Publications
2024
A. Joesaar, M. Holub, L. Lutze, M. Emanuele, J. Kerssemakers, M. Pabst, C. Dekker
A microfluidic platform for extraction and analysis of bacterial genomic DNA
Lab on a chip, submitted
N. De Franceschi, A. Blanch-Jover, C. Dekker
Interaction hierarchy among Cdv proteins drives recruitment to membrane necks in vitro
eLife, under review
A. Martin Gonzalez, M. Tišma, B.T. Analikwu, A. Barth, R. Janissen, H. Antar, G. Kemps, S. Gruber, C. Dekker
DNA supercoiling enhances DNA condensation by ParB proteins
Nucl. Acid Res., accepted, in print
A. Japaridze, V. Struijk, K. Swamy, I. E. Roslon, O. Shoshani, C. Dekker, F. Alijani
Synchronization of E. coli bacteria moving in coupled wells
Small, in print
X. Chen, J. W. van de Sande, J. Ritmejeris, C. Wen, H. Brinkerhoff, A. H. Laszlo, B. Albada, C. Dekker
Resolving sulfation PTMs on a plant peptide hormone using nanopore sequencing
ACS Nano, under review
J. Ritmejeris, X. Chen, C. Dekker
Single-molecule protein sequencing with nanopores
Nature Reviews Bioengineering, accepted, in print
Z. Yu, A. Baptist, S. Reinhardt, E. Bertosin, C. Dekker, R. Jungmann, A. Heuer-Jungemann, S. Caneva
Compliant DNA Origami Nanoactuators as Size-Selective Nanopores
Advanced Mater., in print
I.F. Davidson, R. Barth, S. Horn, R. Janissen, B. Bauer, C. Dekker, J.-M. Peters
Cohesin supercoils DNA during loop extrusion
Molecular Cell, submitted
R. Janissen, R. Barth, I.F. Davidson, M. Taschner, S. Gruber, J.-M. Peters, C. Dekker
All eukaryotic SMC proteins induce a twist of -0.6 at each DNA-loop-extrusion step
Science advances, submitted
C. Wen, S. Schmid, C. Dekker
Understanding Electrophoresis and Electroosmosis in Nanopore Sensing with the help of the NEOtrap
ACS Nano, in print
2023
2022
2021
B. Pradhan, R. Barth, E. Kim, I.F. Davidson, B. Bauer, T. van Laar, W. Yang, J.-K. Ryu, J. van der Torre, J.-M. Peters, C. Dekker
SMC complexes can pass physical roadblocks bigger than their ring size, indicating a nontopological mechanism for DNA loop extrusion
Cell Reports DOI:https://doi.org/10.1016/j.celrep.2022.111491
2020
J. Alfaro, P. Bohländer, M. Dai, M. Filius, C.J. Howard, X. van Kooten, S. Ohayon, A. Pomorski, S. Schmid, S.H. Kim, P. Samaras, B. Kuster, G. Bedran, M. Wilhelm, L. Sepiashvili, U. Kalathiya1, S. Kumar, A. Aksimentiev, D. Stein, N. Drachman, D. Goodlett, C. Masselon, S. Hentz, M. Chinappi, C. Chan, M. Mayer, S. Lindsey, D. Rodriguez Larrea, E.M. Marcotte, G. Maglia, G. Dittmar, J. Marino, Z. Kelman, M. Wanunu, N.L. Kelleher, R. Eelkema, P. Yin, E.V. Anslyn, C. Dekker, A. Meller, C. Joo
The emerging landscape of single-molecule protein sequencing technologies
Nature Meth. 18, 604–617 (2021)
2019
2018
F. Fanalista, S. Deshpande, A. Lau, G. Pawlik, C. Dekker
FtsZ-induced Shape Transformation of Coacervates
Advanced Biosystems 1800136 (2018)
2017
2016
Y. Caspi, C. Dekker
Mapping out Min protein patterns in fully confined fluidic chambers
eLife 5:e19271
2015
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)
2014
2013
2012
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)
C. Dekker
Als fysicus aan de slag in de nanobiologie
Ned. Tijdschr. Natuurk. 78, 286 (2012)
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)
F. Hol and C. Dekker
Bacteriën in nanokanalen en micro-steden
Ned. Tijdschr. Natuurk. 78, 240 (2012)
2011
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|https://ceesdekkerlab.nl/wp-content/uploads/Kowalczyk_4_2011.pdf
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).
