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  • 1. Altfeder, Igor
    et al.
    Voevodin, Andrey A.
    Check, Michael H.
    Eichfeld, Sarah M.
    Robinson, Joshua A.
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Scanning Tunneling Microscopy Observation of Phonon Condensate2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 43214Article in journal (Refereed)
    Abstract [en]

    Using quantum tunneling of electrons into vibrating surface atoms, phonon oscillations can be observed on the atomic scale. Phonon interference patterns with unusually large signal amplitudes have been revealed by scanning tunneling microscopy in intercalated van der Waals heterostructures. Our results show that the effective radius of these phonon quasi-bound states, the real-space distribution of phonon standing wave amplitudes, the scattering phase shifts, and the nonlinear intermode coupling strongly depend on the presence of defect-induced scattering resonance. The observed coherence of these quasi-bound states most likely arises from phase-and frequency-synchronized dynamics of all phonon modes, and indicates the formation of many-body condensate of optical phonons around resonant defects. We found that increasing the strength of the scattering resonance causes the increase of the condensate droplet radius without affecting the condensate fraction inside it. The condensate can be observed at room temperature.

  • 2.
    Andersson, Richard L.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Ström, Valter
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Engineering Material Physics.
    Gedde, Ulf W.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Mallon, Peter E.
    Hedenqvist, Mikael S.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Olsson, Richard T.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Micromechanics of ultra-toughened electrospun PMMA/PEO fibres as revealed by in-situ tensile testing in an electron microscope2014In: Scientific Reports, ISSN 2045-2322, Vol. 4, 6335- p.Article in journal (Refereed)
    Abstract [en]

    A missing cornerstone in the development of tough micro/nano fibre systems is an understanding of the fibre failure mechanisms, which stems from the limitation in observing the fracture of objects with dimensions one hundredth of the width of a hair strand. Tensile testing in the electron microscope is herein adopted to reveal the fracture behaviour of a novel type of toughened electrospun poly(methyl methacrylate)/poly(ethylene oxide) fibre mats for biomedical applications. These fibres showed a toughness more than two orders of magnitude greater than that of pristine PMMA fibres. The in-situ microscopy revealed that the toughness were not only dependent on the initial molecular alignment after spinning, but also on the polymer formulation that could promote further molecular orientation during the formation of micro/nano-necking. The true fibre strength was greater than 150 MPa, which was considerably higher than that of the unmodified PMMA (17 MPa). This necking phenomenon was prohibited by high aspect ratio cellulose nanocrystal fillers in the ultra-tough fibres, leading to a decrease in toughness by more than one order of magnitude. The reported necking mechanism may have broad implications also within more traditional melt-spinning research.

  • 3. Araujo, C. Moyses
    et al.
    Nagar, Sandeep
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Ramzan, Muhammad
    Shukla, R.
    Jayakumar, O. D.
    Tyagi, A. K.
    Liu, Yi-Sheng
    Chen, Jeng-Lung
    Glans, Per-Anders
    Chang, Chinglin
    Blomqvist, Andreas
    Lizarraga, Raquel
    Holmström, Erik
    Belova, Lyubov
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Engineering Material Physics.
    Guo, Jinghua
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Rao, K. Venkat
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Disorder-induced Room Temperature Ferromagnetism in Glassy Chromites2014In: Scientific Reports, ISSN 2045-2322, Vol. 4, 4686- p.Article in journal (Refereed)
    Abstract [en]

    We report an unusual robust ferromagnetic order above room temperature upon amorphization of perovskite [YCrO3] in pulsed laser deposited thin films. This is contrary to the usual expected formation of a spin glass magnetic state in the resulting disordered structure. To understand the underlying physics of this phenomenon, we combine advanced spectroscopic techniques and first-principles calculations. We find that the observed order-disorder transformation is accompanied by an insulator-metal transition arising from a wide distribution of Cr-O-Cr bond angles and the consequent metallization through free carriers. Similar results also found in YbCrO3-films suggest that the observed phenomenon is more general and should, in principle, apply to a wider range of oxide systems. The ability to tailor ferromagnetic order above room temperature in oxide materials opens up many possibilities for novel technological applications of this counter intuitive effect.

  • 4. Arslanov, Temirlan R.
    et al.
    Mollaev, Akhmedbek Yu.
    Kamilov, Ibragimkhan K.
    Arslanov, Rasul K.
    Kilanski, Lukasz
    Minikaev, Roman
    Reszka, Anna
    Lopez-Moreno, Sinhue
    Romero, Aldo H.
    Ramzan, Muhammad
    Panigrahi, Puspamitra
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Trukhan, Vladimir M.
    Chatterji, Tapan
    Marenkin, Sergey F.
    Shoukavaya, Tatyana V.
    Pressure control of magnetic clusters in strongly inhomogeneous ferromagnetic chalcopyrites2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, 7720- p.Article in journal (Refereed)
    Abstract [en]

    Room-temperature ferromagnetism in Mn-doped chalcopyrites is a desire aspect when applying those materials to spin electronics. However, dominance of high Curie-temperatures due to cluster formation or inhomogeneities limited their consideration. Here we report how an external perturbation such as applied hydrostatic pressure in CdGeP2:Mn induces a two serial magnetic transitions from ferromagnet to non-magnet state at room temperature. This effect is related to the unconventional properties of created MnP magnetic clusters within the host material. Such behavior is also discussed in connection with ab initio density functional calculations, where the structural properties of MnP indicate magnetic transitions as function of pressure as observed experimentally. Our results point out new ways to obtain controlled response of embedded magnetic clusters.

  • 5. Ashaduzzaman, Md.
    et al.
    Deshpande, Swapneel R.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mishra, Yogendra Kumar
    Turner, Anthony P. F.
    Tiwari, Ashutosh
    On/off-switchable LSPR nano-immunoassay for troponin-T2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 44027Article in journal (Refereed)
    Abstract [en]

    Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature.

  • 6.
    Asp, Michaela
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Salmen, Fredrik
    KTH, School of Biotechnology (BIO), Gene Technology.
    Stahl, Patrik L.
    Vickovic, Sanja
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Felldin, Ulrika
    Lofling, Marie
    Navarro, Jose Fernandez
    Maaskola, Jonas
    Eriksson, Maria J.
    Persson, Bengt
    Corbascio, Matthias
    Persson, Hans
    Linde, Cecilia
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Spatial detection of fetal marker genes expressed at low level in adult human heart tissue2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 12941Article in journal (Refereed)
    Abstract [en]

    Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.

