Research Output

2020

A Mechanically Tunable Quantum Dot in a Graphene Break Junction

Caneva, S., Hermans, M., Lee, M., García-Fuente, A., Watanabe, K., Taniguchi, T., Dekker, C., Ferrer, J., Van Der Zant, H. S. J. & Gehring, P., 2020, In : Nano Letters. 20, 7, p. 4924-4931

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2 Downloads (Pure)

Comparing Current Noise in Biological and Solid-State Nanopores

Fragasso, A., Schmid, S. & Dekker, C., 2020, In : ACS Nano. 14, 2, p. 1338-1349

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
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5 Citations (Scopus)
28 Downloads (Pure)

Direct observation of independently moving replisomes in Escherichia coli

Japaridze, A., Gogou, C., Kerssemakers, J. W. J., Nguyen, H. M. & Dekker, C., 2020, In : Nature Communications. 11, 1, 10 p., 3109.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Downloads (Pure)

DNA-loop extruding condensin complexes can traverse one another

Kim, E., Kerssemakers, J., Shaltiel, I. A., Haering, C. H. & Dekker, C., 2020, In : Nature. 579, 7799, p. 438-442 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Citations (Scopus)
1 Downloads (Pure)

Dynamics as a cause for the nanoscale organization of the genome

Barth, R., Fourel, G. & Shaban, H. A., 2020, In : Nucleus. 11, 1, p. 83-98

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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1 Citation (Scopus)
7 Downloads (Pure)

Fast, Simultaneous Tagging and Mutagenesis of Genes on Bacterial Chromosomes

Schärfen, L., Tišma, M. & Schlierf, M., 2020, In : ACS Synthetic Biology. 9, 8, p. 2203-2207

Research output: Contribution to journalArticleScientificpeer-review

High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT

Filius, M., Cui, T. J., Ananth, A. N., Docter, M. W., Hegge, J. W., van der Oost, J. & Joo, C., 2020, In : Nano Letters. 20, 4, p. 2264-2270

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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13 Downloads (Pure)

Interplay between Confinement and Drag Forces Determine the Fate of Amyloid Fibrils

Smith, K. B., Wehrli, M., Japaridze, A., Assenza, S., Dekker, C. & Mezzenga, R., 2020, In : Physical Review Letters. 124, 11, 6 p., 118102.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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21 Downloads (Pure)

On-chip reconstitution of an FtsZ-based divisome for synthetic cells

Fanalista, F., 2020, 131 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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43 Downloads (Pure)

pH-Controlled Coacervate-Membrane Interactions within Liposomes

Last, M. G. F., Deshpande, S. & Dekker, C., 2020, In : ACS Nano. 14, 4, p. 4487-4498

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Citations (Scopus)
9 Downloads (Pure)
2019

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

Fragasso, A., Pud, S. & Dekker, C., 2019, In : Nanotechnology. 30, 39, 395202.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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5 Citations (Scopus)
1 Downloads (Pure)

A microfluidic platform for the characterisation of membrane active antimicrobials

Al Nahas, K., Cama, J., Schaich, M., Hammond, K., Deshpande, S., Dekker, C., Ryadnov, M. G. & Keyser, U. F., 2019, In : Lab on a Chip. 19, 5, p. 837-844 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
75 Downloads (Pure)

An Integrated Microfluidic Platform for Quantifying Drug Permeation across Biomimetic Vesicle Membranes

Schaich, M., Cama, J., Al Nahas, K., Sobota, D., Sleath, H., Jahnke, K., Deshpande, S., Dekker, C. & Keyser, U. F., 2019, In : Molecular Pharmaceutics. 16, 6, p. 2494-2501

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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9 Citations (Scopus)
4 Downloads (Pure)

Bacteria-in-paper, a versatile platform to study bacterial ecology

Hol, F. J. H., Whitesides, G. M. & Dekker, C., 2019, In : Ecology Letters. 22, 8, p. 1316-1323 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2 Citations (Scopus)
38 Downloads (Pure)

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Wu, F., Swain, P., Kuijpers, L., Zheng, X., Felter, K., Guurink, M., Solari, J., Jun, S., Dekker, C. & More Authors, 2019, In : Current Biology. 29, 13, p. 2131-2144.e4

Research output: Contribution to journalArticleScientificpeer-review

10 Citations (Scopus)

Direct imaging of the circular chromosome in a live bacterium

Wu, F., Japaridze, A., Zheng, X., Wiktor, J., Kerssemakers, J. W. J. & Dekker, C., 2019, In : Nature Communications. 10, 1, 9 p., 2194.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
48 Downloads (Pure)

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

Elbatsh, A. M. O., Kim, E., Eeftens, J. M., Raaijmakers, J. A., van der Weide, R. H., García-Nieto, A., Bravo, S., Ganji, M., Dekker, C. & More Authors, 2019, In : Molecular Cell. 76, 5, p. 724-737.e5

