Kavli Institute of Nanoscience

Delft, Netherlands

Kavli Institute of Nanoscience

Delft, Netherlands
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News Article | February 16, 2017
Site: www.eurekalert.org

It is the most crucial mechanism in life - the division of cells. For 25 years, it has been known that bacteria split into two by forming a Z ring at their centre. They use this to cut themselves into two daughter cells. Using advanced microscopes, researchers from the universities of Harvard, Indiana, Newcastle, and Delft have succeeded in finding out how bacteria do this. The bacteria appear to build a new cell wall working from the outside in with the help of multiple molecular 'bricklayers', in about a quarter of an hour¬¬. What was completely unexpected was that the 'bricklayers' move along the inside of the wall under construction by 'treadmilling'; the building of the cell wall is performed from scaffolding that is continuously being moved at the front, while at the rear it is continuously being dismantled. The scientists will be publishing an article on the topic in Science on 17 February. They investigated the process by viewing individual bacteria through advanced microscopes. This involved putting coloured labels on the cell wall material. By changing the colours every time, they were able to see that the bacteria were building the cell walls from the outside in. And by changing the colours of the building material with breaks of just a few seconds, they were also able to see that this is not a gradual process, but one that takes place in a different location each time. The engine that drives all of this is FtsZ, a protein that makes an arched -haped piece of polymer, and which appears to move via a phenomenon known as 'treadmilling', named after the old treadmills from the Middle Ages. "With treadmilling, you create movement by adding something on the front, while removing something from the rear," explains Professor Cees Dekker of TU Delft, a co-author on the article. "Our research shows that a cell also uses this phenomenon for building a cell wall." Cell walls are built with the help of a number of collaborating proteins, with FtsZ playing the most important part. "Our new discovery has solved the 25-year-old puzzle of how FtsZ coordinates cell division. The protein appears to work like a kind of scaffolding, on which the building work takes place. However, it is not rolling scaffolding, but fixed scaffolding that is continuously renovating itself: all the time, the cell is building new scaffolding boards for the work on the cell wall on, let's say, the right-hand side of the FtsZ scaffolding, while breaking up the now-superfluous scaffolding on the left-hand side, at the rear end of the work. This way, the scaffolding shifts along the cell wall. The building machine that produces the cell wall is controlled from the scaffolding, therefore moving neatly in tandem with the slowly moving scaffolding. The cell does this with different sets of scaffolding along the cell wall simultaneously, resulting in the construction of a partition wall in ten or fifteen minutes. Meanwhile, other proteins make sure that the DNA is divided properly between the two halves, for example, or that the membrane is properly closed off, and so on. The division of cells is a complex and fascinating process." The study was a collaborative project involving researchers from four scientific groups, in the US, the UK, and Delft. The most significant contribution from Delft consisted of the production of nanostructures in which exactly one bacterium fits, lengthwise. "By placing the nanoboxes upright on the microscope, we were able to see in very sharp focus a cross-section of the cell. This gave us an excellent view of the dynamics of the FtsZ molecules. An important technical contribution." explains Dekker. Although the study is fundamental in nature, Dekker believes that this type of research may be of practical benefit in the future. "Once we have a thorough understanding of how bacterial cells divide, it could pave the way towards alternative antibiotics. That is still some way off, but if we are able to disrupt bacterial cell division in a targeted manner, we may have new weapons in the future that we can use to fight bacteria that cause disease." 1Molecular and Cellular Biology, Faculty of Arts andSciences (FAS) 1Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. 2Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA. 3Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Netherlands. 4Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK. 5Department of Chemistry, Indiana University, Bloomington, IN 47405, USA. 6Department of Biology, Indiana University, Bloomington, IN 47405, USA. *Present address: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. †Present address: Division of Geology and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA. ‡These authors contributed equally to this work. §Corresponding author.

Kouwen M.P.V.,Kavli Institute of Nanoscience | Reimer M.E.,Kavli Institute of Nanoscience | Hidma A.W.,Kavli Institute of Nanoscience | Van Weert M.H.M.,Kavli Institute of Nanoscience | And 6 more authors.
Nano Letters | Year: 2010

We report optical experiments of a charge tunable, single nanowire quantum dot subject to an electric field tuned by two independent voltages. First, we control tunneling events through an applied electric field along the nanowire growth direction. Second, we modify the chemical potential in the nanowire with a back-gate. We combine these two field-effects to isolate a single electron and independently tune the tunnel coupling of the quantum dot with the contacts. Such charge control is a first requirement for opto-electrical single electron spin experiments on a nanowire quantum dot. © 2010 American Chemical Society.