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|https://ceesdekkerlab.nl/wp-content/uploads/Kowalczyk_3_2011.pdf
2010
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)
2009
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|https://ceesdekkerlab.nl/wp-content/uploads/2009_Skinner_Hout.pdf
2008
R. Seidel, J.P.G. Bloom, C. Dekker, and M.D. Szczelkun
Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I
EMBO J. 27, 1388–1398
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)
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|https://ceesdekkerlab.nl/wp-content/uploads/2008_van-der-Heijden.pdf
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|https://ceesdekkerlab.nl/wp-content/uploads/2008_van-der-Heijden02.pdf
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)
R. Smeets, U. F. Keyser, N. H. Dekker, C. Dekker
Noise in Solid-state Nanopores
Proceedings of the National Academy of Sciences
2007
M.G.L. van den Heuvel, S. Bolhuis, C. Dekker
Persistance length measurement from stochastic single-molecule trajectories
Nano Letters
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
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)
2006
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.: undefined
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: undefined
2005
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: 437 (7057): 440-443 (2005) PDF Movie 1 & Movie 2|https://ceesdekkerlab.nl/wp-content/uploads/2005_Moreno-2.pdf
2004
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): undefined
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: undefined
J. Kong, L.P. Kouwenhoven, C. Dekker
Quantum change for nanotubes
Physics World July issue: 17 (2004) WEB LINK: undefined
2003
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: undefined
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): undefined
C. Dekker
Nanotechnologie, fascinatie voor het kleine
Diesrede, 161ste Dies Natalis, 10 januari 2003, TU Delft: undefined
2002
A. Bachtold, P. Hadley, T. Nakanishi, C. Dekker
Logic circuits with carbon nanotubes
AIP Conference Proceedings: 633: 502-507 (2002)
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: 633: 444-448 (2002)
2001
A. Bachtold, P. Hadley, C. Dekker
Logic circuits with carbon nanotube transistors Science 294, 1317 (2001)
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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: Proceedings of the XXXVIth Rencontres de Moriond, Th. Martin and G. Montambaux, Les Ulis (eds), EDP Sciences (France), January 20-27: 433-436, 2001
C. Dekker
Single-molecule electronics from carbon nanotubes to DNA.
Nova Acta Leopoldina Supplementum: 17: 27 (2001).
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,: vol. 80, Springer Verlag, Berlin, 2001, p. 147-171. ISSN: 0303-4216.
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.: undefined
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.): Kirchberg, Oostenrijk, March 3-10 591: 293-297 (2001)
M. van den Hout, J.W. Janssen
Elektrongolven in koolstof nanobuisjes.
Nederlandse Tijdschriften voor Natuurkunde: 67 (10): 294-297 (2001)
2000
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: undefined
L.C. Venema and C. Dekker
Carbon nanotubes
In New Frontiers of Science and Technology , edited by L. Esaki (Frontiers Science Series No. 31, Universal Acad. Press, 293-300 (2000): undefined
1999
C. Dekker
Carbon nanotubes as molecular quantum wires
Physics Today,: 52 (5): 22-28 (1999)
1998
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): undefined
1997
J. Liu, H. Dai, J. H. Hafner, D. T. Colbert, R. E. Smalley, S. J. Tans, and C. Dekker
Fullerene crop circles
Nature 385, 780-781 (1997)
S. J. Tans, M. H. Devoret, H. Dai, A. Thess, R. E. Smalley, L. J. Geerligs, and C. Dekker
Individual single-wall nanotubes as quantum wires
Nature 386, 474 (1997)
C. Dekker, S. J. Tans, L. J. Geerligs, A. Bezryadin, J. Wu, and G. Wegner
Towards transport on single molecules: first results on nanofabrication and phthalocyanine polymers
in Atomic and Molecular Wires, eds. C. Joachim and S. Roth (Kluwer Acad. Publ., 1997), p. 129-138
C. Dekker, S.J. Tans, B. Oberndorff, R. Meyer, and L. Venema
STM imaging and spectroscopy of single copperphthalocyanine molecules
Synthetic Metals 84, 853 (1997)