  • 7.
    Bass, Tarek
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Rosestedt, Maria
    Mitran, Bogdan
    Frejd, Fredrik Y.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Protein Technology.
    Tolmachev, Vladimir
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Orlova, Anna
    In vivo evaluation of a novel format of a bivalent HER3-targeting and albumin- binding therapeutic affibody construct2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 43118Article in journal (Refereed)
    Abstract [en]

    Overexpression of human epidermal growth factor receptor 3 (HER3) is involved in resistance to several therapies for malignant tumours. Currently, several anti-HER3 monoclonal antibodies are under clinical development. We introduce an alternative approach to HER3-targeted therapy based on engineered scaffold proteins, i.e. affibody molecules. We designed a small construct (22.5 kDa, denoted 3A3), consisting of two high-affinity anti-HER3 affibody molecules flanking an albumin-binding domain ABD, which was introduced for prolonged residence in circulation. In vitro, 3A3 efficiently inhibited growth of HER3-expressing BxPC-3 cells. Biodistribution in mice was measured using 3A3 that was site-specifically labelled with In-111 via a DOTA chelator. The residence time of In-111-DOTA-3A3 in blood was extended when compared with the monomeric affibody molecule. In-111-DOTA-3A3 accumulated specifically in HER3-expressing BxPC-3 xenografts in mice. However, In-111-DOTA-3A3 cleared more rapidly from blood than a size-matched control construct In-111-DOTA-TAT, most likely due to sequestering of 3A3 by mErbB3, the murine counterpart of HER3. Repeated dosing and increase of injected protein dose decreased uptake of In-111-DOTA-3A3 in mErbB3-expressing tissues. Encouragingly, growth of BxPC-3 xenografts in mice was delayed in an experimental (pilot-scale) therapy study using 3A3. We conclude that the 3A3 affibody format seems promising for treatment of HER3-overexpressing tumours.

  • 8.
    Belonoshko, Anatoly B.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Lukinov, Timofiy
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Rosengren, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. AlbaNova University Center, Sweden.
    Bryk, Taras
    Litasov, Konstantin D.
    Synthesis of heavy hydrocarbons at the core-mantle boundary2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, 18382Article in journal (Refereed)
    Abstract [en]

    The synthesis of complex organic molecules with C-C bonds is possible under conditions of reduced activity of oxygen. We have found performing ab initio molecular dynamics simulations of the C-O-H- Fe system that such conditions exist at the core-mantle boundary (CMB). H2O and CO2 delivered to the CMB by subducting slabs provide a source for hydrogen and carbon. The mixture of H2O and CO2 subjected to high pressure (130 GPa) and temperature (4000 to 4500 K) does not lead to synthesis of complex hydrocarbons. However, when Fe is added to the system, C-C bonds emerge. It means that oil might be a more abundant mineral than previously thought.

  • 9.
    Belonoshko, Anatoly B.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Ramzan, Muhammad
    Mao, Ho-kwang
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Atomic Diffusion in Solid Molecular Hydrogen2013In: Scientific Reports, ISSN 2045-2322, Vol. 3, 2340- p.Article in journal (Refereed)
    Abstract [en]

    We performed ab initio molecular dynamics simulations of the C2c and Cmca-12 phases of hydrogen at pressures from 210 to 350 GPa. These phases were predicted to be stable at 0 K and pressures above 200 GPa. However, systematic studies of temperature impact on properties of these phases have not been performed so far. Filling this gap, we observed that on temperature increase diffusion sets in the Cmca-12 phase, being absent in C2c. We explored the mechanism of diffusion and computed melting curve of hydrogen at extreme pressures. The results suggest that the recent experiments claiming conductive hydrogen at the pressure around 260 GPa and ambient temperature might be explained by the diffusion. The diffusion might also be the reason for the difference in Raman spectra obtained in recent experiments.

  • 10. Bergman, Anders
    et al.
    Hellsvik, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Bessarab, Pavel F.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. Univ Iceland, Iceland.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Spin relaxation signature of colossal magnetic anisotropy in platinum atomic chains2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 36872Article in journal (Refereed)
    Abstract [en]

    Recent experimental data demonstrate emerging magnetic order in platinum atomically thin nanowires. Furthermore, an unusual form of magnetic anisotropy-colossal magnetic anisotropy (CMA)-was earlier predicted to exist in atomically thin platinum nanowires. Using spin dynamics simulations based on first-principles calculations, we here explore the spin dynamics of atomically thin platinum wires to reveal the spin relaxation signature of colossal magnetic anisotropy, comparing it with other types of anisotropy such as uniaxial magnetic anisotropy (UMA). We find that the CMA alters the spin relaxation process distinctly and, most importantly, causes a large speed-up of the magnetic relaxation compared to uniaxial magnetic anisotropy. The magnetic behavior of the nanowire exhibiting CMA should be possible to identify experimentally at the nanosecond time scale for temperatures below 5 K. This time-scale is accessible in e.g., soft x-ray free electron laser experiments.

  • 11. Bora, Tanujjal
    et al.
    Zoepfl, David
    Dutta, Joydeep
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Importance of Plasmonic Heating on Visible Light Driven Photocatalysis of Gold Nanoparticle Decorated Zinc Oxide Nanorods2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 26913Article in journal (Refereed)
    Abstract [en]

    Herein we explore the role of localized plasmonic heat generated by resonantly excited gold (Au) NPs on visible light driven photocatalysis process. Au NPs are deposited on the surface of vertically aligned zinc oxide nanorods (ZnO NRs). The localized heat generated by Au NPs under 532 nm continuous laser excitation (SPR excitation) was experimentally probed using Raman spectroscopy by following the phonon modes of ZnO. Under the resonant excitation the temperature at the surface of the AuZnO NRs reaches up to about 300 degrees C, resulting in almost 6 times higher apparent quantum yield (AQY) for photocatalytic degradation of methylene blue (MB) compared to the bare ZnO NRs. Under solar light irradiation the Au-ZnO NRs demonstrated visible light photocatalytic activity twice that of what was achieved with bare ZnO NRs, while significantly reduced the activation energy required for the photocatalytic reactions allowing the reactions to occur at a faster rate.

  • 12. Caspeta, Luis
    et al.
    Chen, Yun
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 degrees C2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 27003Article in journal (Refereed)
    Abstract [en]

    Exposure to long-term environmental changes across >100s of generations results in adapted phenotypes, but little is known about how metabolic and transcriptional responses are optimized in these processes. Here, we show that thermotolerant yeast strains selected by adaptive laboratory evolution to grow at increased temperature, activated a constitutive heat stress response when grown at the optimal ancestral temperature, and that this is associated with a reduced growth rate. This preventive response was perfected by additional transcriptional changes activated when the cultivation temperature is increased. Remarkably, the sum of global transcriptional changes activated in the thermotolerant strains when transferred from the optimal to the high temperature, corresponded, in magnitude and direction, to the global changes observed in the ancestral strain exposed to the same transition. This demonstrates robustness of the yeast transcriptional program when exposed to heat, and that the thermotolerant strains streamlined their path to rapidly and optimally reach post-stress transcriptional and metabolic levels. Thus, long-term adaptation to heat improved yeasts ability to rapidly adapt to increased temperatures, but this also causes a trade-off in the growth rate at the optimal ancestral temperature.