Schneider G.F.,Kavli Institute of Nanoscience | Kowalczyk S.W.,Kavli Institute of Nanoscience | Calado V.E.,Kavli Institute of Nanoscience | Pandraud G.,Kavli Institute of Nanoscience | And 3 more authors.
Nano Letters | Year: 2010

Nanopores-nanosized holes that can transport ions and molecules-are very promising devices for genomic screening, in particular DNA sequencing. Solid-state nanopores currently suffer from the drawback, however, that the channel constituting the pore is long, ∼100 times the distance between two bases in a DNA molecule (0.5 nm for single-stranded DNA). This paper provides proof of concept that it is possible to realize and use ultrathin nanopores fabricated in graphene monolayers for single-molecule DNA translocation. The pores are obtained by placing a graphene flake over a microsize hole in a silicon nitride membrane and drilling a nanosize hole in the graphene using an electron beam. As individual DNA molecules translocate through the pore, characteristic temporary conductance changes are observed in the ionic current through the nanopore, setting the stage for future single-molecule genomic screening devices. © 2010 American Chemical Society.

Schneider G.F.,Kavli Institute of Nanoscience | Calado V.E.,Kavli Institute of Nanoscience | Zandbergen H.,Kavli Institute of Nanoscience | Vandersypen L.M.K.,Kavli Institute of Nanoscience | Dekker C.,Kavli Institute of Nanoscience
Nano Letters | Year: 2010

We report a versatile water-based method for transferring nanostructures onto surfaces of various shapes and compositions. The transfer occurs through the intercalation of a layer of water between a hydrophilic substrate and a hydrophobic nanostructure (for example, graphene flakes, carbon nanotubes, metallic nanostructures, quantum dots, etc.) locked within a hydrophobic polymer thin film. As a result, the film entrapping the nanostructure is lifted off and floats at the air-water interface. The nanostructure can subsequently be deposited onto a target substrate by the removal of the water and the dissolution of the polymeric film. We show examples where graphene flakes and patterned metallic nanostructures are precisely transferred onto a specific location on a variety of patterned substrates, even on top of curved objects such as microspheres. The method is simple to use, fast, and does not require advanced equipment. © 2010 American Chemical Society.

Weyher J.L.,Polish Academy of Sciences | Tichelaar F.D.,Kavli Institute of Nanoscience | Van Dorp D.H.,University Utrecht | Kelly J.J.,University Utrecht | Khachapuridze A.,Polish Academy of Sciences
Journal of Crystal Growth | Year: 2010

A recently developed photoetching system for n-type GaN, a KOH solution containing the strong oxidizing agent potassium peroxydisulphate (K 2S2O8), was studied in detail. By careful selection of the etching parameters, such as the ratio of components and the hydrodynamics, two distinct modes were defined: defect-selective etching (denoted by KSO-D) and polishing (KSO-P). Both photoetching methods can be used under open-circuit (electroless) conditions. Well-defined dislocation-related etch whiskers are formed during KSO-D etching. All types of dislocations are revealed, and this was confirmed by cross-sectional TEM examination of the etched samples. Extended electrically active defects are also clearly revealed. The known relationship between etch rate and carrier concentration for photoetching of GaN in KOH solutions was confirmed for KSO-D etch using Raman measurements. It is shown that during KSO-P etching diffusion is the rate-limiting step, i.e. this etch is suitable for polishing of GaN. Some constraints of the KSO etching system for GaN are discussed and peculiar etch features, so far not understood, are described. © 2010 Elsevier B.V. All rights reserved.

Ali M.,Stanford University | Lipfert J.,Kavli Institute of Nanoscience | Seifert S.,Argonne National Laboratory | Herschlag D.,Stanford University | Doniach S.,Stanford University
Journal of Molecular Biology | Year: 2010

Riboswitches are elements of mRNA that regulate gene expression by undergoing structural changes upon binding of small ligands. Although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. The ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the RNA, with conformational heterogeneity that makes it particularly challenging to study. Here, we present models of the ligand-free state of a thiamine pyrophosphate riboswitch that are derived from a combination of complementary experimental and computational modeling approaches. We obtain a global picture of the molecule using small-angle X-ray scattering data and use an RNA structure modeling software, MC-Sym, to fit local structural details to these data on an atomic scale. We have used two different approaches to obtaining these models. Our first approach develops a model of the RNA from the structures of its constituent junction fragments in isolation. The second approach treats the RNA as a single entity, without bias from the structure of its individual constituents. We find that both approaches give similar models for the ligand-free form, but the ligand-bound models differ for the two approaches, and only the models from the second approach agree with the ligand-bound structure known previously from X-ray crystallography. Our models provide a picture of the conformational changes that may occur in the riboswitch upon binding of its ligand. Our results also demonstrate the power of combining experimental small-angle X-ray scattering data with theoretical structure prediction tools in the determination of RNA structures beyond riboswitches. © 2009 Elsevier Ltd. All rights reserved.

Witek B.J.,Kavli Institute of Nanoscience | Heeres R.W.,Kavli Institute of Nanoscience | Perinetti U.,Kavli Institute of Nanoscience | Bakkers E.P.A.M.,Kavli Institute of Nanoscience | And 3 more authors.
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

We perform polarization-resolved magneto-optical measurements on single InAsP quantum dots embedded in an InP nanowire. In order to determine all elements of the electron and hole g-factor tensors, we measure in magnetic fields with different orientations. The results of these measurements are in good agreement with a model based on exchange terms and Zeeman interaction. In our experiment, polarization analysis delivers a powerful tool that not only significantly increases the precision of the measurements, but also enables us to probe the exciton spin-state evolution in magnetic fields. We propose a disentangling scheme of heavy-hole exciton spins enabling a measurement of the electron spin T2-time. © 2011 American Physical Society.

