| 1. |
- Fernandez, Yuri A. Diaz, 1978, et al.
(författare)
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Research Update: Progress in synthesis of nanoparticle dimers by self-assembly
- 2014
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Ingår i: APL Materials. - : AIP Publishing. - 2166-532X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- This article highlights recent advances in the controlled self-assembly of nanoparticles to produce dimeric nanoparticle structures. The relevance of this emergent field is discussed in terms of recent applications in plasmonics and chemical catalysis. The concept of bond-valence applied to nanoparticles will be discussed, emphasizing some general approaches that have been successfully used to build these structures. Further, the asymmetric functionalization of nanoparticles surfaces as a path to drive selective aggregation, the use of biomolecules to self-assemble nanoparticles into dimers in solution, and the confinement of aggregates in small cavities are discussed.
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| 2. |
- Gravgaard Askjær, Thomas, et al.
(författare)
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Multi-centennial Holocene climate variability in proxy records and transient model simulations
- 2022
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 296
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Tidskriftsartikel (refereegranskat)abstract
- Variability on centennial to multi-centennial timescales is mentioned as a feature in reconstructions of the Holocene climate. As more long transient model simulations with complex climate models become available and efforts have been made to compile large proxy databases, there is now a unique opportunity to study multi-centennial variability with greater detail and a large amount of data than earlier. This paper presents a spectral analysis of transient Holocene simulations from 9 models and 120 proxy records to find the common signals related to oscillation periods and geographic dependencies and discuss the implications for the potential driving mechanisms. Multi-centennial variability is significant in most proxy records, with the dominant oscillation periods around 120–130 years and an average of 240 years. Spectra of model-based global mean temperature (GMT) agree well with proxy evidence with significant multi-centennial variability in all simulations with the dominant oscillation periods around 120–150 years. It indicates a comparatively good agreement between model and proxy data. A lack of latitudinal dependencies in terms of oscillation period is found in both the model and proxy data. However, all model simulations have the highest spectral density distributed over the Northern hemisphere high latitudes, which could indicate a particular variability sensitivity or potential driving mechanisms in this region. Five models also have differentiated forcings simulations with various combinations of forcing agents. Significant multi-centennial variability with oscillation periods between 100 and 200 years is found in all forcing scenarios, including those with only orbital forcing. The different forcings induce some variability in the system. Yet, none appear to be the predominant driver based on the spectral analysis. Solar irradiance has long been hypothesized to be a primary driver of multi-centennial variability. However, all the simulations without this forcing have shown significant multi-centennial variability. The results then indicate that internal mechanisms operate on multi-centennial timescales, and the North Atlantic-Arctic is a region of interest for this aspect.
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| 3. |
- Stroth, U., et al.
(författare)
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Progress from ASDEX Upgrade experiments in preparing the physics basis of ITER operation and DEMO scenario development
- 2022
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 62:4
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Tidskriftsartikel (refereegranskat)abstract
- An overview of recent results obtained at the tokamak ASDEX Upgrade (AUG) is given. A work flow for predictive profile modelling of AUG discharges was established which is able to reproduce experimental H-mode plasma profiles based on engineering parameters only. In the plasma center, theoretical predictions on plasma current redistribution by a dynamo effect were confirmed experimentally. For core transport, the stabilizing effect of fast ion distributions on turbulent transport is shown to be important to explain the core isotope effect and improves the description of hollow low-Z impurity profiles. The L-H power threshold of hydrogen plasmas is not affected by small helium admixtures and it increases continuously from the deuterium to the hydrogen level when the hydrogen concentration is raised from 0 to 100%. One focus of recent campaigns was the search for a fusion relevant integrated plasma scenario without large edge localised modes (ELMs). Results from six different ELM-free confinement regimes are compared with respect to reactor relevance: ELM suppression by magnetic perturbation coils could be attributed to toroidally asymmetric turbulent fluctuations in the vicinity of the separatrix. Stable improved confinement mode plasma phases with a detached inner divertor were obtained using a feedback control of the plasma β. The enhanced D α H-mode regime was extended to higher heating power by feedback controlled radiative cooling with argon. The quasi-coherent exhaust regime was developed into an integrated scenario at high heating power and energy confinement, with a detached divertor and without large ELMs. Small ELMs close to the separatrix lead to peeling-ballooning stability and quasi continuous power exhaust. Helium beam density fluctuation measurements confirm that transport close to the separatrix is important to achieve the different ELM-free regimes. Based on separatrix plasma parameters and interchange-drift-Alfvén turbulence, an analytic model was derived that reproduces the experimentally found important operational boundaries of the density limit and between L- and H-mode confinement. Feedback control for the X-point radiator (XPR) position was established as an important element for divertor detachment control. Stable and detached ELM-free phases with H-mode confinement quality were obtained when the XPR was moved 10 cm above the X-point. Investigations of the plasma in the future flexible snow-flake divertor of AUG by means of first SOLPS-ITER simulations with drifts activated predict beneficial detachment properties and the activation of an additional strike point by the drifts.
