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• 1.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Utvärdering av prestanda hos ultraljudsmaskin2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis

The goal of this report is to try to evaluate the performance of an ultrasound scanner, which was bought by the applied physics department in 2014 for a relatively low price. By performing this evaluation we wish to answer the question if a scanner like this can be used to perform simple ultrasound examinations. Seeing that performance is such a broad concept we choose to limit ourselves in this report by focusing on the spatial resolution. The evaluation of spatial resolution was done experimentally by constructing multiple tissue-like phantoms and examining them. The results tell us that the scanner could probably be used on humans for simpler examinations such as estimation of the gestational age given that the scanner fulfils the safety requirements, something we do not investigate in this report.

• 2. Abrahamsson, S.
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics.
Multifocus structured illumination microscopy for fast volumetric super-resolution imaging2017In: Biomedical Optics Express, ISSN 2156-7085, E-ISSN 2156-7085, Vol. 8, no 9, p. 4135-4140, article id #294866Article in journal (Refereed)

We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in superresolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.

• 3. Ackermann, M.
KTH, School of Engineering Sciences (SCI), Applied Physics. Oskar Klein Centre for Cosmoparticle Physics, Alba Nova, Sweden. KTH, School of Engineering Sciences (SCI), Applied Physics. Oskar Klein Centre for Cosmoparticle Physics, Alba Nova, Sweden.
Deep view of the Large Magellanic Cloud with six years of Fermi-LAT observations2016In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 586, article id A71Article in journal (Refereed)

Context. The nearby Large Magellanic Cloud (LMC) provides a rare opportunity of a spatially resolved view of an external star-forming galaxy in gamma-rays. The LMC was detected at 0.1-100 GeV as an extended source with CGRO/EGRET and using early observations with the Fermi-LAT. The emission was found to correlate with massive star-forming regions and to be particularly bright towards 30 Doradus. Aims. Studies of the origin and transport of cosmic rays (CRs) in the Milky Way are frequently hampered by line-of-sight confusion and poor distance determination. The LMC offers a complementary way to address these questions by revealing whether and how the gamma-ray emission is connected to specific objects, populations of objects, and structures in the galaxy. Methods. We revisited the gamma-ray emission from the LMC using about 73 months of Fermi-LAT P7REP data in the 0.2-100 GeV range. We developed a complete spatial and spectral model of the LMC emission, for which we tested several approaches: a simple geometrical description, template-fitting, and a physically driven model for CR-induced interstellar emission. Results. In addition to identifying PSR J0540-6919 through its pulsations, we find two hard sources positionally coincident with plerion N 157B and supernova remnant N 132D, which were also detected at TeV energies with H.E.S.S. We detect an additional soft source that is currently unidentified. Extended emission dominates the total flux from the LMC. It consists of an extended component of about the size of the galaxy and additional emission from three to four regions with degree-scale sizes. If it is interpreted as CRs interacting with interstellar gas, the large-scale emission implies a large-scale population of similar to 1-100 GeV CRs with a density of similar to 30% of the local Galactic value. On top of that, the three to four small-scale emission regions would correspond to enhancements of the CR density by factors 2 to 6 or higher, possibly more energetic and younger populations of CRs compared to the large-scale population. An alternative explanation is that this is emission from an unresolved population of at least two dozen objects, such as pulsars and their nebulae or supernova remnants. This small-scale extended emission has a spatial distribution that does not clearly correlate with known components of the LMC, except for a possible relation to cavities and supergiant shells. Conclusions. The Fermi-LAT GeV observations allowed us to detect individual sources in the LMC. Three of the newly discovered sources are associated with rare and extreme objects. The 30 Doradus region is prominent in GeV gamma-rays because PSR J0540-6919 and N 157B are strong emitters. The extended emission from the galaxy has an unexpected spatial distribution, and observations at higher energies and in radio may help to clarify its origin.

• 4. Agostinho, A.
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Sexual dimorphism in the width of the mouse synaptonemal complex2018In: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 131, no 5, article id jcs212548Article in journal (Refereed)

Sexual dimorphism has been used to describe morphological differences between the sexes, but can be extended to any biologically related process that varies between males and females. The synaptonemal complex (SC) is a tripartite structure that connects homologous chromosomes in meiosis. Here, aided by superresolution microscopy techniques, we show that the SC is subject to sexual dimorphism, in mouse germ cells. We have identified a significantly narrower SC in oocytes and have established that this difference does not arise from a different organization of the lateral elements nor from a different isoform of transverse filament protein SYCP1. Instead, we provide evidence for the existence of a narrower central element and a different integration site for the C-termini of SYCP1, in females. In addition to these female-specific features, we speculate that post-translation modifications affecting the SYCP1 coiled-coil region could render a more compact conformation, thus contributing to the narrower SC observed in females.

• 5. Agostinho, Ana
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
High density of REC8 constrains sister chromatid axes and prevents illegitimate synaptonemal complex formation2016In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 17, no 6, p. 901-913Article in journal (Refereed)

During meiosis, cohesin complexes mediate sister chromatid cohesion (SCC), synaptonemal complex (SC) assembly and synapsis. Here, using super-resolution microscopy, we imaged sister chromatid axes in mouse meiocytes that have normal or reduced levels of cohesin complexes, assessing the relationship between localization of cohesin complexes, SCC and SC formation. We show that REC8 foci are separated from each other by a distance smaller than 15% of the total chromosome axis length in wild-type meiocytes. Reduced levels of cohesin complexes result in a local separation of sister chromatid axial elements (LSAEs), as well as illegitimate SC formation at these sites. REC8 but not RAD21 or RAD21L cohesin complexes flank sites of LSAEs, whereas RAD21 and RAD21L appear predominantly along the separated sister-chromatid axes. Based on these observations and a quantitative distribution analysis of REC8 along sister chromatid axes, we propose that the high density of randomly distributed REC8 cohesin complexes promotes SCC and prevents illegitimate SC formation.

