers, C. Dekker

Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers

Plos One 8 e65329 (2013)

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C. Plesa, S.W. Kowalczyk, R. Zinsmeester, A. Y. Grosberg, Y. Rabin, C. Dekker

Fast Translocation of Proteins through Solid State Nanopores

Nano Lett. 13 658 (2013)

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M.P. Jonsson , C. Dekker

Electrical Profiling of Optical Intensity Landscapes with a Plasmonic Nanopore

Nano Lett. 13 1029 (2013)

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G.V. Soni, M.P. Jonsson , C. Dekker

Periodic modulation of optical tweezers near solid-state membranes

Small 9 679 (2013)

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Q. Xu, M.Y. Wu, G. Schneider, L. Houben, S. Malladi, C. Dekker, E. Yucelen, R. E. Dunin-Borkowski, H.W. Zandbergen

Controllable Atomic Scale Patterning of Freestanding Monolayer Graphene at Elevated Temperature

ACS Nano 7 1566-1572 (2013)

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G.F. Schneider, Q. Xu, S. Hage, S. Luik, J.N.H. Spoor, S. Malladi, H. Zandbergen C. Dekker

Tailoring the hydrophobicity of graphene nanopores

Nature Communications 4 2619 (2013)

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A. Mashaghi, A. Katan

A physicist’s view of DNA

De Physicus 24e 3 59-61 (2013)

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C. Plesa, A. Ananth, V. Linko, C. Gülcher, A. Katan, H. Dietz, C. Dekker

Ionic permeability and mechanical properties of DNA origami nanoplates on solid-state nanopores

ACS Nano 8 35–43 (2014)

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C. Plesa, L. Cornelissen, M.W. Tuijtel, C. Dekker

Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore

Nanotechnology 24 475101 (2013)

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F. J.H. Hol, P. Galajda, K. Nagy, R.G. Woolthuis, C. Dekker, J.E. Keymer

Spatial structure facilitates cooperation in a social dilemma: empirical evidence from a bacterial community

Plos One 8: e77042. doi:10.1371/journal.pone.0077042 (2013)

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2012

I. De Vlaminck and C. Dekker

Recent Advances in Magnetic Tweezers

Ann. Rev. Biophys. 41 453 (2012)

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I. De Vlaminck, Th. Henighan, M.T.J. van Loenhout, D. Burnham, C. Dekker

Magnetic forces and DNA mechanics in multiplexed magnetic tweezers

PLOS One 7 e41432 (2012)

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J. Männik, F. Wu, F.J.H. Hol, P. Bissichia, D. Sherratt, J.E. Keymer, C. Dekker

Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes

Proc. Natl. Acad. Sci. (USA) 109 6957 (2012)

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M.T.J. van Loenhout, J. Kerssemakers , I. De Vlaminck, C. Dekker

Non-bias-limited tracking of spherical particles, enabling nanometer resolution at low magnification

Biophys. J. 102 Issue 10 2362 (2012)

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I. De Vlaminck, M. T.J. van Loenhout, L. Zweifel, J. den Blanken, K. Hooning, S. Hage, J. Kerssemakers, C. Dekker

Mechanism of homology recognition in DNA recombination from dual-molecule experiments

Molec. Cell 46 616 (2012)

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S.W. Kowalczyk, D.B. Wells, A. Aksimentiev, C. Dekker

Slowing down DNA translocation through a nanopore in lithium chloride

Nano Lett.12 1038 (2012)

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A.R. Hall, J.M. Keegstra, M.C. Duch, M.C. Hersam, C. Dekker

Measuring Single-Wall Carbon Nanotubes with Solid-State Nanopores

Book chapter in ‘Nanopore-based technology: single molecule characterization and DNA sequencing’, (Ed. M. Gracheva,; Humana Press, 2011) as the volume on “Nanopore Sequencing technology” in the series ‘Methods in Molecular biology ‘ (series editor J.M. Walker) Volume 870, 2012, DOI: 10.1007/978-1-61779-773-6, p. 227-239 (2012)

R. Vlijm, J. S.J. Smitshuijzen, A. Lusser, C. Dekker

NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers

PLOS One 7 e46306 (2012)

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S.W. Kowalczyk and C. Dekker

Salt and voltage dependence of the conductance blockade induced by translocation of DNA and RecA filaments through solid-state nanopores

in ‘Nanopores for bioanalytical applications’, Edited by J. Edel and T. Albrecht (Royal Society Chemisty, 2012)

V.E. Calado, G.F. Schneider, A.M.M.G. Theulings, C. Dekker, L.M.K. Vandersypen

Formation and control of wrinkles in graphene by the wedging transfer method

Appl. Phys. Lett. 101 103116 – 103116-3 (2012)

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M.T.J. van Loenhout, M.V. de Grunt, C. Dekker

Dynamics of DNA supercoils

Science 338 94-97 (2012)

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X.J.A. Janssen, M.P. Jonsson, C. Plesa, G.V. Soni, C. Dekker, N.H. Dekker

Rapid manifacturing of low-noise membranes for nanopore sensors by Trans-chip Illumination Lithography

Nanotechnology 23 475302 (2012)

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S.W. Kowalczyk and C. Dekker

Measurement of the docking time of a DNA molecule onto a solid-state nanopore

Nano Lett. 12 4159-63 (2012)

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G.V. Soni and C. Dekker

Detection of Nucleosomal Substructures using Solid State Nanopores

Nano Lett. 12 3180 (2012)

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F. Hol and C. Dekker

Bacteriën in nanokanalen en micro-steden

Ned. Tijdschr. Natuurk. 78, 240 (2012)

G. Schneider and C. Dekker

DNA sequencing with nanopores

Nature Biotechn. 30 326 (2012)

