| 41. |
- Nilsson, Adam, et al.
(författare)
-
Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
- 2014
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 42:15, s. 118-118
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.
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| 42. |
- Nilsson, Sara, 1990, et al.
(författare)
-
Competing oxidation mechanisms in Cu nanoparticles and their plasmonic signatures
- 2022
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 14:23, s. 8332-8341
-
Tidskriftsartikel (refereegranskat)abstract
- Chemical reactions involving nanoparticles often follow complex processes. In this respect, real-time probing of single nanoparticles under reactive conditions is crucial for uncovering the mechanisms driving the reaction pathway. Here, we have captured in situ the oxidation of single Cu nanoparticles to unravel a sequential competitive activation of different mechanisms at temperatures 50-200 degrees C. Using environmental scanning transmission electron microscopy, we monitor the evolution of oxide formation with sub-nanometre spatial resolution, and show how the prevalence of oxide island nucleation, Cabrera-Mott, Valensi-Carter and Kirkendall mechanisms under different conditions determines the morphology of the particles. Moreover, using in situ electron energy-loss spectroscopy, we probe the localised surface plasmons of individual particles during oxidation, and with the aid of finite-difference time-domain electrodynamic simulations investigate the signature of each mechanism in their plasmonic response. Our results shed light on the rich and intricate processes involved in the oxidation of nanoparticles, and provide in-depth insight into how these processes govern their morphology and optical response, beneficial for applications in catalysis, sensing, nanomedicine and plasmonics.
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| 43. |
- Nilsson, Sara, 1990, et al.
(författare)
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Probing the role of grain boundaries in single Cu nanoparticle oxidation by in situ plasmonic scattering
- 2022
-
Ingår i: Physical Review Materials. - 2475-9953. ; 6:4
-
Tidskriftsartikel (refereegranskat)abstract
- Grain boundaries determine physical properties of bulk materials including ductility, diffusivity, and electrical conductivity. However, the role of grain boundaries in nanostructures and nanoparticles is much less understood, despite the wide application of nanoparticles in nanophotonics, nanoelectronics, and heterogeneous catalysis. Here, we investigate the role of high-angle grain boundaries in the oxidation of Cu nanoparticles, using a combination of in situ single particle plasmonic nanoimaging and postmortem transmission electron microscopy image analysis, together with ab initio and classical electromagnetic calculations. We find an initial growth of a 5-nm-thick Cu2O shell on all nanoparticles, irrespective of different grain morphologies. This insensitivity of the Cu2O shell on the grain morphology is rationalized by extraction of Cu atoms from the metal lattice being the rate limiting step, as proposed by density functional theory calculations. Furthermore, we find that the change in optical scattering intensity measured from the individual particles can be deconvoluted into one contribution from the oxide layer growth and one contribution that is directly proportional to the grain boundary density. The latter contribution signals accumulation of Cu vacancies at the grain boundaries, which, as corroborated by calculations of the optical scattering, leads to increased absorption losses and thus a decrease of the scattering, thereby manifesting the role of grain boundaries as vacancy sinks and nuclei for Kirkendall void formation at a later stage of the oxidation process.
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| 44. |
- Nilsson, Sara, 1990, et al.
(författare)
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Resolving single Cu nanoparticle oxidation and Kirkendall void formation with in situ plasmonic nanospectroscopy and electrodynamic simulations
- 2019
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 11:43, s. 20725-20733
-
Tidskriftsartikel (refereegranskat)abstract
- Copper nanostructures are ubiquitous in microelectronics and heterogeneous catalysis and their oxidation is a topic of high current interest and broad relevance. It relates to important questions, such as catalyst active phase, activity and selectivity, as well as fatal failure of microelectronic devices. Despite the obvious importance of understanding the mechanism of Cu nanostructure oxidation, numerous open questions remain, including under what conditions homogeneous oxide layer growth occurs and when the nanoscale Kirkendall void forms. Experimentally, this is not trivial to investigate because when a large number of nanoparticles are simultaneously probed, ensemble averaging makes rigorous conclusions difficult. On the other hand, when (in situ) electron-microscopy approaches with single nanoparticle resolution are applied, concerns about beam effects that may both reduce the oxide or prevent oxidation via the deposition and cross-linking of carbonaceous species cannot be neglected. In response we present how single particle plasmonic nanospectroscopy can be used for the in situ real time characterization of multiple individual Cu nanoparticles during oxidation. Our analysis of their optical response combined with post mortem electron microscopy imaging and detailed Finite-Difference Time-Domain electrodynamics simulations enables in situ identification of the oxidation mechanism both in the initial oxide shell growth phase and during Kirkendall void formation, as well as the transition between them. In a wider perspective, this work presents the foundation for the application of single particle plasmonic nanospectroscopy in investigations of the impact of parameters like particle size, shape and grain structure with respect to defects and grain boundaries on the oxidation of metal nanoparticles.
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| 45. |
- Nilsson, Sara, 1990, et al.
