| 1. |
- Agnarsson, Björn, 1977, et al.
(author)
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Low-temperature fabrication and characterization of a symmetric hybrid organic–inorganic slab waveguide for evanescent light microscopy
- 2018
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In: Nano Futures. - : IOP Publishing. - 2399-1984. ; 2:2
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Journal article (peer-reviewed)abstract
- Organic and inorganic solid materials form the building blocks for most of today's high-technological instruments and devices. However, challenges related to dissimilar material properties have hampered the synthesis of thin-film devices comprised of both organic and inorganic films. We here give a detailed description of a carefully optimized processing protocol used for the construction of a three-layered hybrid organic–inorganic waveguide-chip intended for combined scattering and fluorescence evanescent-wave microscopy in aqueous environments using conventional upright microscopes. An inorganic core layer (SiO2 or Si3N4), embedded symmetrically in an organic cladding layer (CYTOP), aids simple, yet efficient in-coupling of light, and since the organic cladding layer is refractive index matched to water, low stray-light (background) scattering of the propagating light is ensured. Another major advantage is that the inorganic core layer makes the chip compatible with multiple well-established surface functionalization schemes that allows for a broad range of applications, including detection of single lipid vesicles, metallic nanoparticles or cells in complex environments, either label-free—by direct detection of scattered light—or by use of fluorescence excitation and emission. Herein, focus is put on a detailed description of the fabrication of the waveguide-chip, together with a fundamental characterization of its optical properties and performance, particularly in comparison with conventional epi illumination. Quantitative analysis of images obtained from both fluorescence and scattering intensities from surface-immobilized polystyrene nanoparticles in suspensions of different concentrations, revealed enhanced signal-to-noise and signal-to-background ratios for the waveguide illumination compared to the epi-illumination.
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| 2. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(author)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
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In: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
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Journal article (peer-reviewed)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 3. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(author)
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Nanoconfined circular DNA
- 2014
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In: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1353-1355
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Conference paper (peer-reviewed)abstract
- Studies of nanoconfined circular DNA are of interest both from a biological as well as a fundamental polymer physics perspective. We here present the use of nanofluidic channels as a tool for comparing statics and dynamics of the linear and circular configuration of the same DNA molecule.
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| 4. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(author)
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Nanoconfined Circular DNA
- 2014
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Conference paper (other academic/artistic)
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| 5. |
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| 6. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(author)
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Unfolding of nanoconfined circular DNA
- 2015
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In: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1
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Journal article (other academic/artistic)
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| 7. |
- Bidabadi, M, et al.
(author)
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The analytical investigation of premixed combustion in cylindrical micro-combustor
- 2011
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In: Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science. - 2041-2983 .- 0954-4062. ; 225:4, s. 931-938
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Journal article (peer-reviewed)abstract
- In this study, an analytical model for heat recirculation in cylindrical micro-combustorsis presented, including the effects of heat transfer from the product gas stream in the reaction zoneand post-flame region to the reactant in the preheat zone, structural heat conduction through thecombustor walls and heat loss to ambient. Eventually, the explicit expression for the flame speedin non-adiabatic condition and the implicit expression for adiabatic condition are obtained in thisresearch. In addition, comparison is made between adiabatic and non-adiabatic flame speeds.It is demonstrated that the streamwise heat conduction through the structure of combustorplays an important role in the flame broadening in both adiabatic and non-adiabatic conditions.Moreover, it is shown that reducing the size of the combustor to a submillimetre scale extremelyincreases the surface-to-volume ratio, leading to the decrease in the flame speed and flamequenching.
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| 8. |
- Fornander, Louise, 1984, et al.
(author)
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Using nanofluidic channels to probe dynamics of RAD51-Filaments
- 2015
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In: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1826-1828
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Conference paper (peer-reviewed)abstract
- Using nanochannels, passivated with a lipid bilayer to avoid sticking of proteins, we study Rad51 filaments bound to single- and double stranded DNA. We demonstrate how we can discern different properties of the filaments by studying them at different degrees of confinement. Unlike the bacterial homologue RecA, that forms homogeneous filaments along DNA, Rad51 forms heterogeneous filaments containing both rigid kinks as well as flexible regions. Varying the counterion, the DNA substrate as well as the initial protein concentration, we try to understand the factors governing the structure of the filaments.
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| 9. |
- Friedrich, R., et al.
(author)
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A nano flow cytometer for single lipid vesicle analysis
- 2017
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In: Lab on a Chip - Miniaturisation for Chemistry and Biology. - : Royal Society of Chemistry (RSC). - 1473-0189 .- 1473-0197. ; 17:5, s. 830-841
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Journal article (peer-reviewed)abstract
- We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 mu l sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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| 10. |
- Frykholm, Karolin, 1977, et al.
(author)
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Probing Physical Properties of a DNA- Protein Complex Using Nanofluidic Channels
- 2014
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In: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 10:5, s. 884-887
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Journal article (peer-reviewed)abstract
- A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 μm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.
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