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C. Dekker

Als fysicus aan de slag in de nanobiologie

Ned. Tijdschr. Natuurk. 78, 286 (2012)

2011

I. De Vlaminck, Th. Henighan, M.T.J. van Loenhout, I. Pfeiffer, J. Huijts, J. Kerssemakers, A. Katan, A. van Langen-Suurling, E. van der Drift, Claire Wyman, C. Dekker

Highly parallel magnetic tweezers by targeted DNA tethering

Nano Lett. 11 5489 (2011)

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A.J. Katan and C. Dekker

High-speed AFM reveals the dynamics of single biomolecules at the nanometer scale

Cell 147 979-982 (2011)

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S.W. Kowalczyk and C. Dekker

Nanogaatjes voor DNA-analyse

Nederlands Tijdschrift voor Natuurkunde 77(5) 2011

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S.W. Kowalczyk, A.Y. Grosberg, Y. Rabin, C. Dekker

Modeling the conductance and DNA blockade of solid-state nanopores

Nanotechnology 22 (2011) 315101. PDF Supplementary Material

A.R. Hall, J. M. Keegstra, M. C. Duch, M. C. Hersam, C. Dekker

Translocation of Single-Wall Carbon Nanotubes Through Solid-State Nanopores

Nano Lett. 11 2446-50 (2011)

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Stefan W. Kowalczyk, Timothy R. Blosser, Cees Dekker

Biomimetic nanopores: learning from and about nature

Trends in Biotechnology. 29 607-614 (2011)

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B. Song, G.F. Schneider, Q. Xu, G. Pandraud, C. Dekker, H. Zandbergen

Atomic-scale electron-beam sculpting of defect-free graphene nanostructures

Nano Lett. 11 2247–2250 (2011)

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A.R. Hall and C. Dekker

Molecular Detection and Force Spectroscopy in Solid-State Nanopores with Integrated Optical Tweezers

Book chapter to be published in ‘Nanopores: Sensing Fundamental Biological Interactions at the Single Molecule Level’ (Eds. R. Bashir, S. Iqbal; Springer, 2011).

J.T. Holthausen, M. van Loenhout, H. Sanchez, D. Ristic, S.i van Rossum-Fikkert, M. Modesti, T. Thorslund, S.C. West, C. Dekker, R. Kanaar, C. Wyman

Effect of the BRCA2 CTRD domain on RAD51 filaments analyzed by an ensemble of single molecule techniques

Nucl. Acid Res.39 6558 (2011)

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S.W. Kowalczyk, L. Kapinos, T.R. Blosser, T. Magalhaes, P. van Nies,R.Y.H. Lim, C. Dekker

Single-molecule transport across an individual biomimetic nuclear pore complex

Nature Nanotechnology 6, 433–438 (2011). PDF Supplementary Material

2010

I. Heller, S. Chatoor, J. Männik, M.A.G. Zevenbergen, J.B. Oostinga, A.F. Morpurgo, C. Dekker, S.G. Lemay

Charge Noise in Graphene Transistors

Nano Lett. 10 1563–1567 (2010)

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S.W. Kowalczyk, A.R. Hall, C. Dekker

Detection of local protein structures along DNA using solid-state nanopores

Nano Lett. 10 324–328 (2010)

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I. Dujovne, J. Kerssemakers, G. Cappello, C. Dekker

Interference technique for minimally invasive, subnanometer, microsecond measurements of displacements

Rev. Sci. Instrum. 81 016103 (2010)

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D. Stein, Z. Deurvorst, F.H.J. van der Heyden, W.J.A. Koopmans, A. Gabel, C. Dekker

Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

Nano Lett. 10 765–772 (2010)

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M. van den Hout, A.R. Hall, M.-Y. Wu, H.W. Zandbergen, C. Dekker, N.H. Dekker

Controlling Nanopore Size, Shape, and Stability

Nanotechnology 21 115304 (2010)

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I. De Vlaminck, I. Vidic, M. van Loenhout, R. Kanaar, J.H.G. Lebbink, C. Dekker

Torsional regulation of hRPA-induced unwinding of double stranded DNA

Nucl. Acid Res. 38 4133-4142 (2010)

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J. Männik, F. Sekhavati, J. E. Keymer, C. Dekker

Bacteria in submicron channels and microvalves

Proc. μTAS2010 (14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 3-7 October 2010 Groningen The Netherlands) p. 1376-1378 (2010)

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A .R. Hall, J.M. Keegstra, M.C. Duch, M.C. Hersam, C. Dekker

Measuring Single-Wall Carbon Nanotubes with Solid-State Nanopores

Book chapter to be published in ‘Nanopore-based technology: single molecule characterization and DNA sequencing’, (Ed. M. Gracheva,; Humana Press, 2011) as the volume on “Nanopore Sequencing technology” in the series ‘Methods in Molecular biology ‘ (series editor J.M. Walker)

I. Heller, S. Chatoor, J. Männik, M.A.G. Zevenbergen, C. Dekker, S.G. Lemay

Influence of electrolyte composition on liquid-gated carbon-nanotube and graphene transistors

J. Am. Chem. Soc. 132 17149–17156 (2010)

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G.F. Schneider, S.W. Kowalczyk, V. E. Calado, G. Pandraud, H. Zandbergen, L.M.K. Vandersypen, C. Dekker

DNA translocation through graphene nanopores

Nano Lett. 10 3163–3167 (2010)

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A.R. Hall, A. Scott, D. Rotem, K.l Mehta, H. Bayley, C. Dekker

Hybrid pore formation by directed insertion of alpha hemolysin into solid-state nanopores

Nature Nanotechnology 5 874–877 (2010)

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G.F. Schneider, V.E. Calado, H. Zandbergen, L.M.K. Vandersypen, C. Dekker