  • 13. Cebula, Marcus
    et al.
    Turan, Ilke Simsek
    Sjodin, Birgitta
    Thulasingam, Madhuranayaki
    Brock, Joseph
    Chmyrov, Volodymyr
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Abe, Hiroshi
    Mannervik, Bengt
    Haeggstrom, Jesper Z.
    Rinaldo-Matthis, Agnes
    Akkaya, Engin U.
    Morgenstern, Ralf
    Catalytic Conversion of Lipophilic Substrates by Phase constrained Enzymes in the Aqueous or in the Membrane Phase2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 38316Article in journal (Refereed)
    Abstract [en]

    Both soluble and membrane-bound enzymes can catalyze the conversion of lipophilic substrates. The precise substrate access path, with regard to phase, has however, until now relied on conjecture from enzyme structural data only (certainly giving credible and valuable hypotheses). Alternative methods have been missing. To obtain the first experimental evidence directly determining the access paths (of lipophilic substrates) to phase constrained enzymes we here describe the application of a BODIPY-derived substrate (PS1). Using this tool, which is not accessible to cytosolic enzymes in the presence of detergent and, by contrast, not accessible to membrane embedded enzymes in the absence of detergent, we demonstrate that cytosolic and microsomal glutathione transferases (GSTs), both catalyzing the activation of PS1, do so only within their respective phases. This approach can serve as a guideline to experimentally validate substrate access paths, a fundamental property of phase restricted enzymes. Examples of other enzyme classes with members in both phases are xenobiotic-metabolizing sulphotransferases/UDP-glucuronosyl transferases or epoxide hydrolases. Since specific GSTs have been suggested to contribute to tumor drug resistance, PS1 can also be utilized as a tool to discriminate between phase constrained members of these enzymes by analyzing samples in the absence and presence of Triton X-100.

  • 14. Chen, Rui-Pin
    et al.
    Chen, Zhaozhong
    Chew, Khian-Hooi
    Li, Pei-Gang
    Yu, Zhongliang
    Ding, Jianping
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Structured caustic vector vortex optical field: manipulating optical angular momentum flux and polarization rotation2015In: Scientific Reports, ISSN 2045-2322, Vol. 5, 10628Article in journal (Refereed)
    Abstract [en]

    A caustic vector vortex optical field is experimentally generated and demonstrated by a caustic-based approach. The desired caustic with arbitrary acceleration trajectories, as well as the structured states of polarization (SoP) and vortex orders located in different positions in the field cross-section, is generated by imposing the corresponding spatial phase function in a vector vortex optical field. Our study reveals that different spin and orbital angular momentum flux distributions (including opposite directions) in different positions in the cross-section of a caustic vector vortex optical field can be dynamically managed during propagation by intentionally choosing the initial polarization and vortex topological charges, as a result of the modulation of the caustic phase. We find that the SoP in the field cross-section rotates during propagation due to the existence of the vortex. The unique structured feature of the caustic vector vortex optical field opens the possibility of multi-manipulation of optical angular momentum fluxes and SoP, leading to more complex manipulation of the optical field scenarios. Thus this approach further expands the functionality of an optical system.

  • 15. Chen, Rui-Pin
    et al.
    Chew, Khian-Hooi
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Dynamic Control of Collapse in a Vortex Airy Beam2013In: Scientific Reports, ISSN 2045-2322, Vol. 3, 1406- p.Article in journal (Refereed)
    Abstract [en]

    Here we study systematically the self-focusing dynamics and collapse of vortex Airy optical beams in a Kerr medium. The collapse is suppressed compared to a non-vortex Airy beam in a Kerr medium due to the existence of vortex fields. The locations of collapse depend sensitively on the initial power, vortex order, and modulation parameters. The collapse may occur in a position where the initial field is nearly zero, while no collapse appears in the region where the initial field is mainly distributed. Compared with a non-vortex Airy beam, the collapse of a vortex Airy beam can occur at a position away from the area of the initial field distribution. Our study shows the possibility of controlling and manipulating the collapse, especially the precise position of collapse, by purposely choosing appropriate initial power, vortex order or modulation parameters of a vortex Airy beam.

  • 16. Chen, Xiaobin
    et al.
    Tian, Fuyang
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Persson, Clas
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling.
    Duan, Wenhui
    Chen, Nan-xian
    Interlayer interactions in graphites2013In: Scientific Reports, ISSN 2045-2322, Vol. 3, 3046- p.Article in journal (Refereed)
    Abstract [en]

    Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Mobius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

  • 17. Cheng, J.
    et al.
    Sun, Xianqiang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, W.
    Liu, G.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tang, Y.
    Molecular switches of the κ opioid receptor triggered by 6′-GNTI and 5′-GNTI2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 18913Article in journal (Refereed)
    Abstract [en]

    The κ opioid receptor (κOR) is a member of G-protein-coupled receptors, and is considered as a promising drug target for treating neurological diseases. κOR selective 6′-GNTI was proved to be a G-protein biased agonist, whereas 5′-GNTI acts as an antagonist. To investigate the molecular mechanism of how these two ligands induce different behaviors of the receptor, we built two systems containing the 5′-GNTI-κOR complex and the 6′-GNTI-κOR complex, respectively, and performed molecular dynamics simulations of the two systems. We observe that transmembrane (TM) helix 6 of the κOR rotates about 4.6° on average in the κOR-6′-GNTI complex. Detailed analyses of the simulation results indicate that E2976.58 and I2946.55 play crucial roles in the rotation of TM6. In the simulation of the κOR-5′-GNTI system, it is revealed that 5′-GNTI can stabilize TM6 in the inactive state form. In addition, the kink of TM7 is stabilized by a hydrogen bond between S3247.47 and the residue V691.42 on TM1.

  • 18. Ch'ng, Jun-Hong
    et al.
    Sirel, Madle
    Zandian, Arash
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Quintana, Maria del Pilar
    Chan, Sherwin Chun Leung
    Moll, Kirsten
    Tellgren-Roth, Asa
    Nilsson, IngMarie
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Qundos, Ulrika
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wahlgren, Mats
    Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 43190Article in journal (Refereed)
    Abstract [en]

    Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.

  • 19. Choong, Ferdinand X.
    et al.
    Back, Marcus
    Steiner, Svava E.
    Melican, Keira
    Nilsson, K. Peter R.
    Edlund, Ulrica
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Richter-Dahlfors, Agneta
    Nondestructive, real-time determination and visualization of cellulose, hemicellulose and lignin by luminescent oligothiophenes2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 35578Article in journal (Refereed)
    Abstract [en]

    Enabling technologies for efficient use of the bio-based feedstock are crucial to the replacement of oil-based products. We investigated the feasibility of luminescent conjugated oligothiophenes (LCOs) for non-destructive, rapid detection and quality assessment of lignocellulosic components in complex biomass matrices. A cationic pentameric oligothiophene denoted p-HTEA (pentamer hydrogen thiophene ethyl amine) showed unique binding affinities to cellulose, lignin, hemicelluloses, and cellulose nanofibrils in crystal, liquid and paper form. We exploited this finding using spectrofluorometric methods and fluorescence confocal laser scanning microscopy, for sensitive, simultaneous determination of the structural and compositional complexities of native lignocellulosic biomass. With exceptional photostability, p-HTEA is also demonstrated as a dynamic sensor for real-time monitoring of enzymatic cellulose degradation in cellulolysis. These results demonstrate the use of p-HTEA as a non-destructive tool for the determination of cellulose, hemicellulose and lignin in complex biomass matrices, thereby aiding in the optimization of biomass-converting technologies.