• 6.
Bu Ali Sina Univ, Fac Chem, Hamadan, Iran..
Karolinska Inst, Ctr Psychiat Res, Dept Clin Neurosci, SE-17176 Stockholm, Sweden.;Stockholm Cty Council, SE-17176 Stockholm, Sweden.. Bu Ali Sina Univ, Fac Chem, Hamadan, Iran.. Bu Ali Sina Univ, Fac Chem, Hamadan, Iran.. Univ Kurdistan, Fac Sci, Dept Chem, Sanandaj, Iran.. KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Karolinska Inst, Ctr Psychiat Res, Dept Clin Neurosci, SE-17176 Stockholm, Sweden.;Stockholm Cty Council, SE-17176 Stockholm, Sweden..
Reduced graphene oxide as an efficient sorbent in microextraction by packed sorbent: Determination of local anesthetics in human plasma and saliva samples utilizing liquid chromatography-tandem mass spectrometry2018In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 1095, p. 177-182Article in journal (Refereed)

Herein, reduced graphene oxide (RGO) has been utilized as an efficient sorbent in microextraction by packed sorbent (MEPS). The combination of MEPS and liquid chromatography-tandem mass spectrometry has been used to develop a method for the extraction and determination of three local anesthetics (i.e. lidocaine, prilocaine, and ropivacaine) in human plasma and saliva samples. The results showed that the utilization of RGO in MEPS could minimize the matrix effect so that no interfering peaks at the retention times of the analytes or internal standard was observed. The high extraction efficiency of this method was approved by mean recoveries of 97.26-106.83% and 95.21-105.83% for the studied analytes in plasma and saliva samples, respectively. Intra- and inter-day accuracies and precisions for all analytes were in good accordance with the international regulations. The accuracy values (as percentage deviation from the nominal value) of the quality control samples were between - 2.1 to 13.9 for lidocaine, - 4.2 to 11.0 for prilocaine and between - 4.5 to - 2.4 for ropivacaine in plasma samples while the values were ranged from - 4.6 to 1.6 for lidocaine, from - 4.2 to 15.5 for prilocaine and from - 3.3 to - 2.3 for ropivacaine in human saliva samples. Lower and upper limit of quantification (LLOQ, ULOQ) were set at 5 and 2000 nmol L-1 for all of the studied drugs. The correlation coefficients values were >= 0.995. The limit of detection values were obtained 4 nmol L-1 for lidocaine and prilocaine, and 2 nmol L-1 for ropivacaine.

• 7.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Design of III-V hybrid membrane laser2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
• 8.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
Reaction control of metal-assisted chemical etching for silicon-based zone plate nanostructures2018In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 8, no 23, p. 12628-12634Article in journal (Refereed)

Metal-assisted chemical etching (MACE) reaction parameters were investigated for the fabrication of specially designed silicon-based X-ray zone plate nanostructures using a gold catalyst pattern and etching solutions composed of HF and H2O2. Etching depth, zone verticality and zone roughness were studied as a function of etching solution composition, temperature and processing time. Homogeneous, vertical etching with increasing depth is observed at increasing H2O2 concentrations and elevated processing temperatures, implying a balance in the hole injection and silica dissolution kinetics at the gold-silicon interface. The etching depth decreases and zone roughness increases at the highest investigated H2O2 concentration and temperature. Possible reasons for these observations are discussed based on reaction chemistry and zone plate design. Optimum MACE conditions are found at HFH2O2 concentrations of 4.7 M:0.68 M and room temperature with an etching rate of ≈0.7 μm min-1, which is about an order of magnitude higher than previous reports. Moreover, our results show that a grid catalyst design is important for successful fabrication of vertical high aspect ratio silicon nanostructures.

• 9.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
Reaction control of metal-assisted chemical etching for silicon-based zone plate nanostructuresManuscript (preprint) (Other academic)

Metal-assisted chemical etching (MACE) reaction parameters were investigated for the fabrication of specially designed silicon-based x-ray zone plate nanostructures using a gold catalyst pattern and etching solutions composed of HF and H2O2. Etching depth, zone verticality and zone roughness were studied as a function of etching solution composition, temperature and processing time. Homogeneous, vertical etching with increasing depth is observed at increasing H2O2 concentrations and elevated processing temperatures, implying a balance in the hole injection and silica dissolution kinetics at the gold-silicon interface. The etching depth decreases and zone roughness increases at the highest investigated H2O2 concentration and temperature. Possible reasons for these observations are discussed based on reaction chemistry and zone plate design. Optimum MACE conditions are found at HF:H2O2 concentrations of 4.7 M:0.68 M and room temperature with an etching rate of 0.7 micrometers per minute, which is about an order of magnitude higher than previous reports. Moreover, our results show that a grid catalyst design is important for successful fabrication of vertical high aspect ratio silicon nanostructures.

• 10.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. St Petersburg State Univ, Inst Translat Biomed, St Petersburg, Russia.
Skolkovo Inst Sci & Technol, Ctr Data Intens Biomed & Biotechnol, Moscow, Russia.;Russian Acad Sci, Inst Informat Transmiss Problems, Moscow, Russia.;Natl Res Univ, Higher Sch Econ, Fac Comp Sci, Moscow, Russia.;MM Lomonosov Moscow State Univ, Dept Bioengn & Bioinformat, Moscow, Russia.. Skolkovo Inst Sci & Technol, Ctr Data Intens Biomed & Biotechnol, Moscow, Russia.;Russian Acad Sci, Inst Informat Transmiss Problems, Moscow, Russia..
Neanderthal and Denisovan ancestry in Papuans: A functional study2018In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, E-ISSN 1757-6334, Vol. 16, no 2, article id 1840011Article in journal (Refereed)

Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.

• 11.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
Photophysical and Chemical Approaches to Cellular Biophysics2008Licentiate thesis, comprehensive summary (Other academic)

The central theme in this thesis is reversibility. Two main attempts has been made to approach reversibility in cellular systems from both chemical and physical points of view. Reversibility of immunolabeling of proteins on the cell surface has been adressed by development of new fluorescent substances optimized for CALI (Chromophore-Assisted Laser Inactivation of protein). Aluminum phthalocyanine (AlPc) is here identified to be a good candidate for a new generation of fluorophores for efficient hydroxyl radical generation. It is shown that cells can be reversibly labeled with antibody-AlPc conjugates. In experiments on living cells the AlPcs were not only active as classic fluorophores but also as photocatalytic substances with destaining properties. Reversibility of cell immobilization is also reported, where cells cultured in microstructures were immobilized and 3D supported using hydrogels. Hydrogel formulation and application was optimized to achieve a system where both viability and ease of use was satisfied. Gel reversibility was actualized with pH and enzyme treatment. The developped method offers the possibility of stop flow culturing cells in controlled and reusable 3D environments.