Wedging transfer of nanostructures

Nano Lett. 10 1912–1916 (2010)

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S.W. Kowalczyk, M.W. Tuijtel, S.P. Donkers, C. Dekker

Unraveling Single-Stranded DNA in a Solid-State Nanopore

Nano Lett 10 1414–1420 (2010)

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J. Männik, F. Sekhavati, J. E. Keymer, C. Dekker

Bacteria in submicron channels and microvalves

Proc. μTAS2010 (14th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 3-7 October 2010, Groningen, The Netherlands), p. 1376-1378 (2010) PDF

2009

M.Y. Wu, R.M.M Smeets, M. Zandbergen, U. Ziese, D. Krapf, P.E. Batson, N.H. Dekker, C. Dekker, H.W. Zandbergen

Control of Shape and Material Composition of Solid-State Nanopores

Nano Letters 9 479-484 (2009)

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R.M.M Smeets, S.W. Kowalczyk, A.R. Hall, N.H. Dekker, C. Dekker

Translocation of RecA-coated Double-Stranded DNA Through Solid-State Nanopores

Nano Letters 9 (9): 3089-3095 (2009)

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I. Heller, J. Mannik, S.G. Lemay, C. Dekker

Optimizing the Signal-to-Noise Ratio for Biosensing with Carbon Nanotube Transistors

Nano Letters 9 377-382 (2009)

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R.M.M. Smeets, N.H. Dekker, C. Dekker

Low Frequency Noise in Solid-State Nanopores

Nanotechnology 20 095501 (2009)

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A.R. Hall, S. van Dorp, S.G. Lemay, C. Dekker

Electrophoretic Force on a Protein-Coated DNA Molecule in a Solid-State Nanopore

Nano Letters 9 4441-4445 (2009)

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I. Heller, W.T.T. Smaal, S.G. Lemay, C. Dekker

Probing macrophage activity with carbon nanotube sensors

Small 5 2528-2532 (2009)

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I.Heller, S. Chatoor, J. Männik, M. A. G. Zevenbergen, C. Dekker, S. G. Lemay

Comparing the weak and strong gate-coupling regimes for nanotube and graphene transistors

Physica Status Solidi – Rapid Research Letters 3 190 – 192 (2009)

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D. Stein, M.G.L. van den Heuvel, C. Dekker

Transport of ions, DNA polymers, and microtubules in the nanofluidic regime

Book chapter in ‘Nanofluidics: nanoscience and nanotechnology’ edited by J.B. Edel and A.J. deMello (RSC Publ Cambridge 2009) p. 1-30

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M.T.J. van Loenhout, T. van der Heijden, R. Kanaar, C. Wyman, C. Dekker

Dynamics of RecA filaments on single stranded DNA

Nucleic Acids Research 37 4089-4099 (2009)

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J. Männik, R. Driessen, P. Galajda, J. E. Keymer, C. Dekker

Bacterial Growth and Motility in Sub-Micron Constrictions

Proceedings of the National Academy of Sciences 106 (35) 14861-6 (2009)

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G.M. Skinner, M. van den Hout, O. Broekmans, C. Dekker, N.H. Dekker

Distinguishing Nucleic Acids Using Solid-State Nanopores

Nano Letters, 9 (8), 2953-2960 (2009) PDF Supporting Information

S. van Dorp, U.F. Keyser, N.H. Dekker, C. Dekker, Serge G. Lemay

Origin of the electrophoretic force on DNA in solid-state nanopores

Nature Physics 5 347-351 (2009)

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2008

R. Smeets, U. F. Keyser, N. H. Dekker, C. Dekker

Noise in Solid-state Nanopores

Proceedings of the National Academy of Sciences

I. Heller, A. M. Janssens, J. Männik, E. D. Minot, S. G. Lemay, C. Dekker

Identifying the Mechanism of Biosensing with Carbon Nanotube Transistors

Nano Letters 8 (2) 591-595 (2008)

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M.G.L. van den Heuvel, M.P. de Graaff, C. Dekker

Microtubule curvatures under perpendicular electric forces reveal a low persistence length

Proceedings of the National Academy of Sciences 105: 7941-6 (2008)

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J. Männik, I. Heller, A.M. Jannsens, S.G. Lemay, C. Dekker

Charge noise in liquid-gated single-wall carbon nanotube Transistors

Nano Letters 8 (2) 685-688 (2008)

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F.J.M. Hoeven, F.S. Meijer, C. Dekker, S.P.J. Albracht, H.A. Heering, S.J. Lemay

Towards single-enzyme voltammetry: [NiFe]-hydrogenase protein film voltammetry at nanoelectrodes

ACS Nano 2 , 2497–2504 (2008)

E. Šišáková, M. Weiserová, C. Dekker, R. Seidel, M. D. Szczelkun

The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I

J. Mol. Biol. 384, 1273–1286 (2008)

M.G.L. van den Heuvel, R. Bondesan, M. Cosentino Lagomarsino, C. Dekker

Single-molecule observation of anomalous electro-hydrodynamic orientation of microtubules

Phys. Rev. Lett.. 101, 118301 (2008)

P. McEuen and C. Dekker

Synthesizing the future

ACS Chemical Biology 3, 10–12 (2008)

I. Dujovne, M. van den Heuvel, Y. Shen, M. de Graaff, C. Dekker

Velocity Modulation of Microtubules in Electric Fields

Nano Letters 8 (12) 4217-4220 (2008)

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M. van den Hout, S. Hage, C. Dekker, N.H. Dekker

End-Joining Long Nucleic Acid Polymers

Nucleic Acids Research 36e104 (2008)

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D.J. Bonthuis, C. Meyer, D. Stein, C. Dekker