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| 4. |
- Sun, Lu, 1982, et al.
(författare)
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Characterization of self-assembled DNA concatemers from synthetic oligonucleotides
- 2014
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Ingår i: Computational and Structural Biotechnology Journal. - : Elsevier BV. - 2001-0370. ; 11:18, s. 66-72
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Tidskriftsartikel (refereegranskat)abstract
- Studies of DNA–ligand interaction on a single molecule level provide opportunities to understand individual behavior of molecules. Construction of DNA molecules with repetitive copies of the same segments of sequences linked in series could be helpful for enhancing the interaction possibility for sequence-specific binding ligand to DNA. Here we report on the use of synthetic oligonucleotides to self-assembly into duplex DNA concatemeric molecules. Two strands of synthetic oligonucleotides used here were designed with 50-mer in length and the sequences are semi-complimentary so to hybridize spontaneously into concatemers of double stranded DNA. In order to optimize the length of the concatemers the oligonucleotides were incubated at different oligomer concentrations, ionic strengths and temperatures for different durations. Increasing the salt concentration to 200 mM NaCl was found to be the major optimizing factor because at this enhanced ionic strength the concatemers formed most quickly and the other parameters had no detectable effect. The size and shape of formed DNA concatemers were studied by gel electrophoresis in agarose, polyacrylamide gels and by AFM. Our results show that linear DNA constructs up to several hundred base pairs were formed and could be separated from a substantial fraction of non-linear constructs.
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| 5. |
- Sun, Lu, 1982
(författare)
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Concatemerization of Synthetic Oligonucleotides
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- DNA nanotechnology has become an important research field because of its advantages in high predictability and accuracy of base-paring recognition. For example, the DNA concatemer, one of the simplest DNA constructs in shape, has been used to enhance signals in biosensing. In this thesis, concatemers were designed and characterized towards sequence-specific target amplifiers for single molecule mechanical studies. The project firstly focuses on exploring how to obtain concatemers of satisfactory length by self-assembly in bulk. Concatemers formed in solution by mixing of the different components were characterized by gel electrophoresis and AFM. Experimental results show that the concatemer yield could be increased primarily by increasing the ionic strength, and linear concatemers of expected length could be separated from mixed sizes and shapes. As an alternative, a platform for concatemer formation based on a planar surface was investigated by immobilizing and sequentially hybridizing oligonucleotides to concatemers. This method was further improved by involving click-reaction to link the nicks on backbones of the concatemers. QCM-D and SPR were utilized to monitor the step-by-step construction process. Gel electrophoresis shows that concatemers with desired length were successfully formed in a controllable manner. Furthermore, the surface-based concatemer formation platform was applied to study DNA-ligand interaction using QCM-D and SPR. We selected three ligands, known to bind to DNA: spermidine, spermine and RAD51. We observed that polyamines condense the DNA layers; by contrast, RAD51 induces an extension of the DNA layer. This study provides some guidelines for QCM-D and SPR-based characterization of changes in the properties of DNA films (e.g., thickness, viscoelastic properties) on sensor surfaces. It is interesting to correlate these changes to structural and mechanical changes induced in single DNA molecules upon ligand binding. The biosensing approach provides rapid access to kinetic data of DNA-ligand interactions, which is typically useful in various screening applications.
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| 6. |
- Sun, Lu, 1982
(författare)
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Concatemerization of Synthetic Oligonucleotides, Assembly on Surface and Ligand Interactions
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- DNA nanotechnology has become an important research field because of its advantages in high predictability and accuracy of base-paring recognition. DNA concatemer, one of the simplest DNA constructs in shape, have been found as efficient signal amplifiers in several biosensors for different applications. In this thesis, formation of concatemers as sequence-specific target amplifier for single molecular mechanical study was constructed and characterized. The research work firstly focuses on exploring to obtain concatemers in satisfactory length by self-assembled method via varying incubation conditions. Formed concatemers were characterized by gel electrophoresis and AFM. Experimental results show that the efficiency of forming concatemers could be optimized primarily by increasing ionic strength. Moreover, linear concatemers with expected length could be separated from mixed sizes and shapes.In the second part, an attempt of establishing a platform on planar surface is investigated by immobilizing and sequentially hybridizing oligonucleotides to concatemers. This method is further improved by involving click-reaction to link the nicks on the backbones. QCM-D and SPR were utilized to monitor the step by step construction process. Gel electrophoresis shows that concatemers with desired length were successfully formed in a controllable manner. Finally, we apply the concatemer formation platform to study DNA-ligand interaction using QCM-D. We selected three ligands to bind to DNA: spermidine, spermine and RAD51. We observe that polyamines condense the DNA layers; by contrast, RAD51 induces an extension of the DNA layer. This study provides some guidelines for a QCM-D biosensor based on ligand-induced structural changes of DNA films.
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| 7. |
- Sun, Lu, 1982, et al.