• 12.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
Photophysical and photochemical parameters of octakis (benzylthio) phthalocyaninato zinc, aluminium and tin: Red shift index concept in solvent effect on the ground state absorption of zinc phthalocyanine derivatives2010In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 984, no 1-3, p. 1-14Article in journal (Refereed)

This paper addresses the synthesis of octa-substituted benzylthio metallophthalocyanines (OBTMPcs) that contain the central metal ions of Zn2+, Al3+ and Sn4+. The ground state absorption of ZnPc(SR)(8) (OBTZnPc) along with the ZnPc derivatives, well documented in literature were used to study a new concept called the red shift index (RsI). The concept is based on the empirical values of RsI of the different complexes in solvent media. Unequivocally, parameters used in this paper show strong correlations that are consistent with the results obtained. For instance, 12,1 of the complexes tend to increase as the refractive index, n(D), and solvent donor, DN, of solvent increases. Photodegradation (photobleaching) quantum yield, phi(d) measurements of these compounds show that they are highly photostable, phi(d) (0.03-0.33 x 10(-5)). The triplet quantum yield, phi(T) (0.40-0.53) and the triplet lifetime, tau(T) (610-810 mu s) are within the typical range for metallophthalocyanines in DMSO. The photosensitisation efficiency. S-Delta, is relatively high for all the molecules (0.74-0.90). (C) 2010 Elsevier B.V. All rights reserved.

• 13.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
Photophysics and photochemistry of zinc, aluminium and tin octakis (benzylthio) phthalocyanines2008Report (Other academic)
• 14.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
Red-Shift Index Concept in Solvent Effects of Chromophore-Substituted Metallophthalocyanines: A Look at the Empirical Relationship of the Macroscopic Properties of the Solute-Solvent Interactions2015In: Journal of Solution Chemistry, ISSN 0095-9782, E-ISSN 1572-8927, Vol. 44, no 2, p. 307-326Article in journal (Refereed)

Solvent effects on the UV/vis spectra of metallopthalocyanines (MPcs) have been interpreted using the red-shift index concept (R (s) I). The concept connects empirically, direct, experimental, easily accessible optical spectral data, which are explained by considering the differential behavior of the solute-solvent interactions at the ground state and excited state using the spectral values of MPcs along with the derived concept, called the associated solvation energy (ASE). R (s) I is formulated from three fundamental parameters, which are: ground state electronic absorption spectrum, polarization red-shift and a scaling factor of MPc (N (dye)) in the respective solvents. The R (s) I is a reflection of the index value of the chromophore substituent of MPc in the solvent; thus, the concept can be used as a solvatochromic parameter to study a wide range of supramolecular and heterocyclic compounds that can be modified at their periphery or 'handles'. Particularly, in this study, the concept has been used to rank MPc candidates by using the statistical mean performance of the solvatochromic parameters, which are red shift index, polarizability efficiency and ASE. We hereby review the solvent effects on the UV/vis spectra of substituted and unsubstituted MPcs.

• 15.
KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
KTH, School of Biotechnology (BIO), Molecular Biotechnology. KTH, School of Biotechnology (BIO), Molecular Biotechnology. KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
Characterization studies of aluminum phthalocyanine binding to antibodies from SKBR 3 cell line2008Report (Other academic)
• 16.
KTH, School of Engineering Sciences (SCI), Applied Physics.
KTH, School of Biotechnology (BIO), Protein Technology. KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
Understanding the Photochemical Pathway of In Vitro Target Delivery of Aluminium Phthalocyanine: A Mechanistic Approach Using Radical Reaction Chemistry2014In: ChemPlusChem, ISSN 2192-6506, Vol. 79, no 5, p. 671-679Article in journal (Refereed)

A classical dye, aluminium phthalocyanine (AlPc), is used to study the photochemical processes involved in the chromophore-assisted laser inactivation technique. Both cell-free and cell-based systems are investigated by novel methods and radical reaction chemistry. Findings on the photochemical pathways in two models representing cell-free and a cell-based systems are reported. In the cell-free system, the unsubstituted, free, fluorescence-active photosensitiser AlPc recovers its fluorescence signal by means of phosphorescence through a reversible photobleaching process. In the cell-based system, photoactivation of substituted AlPc conjugated to an antibody results in the loss of fluorescence signal at the area examined. Reinjection of the AlPc-conjugated antibodies restores the fluorescence signal.

• 17. Aktas, O.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Interfacing telecom fibers and silicon core fibers with nano-spikes for in-fiber silicon devices2018In: Optics InfoBase Conference Papers, Optics Info Base, Optical Society of America, 2018, article id u12d3i3mConference paper (Refereed)

We report fabrication of tapered silicon core fibers with nano-spikes enabling efficient optical coupling into the core, as well as their seamless integration with single mode fibers. A proof-of-concept integrated in-fiber silicon device is demonstrated. © OSA 2018.

• 18.
Univ Southampton, Optoelect Res Ctr, Southampton SO17 1BJ, Hants, England..
Univ Southampton, Optoelect Res Ctr, Southampton SO17 1BJ, Hants, England.. Univ Southampton, Optoelect Res Ctr, Southampton SO17 1BJ, Hants, England.. Univ Southampton, Optoelect Res Ctr, Southampton SO17 1BJ, Hants, England.. Clemson Univ, COMSET, Clemson, SC 29634 USA.;Clemson Univ, Dept Mat Sci & Engn, Clemson, SC 29634 USA.. Clemson Univ, COMSET, Clemson, SC 29634 USA.;Clemson Univ, Dept Mat Sci & Engn, Clemson, SC 29634 USA.. KTH, School of Engineering Sciences (SCI), Applied Physics. Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway.
Interfacing Telecom Fibers and Silicon Core Fibers with Nano-Spikes for In-Fiber Silicon Devices2018In: 2018 Optical Fiber Communications Conference and Exposition, OFC 2018 - Proceedings, Institute of Electrical and Electronics Engineers (IEEE), 2018Conference paper (Refereed)

We report fabrication of tapered silicon core fibers with nano-spikes enabling efficient optical coupling into the core, as well as their seamless integration with single mode fibers. A proof-of-concept integrated in-fiber silicon device is demonstrated.

• 19.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Virginia Commonwealth Univ Qatar, Liberal Arts & Sci Program, POB 8095, Doha, Qatar.. KTH, School of Engineering Sciences (SCI), Applied Physics.
Critical Review of Low-Temperature CO Oxidation and Hysteresis Phenomenon on Heterogeneous Catalysts2018In: Catalysts, ISSN 2073-4344, Vol. 8, no 12, article id 660Article, review/survey (Refereed)

There is a growing demand for new heterogeneous catalysts for cost-effective catalysis. Currently, the hysteresis phenomenon during low-temperature CO oxidation is an important topic in heterogeneous catalysis. Hysteresis provides important information about fluctuating reaction conditions that affect the regeneration of active sites and indicate the restoration of catalyst activity. Understanding its dynamic behavior, such as hysteresis and self-sustained kinetic oscillations, during CO oxidation, is crucial for the development of cost-effective, stable and long-lasting catalysts. Hysteresis during CO oxidation has a direct influence on many industrial processes and its understanding can be beneficial to a broad range of applications, including long-life CO2 lasers, gas masks, catalytic converters, sensors, indoor air quality, etc. This review considers the most recent reported advancements in the field of hysteresis behavior during CO oxidation which shed light on the origin of this phenomenon and the parameters that influence the type, shape, and width of the conversion of the hysteresis curves.