O. C. Mantel, H.S.J. van der Zant, A.J. Steinfort, C. Traeholt, and C. Dekker
Orientation of the charge-density-wave chains in thin films of Rb0.30MoO3
Synthetic Metals 86, 2193 (1997)
S. J. Tans, L.J. Geerligs, C. Dekker, J. Wu, and G. Wegner
Electrical transport in monolayers of phthalocyanine molecular wires and AFM imaging of a single wire bridging two electrodes
Synthetic Metals 84, 733 (1997)
H. S. J. van der Zant, O. C. Mantel, C. P. Heij, and C. Dekker
Photolithographic patterning of the charge-density-wave conductor Rb0.30MoO3
Synthetic Metals 86, 1781 (1997)
O. C. Mantel, H.S.J. van der Zant, A. J. Steinfort, C. Dekker, C. Traeholt, and H. W. Zandbergen
Thin films of the charge-density-wave oxide Rb0.30MoO3 by pulsed-laser deposition
Phys. Rev. B 55, 4817 (1997)
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): undefined
1996
1995
1994
1993
1992
F. Liefrink, A. J. Scholten, C. Dekker, J. I. Dijkhuis, B. W. Alphenaar, H. van Houten, and C. T. Foxon
Magnetic Field Effects on Switching Noise in a Quantum Point Contact
Phys. Rev. B 46, 15523 (1992)
C. Dekker, W. Eidelloth, and R. H. Koch
Measurement of the Exponent mu in the Low-Temperature Phase of YBa2Cu3O7 Films in a Magnetic Field: Direct Evidence for a Vortex-Glass Phase
Phys. Rev. Lett. 68, 3347 (1992)
C. Dekker, P. J. M. Woltgens, R. H. Koch, B. W. Hussey, and A. Gupta
Absence of a Finite-Temperature Vortex-Glass Phase Transition in Two-Dimensional YBa2Cu3O7 Films
Phys. Rev. Lett. 69, 2717 (1992)
1991
C. Dekker, A. J. Scholten, F. Liefrink, R. Eppenga, H. van Houten, and C. T. Foxon
Spontaneous Resistance Switching and Low-Frequency Noise in Quantum Point Contacts
Phys. Rev. Lett. 66, 2148 (1991)
F. Liefrink, A. J. Scholten, C. Dekker, R. Eppenga, H. van Houten, and C. T. Foxon
Low-Frequency Noise of Quantum Point Contacts in the Ballistic and Quantum Hall Regime
Physica B 175, 213 (1991)
F. Liefrink, A. J. Scholten, C. Dekker, J. I. Dijkhuis, R. Eppenga, H. van Houten, and C. T. Foxon
Low-Frequency Noise in Quantum Point Contacts
in Noise in physical systems and 1/f fluctuations, ed. by T. Musha, S. Sato, and M. Yamamoto (Ohmsha, Tokyo, 1991), p. 363
C. Dekker, R. H. Koch, B. Oh, and A. Gupta
Dimensionality Crossover of the Superconducting-Normal Transition in YBa2Cu3O7 Thin Films both at High Magnetic Field and at Zero Field
Physica C 185-189, 1799 (1991)
1990
A. F. M. Arts, C. Dekker, and H. W. de Wijn
Spin-glass dynamics in the two-dimensional Ising Rb2Cu1-xCoxF4
in Relaxation and Related Topics in Complex Systems, ed. by I. A. Campbell and C. Giovannella (Plenum Press, New York, 1990), p. 23
1989
C. Dekker, A. F. M. Arts, H. W. de Wijn, A. J. van Duyneveldt, and J. A. Mydosh
Activated dynamics in a two-dimensional Ising spin-glass Rb2Cu1-xCoxF4
Phys. Rev. B 40, 11243 (1989)
1988
C. Dekker, A. F. M. Arts, and H. W. de Wijn
Rb2Cu1-xCoxF4, a two-dimensional Ising spin glass
J. Appl. Phys. 63, 4334 (1988)
C. Dekker, A. F. M. Arts, H. W. de Wijn, A. J. van Duyneveldt, and J. A. Mydosh
Activated dynamics in the two-dimensional Ising spin-glass Rb2Cu1-xCoxF4
Phys. Rev. Lett. 61, 1780 (1988)
C. Dekker, A. F. M. Arts, and H. W. de Wijn
Static critical behavior of the two-dimensional Ising spin glass Rb2Cu1-xCoxF4
Phys. Rev. B 38, 8985 (1988).
C. Dekker, A. F. M. Arts, and H. W. de Wijn
Magnetic order in the two-dimensional randomly mixed ferromagnet-antiferromagnet Rb2Cu1-xCoxF4
Phys. Rev. B 38, 11512 (1988)
C. Dekker, A. F. M. Arts, and H. W. de Wijn
Static and dynamic properties of the two-dimensional Ising spin glass Rb2Cu1-xCoxF4
J. Phys. (Paris) 49, C8-1013 (1988)
C. Dekker
Two-dimensional spin glasses
Ph. D. thesis, University of Utrecht
C. Dekker en A. F. M. Arts
Dynamica van spinglazen
Nederlands Tijdschrift voor Natuurkunde B 54, 149 (1988) [in Dutch]
1987
C. Dekker, A. F. M. Arts, H. W. de Wijn, and J. K. Kjems
Breakup of long-range order in the diluted antiferromagnet K2MnxZn1-xF4 in zero magnetic field
Phys. Rev. B 35, 7157 (1987)
1985
B. J. Dikken, C. Dekker, A. F. M. Arts, and H. W. de Wijn
NMR study of local magnetizations in diluted two-dimensional antiferromagnets
Phys. Rev. B 32, 5787 (1985)
C. Dekker, B. J. Dikken, and A. F. M. Arts
Monte Carlo investigation of diluted antiferromagnets in high magnetic fields
Solid State Commun. 54, 887 (1985)