Johan R. C. van der Maarel

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Encapsulation of dsDNA fragments (contour length 54 nm) by the cationic diblock copolymer poly(butadiene-b-N-methyl-4-vinyl pyridinium) [PBd-b-P4VPQ] has been studied with phase contrast, polarized light, and fluorescence microscopies, as well as scanning electron microscopy. Encapsulation was achieved with a single emulsion technique. For this purpose, an(More)
Increasing evidence supports the contribution of local inflammation to the development of Alzheimer's disease (AD) pathology, although the precise mechanisms are not clear. In this study, we demonstrate that the pro-inflammatory protein S100A9 interacts with the Aβ1-40 peptide and promotes the formation of fibrillar β-amyloid structures. This interaction(More)
Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its(More)
We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and(More)
We report an approach to study the in situ conformational response of single biomolecules such as DNA to a change in environmental solution conditions. These conditions are, for example, the composition of the buffer or the presence of protein. For this purpose, we designed and fabricated a nanofluidic device featuring two arrays of parallel nanochannels in(More)
The effect of the bacterial heat-stable nucleoid-structuring protein (H-NS) on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. With increasing concentration of H-NS, the DNA molecules either elongate or contract. The conformational response is related to filamentation of H-NS on DNA through(More)
The effects of the like-charged proteins bovine serum albumin and hemoglobin on the conformation and compaction of single DNA molecules confined in rectangular nanochannels were investigated with fluorescence microscopy. The channels have lengths of 50 μm and cross-sectional diameters in the range of 80-300 nm. In the wider channels, the DNA molecules are(More)
Artificial nanowalkers are inspired by biomolecular counterparts from living cells, but remain far from comparable to the latter in design principles. The walkers reported to date mostly rely on chemical mechanisms to gain a direction; they all produce chemical wastes. Here we report a light-powered DNA bipedal walker based on a design principle derived(More)
DNA conformation in slitlike confinement is studied using Monte Carlo simulation and scaling theory. We focus on analysing the in-plane DNA extension as a function of slit height and DNA properties, such as contour length, persistence length and width. Similar to tube confinement, we identify an extended de Gennes regime which is prevalent in many(More)
Monte Carlo simulations are used to study the knotting probability of circular DNA confined in a slit. We systematically vary the slit height, the width, and the contour length of the DNA molecule. We find that the trend in knotting probability with respect to slit height can be monotonic or nonmonotonic, depending on the width and contour length. The(More)