• 20.
Sultan Qaboos Univ, Dept Chem & Petr Engn, Coll Engn, POB 33, Al Khoud 123, Oman.;Sultan Qaboos Univ, Nanotechnol Res Ctr, POB 17, Al Khoud 123, Oman..
Sultan Qaboos Univ, Nanotechnol Res Ctr, POB 17, Al Khoud 123, Oman.. Asian Inst Technol, Ctr Excellence Nanotechnol, POB 4, Klong Luangpathumthani 12120, Thailand.. Sultan Qaboos Univ, Dept Marine Sci & Fisheries, Coll Agr & Marine Sci, POB 34, Al Khoud 123, Oman.;Sultan Qaboos Univ, Ctr Excellence Marine Biotechnol, POB 50, Muscat 123, Oman.. KTH, School of Engineering Sciences (SCI), Applied Physics. RMIT Univ, Sch Engn, Bundoora, Vic 3083, Australia.. Univ Modena & Reggio Emilia, Dept Engn Enzo Ferrari, Via Vivarelli 10, I-41125 Modena, Italy.. 14 Chancellor Ave, Bundoora, Vic 3083, Australia..
Chlorination disadvantages and alternative routes for biofouling control in reverse osmosis desalination (vol 2, 2, 2019)2019In: NPJ CLEAN WATER, ISSN 2059-7037, Vol. 2, article id 8Article in journal (Refereed)
• 21.
Iraq.
Ireland. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. Ireland. Ireland.
Wide-field surface-enhanced Raman scattering from ferroelectrically defined Au nanoparticle microarrays for optical sensing2018In: Optics InfoBase Conference Papers, OSA - The Optical Society , 2018Conference paper (Refereed)

The acquisition-time in optical sensors using SERS is vital value. Wide-field SERS is used to perform high-density of hot-spots of GNPs photodeposition on a periodically-protonexchanged- LiNbO3 which, leads to increase the sensitivity at ultralow probe concentrations.

• 22.
KTH, School of Electrical Engineering and Computer Science (EECS), Electronics, Integrated devices and circuits.
Department of Physics, University of Gothenburg. KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Department of Physics, University of Gothenburg. KTH, School of Electrical Engineering and Computer Science (EECS), Electronics, Integrated devices and circuits. KTH, School of Electrical Engineering and Computer Science (EECS), Electronics, Integrated devices and circuits.
Compact Macrospin-Based Model of Three-Terminal Spin-Hall Nano Oscillators2019In: IEEE transactions on magnetics, ISSN 0018-9464, E-ISSN 1941-0069, Vol. 55, no 10, article id 4003808Article in journal (Refereed)

Emerging spin-torque nano oscillators (STNOs) and spin-Hall nano oscillators (SHNOs) are potential candidates for microwave applications. Recent advances in three-terminal magnetic tunnel junction (MTJ)-based SHNOs opened the possibility to develop more reliable and well-controlled oscillators, thanks to individual spin Hall-driven precession excitation and read-out paths. To develop hybrid systems by integrating three-terminal SHNOs and CMOS circuits, an electrical model able to capture the analog characteristics of three-terminal SHNOs is needed. This model needs to be compatible with current electric design automation (EDA) tools. This work presents a comprehensive macrospin-based model of three-terminal SHNOs able to describe the dc operating point, frequency modulation, phase noise, and output power. Moreover, the effect of voltage-controlled magnetic anisotropy (VCMA) is included. The model shows good agreement with experimental measurements and could be used in developing hybrid three-terminal SHNO/CMOS systems.

• 23.
Stockholm Univ, Dept Biochem & Biophys, Svante Arrhenius Vag 16C, SE-10691 Stockholm, Sweden..
KTH, School of Engineering Sciences (SCI), Applied Physics. Stockholm Univ, Dept Biochem & Biophys, Svante Arrhenius Vag 16C, SE-10691 Stockholm, Sweden.;Umea Univ, Dept Med Biochem & Biophys, SE-90187 Umea, Sweden.. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.. KTH, School of Engineering Sciences (SCI), Applied Physics. Stockholm Univ, Dept Biochem & Biophys, Svante Arrhenius Vag 16C, SE-10691 Stockholm, Sweden..
Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 17234Article in journal (Refereed)

Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd(1) nitrite reductase (cd(1)NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd(1)NiR, presumably because cd(1)NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd(1)NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd(1)NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd(1)NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.

• 24.
ICMUV, Dept Fis Aplicada & Electromagnetismo, Dr Moliner 50, Burjassot 46100, Spain..
ICMUV, Dept Fis Aplicada & Electromagnetismo, Dr Moliner 50, Burjassot 46100, Spain.. KTH, School of Engineering Sciences (SCI), Applied Physics. Acreo AB, Dept Fiber Photon, Elect 236, S-16440 Kista, Sweden.. KTH, School of Engineering Sciences (SCI), Applied Physics. Acreo AB, Dept Fiber Photon, Elect 236, S-16440 Kista, Sweden.. ICMUV, Dept Fis Aplicada & Electromagnetismo, Dr Moliner 50, Burjassot 46100, Spain..
Acousto-optic interaction in polyimide coated optical fibers2017In: 2017 CONFERENCE ON LASERS AND ELECTRO-OPTICS EUROPE & EUROPEAN QUANTUM ELECTRONICS CONFERENCE (CLEO/EUROPE-EQEC), IEEE , 2017Conference paper (Refereed)
• 25. Alcusa-Saez, E. P.
KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. ACREO.
Acousto-optic interaction in polyimide coated optical fibers with flexural waves2017In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 25, no 15, p. 17167-17173Article in journal (Refereed)

Acousto-optic coupling in polyimide-coated single-mode optical fibers using flexural elastic waves is demonstrated. The effect of the polyimide coating on the acoustooptic interaction process is analyzed in detailed. Theoretical and experimental results are in good agreement. Although the elastic attenuation is significant, we show that acousto-optic coupling can be produced with a reasonably good efficiency. To our knowledge, it is the first experimental demonstration of acousto-optic coupling in optical fibers with robust protective coating.