  • 20. Clausson, Carl-Magnus
    et al.
    Arngarden, Linda
    Ishaq, Omer
    Klaesson, Axel
    Kuhnemund, Malte
    Grannas, Karin
    Koos, Bjorn
    Qian, Xiaoyan
    Ranefall, Petter
    Krzywkowski, Tomasz
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Mats
    Wahlby, Carolina
    Soderberg, Ola
    Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio2015In: Scientific Reports, ISSN 2045-2322, Vol. 5, 12317Article in journal (Refereed)
    Abstract [en]

    Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.

  • 21. Conti, Luca
    et al.
    Renhorn, Jakob
    Gabrielsson, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Turesson, Fredrik
    Liin, Sara I.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. Stockholm University, Sweden.
    Elinder, Fredrik
    Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 27562Article in journal (Refereed)
    Abstract [en]

    Voltage-gated potassium channels open at depolarized membrane voltages. A prolonged depolarization causes a rearrangement of the selectivity filter which terminates the conduction of ions - a process called slow or C-type inactivation. How structural rearrangements in the voltage-sensor domain (VSD) cause alteration in the selectivity filter, and vice versa, are not fully understood. We show that pulling the pore domain of the Shaker potassium channel towards the VSD by a Cd2+ bridge accelerates C-type inactivation. Molecular dynamics simulations show that such pulling widens the selectivity filter and disrupts the K+ coordination, a hallmark for C-type inactivation. An engineered Cd2+ bridge within the VSD also affect C-type inactivation. Conversely, a pore domain mutation affects VSD gating-charge movement. Finally, C-type inactivation is caused by the concerted action of distant amino acid residues in the pore domain. All together, these data suggest a reciprocal communication between the pore domain and the VSD in the extracellular portion of the channel.

  • 22.
    Couto, Rafael C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Univ Fed Goias, Brazil.
    Guarise, Marco
    Nicolaou, Alessandro
    Jaouen, Nicolas
    Chiuzbaian, Gheorghe S.
    Luening, Jan
    Ekholm, Victor
    Rubensson, Jan-Erik
    Sathe, Conny
    Hennies, Franz
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Guimaraes, Freddy F.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Journel, Loic
    Simon, Marc
    Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 20947Article in journal (Refereed)
    Abstract [en]

    The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12-14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of "dark" with "bright" final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past.

  • 23.
    Dahlberg, Carl F. O.
    et al.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Solid Mechanics (Div.).
    Mitchell-Thomas, R. C.
    Quevedo-Teruel, Oscar
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering.
    Reducing the Dispersion of Periodic Structures with Twist and Polar Glide Symmetries2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 10136Article in journal (Refereed)
    Abstract [en]

    In this article, a number of guiding structures are proposed which take advantage of higher symmetries to vastly reduce the dispersion. These higher symmetries are obtained by executing additional geometrical operations to introduce more than one period into the unit cell of a periodic structure. The specific symmetry operations employed here are a combination of p-fold twist and polar glide. Our dispersion analysis shows that a mode in a structure possessing higher symmetries is less dispersive than in a conventional structure. It is also demonstrated that, similar to the previously studied Cartesian glide-symmetric structures, polar glide-symmetric structures also exhibit a frequency independent response. Promising applications of these structures are leaky-wave antennas which utilize the low frequency dependence.

  • 24.
    Dias, Jorge T
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Svedberg, Gustav
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Nystrand, Mats
    Andersson-Svahn, Helene
    Gantelius, Jesper
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rapid signal enhancement method for nanoprobe-based biosensing2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 6837Article in journal (Refereed)
    Abstract [en]

    The introduction of nanomaterials as detection reagents has enabled improved sensitivity and facilitated detection in a variety of bioanalytical assays. However, high nanoprobe densities are typically needed for colorimetric detection and to circumvent this limitation several enhancement protocols have been reported. Nevertheless, there is currently a lack of universal, enzyme-free and versatile methods that can be readily applied to existing as well as new biosensing strategies. The novel method presented here is shown to enhance the signal of gold nanoparticles enabling visual detection of a spot containing < 10 nanoparticles. Detection of Protein G on paper arrays was improved by a 100-fold amplification factor in under five minutes of assay time, using IgG-labelled gold, silver, silica and iron oxide nanoprobes. Furthermore, we show that the presented protocol can be applied to a commercial allergen microarray assay, ImmunoCAP ISAC sIgE 112, attaining a good agreement with fluorescent detection when analysing human clinical samples.

  • 25. Ding, Fei
    et al.
    Dai, Jin
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Chen, Yiting
    Zhu, Jianfei
    Jin, Yi
    Bozhevolnyi, Sergey I.
    Broadband near-infrared metamaterial absorbers utilizing highly lossy metals2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 39445Article in journal (Refereed)
    Abstract [en]

    Radiation absorbers have increasingly been attracting attention as crucial components for controllable thermal emission, energy harvesting, modulators, etc. However, it is still challenging to realize thin absorbers which can operate over a wide spectrum range. Here, we propose and experimentally demonstrate thin, broadband, polarization-insensitive and omnidirectional absorbers working in the near-infrared range. We choose titanium (Ti) instead of the commonly used gold (Au) to construct nano-disk arrays on the top of a silicon dioxide (SiO2) coated Au substrate, with the quality (Q) factor of the localized surface plasmon (LSP) resonance being decreased due to the intrinsic high loss of Ti. The combination of this low-Q LSP resonance and the propagating surface plasmon (PSP) excitation resonance, which occur at different wavelengths, is the fundamental origin of the broadband absorption. The measured (at normal light incidence) absorption is over 90% in the wavelength range from 900 nm to 1825 nm, with high absorption persisting up to the incident angle of similar to 40 degrees. The demonstrated thin-film absorber configuration is relatively easy to fabricate and can be realized with other properly selected materials.

  • 26.
    Edsgärd, Daniel
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Iglesias, Maria Jesus
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden .
    Reilly, Sarah-Jayne
    Hamsten, Anders
    Tornvall, Per
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden; .
    Emanuelsson, Olof
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 21134Article in journal (Refereed)
    Abstract [en]

    Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively.

  • 27. El-Sayed, Ramy
    et al.
    Bhattacharya, Kunal
    Gu, Zonglin
    Yang, Zaixing
    Weber, Jeffrey K.
    Li, Hu
    Leifer, Klaus
    Zhao, Yichen
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Toprak, Muhammet S.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Zhou, Ruhong
    Fadeel, Bengt
    Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A42016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 21316Article in journal (Refereed)
    Abstract [en]

    We report a detailed computational and experimental study of the interaction of single-walled carbon nanotubes (SWCNTs) with the drug-metabolizing cytochrome P450 enzyme, CYP3A4. Dose-dependent inhibition of CYP3A4-mediated conversion of the model compound, testosterone, to its major metabolite, 6 beta-hydroxy testosterone was noted. Evidence for a direct interaction between SWCNTs and CYP3A4 was also provided. The inhibition of enzyme activity was alleviated when SWCNTs were pre-coated with bovine serum albumin. Furthermore, covalent functionalization of SWCNTs with polyethylene glycol (PEG) chains mitigated the inhibition of CYP3A4 enzymatic activity. Molecular dynamics simulations suggested that inhibition of the catalytic activity of CYP3A4 is mainly due to blocking of the exit channel for substrates/products through a complex binding mechanism. This work suggests that SWCNTs could interfere with metabolism of drugs and other xenobiotics and provides a molecular mechanism for this toxicity. Our study also suggests means to reduce this toxicity, eg., by surface modification.