Conformation and dynamics of DNA confined in slit-like nanofluidic channels

Phys. Rev. Lett. 101, 108303 (2008)

T. van der Heijden and C. Dekker

Monte Carlo simulations of protein assembly, disassembly, and linear motion on DNA

Biophysical Journal, doi:10.1529/biophysj.108.135061, (2008) PDF Monte Carlo code

T. van der Heijden, M. Modesto, S. Hage, R. Kanaar, C. Wyman, C. Dekker

Homologous recombination in real time: DNA strand exchange by RecA

Molecular Cell, 30, 530-538 (2008) PDF Supplementary Material

F.J.M. Hoeben, I. Heller, S.P.J. Albracht, C. Dekker, S.G. Lemay, H.A. Heering

Polymyxin-coated Au and carbon nanotube electrodes for stable [NiFe]-hydrogenase film voltammetry

Langmuir 24 5925-5931 (2008)

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2007

T. van der Heijden, R. Seidel, M. Modesti, R. Kanaar, C. Wyman, C. Dekker

Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules

Nucleic Acids Research 35: 5646-5657 (2007): doi: 10.1093/nar/gkm629 (2007)

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E.D. Minot, A.M. Janssens, I. Heller, H.A. Heering, C. Dekker, S. G. Lemay

Carbon nanotube biosensors: the critical role of the reference electrode

Applied Physics Letters

M.G.L. van den Heuvel, S. Bolhuis, C. Dekker

Persistance length measurement from stochastic single-molecule trajectories

Nano Letters

B.J. LeRoy, I. Heller, V.K. Pahilwani, C. Dekker, S.G. Lemay

Simultaneous electrical transport and scanning tunneling spectroscopy of carbon nanotubes

Nano Letters : Accepted (2007)

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M.G.L. van den Heuvel, C. Dekker

Motor Proteins at Work for Nanotechnology

Science 317: 333-336 (2007)

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F.H.J. van der Heyden, D.J. Bonthuis, D. Stein, C. Meyer, C. Dekker

Power Generation by Pressure-Driven Transport of Ions in Nanofluidic Channels

Nano Letters 7: 1022-1025 (2007)

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M. Modesti, D. Ristic, T. van der Heijden, C. Dekker, J. van Mameren, E.J.G. Peterman, G.J.L. Wuite, R. Kanaar, C. Wyman

Fluorescent Human RAD51 Reveals Multiple Nucleation Sites and Filament Segments Tightly Associated along a Single DNA Molecule

Structure

T. van der Heijden, F. Moreno-Herrero, R. Kanaar, C. Wyman, C. Dekker

AFM Tip-Induced Dissociation of RecA-dsDNA Filaments

NanoLetters

C. Dekker

Solid-State Nanopores

Nature Nanotechnology 2 (4): 209-215 (2007)

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P.A. Wiggins, T. Van der Heijden, F. Moreno-Herrero, A. Spakowitz, R. Phillips, J. Widom, C. Dekker, P.C. Nelson

High flexibility of DNA on short length scales probed by atomic force microscopy

Nature Nanotechn. 1, 137-141 (2006)

M.G.L. van den Heuvel, M.P. de Graaff, S.G. Lemay, C. Dekker

Electrophoresis of individual Microtubules in Microchannels

Proceedings of the National Academy of Science USA 104 (19): 7770-7775 (2007)

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2006

M.G.L. van den Heuvel, M.P. de Graaff, C. Dekker

Op afstand bestuurbare eiwit

Nederlands Tijdschrift voor Natuurkunde 1-4 September 2006

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S. Sapmaz, P. Jarillo-Herrero, Ya. M. Blanter, C. Dekker, and H.S.J. van der Zant

Tunneling in suspended carbon nanotubes assisted by stretching modes

Physical Review Letters

D. Krapf, M.Y. Wu, R. M. M. Smeets, H. W. Zandbergen, C. Dekker, S.G. Lemay

Fabrication and Characterization of Nanopore-Based Electrodes with Radii down to 2 nm.

Nano Letters

R.M.M. Smeets, U.F. Keyser, D. Krapf, M.Y. Wu, N.H. Dekker, C. Dekker

Salt dependence of ion transport and DNA translocation through solid-state nanopores.

Nano Letters

F.H.J. van der Heyden, D. Stein, K. Besteman, S.G. Lemay, C. Dekker

Charge inversion at high ionic strength studied by streaming currents

Physical Review Letters

P.A. Wiggins, T. van der Heijden, F.Moreno-Herrero, A. spakowitz, R. Phillips, J. Widom, C. Dekker, P.C. Nelson

High flexibility of DNA on short length scales probed by atomic force microscopy

Nature Nanotechnology

T. van der Heijden, F. Moreno-Herrero, R. Kanaar, C. Wyman, C. Dekker

Comment on: “Direct and Real-Time Visualization of the Disassembly of a Single RecA-DNA-ATP S Complex Using AFM Imaging in Fluid”

Nano Letters (1): 137-141 (2006) PDF

U. F. Keyser, J. van der Does, C. Dekker, N.H. Dekker

Optical tweezers for force measurements on DNA in nanopores

Review of Scientific Instruments

F.H.J. van der Heyden, D.J. Bonthuis, D. Stein, C. Meyer, C. Dekker

Electrokinetic energy conversion effciency in nanofluidic channels

Nano Letters

H. A. Heering, K.A. Williams, S. de Vries, C. Dekker

Specific Vectorial Immobilization of Oligonucleotide-Modified Yeast Cytochrome c on Carbon Nanotubes