• 26. Alcusa-Saez, E. P.
KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
All-fiber acousto-optic tunable filter in polyimide coated optical fibers2017In: 2017 19th International Conference on Transparent Optical Networks (ICTON), IEEE Computer Society, 2017, article id 8025093Conference paper (Refereed)

We present the experimental demonstration of in-fiber acousto-optic coupling in a polyimide-coated optical fiber. Although the presence of the polyimide coating increases is significantly the attenuation of the acoustic wave, we show that acousto-optic interaction can still be produced with reasonable efficiency. The effect of the polyimide coating on the acousto-optic interaction process is analyzed in detailed. Theoretical and experimental results are in good agreement. To our knowledge, this is the first experimental demonstration of acousto-optic coupling in optical fibers with robust protective coating.

• 27.
Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.;Minist Hlth, Cent Publ Hlth Labs, Muscat, Oman..
Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.;Sultan Qaboos Univ, Coll Agr & Marine Sci, Dept Anim & Vet Sci, Muscat, Oman.. Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.. Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.. Minist Hlth, Cent Publ Hlth Labs, Muscat, Oman.. Minist Hlth, Cent Publ Hlth Labs, Muscat, Oman.. Sultan Qaboos Univ, Coll Med & Hlth Sci, Dept Microbiol & Immunol, Muscat, Oman.. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Microbiol, Stockholm, Sweden.. Karolinska Inst, Dept Lab Med, Div Clin Microbiol, Stockholm, Sweden.;Karolinska Univ Hosp, Immunodeficiency Unit, Infect Dis Clin, Stockholm, Sweden..
Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, article id 2632Article in journal (Refereed)

Background Colistin is a polypeptide antibiotic drug that targets lipopolysaccharides in the outer membrane of Gram-negative bacteria. Inactivation of the mgrB-gene is a common mechanism behind colistin-resistance in Klebsiella pneumoniae (Kpn). Since colistin is a cyclic polypeptide, it may exhibit cross-resistance with the antimicrobial peptide LL-37, and with other innate effector mechanisms, but previous results are inconclusive. Objective To study potential cross-resistance between colistin and LL-37, as well as with other innate effector mechanisms, and to compare virulence of colistin-resistant and susceptible Kpn strains. Materials/Methods Carbapenemase-producing Kpn from Oman (n = 17) were subjected to antimicrobial susceptibility testing and whole genome sequencing. Susceptibility to colistin and LL-37 was studied. The surface charge was determined by zeta-potential measurements and the morphology of treated bacteria was analyzed with electron microscopy. Bacterial survival was assessed in human whole blood and serum, as well as in a zebrafish infection-model. Results Genome-analysis revealed insertion-sequences in the mgrB gene, as a cause of colistin resistance in 8/17 isolates. Colistin-resistant (Col-R) isolates were found to be more resistant to LL-37 compared to colistin-susceptible (Col-S) isolates, but only at concentrations >= 50 mu g/ml. There was no significant difference in surface charge between the isolates. The morphological changes were similar in both Col-R and Col-S isolates after exposure to LL-37. Finally, no survival difference between the Col-R and Col-S isolates was observed in whole blood or serum, or in zebrafish embryos. Conclusion Cross-resistance between colistin and LL-37 was observed at elevated concentrations of LL-37. However, Col-R and Col-S isolates exhibited similar survival in serum and whole blood, and in a zebrafish infection-model, suggesting that cross-resistance most likely play a limited role during physiological conditions. However, it cannot be ruled out that the observed cross-resistance could be relevant in conditions where LL-37 levels reach high concentrations, such as during infection or inflammation.

• 28. Al-Hinai, Muna H.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Antimicrobial Activity Enhancement of Poly(ether sulfone) Membranes by in Situ Growth of ZnO Nanorods2017In: ACS OMEGA, ISSN 2470-1343, Vol. 2, no 7, p. 3157-3167Article in journal (Refereed)

Composite poly(ether sulfone) membranes integrated with ZnO nanostructures either directly blended or grown in situ have enhanced antibacterial activity with improved functionality in reducing the biofouling in water treatment applications. The pore structure and surface properties of the composite were studied to investigate the effect of the addition of ZnO nanostructures. The hydrophilicity of the blended membranes increased with a higher content of ZnO nanoparticles in the membrane (2-6%), which could be further controlled by varying the growth conditions of ZnO nanorods on the polymer surface. Improved water flux, bovine serum albumin rejection, and inhibition of Escherichia coli bacterial growth under visible light irradiation was observed for the membranes decorated with ZnO nanorods compared to those in the membranes simply blended with ZnO nanoparticles. No regrowth of E. coli was recorded even 2 days after the incubation.

• 29.
Sultan Qaboos Univ, Petr & Chem Engn, Muscat, Oman.;Water Res Ctr, Nanotechnol, Muscat, Oman..
Water Res Ctr, Nanotechnol, Muscat, Oman.;Sultan Qaboos Univ, Dept Marine Sci & Fisheries, Muscat, Oman.. Petr Dev Oman LLC, Mat & Corros Dept, Muscat, Oman.. Sultan Qaboos Univ, Petr & Chem Engn, Muscat, Oman.;Water Res Ctr, Nanotechnol, Muscat, Oman.. Sultan Qaboos Univ, Dept Marine Sci & Fisheries, Muscat, Oman.. KTH, School of Engineering Sciences (SCI), Applied Physics, Functional Materials, FNM.
Modification of blended polyethersulfone membranes by in-situ growth of zinc oxide nanostructures for prevention of biofouling during water treatment2016In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 251Article in journal (Other academic)
• 30.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
Quantum error correction2016Doctoral thesis, comprehensive summary (Other academic)

Quantum error correction is the art of protecting quantum states from the detrimental influence from the environment. To master this art, one must understand how the system interacts with the environment and gives rise to a full set of quantum phenomena, many of which have no correspondence in classical information theory. Such phenomena include decoherence, an effect that in general destroys superpositions of pure states as a consequence of entanglement with the environment. But decoherence can also be understood as “information leakage”, i.e., when knowledge of an encoded code block is transferred to the environment. In this event, the block’s information or entanglement content is typically lost.

In a typical scenario, however, not all types of destructive events are likely to occur, but only those allowed by the information carrier, the type of interaction with the environment, and how the environment “picks up” information of the error events. These characteristics can be incorporated into a code, i.e., a channel-adapted quantum error-correcting code.

Often, it is assumed that the environment’s ability to distinguish between error events is small, and I will denote such environments “memory-less”. But this assumption is not always valid, since the ability to distinguish error events is related to the temperature of the environment, and in the particular case of information coded onto photons, kBTR «ℏω typically holds, and one must then assume that the environment has a “memory”. In the thesis I describe a short quantum error-correction code adapted for photons interacting with a “cold” reservoir, i.e., a reservoir which continuously probes what error occurred in the coded state.