  • 28.
    Ergül, Adem
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics. Stockholm University, Sweden.
    Weissl, Thomas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Johansson, Jan
    Lidmar, Jack
    KTH, School of Engineering Sciences (SCI), Physics, Statistical Physics.
    Haviland, David B.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Spatial and temporal distribution of phase slips in Josephson junction chains2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 11447Article in journal (Refereed)
    Abstract [en]

    The Josephson effect, tunnelling of a supercurrent through a thin insulator layer between two superconducting islands, is a phenomena characterized by a spatially distributed phase of the superconducting condensate. In recent years, there has been a growing focus on Josephson junction devices particularly for the applications of quantum metrology and superconducting qubits. In this study, we report the development of Josephson junction circuit formed by serially connecting many Superconducting Quantum Interference Devices, SQUIDs. We present experimental measurements as well as numerical simulations of a phase-slip center, a SQUID with weaker junctions, embedded in a Josephson junction chain. The DC transport properties of the chain are the result of phase slips which we simulate using a classical model that includes linear external damping, terminating impedance, as well as internal nonlinear quasiparticle damping. We find good agreement between the simulated and the experimental current voltage characteristics. The simulations allow us to examine the spatial and temporal distribution of phase-slip events occurring across the chains and also the existence of travelling voltage pulses which reflect at the chain edges.

  • 29.
    Etcheverry, Sebastian
    et al.
    Center for optics and photonics,Univesity of Concepcion.
    Cañas, Gustavo
    S. Gomez, Esteban
    Nogueira, Wallon
    Saaveda, Carlos
    Xavier, Guilherme
    Lima, Gustavo
    Quantum key distribution session with 16-dimensional photonic states2013In: Scientific Reports, ISSN 2045-2322, no 3, 2316- p.Article in journal (Refereed)
    Abstract [en]

    The secure transfer of information is an important problem in modern telecommunications. Quantum key distribution (QKD) provides a solution to this problem by using individual quantum systems to generate correlated bits between remote parties, that can be used to extract a secret key. QKD with D-dimensional quantum channels provides security advantages that grow with increasing D. However, the vast majority of QKD implementations has been restricted to two dimensions. Here we demonstrate the feasibility of using higher dimensions for real-world quantum cryptography by performing, for the first time, a fully automated QKD session based on the BB84 protocol with 16-dimensional quantum states. Information is encoded in the single-photon transverse momentum and the required states are dynamically generated with programmable spatial light modulators. Our setup paves the way for future developments in the field of experimental high-dimensional QKD.

  • 30.
    Etcheverry, Sebastián
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. RISE Acreo AB, Sweden.
    Faridi, Muhammad Asim
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ramachandraiah, Harisha
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kumar, T.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Margulis, Walter
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. RISE Acreo AB, Sweden.
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    High performance micro-flow cytometer based on optical fibres2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 5628Article in journal (Refereed)
    Abstract [en]

    Flow cytometry is currently the gold standard for analysis of cells in the medical laboratory and biomedical research. Fuelled by the need of point-of-care diagnosis, a significant effort has been made to miniaturize and reduce cost of flow cytometers. However, despite recent advances, current microsystems remain less versatile and much slower than their large-scale counterparts. In this work, an all-silica fibre microflow cytometer is presented that measures fluorescence and scattering from particles and cells. It integrates cell transport in circular capillaries and light delivery by optical fibres. Single-stream cell focusing is performed by Elasto-inertial microfluidics to guarantee accurate and sensitive detection. The capability of this technique is extended to high flow rates (up to 800 mu l/min), enabling a throughput of 2500 particles/s. The robust, portable and low-cost system described here could be the basis for a point-of-care flow cytometer with a performance comparable to commercial systems.

  • 31.
    Fleetwood, Filippa
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Klint, Susanne
    Hanze, Martin
    KTH, School of Biotechnology (BIO), Protein Technology.
    Gunneriusson, Elin
    Frejd, Fredrik
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Protein Technology.
    Simultaneous targeting of two ligand-binding sites on VEGFR2 using biparatopic Affibody molecules results in dramatically improved affinity2014In: Scientific Reports, ISSN 2045-2322, Vol. 4, 7518- p.Article in journal (Refereed)
    Abstract [en]

    Angiogenesis plays an important role in cancer and ophthalmic disorders such as age-related macular degeneration and diabetic retinopathy. The vascular endothelial growth factor (VEGF) family and corresponding receptors are regulators of angiogenesis and have been much investigated as therapeutic targets. The aim of this work was to generate antagonistic VEGFR2-specific affinity proteins having adjustable pharmacokinetic properties allowing for either therapy or molecular imaging. Two antagonistic Affibody molecules that were cross-reactive for human and murine VEGFR2 were selected by phage and bacterial display. Surprisingly, although both binders independently blocked VEGF-A binding, competition assays revealed interaction with non-overlapping epitopes on the receptor. Biparatopic molecules, comprising the two Affibody domains, were hence engineered to potentially increase affinity even further through avidity. Moreover, an albumin-binding domain was included for half-life extension in future in vivo experiments. The best-performing of the biparatopic constructs demonstrated up to 180-fold slower dissociation than the monomers. The new Affibody constructs were also able to specifically target VEGFR2 on human cells, while simultaneously binding to albumin, as well as inhibit VEGF-induced signaling. In summary, we have generated small antagonistic biparatopic Affibody molecules with high affinity for VEGFR2, which have potential for both future therapeutic and diagnostic purposes in angiogenesis-related diseases.

  • 32.
    Fogelqvist, Emelie
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Kördel, Mikael
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Carannante, Valentina
    Önfelt, Björn
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics.
    Hertz, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. Karolinska Institutet, Sweden.
    Laboratory cryo x-ray microscopy for 3D cell imaging2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 13433Article in journal (Refereed)
    Abstract [en]

    Water-window x-ray microscopy allows two-and three-dimensional (2D and 3D) imaging of intact unstained cells in their cryofixed near-native state with unique contrast and high resolution. Present operational biological water-window microscopes are based at synchrotron facilities, which limits their accessibility and integration with complementary methods. Laboratory-source microscopes have had difficulty addressing relevant biological tasks with proper resolution and contrast due to long exposure times and limited up-time. Here we report on laboratory cryo x-ray microscopy with the exposure time, contrast, and reliability to allow for routine high-spatial resolution 3D imaging of intact cells and cell-cell interactions. Stabilization of the laser-plasma source combined with new optics and sample preparation provide high-resolution cell imaging, both in 2D with ten-second exposures and in 3D with twenty-minute tomography. Examples include monitoring of the distribution of carbon-dense vesicles in starving HEK293T cells and imaging the interaction between natural killer cells and target cells.