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Citations (Scopus)
17 Downloads (Pure)

Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate

Zhao, S., Restrepo-Pérez, L., Soskine, M., Maglia, G., Joo, C., Dekker, C. & Aksimentiev, A., 2019, In : ACS Nano. 13, 2, p. 2398-2409

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Citations (Scopus)
19 Downloads (Pure)

Hybrid particles derived from alendronate and bioactive glass for treatment of osteoporotic bone defects

Diba, M., Camargo, W. A., Zinkevich, T., Grünewald, A., Detsch, R., Kabiri, Y., Kentgens, A. P. M., Boccaccini, A. R., Van Den Beucken, J. J. J. P. & Leeuwenburgh, S. C. G., 2019, In : Journal of Materials Chemistry B. 7, 5, p. 796-808

Research output: Contribution to journalArticleScientificpeer-review

4 Citations (Scopus)

Imaging DNA nanostructures with advanced TEM techniques

Kabiri, Y., 2019, 140 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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48 Downloads (Pure)

Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level

Kabiri, Y., Angelin, A., Ahmed, I., Mutlu, H., Bauer, J., Niemeyer, C. M., Zandbergen, H. & Dekker, C., 2019, In : ChemBioChem. 20, 6, p. 822-830

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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1 Citation (Scopus)
102 Downloads (Pure)

Label-Free Detection of Post-translational Modifications with a Nanopore

Restrepo-Pérez, L., Wong, C. H., Maglia, G., Dekker, C. & Joo, C., 2019, In : Nano Letters. 19, 11, p. 7957-7964 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Citations (Scopus)
28 Downloads (Pure)

Membrane Tension–Mediated Growth of Liposomes

Deshpande, S., Wunnava, S., Hueting, D. & Dekker, C., 2019, In : Small. 15, 38, 10 p., 1902898.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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6 Citations (Scopus)
1 Downloads (Pure)

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

Perez, A. J., Cesbron, Y., Shaw, S. L., Villicana, J. B., Tsui, H. C. T., Boersma, M. J., Ye, Z. A., Tovpeko, Y., Dekker, C. & More Authors, 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 8, p. 3211-3220 10 p.

Research output: Contribution to journalArticleScientificpeer-review

14 Citations (Scopus)

Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores

Verschueren, D., Shi, X. & Dekker, C., 2019, In : SMALL METHODS. 3, 5, 9 p., 1800465.

Research output: Contribution to journalArticleScientificpeer-review

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13 Citations (Scopus)
4 Downloads (Pure)

Nanopore Formation via Tip-Controlled Local Breakdown Using an Atomic Force Microscope

Zhang, Y., Miyahara, Y., Derriche, N., Yang, W., Yazda, K., Capaldi, X., Liu, Z., Grutter, P. & Reisner, W., 2019, In : SMALL METHODS. 3, 7, 1900147.

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)

Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore

Restrepo-Pérez, L., Huang, G., Bohländer, P. R., Worp, N., Eelkema, R., Maglia, G., Joo, C. & Dekker, C., 2019, In : ACS Nano. 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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8 Citations (Scopus)
27 Downloads (Pure)

Shape and Size Control of Artificial Cells for Bottom-Up Biology

Fanalista, F., Birnie, A., Maan, R., Burla, F., Charles, K., Pawlik, G., Deshpande, S., Koenderink, G. H., Dogterom, M. & Dekker, C., 2019, In : ACS Nano. 13, 5, p. 5439-5450

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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16 Citations (Scopus)
60 Downloads (Pure)

Spatiotemporal control of coacervate formation within liposomes

Deshpande, S., Brandenburg, F., Lau, A., Last, M. G. F., Spoelstra, W. K., Reese, L., Wunnava, S., Dogterom, M. & Dekker, C., 2019, In : Nature Communications. 10, 1, 11 p., 1800.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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21 Citations (Scopus)
83 Downloads (Pure)

Unraveling proteins at the single molecule level using nanopores

Restrepo Perez, L., 2019, 161 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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73 Downloads (Pure)

Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques

Kabiri, Y., Ravelli, R. B. G., Lehnert, T., Qi, H., Katan, A. J., Roest, N., Kaiser, U., Dekker, C., Peters, P. J. & Zandbergen, H., 2019, In : Scientific Reports. 9, 1, 7218.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Citations (Scopus)
64 Downloads (Pure)
2018

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

Shi, X., Verschueren, D. V. & Dekker, C., 2018, In : Nano Letters. 18, 12, p. 8003-8010

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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16 Citations (Scopus)
47 Downloads (Pure)

A nanopore-based system for trapping, controlled displacement, and sequencing of (bio)macromolecules