I also study other types of environments, and show how to distill meaningful figures of merit from codes adapted for these channels, as it turns out that resource-based figures reflecting both information and entanglement can be calculated exactly for a well-studied class of channels: the Pauli channels. Starting from these resource-based figures, I establish the notion of efficiency and quality and show that there will be a trade-off between efficiency and quality for short codes. Finally I show how to incorporate, into these calculations, the choices one has to make when handling quantum states that have been detected as incorrect, but where no prospect of correcting them exists, i.e., so-called detection errors.

• 31.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
Quantum error correction2012Licentiate thesis, comprehensive summary (Other academic)

This thesis intends to familiarise the reader with quantum error correction, and also show some relations to the well known concept of information - and the lesser known quantum information. Quantum information describes how information can be carried by quantum states, and how interaction with other systems give rise to a full set of quantum phenomena, many of which have no correspondence in classical information theory. These phenomena include decoherence, as a consequence of entanglement. Decoherence can also be understood as "information leakage", i.e., knowledge of an event is transferred to the reservoir - an effect that in general destroys superpositions of pure states.

It is possible to protect quantum states (e.g., qubits) from interaction with the environment - but not by amplification or duplication, due to the "no-cloning" theorem. Instead, this is done using coding, non-demolition measurements, and recovery operations. In a typical scenario, however, not all types of destructive events are likely to occur, but only those allowed by the information carrier, the type of interaction with the environment, and how the environment "picks up" information of the error events. These characteristics can be incorporated into a code, i.e., a channel-adapted quantum error-correcting code. Often, it is assumed that the environment's ability to distinguish between error events is small, and I will denote such environments "memory-less".

This assumption is not always valid, since the ability to distinguish error events is related to the \emph{temperature} of the environment, and in the particular case of information coded onto photons, $k_{\text{B}}T_{\text{R}}\ll\hbar\omega$ typically holds, and one must then assume that the environment has a "memory". In this thesis, I describe a short quantum error-correcting code (QECC), adapted for photons interacting with a cold environment, i.e., this code protects from an environment that continuously records which error occurred in the coded quantum state.

Also, it is of interest to compare the performance of different QECCs - But which yardstick should one use? We compare two such figures of merit, namely the quantum mutual information and the quantum fidelity, and show that they can not, in general, be simultaneously maximised in an error correcting procedure. To show this, we have used a five-qubit perfect code, but assumed a channel that only cause bit-flip errors. It appears that quantum mutual information is the better suited yardstick of the two, however more tedious to calculate than quantum fidelity - which is more commonly used.

• 32.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
Fidelity as a figure of merit in quantum error correction2013In: Quantum information & computation, ISSN 1533-7146, Vol. 13, no 1-2, p. 0009-0020Article in journal (Refereed)

We discuss the fidelity as a figure of merit in quantum error correction schemes. We show that when identifiable but uncorrectable errors occur as a result of the action of the channel, a common strategy that improves the fidelity actually decreases the transmitted mutual information. The conclusion is that while the fidelity is simple to calculate and therefore often used, it is perhaps not always a recommendable figure of merit for quantum error correction. The reason is that while it roughly speaking encourages optimisation of the "mean probability of success", it gives no incentive for a protocol to indicate exactly where the errors lurk. For small error probabilities, the latter information is more important for the integrity of the information than optimising the mean probability of success.

• 33.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
On the efficiency of quantum error correction codes for the depolarising channelManuscript (preprint) (Other academic)
• 34.
Sultan Qaboos Univ, Dept Marine Sci & Fisheries, POB 34, Muscat 123, Oman.;Minist Municipal & Water Resources, Muscat 112, Oman..
KTH, School of Engineering Sciences (SCI), Applied Physics. Sultan Qaboos Univ, Dept Marine Sci & Fisheries, POB 34, Muscat 123, Oman.;Sultan Qaboos Univ, Ctr Excellence Marine Biotechnol, POB 50, Muscat 123, Oman..
Nanocomposite Zinc Oxide-Chitosan Coatings on Polyethylene Films for Extending Storage Life of Okra (Abelmoschus esculentus)2018In: NANOMATERIALS, ISSN 2079-4991, Vol. 8, no 7, article id 479Article in journal (Refereed)

Efficiency of nanocomposite zinc oxide-chitosan antimicrobial polyethylene packaging films for the preservation of quality of vegetables was studied using okra Abelmoschus esculentus. Low density polyethylene films (LDPE) coated with chitosan-ZnO nanocomposites were used for packaging of okra samples stored at room temperature (25 degrees C). Compared to the control sample (no coating), the total bacterial concentrations in the case of chitosan and nanocomposite coatings were reduced by 53% and 63%, respectively. The nanocomposite coating showed a 2-fold reduction in total fungal concentrations in comparison to the chitosan treated samples. Results demonstrate the effectiveness of the nanocomposite coatings for the reduction of fungal and bacterial growth in the okra samples after 12 storage days. The nanocomposite coatings did not affect the quality attributes of the okra, such as pH, total soluble solids, moisture content, and weight loss. This work demonstrates that the chitosan-ZnO nanocomposite coatings not only maintains the quality of the packed okra but also retards microbial and fungal growth. Thus, chitosan-ZnO nanocomposite coating can be used as a potential coating material for active food packaging applications.

• 35. Al-Naamani, Laila
KTH, School of Engineering Sciences (SCI), Applied Physics, Functional Materials, FNM. KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
Antifouling properties or chitosan coatings on plastic substrates2019In: Journal of Agricultural and Marine Sciences, Vol. 23, no 1, p. 92-98Article in journal (Refereed)
• 36. Al-Sabahi, J.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Visible light photocatalytic degradation of HPAM polymer in oil produced water using supported zinc oxide nanorods2018In: Chemical Engineering Journal, ISSN 1385-8947, E-ISSN 1873-3212, Vol. 351, p. 56-64Article in journal (Refereed)

Polymer flooding displacement ability during petroleum extraction from the earth's crust plays an important role in enhanced oil recovery processes. Produced water, as a byproduct, still contain high concentrations of petroleum hydrocarbons and partially hydrolyzed polyacrylamide (HPAM) which is a serious environmental concern. Remediating produced water economically is a big challenge for meeting the permissible discharge limits leading to failure in the effectiveness of the conventional water treatment technologies. Advanced oxidation processes (AOPs) are playing increasing role in the treatment of polluted water and is receiving much attention in recent times as a green and safer water treatment technology. Here we report a new approach to use vertically aligned zinc oxide nanorods (ZnO NRs) supported on substrates engineered for improving their visible light harvesting capacity for effective solar photocatalytic degradation of HPAM. The viscosity of collected oilfield produced water containing HPAM were found to be reduced dramatically when the samples are photocatalytically degraded using ZnO nanorod catalysts irradiated with simulated solar light showing a reduction of 51% within 6 h. With high pressure liquid chromatography 68, 62, 56 and 45% removal of 25, 50, 100 and 150 ppm HPAM, respectively, was demonstrated. The pH of the solution was observed to move to acidic region due to acetamide, nitrate, propionamide and acetic acid which are the intermediate byproducts formed during degradation as determined by mass spectrometry. Zinc oxide nanorod coatings showed about 74% removal efficiency over 5 cycles with less than 1.2% removal of zinc ions after 6 h of light irradiation.