ChemPhysChem

D. Krapf, B.M. Quinn, M.-Y. Wu, H.W. Zandbergen, C. Dekker, S.G. Lemay

Experimental observation of nonlinear ionic transport at the nanometer scale

Nano Letters

R.M.M. Smeets, U.F. Keyser, M.Y. Wu, N.H. Dekker, C. Dekker

Nanobubbles in solid-state nanopores

Physical Review Letters

I. Heller, J. Kong, K. A. Williams, C. Dekker, S.G. Lemay

Electrochemistry at Single-Walled Carbon Nanotubes: The Role of Band Structure and Quantum Capacitance

Journal of the American Chemical Society

L.K. Stanley, R. Seidel, C. van der Scheer, N.H. Dekker, M.D. Szczelkun, C. Dekker

When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I

EMBO Journal

P.D. Jarillo-Herrero, J.Kong, H.S.J. van der Zant, C. Dekker, L.P. Kouwenhoven, S. De Franceschi

Tunable orbital pseudospin and multi-level Kondo effect in carbon nanotubes

Properties of Novel Nanostructures AIP conference proceedings H Kuzmany, J Fink, M Mehring, & S Roth (Eds.) 786: 482-489 (2005) Kirchberg, Austria: AIP.

M.G.L. van den Heuvel, M.P. de Graaff, C. Dekker

Molecular sorting by electrical steering of microtubules in kinesin-coated channels

Science

D. Stein, F.H.J. van der Heyden, W. Koopmans, C. Dekker

Pressure-driven transport of DNA polymers confined in fluidic channels

Proceedings of the National Academy of Science USA 103 (43): 15853-15858 (2006)

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U.F. Keyser, B.N. Koeleman, D. Krapf, R.M.M. Smeets, S.G. Lemay, N.H. Dekker, C. Dekker

Direct force measurements on DNA in a solid-state nanopore

Nature Physics

2005

D.A. Koster, V. Croquette, C. Dekker, S. Shuman, N.H. Dekker

Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB

Nature

I. Heller, J. Kong, H. A. Heering, K. Williams, S. Lemay, C. Dekker

Individual single-walled carbon nanotubes as nanoelectrodes for electrochemistry

Nano Letters

M.G.L. van den Heuvel, C.T. Butcher, S.G. Lemay, S. Diez, C. Dekker

Electrical docking of microtubules for kinesin-driven motility in nanostructures

Nano Letters

J.A. Abels, F. Moreno-Herrero, T. van der Heijden, C. Dekker, N.H. Dekker

Single-Molecule Measurements of the Persistence Length of double-stranded RNA

Biophysical Journal

J. Kong, B.J. LeRoy, S.G. Lemay, C. Dekker

Integration of a gate electrode into carbon nanotube devices for scanning tunneling microscopy

Applied Physics Letters

S. Sapmaz, P. Jarillo-Herrero, J. Kong, C. Dekker, L.P. Kouwenhoven, H.S.J. van der Zant

Electronic excitation spectrum of metallic carbon nanotubes

Physical Review B

S.G. Lemay, D.M. van den Broek, A.J. Storm, D. Krapf, R.M.M. Smeets, H.A. Heering, C. Dekker

Lithographically fabricated nanopore-based electrodes for electrochemistry

Analytical Chemistry

A. J. Storm, C. Storm, J. Chen, H.W. Zandbergen, J.F. Joanny, C. Dekker

Fast DNA translocation through a solid-state nanopore

Nano Letters

H.W. Zandbergen, B.J.H.A. van Duuren, P.F.A. Alkemade, G. Lientschnig, O.Vasquez, C. Dekker, F.D. Tichelaar

Sculpting nano-electrodes with a transmission electron beam for electrical and geometrical characterization of nanoparticles.

Nano Letters

A.J. Storm, J. Chen, H.W. Zandbergen, C. Dekker

Translocation of double-strand DNA through a siliconoxide nanopore

Physical Review E

P. Jarillo-Herrero, J. Kong, H. S.J. van der Zant, C. Dekker, L. P. Kouwenhoven, S. De Franceschi

Electronic transport spectroscopy of carbon nanotubes in a magnetic field

Physical Review Letters

P. Jarillo-Herrero, J. Kong, H. S.J. van der Zant, C. Dekker, L. P. Kouwenhoven, S. De Franceschi

Orbital Kondo effect in carbon nanotubes

Nature

F. Moreno-Herrero, L. Holtzer, D. Koster, S. Shuman, C. Dekker, N.H. Dekker

Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion

Nucleic Acids Research

F. Moreno-Herrero, M. de Jager, N. H. Dekker, R. Kanaar, C. Wyman, C. Dekker

Meso-scale conformational changes in Rad50/Mre11 upon DNA binding: implications for DNA tethering

Nature

R. Seidel, J. G. P. Bloom, J. van Noort, C. F. Dutta, N. H. Dekker, K. Firman, M. D. Szczelkun, C. Dekker

Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I

EMBO Journal

F.H.J. van der Heyden, D. Stein, C. Dekker

Streaming currents in a single nanofluidic channel

Physical Review Letters

U.F. Keyser, D. Krapf, B. N. Koeleman, R. M. M. Smeets, N. H. Dekker, C. Dekker

Nanopore tomography of a laser focus

Nano Letters

M.G.L. van den Heuvel, C.T. Butcher, R.M.M. Smeets, S. Diez, C. Dekker

High Rectifying Efficiencies of Microtubule Motility on Kinesin-Coated Gold Nanostructures

Nano Letters

D. Ristic, M. Modesti, T. van der Heijden, S.J.T. van Noort, C. Dekker, R. Kanaar, C. Wyman

Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function.