(författare)
-
The Role of Grain Boundary Sites for the Oxidation of Copper Catalysts during the CO Oxidation Reaction
- 2023
-
Ingår i: ACS Nano. - 1936-086X .- 1936-0851. ; 17:20, s. 20284-20298
-
Tidskriftsartikel (refereegranskat)abstract
- The oxidation of transition metal surfaces is a process that takes place readily at ambient conditions and that, depending on the specific catalytic reaction at hand, can either boost or hamper activity and selectivity. Cu catalysts are no exception in this respect since they exhibit different oxidation states for which contradicting activities have been reported, as, for example, in the catalytic oxidation of CO. Here, we investigate the impact of low-coordination sites on nanofabricated Cu nanoparticles with engineered grain boundaries on the oxidation of the Cu surface under CO oxidation reaction conditions. Combining multiplexed in situ single particle plasmonic nanoimaging, ex situ transmission electron microscopy imaging, and density functional theory calculations reveals a distinct dependence of particle oxidation rate on grain boundary density. Additionally, we found that the oxide predominantly nucleates at grain boundary-surface intersections, which leads to nonuniform oxide growth that suppresses Kirkendall-void formation. The oxide nucleation rate on Cu metal catalysts was revealed to be an interplay of surface coordination and CO oxidation behavior, with low coordination favoring Cu oxidation and high coordination favoring CO oxidation. These findings explain the observed single particle-specific onset of Cu oxidation as being the consequence of the individual particle grain structure and provide an explanation for widely distributed activity states of particles in catalyst bed ensembles.
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| 46. |
- Nugroho, Ferry, 1986, et al.
(författare)
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Inverse designed plasmonic metasurface with parts per billion optical hydrogen detection
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Plasmonic sensors rely on optical resonances in metal nanoparticles and are typically limited by their broad spectral features. This constraint is particularly taxing for optical hydrogen sensors, in which hydrogen is absorbed inside optically-lossy Pd nanostructures and for which state-of-the-art detection limits are only at the low parts-per-million (ppm) range. Here, we overcome this limitation by inversely designing a plasmonic metasurface based on a periodic array of Pd nanoparticles. Guided by a particle swarm optimization algorithm, we numerically identify and experimentally demonstrate a sensor with an optimal balance between a narrow spectral linewidth and a large field enhancement inside the nanoparticles, enabling a measured hydrogen detection limit of 250 parts-per-billion (ppb). Our work significantly improves current plasmonic hydrogen sensor capabilities and, in a broader context, highlights the power of inverse design of plasmonic metasurfaces for ultrasensitive optical (gas) detection.
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| 47. |
- Nugroho, Ferry, 1986, et al.
(författare)
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Topographically Flat Nanoplasmonic Sensor Chips for Biosensing and Materials Science
- 2017
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Ingår i: ACS Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 2:1, s. 119-127
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Tidskriftsartikel (refereegranskat)abstract
- Nanoplasmonic sensors typically comprise arrangements of noble metal nanoparticles on a dielectric support. Thus they are intrinsically characterized by surface topography with corrugations at the 10–100 nm length scale. While irrelevant in some bio- and chemosensing applications, it is also to be expected that the surface topography significantly influences the interaction between solids, fluids, nanoparticles and (bio)molecules, and the nanoplasmonic sensor surface. To address this issue, we present a wafer-scale nanolithography-based fabrication approach for high-temperature compatible, chemically inert and topographically flat and laterally homogeneous nanoplasmonic sensor chips. We demonstrate their sensing performance on three different examples, for which we also carry out a direct comparison with a traditional nanoplasmonic sensor with representative surface corrugation. Specifically, we (i) quantify the film-thickness dependence of the glass transition temperature in poly(methyl metacrylate) thin films, (ii) characterize the adsorption and specific binding kinetics of the avidin – b-BSA protein system and (iii) analyze supported lipid bilayer formation on SiO2 surfaces.
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| 48. |
- Nyberg, Lena, 1979, et al.
(författare)
-
Optical mapping of single DNA molecules in nanochannels: A novel method for identification and characterization of antibiotic resistance
- 2015
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Ingår i: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1045-1047
-
Konferensbidrag (refereegranskat)abstract
- The use, and overuse, of antibiotics has during the last decade led to a dramatic increase in antibiotic resistance and there is a crying need for novel methods for fast identification of antibiotic resistance genes. We here demonstrate how our previously developed assay for optical mapping of DNA in nanochannels can be used for characterization of resistance genes located on plasmid DNA from bacteria. The assay requires extremely small sample volumes and does neither rely on PCR, nor culturing of bacteria, which greatly reduces the time for analysis.
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| 49. |
- Nyberg, Lena, 1979, et al.
(författare)
-
Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- The rapid spread of antibiotic resistance - currently one of the greatest threats to human health according to WHO - is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.
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| 50. |
- Persson, Fredrik, 1979, et al.
(författare)
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Lipid-Based Passivation in Nanofluidics
- 2012
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 12:5, s. 2260-2265
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Tidskriftsartikel (refereegranskat)abstract
- Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.
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