• 37. Al-Sabahi, Jamal
KTH, School of Engineering Sciences (SCI), Applied Physics.
Efficient visible light photocatalysis of benzene, toluene, ethylbenzene and xylene (BTEX) in aqueous solutions using supported zinc oxide nanorods2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 12, article id e0189276Article in journal (Refereed)

Benzene, toluene, ethylbenzene and xylenes (BTEX) are some of the common environmental pollutants originating mainly from oil and gas industries, which are toxic to human as well as other living organisms in the ecosystem. Here we investigate photocatalytic degradation of BTEX under visible light irradiation using supported zinc oxide (ZnO) nanorods grown on glass substrates using a microwave assisted hydrothermal method. ZnO nanorods were characterized by electron microscopy, X-ray diffraction (XRD), specific surface area, UV/visible absorption and photoluminescence spectroscopy. Visible light photocatalytic degradation products of BTEX are studied for individual components using gas chromatograph/mass spectrometer (GC/MS). ZnO nanorods with significant amount of electronic defect states, due to the fast crystallization of the nanorods under microwave irradiation, exhibited efficient degradation of BTEX under visible light, degrading more than 80% of the individual BTEX components in 180 minutes. Effect of initial concentration of BTEX as individual components is also probed and the photocatalytic activity of the ZnO nanorods in different conditions is explored. Formation of intermediate byproducts such as phenol, benzyl alcohol, benzaldehyde and benzoic acid were confirmed by our HPLC analysis which could be due to the photocatalytic degradation of BTEX. Carbon dioxide was evaluated and showed an increasing pattern over time indicating the mineralization process confirming the conversion of toxic organic compounds into benign products.

• 38. Al-Shammari, R. M.
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
Label-free cell membrane detection by Raman spectroscopy using biocompatible gold nanostructure microscale arrays on a ferroelectric template2017In: Optics InfoBase Conference Papers, OSA - The Optical Society , 2017Conference paper (Refereed)
• 39.
Univ Coll Dublin, Sch Phys, Dublin D04 N2E5, Ireland.;Univ Coll Dublin, Conway Inst Biomol & Biomed Res, Dublin D04 N2E5, Ireland..
Univ Coll Dublin, Sch Phys, Dublin D04 N2E5, Ireland.;Univ Technol Baghdad, Laser & Optoelect Engn Dept, Baghdad 10066, Iraq.. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Coll Dublin, Sch Phys, Dublin D04 N2E5, Ireland.;Univ Coll Dublin, Conway Inst Biomol & Biomed Res, Dublin D04 N2E5, Ireland.. Univ Coll Dublin, Sch Phys, Dublin D04 N2E5, Ireland..
Single-Molecule Nonresonant Wide-Field Surface-Enhanced Raman Scattering from Ferroelectrically Defined Au Nanoparticle Microarrays2018In: ACS OMEGA, ISSN 2470-1343, Vol. 3, no 3, p. 3165-3172Article in journal (Refereed)

Single-molecule detection by surface-enhanced Raman scattering (SERS) is a powerful spectroscopic technique that is of interest for the sensor development field. An important aspect of optimizing the materials used in SERS-based sensors is the ability to have a high density of "hot spots" that enhance the SERS sensitivity to the single-molecule level. Photodeposition of gold (Au) nanoparticles through electric-field-directed self-assembly on a periodically proton-exchanged lithium niobate (PPELN) substrate provides conditions to form well-ordered microscale features consisting of closely packed Au nanoparticles. The resulting Au nanoparticle microstructure arrays (microarrays) are plasmon-active and support nonresonant single-molecule SERS at ultralow concentrations (<10(-9)-10(-13) M) with excitation power densities <1 x 10(-3) W cm(-2) using wide-field imaging. The microarrays offer excellent SERS reproducibility, with an intensity variation of <7.5% across the substrate. As most biomarkers and molecules do not support resonance enhancement, this work demonstrates that PPELN is a suitable template for high-sensitivity, nonresonant sensing applications.

• 40. Al-Shammari, Rusul M.
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics.
Photoinduced Enhanced Raman from Lithium Niobate on Insulator Template2018In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 10, no 36, p. 30871-30878Article in journal (Refereed)

• 41. Al-Shammari, Rusul M.
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
Tunable Wettability of Ferroelectric Lithium Niobate Surfaces: The Role of Engineered Microstructure and Tailored Metallic Nanostructures2017In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 121, no 12, p. 6643-6649Article in journal (Refereed)

An important aspect of optimizing micro- and optofluidic devices for lab on -a-chip systems is the ability to engineer materials properties including surface structure and charge to control wettability. Biocompatible ferroelectric lithium niobate (LN), which is well-known for acoustic and nonlinear optical applications, has recently found potential micro- and optofluidic applications. However, the tunable wettability of such substrates has yet to be explored in detail. Here, we show that the contact angle of LN substrates can be reproducibly tailored between similar to 7 degrees and similar to 421 degrees by controlling the surface topography and chemistry at the nano- and micrometer scale via ferroelectric domain and polarization engineering and polarization-directed photoassisted deposition of metallic nanostructures.

• 42.
KTH, School of Engineering Sciences (SCI), Applied Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Silica and carbon decorated silica nanosheet impact on primary human immune cells2018In: Colloids and Surfaces B: Biointerfaces, ISSN 0927-7765, E-ISSN 1873-4367, Vol. 172, p. 779-789Article in journal (Refereed)

Silica nanosheets (SiO 2 NS) are considered to be a promising material in clinical practice for diagnosis and therapy applications. However, an appropriate surface functionalization is essential to guarantee high biocompatibility and molecule loading ability. Although SiO 2 NS are chemically stable, its effects on immune systems are still being explored. In this work, we successfully synthesized a novel 2D multilayer SiO 2 NS and SiO 2 NS coated with carbon (C/SiO 2 NS), and evaluated their impact on human Peripheral Blood Mononuclear Cells (PBMCs) and some immune cell subpopulations. We demonstrated that the immune response is strongly dependent on the surface functionalities of the SiO 2 NS. Ex vivo experiments showed an increase in biocompatibility of C/SiO 2 NS compared to SiO 2 NS, resulting in a lowering of hemoglobin release together with a reduction in cellular toxicity and cellular activation. However, none of them are directly involved in the activation of the acute inflammation process with a consequent release of pro-inflammatory cytokines. The obtained results provide an important direction towards the biomedical applications of silica nanosheets, rendering them an attractive material for the development of future immunological therapies.