Nucelic Acids Research

T. van der Heijden, J. van Noort, H. van Leest, R. Kanaar, C. Wyman, N.H. Dekker, C. Dekker

Torque-limited RecA polymerization on dsDNA

Nucleic Acids Research

B.J. LeRoy, J. Kong, V.K. Pahilwani, C. Dekker, S.G. Lemay

Three-terminal scanning tunneling spectroscopy of suspended carbon nanotubes

Physical Review B

B.M. Quinn, C. Dekker, S.G. Lemay

Electrodeposition of noble metals nanoparticles on carbon nanotubes

Journal of the American Chemical Society

A. J. Storm, J.H. Chen, X.S. Ling, H.W. Zandbergen, C. Dekker

Electron-beam-induced deformations of SiO2 nanostructures

Journal of Applied Physics

2004

H. A. Heering, F.G.M. Wiertz, C. Dekker, S. de Vries

Direct immobilization of native yeast iso-1 cytochrome c on bare gold: fast electron relay to redox enzymes and zeptomole protein-film voltammetry

Journal of the American Chemical Society

B.J. , S.G. Lemay, J. Kong, C. Dekker

Electrical generation and absorption of phonons in carbon nanotubes

Nature

R. den Dulk, K.A. Williams, P. T.M. Veenhuizen, M. de Koning, M. Overhand, C. Dekker

Self-Assembly Experiments with PNA-Derivatized Carbon Nanotubes

AIP Proceedings of the Symposium on DNA-Based Molecular Electronics, May 13-15, 2004, Jena, Germany

P. Jarillo-Herrero, S. Sapmaz, C. Dekker, L.P. Kouwenhoven, H.S.J. van der Zant

A Few Electron-Hole Semiconducting Carbon Nanotube Quantum Dot

Proceedings of the International Winterschool on Electronic Properties of Novel Materials (Kirchberg, 2004)

R. Seidel, J. van Noort, C. van der Scheer, J. Bloom, N. Dekker, C. F. Dutta, A. Blundell, T. Robinson, K. Firman, C. Dekker

Real-Time Observation of DNA Translocation by the Type I Restriction-Modification Enzyme EcoR124I

Nature Structural & Molecular Biology

D. Stein, M. Kruithof, C. Dekker

Surface-charge-governed ion transport in nanofluidic channels

Physical Review Letters

B.J. LeRoy, S.G. Lemay, J. Kong, C. Dekker

Scanning tunneling spectroscopy of suspended single-wall carbon nanotubes

Applied Physics Letters

S.J.T. van Noort, S. Verbrugge, N. Goosens, C. Dekker, R.T. Dame

Dual Architectural Roles of HU: Formation of Flexible Hinges and Rigid Filaments

Proceedings of the National Academy of Science USA

S.J.T. van Noort, T. van der Heijden, C. F. Dutta, W. Lisle, K. Firman, C. Dekker

Initiation of Translocation by Type I Restriction-Modification Enzymes is Associated with a Short DNA Extrusion

Nucleic Acids Research

P. Jarillo-Herrero, S. Sapmaz, C. Dekker, L.P. Kouwenhoven, H.S.J. van der Zant

Electron-hole symmetry in a semiconducting carbon nanotube quantum dot

Nature

N. H. Dekker, J. A. Abels, P. T. M. Veenhuizen, C. Dekker

Joining of Long Double-stranded RNA Molecules through Controlled Overhangs

Nucleic Acids Research

J. Kong, L.P. Kouwenhoven, C. Dekker

Quantum change for nanotubes

Physics World July issue: 17 (2004) WEB LINK

2003

Th. Maltezopoulos, A. Kubetzka, M. Morgenstern, R. Wiesendanger, S.G. Lemay, C. Dekker

Confined states in extended metallic nanotubes

Applied Physics Letters

S.J. Tans, R.G. Miedema, L.J. Geerligs, C. Dekker, J. Wu, D. Neher, G. Wegner

Electronic transport in monolayers of phthalocyanine polymers

Nanotechnology

A. Filoramo, C. Dekker, U. Sivan, C. Schönenberger, M.E. Michel-Beyerle

Highlights from DNA-based electronic project

Phantoms Newsletter Issue 10/11: 4-6 (2003)

A.J. Storm, J.H. Chen, X.S. Ling, H.W. Zandbergen, C. Dekker

Fabrication of solid-state nanopores with single nanometer precision

Nature Materials

J.-O Lee, G. Lientschnig, F.G.M. Wiertz, M. Struijk, R.A.J. Janssen, R. Egberink, D.N. Reinhoudt, A. Grimsdale, K. Mullen, P. Hadley, C. Dekker

Electrical transport study of phenylene-based p-conjugated molecules in a three-terminal geomtery

Annals New York Acad. Sciences, accepted for publication

S.J.T. van Noort, T. van der Heijden, M. de Jager, C. Wyman, R. Kanaar, C. Dekker

The coiled-coil of the human Rad50 DNA repair protein contains specific segments of increased flexibility

Proceedings of the National Academy of Science USA

K. Besteman, J.-O Lee, F.G.M. Wiertz, H.A. Heering, C. Dekker

Enzyme-coated carbon nanotubes as single-molecule biosensors

Nano Letters

C. Dekker

Nanotechnologie, fascinatie voor het kleine

Diesrede, 161ste Dies Natalis, 10 januari 2003, TU Delft

J.-O Lee, G. Lientschnig, F.G.M. Wiertz, M. Struijk, R.A.J. Janssen, R. Egberink, D.N. Reinhoudt, P. Hadley, C. Dekker

Absence of strong gate effects in electrical measurements on phenylene-based conjugated molecules

Nano Letters

2002

K.A. Williams, P.T.M. Veenhuizen, B.G. de la Torre, R. Eritja, and C. Dekker

Carbon Nanotubes with DNA recognition

Nature

K.A. Williams, P.T.M. Veenhuizen, B.G. de la Torre, R. Eritja, C. Dekker

Towards DNA-Mediated Self Assembly of Carbon Nanotube Molecular Devices

AIP Conference Proceedings

A. Bachtold, P. Hadley, T. Nakanishi, C. Dekker

Logic circuits with carbon nanotubes

AIP Conference Proceedings

T. Nakanishi, A. Bachtold, C. Dekker

Transport through the interface between a semiconducting carbon nanotube and a metal electrode

Physical Review B

G. Cuniberti, L. Craco, D. Porath, C. Dekker

Backbone-induced semiconducting behavior in short DNA wires

Physical Review B

J.W. Janssen, S.G. Lemay, L.P. Kouwenhoven, C. Dekker

Scanning tunneling spectroscopy on crossed carbon nanotubes.