  • 33.
    Garaud, Julien
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Babaev, Egor
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics.
    Properties of skyrmions and multi-quanta vortices in chiral p-wave superconductors2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, 17540Article in journal (Refereed)
    Abstract [en]

    Chiral p-wave superconducting state supports a rich spectrum of topological excitations different from those in conventional superconducting states. Besides domain walls separating different chiral states, chiral p-wave state supports both singular and coreless vortices also interpreted as skyrmions. Here, we present a numerical study of the energetic properties of isolated singular and coreless vortex states as functions of anisotropy and magnetic field penetration length. In a given chiral state, single quantum vortices with opposite winding have different energies and thus only one kind is energetically favoured. We find that with the appropriate sign of the phase winding, two-quanta (coreless) vortices are always energetically preferred over two isolated single quanta (singular) vortices. We also report solutions carrying more flux quanta. However those are typically more energetically expensive/metastable as compared to those carrying two flux quanta.

  • 34. Garousi, Javad
    et al.
    Andersson, Ken G.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Dam, Johan H.
    Olsen, Birgitte B.
    Mitran, Bogdan
    Orlova, Anna
    Buijs, Jos
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Protein Technology.
    Thisgaard, Helge
    Tolmachev, Vladimir
    The use of radiocobalt as a label improves imaging of EGFR using DOTA-conjugated Affibody molecule2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 5961Article in journal (Refereed)
    Abstract [en]

    Several anti-cancer therapies target the epidermal growth factor receptor (EGFR). Radionuclide imaging of EGFR expression in tumours may aid in selection of optimal cancer therapy. The In-111-labelled DOTA-conjugated Z(EGFR:2377) Affibody molecule was successfully used for imaging of EGFR-expressing xenografts in mice. An optimal combination of radionuclide, chelator and targeting protein may further improve the contrast of radionuclide imaging. The aim of this study was to evaluate the targeting properties of radiocobalt-labelled DOTA-Z(EGFR:2377). DOTA-Z(EGFR:2377) was labelled with Co-57 (T-1/2 = 271.8 d), Co-55 (T-1/2 = 17.5 h), and, for comparison, with the positron-emitting radionuclide Ga-68 (T-1/2 = 67.6 min) with preserved specificity of binding to EGFR-expressing A431 cells. The long-lived cobalt radioisotope Co-57 was used in animal studies. Both Co-57-DOTA-Z(EGFR:2377) and Ga-68-DOTA-Z(EGFR:2377) demonstrated EGFR-specific accumulation in A431 xenografts and EGFR-expressing tissues in mice. Tumour-to-organ ratios for the radiocobalt-labelled DOTA-Z(EGFR:2377) were significantly higher than for the gallium-labelled counterpart already at 3 h after injection. Importantly, Co-57-DOTA-Z(EGFR:2377) demonstrated a tumour-to-liver ratio of 3, which is 7-fold higher than the tumour-to-liver ratio for (68)GaDOTA-Z(EGFR:2377). The results of this study suggest that the positron-emitting cobalt isotope 55Co would be an optimal label for DOTA-Z(EGFR:2377) and further development should concentrate on this radionuclide as a label.

  • 35. Garousi, Javad
    et al.
    Lindbo, Sarah
    KTH, School of Biotechnology (BIO), Protein Technology.
    Mitran, Bogdan
    Buijs, Jos
    Vorobyeva, Anzhelika
    Orlova, Anna
    Tolmachev, Vladimir
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Protein Technology.
    Comparative evaluation of tumor targeting using the anti-HER2 ADAPT scaffold protein labeled at the C-terminus with indium-111 or technetium-99m2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 14780Article in journal (Refereed)
    Abstract [en]

    ABD-Derived Affinity Proteins (ADAPTs) is a novel class of engineered scaffold proteins derived from an albumin-binding domain of protein G. The use of ADAPT6 derivatives as targeting moiety have provided excellent preclinical radionuclide imaging of human epidermal growth factor 2 (HER2) tumor xenografts. Previous studies have demonstrated that selection of nuclide and chelator for its conjugation has an appreciable effect on imaging properties of scaffold proteins. In this study we performed a comparative evaluation of the anti-HER2 ADAPT having an aspartate-glutamate-alanine-valine-aspartate-alanine-asparagine-serine (DEAVDANS) N-terminal sequence and labeled at C-terminus with (99)mTc using a cysteine-containing peptide based chelator, glycine-serine-serine-cysteine (GSSC), and a similar variant labeled with In-111 using a maleimido derivative of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelator. Both (99)mTc-DEAVDANS-ADAPT6-GSSC and In-111-DEAVDANS-ADAPT6-GSSC-DOTA accumulated specifically in HER2-expressing SKOV3 xenografts. The tumor uptake of both variants did not differ significantly and average values were in the range of 19-21% ID/g. However, there was an appreciable variation in uptake of conjugates in normal tissues that resulted in a notable difference in the tumor-to-organ ratios. The In-111-DOTA label provided 2-6 fold higher tumor-to-organ ratios than (99)mTc-GSSC and is therefore the preferable label for ADAPTs.

  • 36. Ge, Xiaochen
    et al.
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, Zhejiang University, China.
    Experimental realization of an open cavity2014In: Scientific Reports, ISSN 2045-2322, Vol. 4, 5965- p.Article in journal (Refereed)
    Abstract [en]

    The design and experimental demonstration of an open cavity in the microwave region is presented. The resonance condition is achieved through the cancellation of lightpaths in positive and negative refractive index materials. The positive index material is a structured aluminium surface supporting a spoof surface plasmon mode, and the negative index material is a photonic crystal made of alumina. A resonance peak is observed in the measured spectrum at which the electric field distribution agrees with numerical simulation.

  • 37. Ghaffari, Pouyan
    et al.
    Mardinoglu, Adil
    Asplund, Anna
    Shoaie, Saeed
    Kampf, Caroline
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nielsen, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Chalmers, Dept Biol & Biol Engn, Sweden.
    Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling2015In: Scientific Reports, ISSN 2045-2322, Vol. 5, 8183- p.Article in journal (Refereed)
    Abstract [en]

    Human cancer cell lines are used as important model systems to study molecular mechanisms associated with tumor growth, hereunder how genomic and biological heterogeneity found in primary tumors affect cellular phenotypes. We reconstructed Genome scale metabolic models (GEMs) for eleven cell lines based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling. We used cell line-specific GEMs to analyze the differences in the metabolism of cancer cell lines, and to explore the heterogeneous expression of the metabolic subsystems. Furthermore, we predicted 85 antimetabolites that can inhibit growth of, or even kill, any of the cell lines, while at the same time not being toxic for 83 different healthy human cell types. 60 of these antimetabolites were found to inhibit growth in all cell lines. Finally, we experimentally validated one of the predicted antimetabolites using two cell lines with different phenotypic origins, and found that it is effective in inhibiting the growth of these cell lines. Using immunohistochemistry, we also showed high or moderate expression levels of proteins targeted by the validated antimetabolite. Identified anti-growth factors for inhibition of cell growth may provide leads for the development of efficient cancer treatment strategies.