Dekker, C. & Aksimentiev, A., 2018, Priority date 7 Sep 2016, Priority No. US 2018/0088104

Research output: Patent

Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores

Yang, W., Restrepo-Pérez, L., Bengtson, M., Heerema, S. J., Birnie, A., Van Der Torre, J. & Dekker, C., 2018, In : Nano Letters. 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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15 Citations (Scopus)
32 Downloads (Pure)

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

Wiktor, J., Van Der Does, M., Büller, L., Sherratt, D. J. & Dekker, C., 2018, In : Nucleic Acids Research. 46, 4, p. 1821-1833 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
14 Downloads (Pure)

Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery

Caspi, Y. & Dekker, C., 2018, In : Frontiers in Microbiology. 9, 25 p., 174.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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11 Citations (Scopus)
59 Downloads (Pure)

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

Ketterer, P., Ananth, A. N., Laman Trip, D. S., Mishra, A., Bertosin, E., Ganji, M., Van Der Torre, J., Onck, P., Dietz, H. & Dekker, C., 2 Mar 2018, In : Nature Communications. 9, 1, 902.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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30 Citations (Scopus)
25 Downloads (Pure)

DNA sensing with nanopores in graphene nanoribbons

Heerema, S., 2018, 137 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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73 Downloads (Pure)

DNA sequence encodes the position of DNA supercoils

Kim, S. H., Ganji, M., Kim, E., van der Torre, J., Abbondanzieri, E. & Dekker, C., 2018, In : eLife. 7, 23 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Citations (Scopus)
33 Downloads (Pure)

Double Barrel Nanopores as a New Tool for Controlling Single-Molecule Transport

Cadinu, P., Campolo, G., Pud, S., Yang, W., Edel, J. B., Dekker, C. & Ivanov, A. P., 2018, In : Nano Letters. 18, 4, p. 2738-2745 8 p.

Research output: Contribution to journalArticleScientificpeer-review

19 Citations (Scopus)

Effects of Inhibitors on Hsp90′s Conformational Dynamics, Cochaperone and Client Interactions

Schmid, S., Götz, M. & Hugel, T., 17 Jul 2018, In : ChemPhysChem. 19, 14, p. 1716-1721

Research output: Contribution to journalArticleScientificpeer-review

3 Citations (Scopus)

Embedded Multimaterial Extrusion Bioprinting

Rocca, M., Fragasso, A., Liu, W., Heinrich, M. A. & Zhang, Y. S., 2018, In : SLAS Technology. p. 154-163 10 p.

Research output: Contribution to journalArticleScientificpeer-review

18 Citations (Scopus)

FtsZ-Induced Shape Transformation of Coacervates

Fanalista, F., Deshpande, S., Lau, A., Pawlik, G. & Dekker, C., 2018, In : ADVANCED BIOSYSTEMS. 2, 9, 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
34 Downloads (Pure)

High-Speed Atomic Force Microscopy of SMC Proteins

Ryu, J-K., Katan, A., Minamino, M., Bouchoux, C., Bisht, S., Eeftens, J., Hearing, C., Uhlmann, F. & Dekker, C., 2018, In : Biophysical Journal. 114, 3, p. 564A-564A

Research output: Contribution to journalMeeting AbstractScientific

How we made the carbon nanotube transistor

Dekker, C., 2018, In : Nature Electronics. 1, 9, 3 p.

Research output: Contribution to journalComment/Letter to the editorScientificpeer-review

Open Access
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5 Citations (Scopus)

Label-Free Optical Detection of DNA Translocations through Plasmonic Nanopores

Verschueren, D. V., Pud, S., Shi, X., De Angelis, L., Kuipers, L. & Dekker, C., 2018, In : ACS Nano.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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26 Citations (Scopus)
29 Downloads (Pure)

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

Verschueren, D. V., Yang, W. & Dekker, C., 2018, In : Nanotechnology. 29, 14, 145302.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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24 Citations (Scopus)
21 Downloads (Pure)

Mechanical Division of Cell-Sized Liposomes

Deshpande, S., Spoelstra, W. K., Van Doorn, M., Kerssemakers, J. & Dekker, C., 2018, In : ACS Nano. 12, 3, p. 2560-2568 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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29 Citations (Scopus)
40 Downloads (Pure)

Mechanically controlled quantum interference in graphene break junctions

Caneva, S., Gehring, P., García-Suárez, V. M., García-Fuente, A., Stefani, D., Olavarria-Contreras, I. J., Ferrer, J., Dekker, C. & van der Zant, H. S. J., 2018, In : Nature Nanotechnology. p. 1126-1131

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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20 Citations (Scopus)
28 Downloads (Pure)

Mimicking the nuclear pore complex using nanopores

Ananth, A., 2018, 207 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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31 Downloads (Pure)