• 43.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Virginia Commonwealth University in Qatar, Libral Arts and Sciences Program, P.O. Box 8095, Doha, Qatar. KTH, School of Engineering Sciences (SCI), Applied Physics. Department of Physics, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat, PC 123, Oman. Department of Chemistry, Paksitan Institute of Engineering and Applied Sciences (PIEAS), PO Nilore, Islamabad, 45650, Pakistan. KTH, School of Engineering Sciences (SCI), Applied Physics.
Synthesis of hierarchically porous silica aerogel supported Palladium catalyst for low-temperature CO oxidation under ignition/extinction conditions2020In: Microporous and Mesoporous Materials, ISSN 1387-1811, E-ISSN 1873-3093, Vol. 292, article id 109758Article in journal (Refereed)

Synthesis of well-dispersed palladium nanoparticles within silica aerogel pores with controlled size was carried out using sol-gel synthesis under supercritical ethanol drying. The high concentration of silanol groups on silica (SiO2) surface facilitated a superior palladium (Pd) loading up to 10 wt %. The synthesized Pd/SiO2 nanocomposite aerogels were characterized by X-ray diffraction (XRD), N2 adsorption-desorption, X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and Fourier transform infrared (FTIR) spectroscopic methods. The silica aerogel supported catalysts were found to have a wide pore size distribution. TEM investigations confirmed that Pd nanocrystals were located within the SiO2 microspores and mesopores. The catalyst was evaluated for carbon monoxide (CO) oxidation reaction under ignition/extinction conditions. The synthesized catalyst demonstrated a high catalytic activity at low operating temperatures (&lt;200 °C) compared to unsupported Pd nanoparticles or bare SiO2 aerogels. This enhancement in CO oxidation activity with Pd/SiO2 aerogel catalysts are attributed to the small Pd particles, Pd interaction with the surface of the underlying SiO2 and the better dispersion of Pd particles within the SiO2 pores. Porosity played a more important role during the extinction cycle as a result of the slow dissipation of the heat leading to hysteresis. We demonstrate the influence of porosity of catalyst supports on the size, dispersion, and catalytic activity of Pd nanoparticles.

• 44.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Investigation of the Photophysical Properties of Quantum Dots for Super-Resolution Imaging2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
• 45.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Fluorescence microscopy at the molecular scale2019In: Current Opinion in Biomedical Engineering, ISSN 2468-4511, Vol. 12, p. 34-42Article, review/survey (Refereed)

The diffraction limit is no longer a concept that stands as a true constant in imaging, with fluorescence switching–based methods having made the breakthrough to circumvent this limit. Multiple ingenious solutions have been presented over the last decades and continue to be explored. The techniques used today have undergone constant development both conceptually and technically, which has enabled an increased number of biological studies at the molecular scale. Here we review recent developments to stimulated emission depletion microscopy, reversible saturable optical fluorescence transitions microscopy, single-molecule localization microscopy, and MINFLUX and mention key applications of these methods. Finally, we present our view on what the future holds for super-resolution imaging, especially in terms of even more challenging live-cell imaging in different biological model systems.

• 46.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Stable stimulated emission depletion imaging of extended sample regions2020In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 53, no 2, article id 024001Article in journal (Refereed)

Stimulated emission depletion (STED) nanoscopy has become one of the most used nanoscopy techniques over the last decade. However, most recordings are done in specimen regions no larger than 10–30  ×  10–30 μm2 due to aberrations, instability and manual mechanical stages. Here, we demonstrate automated 2D and 3D STED nanoscopy of extended sample regions up to 0.5  ×  0.5 mm2 by using a scanning system that maintains stationary beams in the back focal plane. The setup allows up to 80–100  ×  80–100 μm2 field of view (FOV) with uniform spatial resolution, a mechanical stage allowing sequential tiling to record larger sample areas, and a feedback system keeping the sample in focus at all times. Taken together, this allows automated recording of theoretically unlimited-sized sample areas and volumes, without compromising the achievable spatial resolution and image quality.

• 47. Amaya, Andrew J.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
How Cubic Can Ice Be?2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 14, p. 3216-3222Article in journal (Refereed)

Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r approximate to 10 nm) at similar to 225 K The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 mu s of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, chi, in the range of 0.78 +/- 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. The high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a similar to 1 mu s time scale in single nanodroplets.

• 48.
KTH, School of Engineering Sciences (SCI), Applied Physics.
Ion removal trends in capacitivedeionization and its applicationfor treating industrial effluents2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
• 49.
KTH, School of Engineering Sciences (SCI), Applied Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics. CEA LETI MINATEC, Grenoble, France. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Engineering Sciences (SCI), Applied Physics.
Optical Coatings and Films Based on Photonic Semiconductor Nanostructure Assemblies2017In: 2017 19TH INTERNATIONAL CONFERENCE ON TRANSPARENT OPTICAL NETWORKS (ICTON), IEEE , 2017Conference paper (Refereed)

Photonic semiconductor nanostructure assemblies offer unique possibilities for light manipulation as well as for tailoring light-matter interaction by appropriate choice of their geometrical and material properties. The material-structure combination offers a variety of options for wavelength specific applications, deriving from the electronic properties of semiconductors and optical properties of individual and assemblies of nanostructures (particles, disks, pillars/wires etc.). We present an overview of our research on optical coatings based on semiconductor nanostructure assemblies focusing on their optical properties, different fabrication technologies and selected application examples. Design and simulations of the optical coatings are performed by finite difference time domain calculations, and are used as a guideline for fabrication. We discuss different routes for fabrication of nanostructured optical films/coatings including directed assembly and patterning of nanoparticles from solution phase, solution synthesis, combination of dry etching and colloidal lithography, transfer printing, and generation of flexible polymer films with embedded nanostructures. The fabricated films are validated by optical measurements and some device specific properties such as omni-directional broad-band anti-reflection in solar cells and efficient light extraction in light emitting diodes are demonstrated.

KTH, School of Engineering Sciences (SCI), Applied Physics.
Multimode interferometer for guided matter waves2002In: Physical review letters, Vol. 88, no 10Article in journal (Refereed)
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