  • 38. Gkotsis, George
    et al.
    Oellrich, Anika
    Velupillai, Sumithra
    KTH, School of Computer Science and Communication (CSC), Theoretical Computer Science, TCS.
    Liakata, Maria
    Hubbard, Tim J. P.
    Dobson, Richard J. B.
    Dutta, Rina
    Characterisation of mental health conditions in social media using Informed Deep Learning2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7Article in journal (Refereed)
    Abstract [en]

    The number of people affected by mental illness is on the increase and with it the burden on health and social care use, as well as the loss of both productivity and quality-adjusted life-years. Natural language processing of electronic health records is increasingly used to study mental health conditions and risk behaviours on a large scale. However, narrative notes written by clinicians do not capture first-hand the patients' own experiences, and only record cross-sectional, professional impressions at the point of care. Social media platforms have become a source of 'in the moment' daily exchange, with topics including well- being and mental health. In this study, we analysed posts from the social media platform Reddit and developed classifiers to recognise and classify posts related to mental illness according to 11 disorder themes. Using a neural network and deep learning approach, we could automatically recognise mental illness-related posts in our balenced dataset with an accuracy of 91.08% and select the correct theme with a weighted average accuracy of 71.37%. We believe that these results are a first step in developing methods to characterise large amounts of user-generated content that could support content curation and targeted interventions.

  • 39. Gliga, Anda R.
    et al.
    Edoff, Karin
    Caputo, Fanny
    Kallman, Thomas
    Blom, Hans
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Karlsson, Hanna L.
    Ghibelli, Lina
    Traversa, Enrico
    Ceccatelli, Sandra
    Fadeel, Bengt
    Cerium oxide nanoparticles inhibit differentiation of neural stem cells2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 9284Article in journal (Refereed)
    Abstract [en]

    Cerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific beta 3-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.

  • 40. Gong, Hanmo
    et al.
    Yang, Yuanqing
    Chen, Xingxing
    Zhao, Ding
    Chen, Xi
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Chen, Yiting
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Yan, Min
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Li, Qiang
    Qiu, Min
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO. Zhejiang University, Hangzhou, China.
    Gold nanoparticle transfer through photothermal effects in a metamaterial absorber by nanosecond laser2014In: Scientific Reports, ISSN 2045-2322, Vol. 4, 6080- p.Article in journal (Refereed)
    Abstract [en]

    A non-complicated, controllable method of metallic nanoparticle fabrication at low operating light power is proposed. The method is based on laser-induced forward transfer, using a metamaterial absorber as the donor to significantly enhance the photothermal effect and reduce the operating light fluence to 35 mJ/cm(2), which is much lower than that in previous works. A large number of metallic nanoparticles can be transferred by one shot of focused nanosecond laser pulses. Transferred nanoparticles exhibit good size uniformity and the sizes are controllable. The optical properties of transferred particles are characterized by dark-field spectroscopy and the experimental results agree with the simulation results.

  • 41. Gunaydin, Gokce
    et al.
    Yu, Shengze
    KTH, School of Biotechnology (BIO), Protein Technology.
    Graslund, Torbjorn
    KTH, School of Biotechnology (BIO), Protein Technology.
    Hammarstrom, Lennart
    Marcotte, Harold
    Fusion of the mouse IgG1 Fc domain to the VHH fragment (ARP1) enhances protection in a mouse model of rotavirus2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 30171Article in journal (Refereed)
  • 42.
    Gustavsson, Martin
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Hörnström, David
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Lundh, Susanna
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Belotserkovsky, Jaroslav
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Larsson, Gen
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Biocatalysis on the surface of Escherichia coli: melanin pigmentation of the cell exterior2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 36117Article in journal (Refereed)
    Abstract [en]

    Today, it is considered state-of-the-art to engineer living organisms for various biotechnology applications. Even though this has led to numerous scientific breakthroughs, the enclosed interior of bacterial cells still restricts interactions with enzymes, pathways and products due to the mass-transfer barrier formed by the cell envelope. To promote accessibility, we propose engineering of biocatalytic reactions and subsequent product deposition directly on the bacterial surface. As a proof-of-concept, we used the AIDA autotransporter vehicle for Escherichia coli surface expression of tyrosinase and fully oxidized externally added tyrosine to the biopolymer melanin. This resulted in a color change and creation of a black cell exterior. The capture of ninety percent of a pharmaceutical wastewater pollutant followed by regeneration of the cell bound melanin matrix through a simple pH change, shows the superior function and facilitated processing provided by the surface methodology. The broad adsorption spectrum of melanin could also allow removal of other micropollutants.

  • 43. Gyarmati, P.
    et al.
    Kjellander, C.
    Aust, C.
    Song, Yajing
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ohrmalm, L.
    Giske, C. G.
    Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 23532Article in journal (Refereed)
    Abstract [en]

    Leukemic patients are often immunocompromised due to underlying conditions, comorbidities and the effects of chemotherapy, and thus at risk for developing systemic infections. Bloodstream infection (BSI) is a severe complication in neutropenic patients, and is associated with increased mortality. BSI is routinely diagnosed with blood culture, which only detects culturable pathogens. We analyzed 27 blood samples from 9 patients with acute leukemia and suspected BSI at different time points of their antimicrobial treatment using shotgun metagenomics sequencing in order to detect unculturable and non-bacterial pathogens. Our findings confirm the presence of bacterial, fungal and viral pathogens alongside antimicrobial resistance genes. Decreased white blood cell (WBC) counts were associated with the presence of microbial DNA, and was inversely proportional to the number of sequencing reads. This study could indicate the use of high-throughput sequencing for personalized antimicrobial treatments in BSIs.

  • 44. Hansen, Henning Gram
    et al.
    Nilsson, Claes Nymand
    Lund, Anne Mathilde
    Kol, Stefan
    Grav, Lise Marie
    Lundqvist, Magnus
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Lee, Gyun Min
    Andersen, Mikael Rordam
    Kildegaard, Helene Faustrup
    Versatile microscale screening platform for improving recombinant protein productivity in Chinese hamster ovary cells2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, 18016Article in journal (Refereed)
    Abstract [en]

    Chinese hamster ovary (CHO) cells are widely used as cell factories for the production of biopharmaceuticals. In contrast to the highly optimized production processes for monoclonal antibody (mAb)-based biopharmaceuticals, improving productivity of non-mAb therapeutic glycoproteins is more likely to reduce production costs significantly. The aim of this study was to establish a versatile target gene screening platform for improving productivity for primarily non-mAb glycoproteins with complete interchangeability of model proteins and target genes using transient expression. The platform consists of four techniques compatible with 96-well microplates: lipid-based transient transfection, cell cultivation in microplates, cell counting and antibody-independent product titer determination based on split-GFP complementation. We were able to demonstrate growth profiles and volumetric productivity of CHO cells in 96-half-deepwell microplates comparable with those obtained in shake flasks. In addition, we demonstrate that split-GFP complementation can be used to accurately measure relative titers of therapeutic glycoproteins. Using this platform, we were able to detect target gene-specific increase in titer and specific productivity of two non-mAb glycoproteins. In conclusion, the platform provides a novel miniaturized and parallelisable solution for screening target genes and holds the potential to unravel genes that can enhance the secretory capacity of CHO cells.