Physical Review B

A.W. Dunn, E. D. Svensson, C. Dekker

Scanning tunneling spectroscopy of C60 adsorbed on Si(100)-(2×1).

Surface Science

M. Thorwart, M. Grifoni, H.W.Ch. Postma, C. Dekker

Correlated tunneling in intramolecular carbon nanotube quantum dots.

Physical Review Letters

2001

A. Bachtold, P. Hadley, C. Dekker

Logic circuits with carbon nanotube transistors Science 294, 1317 (2001)

C. Dekker, M. A. Ratner

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Physics World

M. de Jager, S.J.T. van Noort, D.C. van Gent, C. Dekker, R. Kanaar, C. Wyman

Human Rad50/Mre11 is a flexible complex that can tether DNA ends.

Molecular Cell

C. Dekker

Single-molecule electronics from carbon nanotubes to DNA.

Nova Acta Leopoldina Supplementum

M. van den Hout, J.W. Janssen

Elektrongolven in koolstof nanobuisjes.

Nederlandse Tijdschriften voor Natuurkunde

A.J. Storm, S.J.T. van Noort, S. de Vries, C. Dekker

Insulating behavior for DNA molecules between nanoelectrodes.

Applied Physics Letters

J.W. Janssen, S. G. Lemay, M. van den Hout, M. Mooij, L. P. Kouwenhoven, C. Dekker

Scanning tunneling spectroscopy on a carbon nanotube buckle.

Proceedings of the American Institute of Physics Conference, H. Kuzmany, S. Roth, M. Mehring, J. Fink (eds.)

H.W.Ch. Postma, T.F. Teepen, Z. Yao, M. Grifoni, C. Dekker

Carbon nanotubes single-electron transistors at room temperature.

Science

P. Hadley, C.P. Heij, G. Lientschnig, T.F. Teepen, H.W.Ch. Postma, C. Dekker

Single-electron effects in metals and nanotubes for nanoscale circuits.

Proceedings of the MIOP – The German Wireless Week, 11th Conference on Microwaves, Radio Communication and Electromagnetic Compatibility, Stuttgart, Germany, May 8-10, 2001, p. 408-412. ISBN: 3-924651-91-4.

Z. Yao, C. Dekker, Ph. Avouris

Electrical transport through single-wall carbon nanotubes.

M.S. Dresselhaus, G. Dresselhaus, Ph. Avouris (eds.), Carbon Nanotubes; Topics in Applied Physics,

S.G. Lemay, J.W. Janssen, M. van den Hout, M. Mooij, M.J. Bronikowski, P.A. Willis, R.E. Smalley, L.P. Kouwenhoven, C. Dekker

Two-dimensional imaging of electronic wavefunctions in carbon nanotubes.

Nature 412 (6847): 617-620 (2001) cover article

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H.W. Ch. Postma, T.F. Teepen, Z. Yao, C. Dekker;

1/f noise in carbon nanotubes.

Electronic correlations: from meso- to nano-physics

2000

O.C. Mantel, F. Chalin, C. Dekker, H.S.J. van der Zant, Y.I. Latyshev, B. Pannetier, P. Monceau

Charge-density-wave current conversion in submicron NbSe3 wires

Physical Review Letters,

D. Porath, A. Bezryadin, S. de Vries, C. Dekker

Direct measurements of electrical transport through DNA molecules

Nature,

L.C. Venema, V. Meunier, Ph. Lambin, C. Dekker

Atomic structure of carbon nanotubes from scanning tunneling microscopy

Physical Review B,

H.W.Ch. Postma, Z. Yao, C. Dekker

Electron addition and excitation spectra of individual single-wall carbon nanotubes

Journal of Low Temperature Physics,

S. Rogge, A. W. Dunn, T. Melin, C. Dekker, L.J. Geerligs

Electrical transport through ultrathin ordered K3C60 films on Si

Carbon,

Z. Yao, C.L. Kane, C. Dekker

High-field electrical transport in single-wall carbon nanotubes

Physical Review Letters,

Ph. Lambin, A.A. Lucas, S. Amelinckx, C. Dekker

Determination of the helicity of the nanotubes

In Nanotubular structures, characterization and simulation at the atomic scale , edited by A. Loiseau, A. Rubio, and F. Willaime

H.W.Ch. Postma, A. Sellmeijer, C. Dekker

Manipulation and imaging of individual single-wall carbon nanotubes with an atomic force microscope

Advanced Materials,

S.J. Tans and C. Dekker

Molecular Transistors – Potential modulations along carbon nanotubes

Nature,

S.P. Rubio, Apell, L.C. Venema, C. Dekker

A mechanism for cutting carbon nanotubes with a scanning tunneling microscope

The European Physical Journal B,

L.C. Venema, J.W. Janssen, M.R. Buitelaar, J.W.G. Wildoer, S. Lemay, L.P. Kouwenhoven, C. Dekker

Spatially resolved scanning tunneling spectroscopy on single-walled carbon nanotubes

Physical Review B,

L.C. Venema and C. Dekker

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In New Frontiers of Science and Technology , edited by L. Esaki (Frontiers Science Series No. 31, Universal Acad. Press, 293-300 (2000)

H.W.Ch. Postma, M. de Jonge, Z. Yao, C. Dekker;

Electrical transport through carbon nanotube junctions created by mechanical manipulation.

