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Burnham, D.R. (author), De Vlaminck, I. (author), Henighan, T. (author), Dekker, C. (author)Measurements in magnetic tweezers rely upon precise determination of the position of a magnetic microsphere. Fluctuations in the position due to Brownian motion allows calculation of the applied force, enabling deduction of the force-extension response function for a single DNA molecule that is attached to the microsphere. The standard approach...journal article 2014
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Ferrari, A.C. (author), Dekker, C. (author), Vandersypen, L.M.K. (author), Van Der Zant, H.S.J. (author)We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and...journal article 2014
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Hol, F.J.H. (author), Voges, M.J. (author), Dekker, C. (author), Keymer, J.E. (author)Background: Antagonistic interactions mediated by antibiotics are strong drivers of bacterial community dynamics which shape biodiversity. Colicin production by Escherichia coli is such an interaction that governs intraspecific competition and is involved in promoting biodiversity. It is unknown how environmental cues affect regulation of the...journal article 2014
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Janissen, R. (author), Berghuis, B.A. (author), Dulin, D. (author), Wink, M. (author), Van Laar, T. (author), Dekker, N.H. (author)Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the...journal article 2014
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Hertzberger, R. (author), Arents, J. (author), Dekker, H.L. (author), Pridmore, D. (author), Gysler, C. (author), Kleerebezem, M. (author), Teixeira de Mattosa, M.J. (author)Hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. In the presence of oxygen, the probiotic lactic acid bacterium Lactobacillus johnsonii NCC 533 excretes up to 1 mM H2O2, inducing growth stagnation and cell death. Disruption of genes commonly assumed to be involved in H2O2 production (e...journal article 2014
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Hol, F.J.H. (author), Galajda, P. (author), Nagy, K. (author), Woolthuis, R.G. (author), Dekker, C. (author), Keymer, J.E. (author)Cooperative organisms are ubiquitous in nature, despite their vulnerability to exploitation by cheaters. Although numerous theoretical studies suggest that spatial structure is critical for cooperation to persist, the spatial ecology of microbial cooperation remains largely unexplored experimentally. By tracking the community dynamics of...journal article 2013
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Van Riessen, B. (author), Negenborn, R.R. (author), Dekker, R. (author), Lodewijks, G. (author)An intermodal container transportation network is being developed between Rotterdam and several inland terminals in North West Europe: the EUROPEAN GATEWAY SERVICES network. This network is developed and operated by the sea terminals of EUROPE CONTAINER TERMINALS (ECT). To use this network cost-efficiently, centralised planning by the sea...journal article 2013
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Van Loenhout, M.T. (author), De Vlaminck, I. (author), Flebus, B. (author), Den Blanken, J.F. (author), Zweifel, L.P. (author), Hooning, K.M. (author), Kerssemakers, J.W. (author), Dekker, C. (author)The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that...journal article 2013
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Genani, G. (author), Dekker, M.C. (author), Molenbroek, J.F.M. (author)An investigation of existing literature reveals that guitar players are most prone to musculoskeletal injuries amongst all musicians. In the light of recent injuries to prominent guitar players such as Eddie Van Halen, this article explores ergonomics of electric guitars. By means of surveys, user observations, biomechanical analysis and...journal article 2013
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Lee, M. (author), Lipfert, J. (author), Sanchez, H. (author), Wyman, C. (author), Dekker, N.H. (author)Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two...journal article 2013
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Dekker, R. (author)“A what on a chip?” is what most people ask with disbelief when they hear for the first time of the new and very exciting research area “Organ on a Chip.” The topic has nothing to do with Science Fiction, but everything with a very surprising encounter between two completely different research fields: Microfabrication and Stem-Cell Biology! The...journal article 2013
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Moolman, M.C. (author), Huang, Z. (author), Krishnan, S.T. (author), Kerssemakers, J.W.J. (author), Dekker, N.H. (author)Background: Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this...journal article 2013
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Mimoun, B.A.Z. (author), Pham, H.T.M. (author), Henneken, V. (author), Dekker, R. (author)The authors have found that patterning polyimide coatings containing organosilane adhesion promoter using pure oxygen plasma resulted in a thin silicon-rich residue layer. They show in this paper that adding small amounts of fluorine-containing gas to the etching gas mixture is necessary in order to achieve residue-free polyimide plasma etching....journal article 2013
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Dulin, D. (author), Lipfert, J. (author), Moolman, M.C. (author), Dekker, N.H. (author)To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in...journal article 2013
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Vlijm, R. (author), Smitshuijzen, J.S.J. (author), Lusser, A. (author), Dekker, C. (author)While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching...journal article 2012
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Khoshfetrat Pakazad, S. (author), Savov, A. (author), Braam, S.R. (author), Dekker, R. (author)A platform for the batch fabrication of pneumatically actuated Stretchable Micro-Electrode Arrays (SMEAs) by using state-of-the-art micro-fabrication techniques and materials is demonstrated. The proposed fabrication process avoids the problems normally associated with processing of thin film structures on polydimethylsiloxane (PDMS), by first...journal article 2012
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Calado, V.E. (author), Schneider, G.F. (author), Theulings, A.M.M.G. (author), Dekker, C. (author), Vandersypen, L.M.K. (author)We study the formation of wrinkles in graphene upon wet transfer onto a hydrophilic target substrate, whereby draining of water appears to play an important role. We are able to control the orientation of the wrinkles by tuning the surface morphology. Wrinkles are absent in flakes transferred to strongly hydrophobic substrates, a further...journal article 2012
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De Vlaminck, I. (author), Henighan, T. (author), Van Loenhout, M.T.J. (author), Burnham, D.R. (author), Dekker, C. (author)Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization...journal article 2012
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De Vlaminck, I. (author), Van Loenhout, M.T.J. (author), Zweifel, L. (author), Den Blanken, J. (author), Hooning, K. (author), Hage, S. (author), Kerssemakers, J. (author), Dekker, C. (author)In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining...journal article 2012
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Non-Bias-Limited Tracking of Spherical Particles, Enabling Nanometer Resolution at Low MagnificationVan Loenhout, M.T.J. (author), Kerssemakers, J.W.J. (author), De Vlaminck, I. (author), Dekker, C. (author)We present a three-dimensional tracking routine for nondiffraction-limited particles, which significantly reduces pixel bias. Our technique allows for increased resolution compared to that of previous methods, especially at low magnification or at high signal/noise ratio. This enables tracking with nanometer accuracy in a wide field of view and...journal article 2012