(författare)
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Construction and Modeling of Concatemeric DNA Multilayers on a Planar Surface as Monitored by QCM-D and SPR
- 2014
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 30:28, s. 8432-8441
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Tidskriftsartikel (refereegranskat)abstract
- The sequential hybridization of a 534 base pair DNA concatemer layer was monitored by QCM-D and SPR, and the QCM-D data were analyzed by Voigt viscoelastic models. The results show that Voigt-based modeling gives a good description of the experimental data but only if shear viscosity and elasticity are allowed to depend on the shear frequency. The derived layer thickness, shear viscosity and elasticity of the growing film give a representation of the DNA film in agreement with known bulk properties of DNA, and reveal a maximum in film viscosity when the molecules in the layer contain 75 base pairs. The experimental data during construction of a 3084 bp DNA concatemer layer were compared to predictions of the QCM-D response of a 1 mu m thick film of rod-like polymers. A predicted nonmonotonous variation of dissipation with frequency (added mass) is in qualitative agreement with the experiments, but with a quantitative disagreement which likely reflects that the flexibility of such long DNA molecules is not included in the model.
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| 8. |
- Sun, Lu, 1982
(författare)
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Formation and Characterization of DNA Concatemers for Single Molecule Mechanism Studies
- 2012
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Well known as genetic information carrier, DNA however, in the past three decade experienced a revolution to become a fashionable fabrication material in nanotechnology as a consequence of the high predictability and accuracy of base-paring recognition. Although DNA can be constructed in many fancy 2D and 3D structures, this thesis work focused on constructing one-dimension linear DNA concatemers in order to study sequence specific DNA-ligand binding at the single-molecule level. This thesis presents two methods of assembly of DNA concatemers by synthetic oligonucleotides. The first method investigated hybridization of desired oligonucleotides insolution with aiming to optimize the length of the concatemers. Gel electrophoresis and AFM were used to check the size and shapes of the formed concatemers. Results showed by inceasing ionic strength at 200 mM NaCl, concatemers were formed most quickly. Concatemers with lengths up to several hundred base pairs was successfully constructed and separated from those non-linear shaped DNA. With the same purpose of forming linear DNA concatemers, the second method provide a strategy of building DNA concatemers on a solid surface with the same sequence of oligonucleotides. Biotin-oligonucleotides were involved to immobilize on the surface. Furthermore, to avoid formation of non-linear DNA constructs, DNA were hybridized layer by layer. QCM-D was used to monitor the process of construction as well as study the viscoelasticity of the formed DNA layers. Result indicated that DNA multilayers were constructed. To confirm this, constructed DNA were cleaved off the surface and checked for sizes by running in gel electrophoresis. Clear bands in the image strongly supported that each hybridization step on surface was complete and DNA concatemers were successfully constructed.
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| 9. |
- Sun, Lu, 1982, et al.
(författare)
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Sensing Conformational Changes in DNA upon Ligand Binding Using QCM-D. Polyamine Condensation and Rad51 Extension of DNA Layers
- 2014
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:41, s. 11895-11904
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Tidskriftsartikel (refereegranskat)abstract
- Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59–184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film deformation allows comparative studies of two or more analytes using the same DNA layer as demonstrated here by spermine and spermidine.
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| 10. |
- Ulfkjær, Anne, et al.
(författare)
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A gold-nanoparticle stoppered [2]rotaxane
- 2018
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 10:19, s. 9133-9140
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Tidskriftsartikel (refereegranskat)abstract
- The construction of molecular machines has captured the imagination of scientists for decades. Despite significant progress in the synthesis and studies of the properties of small-molecule components (smaller than 2-5 kilo Dalton), challenges regarding the incorporation of molecular components into real devices are still eminent. Nano-sized molecular machines operate the complex biological machinery of life, and the idea of mimicking the amazing functions using artificial nano-structures is intriguing. Both in small-molecule molecular machine components and in many naturally occurring molecular machines, mechanically interlocked molecules and structures are key functional components. In this work, we describe our initial efforts to interface mechanically-interlocked molecules and gold-nanoparticles (AuNPs); the molecular wire connecting the AuNPs is covered in an insulating rotaxane-layer, thus mimicking the macroscopic design of a copper wire. Taking advantage of recent progress in the preparation of supramolecular complexes of the cucurbit[7]uril (CB[7] ) macrocycle, we have prepared a bis-thiol functionalised pseudo-rotaxane that enables us to prepare a AuNP-stoppered [2]rotaxane in water. The pseudo-rotaxane is held together extremely tightly (K a > 10 13 M -1 ), K a being the association constant. We have studied the solution and gas phase guest-host chemistry using NMR spectroscopy, mass spectroscopy, and electrochemistry. The bis-thiol functionalised pseudo-rotaxane holds further a ferrocene unit in the centre of the rotaxane; this ferrocene unit enables us to address the system in detail with and without CB[7] and AuNPs using electrochemical methods.
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