Physical Review B,

D. Porath, A. Bezryadin, S. de Vries, C. Dekker

Direct Measurements of Electrical Transport Through DNA Molecules

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1999

O.C. Mantel, C.A.W. Bal, C. Langezaal, C. Dekker, H.S.J. van der Zant

Lithographic patterned wires of the charge-density-wave conductor Rb0.30Mo03

Journal of Applied Physics,

O.C. Mantel, F. Chalin, C. Dekker, H.S.J. van der Zant, Y.I. Latyshev, B. Pannetier, P. Monceau

Submicron structures of the charge-density-wave conductor NbSe3

Synthetic Metals,

O.C. Mantel, C.A.W. Bal, C. Langezaal, C. Dekker, H.S.J. van der Zant

Sliding charge-density-wave transport in micron-sized wires of Rb0.30Mo03

Physical Review B,

Z. Yao, H.W.Ch. Postma, L. Balents, C. Dekker

Carbon nanotube intramolecular junctions

Nature,

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Carbon nanotubes as molecular quantum wires

Physics Today,

L.C. Venema, J.W.G. Wildoer, S.J. Tans, J.W. Janssen, H. Temminck Tuinstra, L. P. Kouwenhoven, C. Dekker

Imaging electron wave functions of quantized energy levels in carbon nanotubes

Science,

1998

S. J. Tans, A. R. M. Verschueren, C. Dekker

Room-temperature transistor based on a single carbon nanotube

Nature,

S.J. Tans, M.H. Devoret, R.J.A. Groeneveld, C. Dekker

Electron-electron correlations in carbon nanotubes

Nature,

Bezryadin, A. R. M. Verschueren, S. J. Tans, C. Dekker

Multiprobe transport experiments on individual single-wall carbon nanotubes

Physics Review Letters,

J. W. G.Wildoer, L. C. Venema, A. G. Rinzler, R. E. Smalley, C. Dekker

Electronic structure of atomically resolved carbon nanotubes

Nature,

L.C. Venema, J.W.G. Wildoer, C. Dekker, A.G. Rinzler, R.E. Smalley

STM atomic resolution images of single-wall carbon nanotubes

Applied Physics A,

C.L. Kane, E.J. Mele, R.S. Lee, J.E. Fisher, P. Petit, H. Dai, A. Thess, R.E. Smalley, A.R.M. Verschueren, S.J. Tans, C. Dekker

Temperature dependent resistivity of single-wall carbon nanotubes

Europhysics Letters,

C. Dekker, S.J. Tans, M.H. Devoret, L.J. Geerligs, R.J.A. Groenveld, L. C. Venema, J.W.G. Wildoer, A.R.M. Verschuren, A. Bezryadin, A. Thess, H. Dai, R. A. Smalley

Electronic properties of individual single-wall nanotubes: Transport and STM results

in Molecular Nanostructures (World Scientific), Eds. H. Kuzmany, J. Fink, M. Mehring, and S. Roth, 467-471 (1998)

1997

J. Liu, H. Dai, J. H. Hafner, D.T. Colbert, R.E. Smalley, S.J. Tans, C. Dekker

Fullerene crop circles

Nature 385 (6619): 780-781 (1997)

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Bezryadin and C. Dekker

Nanofabrication of electrodes with sub-5 nm spacing for transport experiments on single molecules and metal clusters

Journal of Vacuum Science and Technology B,

S.J. Tans, M.H. Devoret, H. Dai, A. Thess, R.E. Smalley, L.J. Geerligs, C. Dekker

Individual single-wall nanotubes as quantum wires

Nature 386 (6624): 474-477 (1997)

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C. Dekker, S. J. Tans, L. J. Geerligs, A. Bezryadin, J. Wu, G. Wegner

Towards transport on single molecules: first results on nanofabrication and phthalocyanine polymers

Atomic and Molecular Wires, eds. C. Joachim and S. Roth Kluwer Acad. Publ., 129-138 (1997)

C. Dekker, S. J. Tans, B. Oberndorff, R. Meyer, L. Venema

STM imaging and spectroscopy of single copperphthalocyanine molecules

Synthetic Metals,

O.C. Mantel, H.S.J. van der Zant, A.J. Steinfort, C. Traeholt, C. Dekker

Orientation of the charge-density-wave chains in thin films of Rb0.30Mo03

Synthetic Metals,

O.C. Mantel, H.S.J. van der Zant, A.J. Steinfort, C. Dekker, C. Traeholt, H.W. Zandbergen

Thin films of the charge-density-wave oxide Rb0.30Mo03 by pulsed-laser depostition

Physical Review B,

S.J. Tans, L.J. Geerligs, C. Dekker, J. Wu, G. Wegner

Electrical transport in monolayers of phthalocyanine molecular wires and AFM imaging of a single wire bridging two electrodes

Synthetic Metals,

S.J. Tans, L.J. Geerligs, C. Dekker, J. Wu, G. Wegner

Deposition and atomic force microscopy of individual phthalocyanine polymers between nanofabricated electrodes

Journal of Vacuum Science and Technology B,

Bezryadin, C. Dekker, G. Schmid

Electrostatic trapping of single conducting nanoparticles between nanoelectrodes

Applied Physics Letters,

L.C. Venema, J.W.G. Wildoer, H.L.J. Temminck Tuinstra, C. Dekker, A.G. Rinzler, and R.E. Smalley

Length control of individual carbon nanotubes by nanostructuring with the scanning tunneling microscope

Applied Physics Letters,