  • 45.
    Hevekerl, Heike
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Tornmalm, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Fluorescence-based characterization of non-fluorescent transient states of tryptophan - prospects for protein conformation and interaction studies2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 35052Article in journal (Refereed)
    Abstract [en]

    Tryptophan fluorescence is extensively used for label-free protein characterization. Here, we show that by analyzing how the average tryptophan fluorescence intensity varies with excitation modulation, kinetics of tryptophan dark transient states can be determined in a simple, robust and reliable manner. Thereby, highly environment-, protein conformation- and interaction-sensitive information can be recorded, inaccessible via traditional protein fluorescence readouts. For verification, tryptophan transient state kinetics were determined under different environmental conditions, and compared to literature data. Conformational changes in a spider silk protein were monitored via the triplet state kinetics of its tryptophan residues, reflecting their exposure to an air-saturated aqueous solution. Moreover, tryptophan fluorescence anti-bunching was discovered, reflecting local pH and buffer conditions, previously observed only by ultrasensitive measurements in highly fluorescent photo-acids. Taken together, the presented approach, broadly applicable under biologically relevant conditions, has the potential to become a standard biophysical approach for protein conformation, interaction and microenvironment studies.

  • 46. Hong, Jongbae
    et al.
    Abergel, David S. L.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Institute for Basic Science, South Korea.
    A universal explanation of tunneling conductance in exotic superconductors2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 31352Article in journal (Refereed)
    Abstract [en]

    A longstanding mystery in understanding cuprate superconductors is the inconsistency between the experimental data measured by scanning tunneling spectroscopy (STS) and angle-resolved photoemission spectroscopy (ARPES). In particular, the gap between prominent side peaks observed in STS is much bigger than the superconducting gap observed by ARPES measurements. Here, we reconcile the two experimental techniques by generalising a theory which was previously applied to zero-dimensional mesoscopic Kondo systems to strongly correlated two-dimensional (2D) exotic superconductors. We show that the side peaks observed in tunneling conductance measurements in all these materials have a universal origin: They are formed by coherence-mediated tunneling under bias and do not directly reflect the underlying density of states (DOS) of the sample. We obtain theoretical predictions of the tunneling conductance and the density of states of the sample simultaneously and show that for cuprate and pnictide superconductors, the extracted sample DOS is consistent with the superconducting gap measured by ARPES.

  • 47. Horsley, S. A. R.
    et al.
    Hooper, I. R.
    Mitchell-Thomas, R. C.
    Quevedo-Teruel, Oscar
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering.
    Removing singular refractive indices with sculpted surfaces2014In: Scientific Reports, ISSN 2045-2322, Vol. 4, 4876- p.Article in journal (Refereed)
    Abstract [en]

    The advent of Transformation Optics established the link between geometry and material properties, and has resulted in a degree of control over electromagnetic fields that was previously impossible. For waves confined to a surface it is known that there is a simpler, but related, geometrical equivalence between the surface shape and the refractive index, and here we demonstrate that conventional devices possessing a singularity-that is, the requirement of an infinite refractive index-can be realised for waves confined to an appropriately sculpted surface. In particular, we redesign three singular omnidirectional devices: the Eaton lens, the generalized Maxwell Fish-Eye, and the invisible sphere. Our designs perfectly reproduce the behaviour of these singular devices, and can be achieved with simple isotropic media of low refractive index contrast.

  • 48. Hu, Lei
    et al.
    Zhang, Yang
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Ramström, Olof
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Gelation-driven Dynamic Systemic Resolution: in situ Generation and Self-Selection of an Organogelator2015In: Scientific Reports, ISSN 2045-2322, Vol. 5, 11065Article in journal (Refereed)
    Abstract [en]

    An organogelator was produced and identified from a dynamic imine system, resolved and amplified by selective gelation. The formation of the organogel was monitored in situ by H-1 NMR, showing the existence of multiple reversible reactions operating simultaneously, and the redistribution of the involved species during gelation. The formed organogelator proved effective with a range of organic solvents, including DMSO, toluene, and longer, linear alcohols.

  • 49. Hu, Mengzhu
    et al.
    Yang, Liu
    Dai, Hao
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Broadband Absorption and Efficient Hot-Carrier Photovoltaic Conversion based on Sunlight-induced Non-radiative Decay of Propagating Surface Plasmon Polaritons2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 4809Article in journal (Refereed)
    Abstract [en]

    Localized surface plasmon polaritons (SPPs), which can decay non-radiatively into hot carriers, have been widely employed to extend the responses of traditional semiconductor-based photocatalytic and photovoltaic devices to sub-bandgap photons. However, radiative decay is unavoidable and adverse to device performances. Here, we propose to take advantage of propagating SPPs, another form of SPPs, which possess non-radiative decay only. A special gold-titanium dioxide nanowire array with each nanowire capped with a nanocone is proposed. The adjacent nanocones forming top gradual openings attribute to efficient sunlight harvesting, while the neighbouring nanowires forming bottom nanoslots allow sufficient absorption due to the propagating SPPs. With the combined advantages, almost 100% of light is absorbed by a very thin gold film in the visible range, and 73% in the whole considered range of 400-1170 nm, superior to the nanocone cell based on localized SPPs, let alone the nanowire-based and planar counterparts. Therefore, much better photovoltaic conversion performance is achieved with short-circuit current density of 0.74 mA/cm(2) and open-circuit voltage of 0.41 V. This work confirms the superiority of non-radiative decay of propagating SPPs to the localized SPPs in terms of generation of hot carriers, providing a promising way of extracting electrons in metal into photocurrent.

  • 50.
    Ignatova, Nina
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University.
    V. Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Couto, Rafael C.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Zimin, Andrey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    F. Guimarães, Freddy
    Polyutov, Sergey
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gradual collapse of nuclear wavefunctions regulated by frequencytuned X-ray scattering2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, ISSN 2045-2322, Vol. 7, no 43891, 10.1038/srep43891Article in journal (Refereed)
    Abstract [en]

    As is well established, the symmetry breaking by isotope substitution in the water molecule results in localisation of the vibrations along one of the two bonds in the ground state. In this study we find that this localisation may be broken in excited electronic states. Contrary to the ground state, the stretching vibrations of HDO are delocalised in the bound core-excited state in spite of the mass difference between hydrogen and deuterium. The reason for this effect can be traced to the narrow “canyon-like” shape of the potential of the state along the symmetric stretching mode, which dominates over the localisation mass-difference effect. In contrast, the localisation of nuclear motion to one of the HDO bonds is preserved in the dissociative core-excited state . The dynamics of the delocalisation of nuclear motion in these core-excited states is studied using resonant inelastic X-ray scattering of the vibrationally excited HDO molecule. The results shed light on the process of a wave function collapse. After core-excitation into the state of HDO the initial wave packet collapses gradually, rather than instantaneously, to a single vibrational eigenstate.

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