Mejia J.,University of Namur | Tichelaar F.,Kavli Institute of Nanoscience | Saout C.,University of Namur | Toussaint O.,University of Namur | And 4 more authors.
Journal of Nanoparticle Research | Year: 2011

Multi-walled carbon nanotubes (MWC NTs) were dispersed in water and in a Pluronic F108 solution by four different dispersion methods (stirring, bath sonication, stirring followed by bath sonication, and sonication probe). The effect of the dispersion methods were evaluated in terms of the particle size distribution, the agglomerates size, and the exfoliated fraction produced, as well as in terms of the surface and bulk chemical composition. Energy dispersive X-ray, X-ray photoelectron spectroscopy, and centrifugal liquid sedimentation techniques were used to characterize pristine MWCNTs and their dispersion. It is shown that, irrespective of the dispersion methods used, the MWCNTs are strongly wrapped with the biocompatible surfactant Pluronic F108, thereby modifying the external surface of the MWCNTs. Some shortening of MWCNTs and more wrapping are also observed when sonication methods are used. These observations raise questions as to the validity of results obtained in toxicology tests, in vitro and in vivo, were such methods of dispersion procedures are used. © Springer Science+Business Media B.V. 2010.

News Article | April 25, 2016
Site: www.rdmag.com

Small objects like electrons and atoms behave according to quantum mechanics, with quantum effects like superposition, entanglement and teleportation. One of the most intriguing questions in modern science is if large objects – like a coffee cup - could also show this behavior. Scientists at the TU Delft have taken the next step towards observing quantum effects at everyday temperatures in large objects. They created a highly reflective membrane, visible to the naked eye, that can vibrate with hardly any energy loss at room temperature. The membrane is a promising candidate to research quantum mechanics in large objects. The team has reported their results in Physical Review Letters. "Imagine you're given a single push on a playground swing. Now imagine this single push allows you to gleefully swing non-stop for nearly a decade. We have created a millimeter-sized version of such a swing on a silicon chip", says prof. Simon Gröblacher of the Kavli Institute of Nanoscience at the TU Delft. "In order to do this, we deposit ultra-thin films of ceramic onto silicon chips. This allows us to engineer a million psi of tensile stress, which is the equivalent of 10,000 times the pressure in a car tire, into millimeter-sized suspended membranes that are only eight times thicker than the width of DNA", explains dr. Richard Norte, lead author of the publication. "Their immense stored energies and ultra-thin geometry mean that these membranes can oscillate for tremendously long times by dissipating only small amounts of energy." To efficiently monitor the motion of the membranes with a laser they need to be extremely reflective. In such a thin structure, this can only be achieved by creating a meta-material through etching a microscopic pattern into the membrane. "We actually made the thinnest super-mirrors ever created, with a reflectivity exceeding 99%. In fact, these membranes are also the world's best force sensors at room temperature, as they are sensitive enough to measure the gravitational pull between two people 100 km apart from each other", Richard Norte says. "The high-reflectivity, in combination with the extreme isolation, allows us to overcome a major hurdle towards observing quantum physics with massive objects, for the first time, at room temperature", says Gröblacher. Because even a single quantum of vibration is enough to heat up and destroy the fragile quantum nature of large objects (in a process called decoherence), researchers have relied on large cryogenic systems to cool and isolate their quantum devices from the heat present in our everyday environments. Creating massive quantum oscillators which are robust to decoherence at room temperature has remained an elusive feat for physicists. This is extremely interesting from a fundamental theoretical point of view. One of the strangest predictions of quantum mechanics is that things can be in two places at the same time. Such quantum 'superpositions' have now been clearly demonstrated for tiny objects such as electrons or atoms, where we now know that quantum theory works very well. But quantum mechanics also tells us that the same rules should also apply for macroscopic objects: a coffee cup can be on the table and in the dishwasher at the same time, or Schrödinger's cat can be in a quantum superposition of being dead and alive. This is however not something we see in our daily lives: the coffee cup is either clean or dirty and the cat is either dead or alive. Experimentally demonstrating a proverbial cat that is simultaneously dead and alive at ambient temperatures is still an open question in quantum mechanics. The steps taken in this research might allow to eventually observe 'quantum cats' on everyday life scales and temperatures.

News Article | January 22, 2016
Site: phys.org

By blowing extremely small bubbles, researchers from the Kavli Institute of Nanoscience at Delft University of Technology (TU Delft) have found an efficient way of producing so-called liposomes – very small bubble-like structures often used to deliver medicine, but also key to generating artificial cells. The scientists publish their findings in the online edition of Nature Communications on Friday 22 January.

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