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  • 1. Aad, G.
    et al.
    Grahn, Karl-Johan
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Lund-Jensen, Bengt
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Strandberg, Jonas
    University of Chicago.
    Lafaye, Remi
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Zwalinski, L.
    et al.,
    Measurement of the inelastic proton-proton cross-section at root s=7 TeV with the ATLAS detector2011In: Nature Communications, E-ISSN 2041-1723, Vol. 2, p. 463-Article in journal (Refereed)
    Abstract [en]

    The dependence of the rate of proton-proton interactions on the centre-of-mass collision energy, root s, is of fundamental importance for both hadron collider physics and particle astrophysics. The dependence cannot yet be calculated from first principles; therefore, experimental measurements are needed. Here we present the first measurement of the inelastic proton-proton interaction cross-section at a centre-of-mass energy, root s, of 7 TeV using the ATLAS detector at the Large Hadron Collider. Events are selected by requiring hits on scintillation counters mounted in the forward region of the detector. An inelastic crosssection of 60.3 +/- 2.1 mb is measured for xi > 5x10(-6), where xi is calculated from the invariant mass, M(X), of hadrons selected using the largest rapidity gap in the event. For diffractive events, this corresponds to requiring at least one of the dissociation masses to be larger than 15.7 GeV.

  • 2.
    Abdellah, Tebani
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Gummesson, Anders
    Zhong, Wen
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Koistinen, Ina Schuppe
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lakshmikanth, Tadepally
    Olsson, Lisa M.
    Boulund, Fredrik
    Neiman, Maja
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Stenlund, Hans
    Hellström, Cecilia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Karlsson, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arif, Muhammad
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Dodig-Crnkovic, Tea
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England.
    Lee, Sunjae
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Zhang, Cheng
    Chen, Yang
    Olin, Axel
    Mikes, Jaromir
    Danielsson, Hanna
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jansson, Per-Anders
    Angerås, Oskar
    Huss, Mikael
    Kjellqvist, Sanela
    Odeberg, Jacob
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Edfors, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Tremaroli, Valentina
    Forsström, Björn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Schwenk, Jochen M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Moritz, Thomas
    Bäckhed, Fredrik
    Engstrand, Lars
    Brodin, Petter
    Bergström, Göran
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Danish Tech Univ, Ctr Biosustainabil, Copenhagen, Denmark.
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Integration of molecular profiles in a longitudinal wellness profiling cohort2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4487Article in journal (Refereed)
  • 3. Adhikari, Subash
    et al.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Baker, Mark S.
    A high-stringency blueprint of the human proteome2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5301Article in journal (Refereed)
    Abstract [en]

    The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases. The Human Proteome Project (HPP) was launched in 2010 to enhance accurate annotation of the genome-encoded proteome. Ten years later, the HPP releases its first blueprint of the human proteome, annotating 90% of all known proteins at high-stringency and discussing the implications of proteomics for precision medicine.

  • 4. Aghion, S.
    et al.
    Ahlén, O.
    Amsler, C.
    Ariga, A.
    Ariga, T.
    Belov, A. S.
    Berggren, Karl
    Physics Department, European Organisation for Nuclear Research, Switzerland.
    Bonomi, G.
    Bräunig, P.
    Bremer, J.
    Brusa, R. S.
    Cabaret, L.
    Canali, C.
    Caravita, R.
    Castelli, F.
    Cerchiari, G.
    Cialdi, S.
    Comparat, D.
    Consolati, G.
    Derking, H.
    Di Domizio, S.
    Di Noto, L.
    Doser, M.
    Dudarev, A.
    Ereditato, A.
    Ferragut, R.
    Fontana, A.
    Genova, P.
    Giammarchi, M.
    Gligorova, A.
    Gninenko, S. N.
    Haider, S.
    Huse, T.
    Jordan, E.
    Jørgensen, L. V.
    Kaltenbacher, T.
    Kawada, J.
    Kellerbauer, A.
    Kimura, M.
    Knecht, A.
    Krasnický, D.
    Lagomarsino, V.
    Lehner, S.
    Magnani, A.
    Malbrunot, C.
    Mariazzi, S.
    Matveev, V. A.
    Moia, F.
    Nebbia, G.
    Nédélec, P.
    Oberthaler, M. K.
    Pacifico, N.
    Petràček, V.
    Pistillo, C.
    Prelz, F.
    Prevedelli, M.
    Regenfus, C.
    Riccardi, C.
    Røhne, O.
    Rotondi, A.
    Sandaker, H.
    Scampoli, P.
    Storey, J.
    Vasquez, M.A. Subieta
    Špaček, M.
    Testera, G.
    Vaccarone, R.
    Widmann, E.
    Zavatarelli, S.
    Zmeskal, J.
    A moiré deflectometer for antimatter2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, article id 2538Article in journal (Refereed)
    Abstract [en]

    The precise measurement of forces is one way to obtain deep insight into the fundamental interactions present in nature. In the context of neutral antimatter, the gravitational interaction is of high interest, potentially revealing new forces that violate the weak equivalence principle. Here we report on a successful extension of a tool from atom optics—the moiré deflectometer—for a measurement of the acceleration of slow antiprotons. The setup consists of two identical transmission gratings and a spatially resolving emulsion detector for antiproton annihilations. Absolute referencing of the observed antimatter pattern with a photon pattern experiencing no deflection allows the direct inference of forces present. The concept is also straightforwardly applicable to antihydrogen measurements as pursued by the AEgIS collaboration. The combination of these very different techniques from high energy and atomic physics opens a very promising route to the direct detection of the gravitational acceleration of neutral antimatter.

  • 5.
    Ahlberg, Martina
    et al.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Chung, Sunjae
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden.;Korea Natl Univ Educ, Dept Phys Educ, Cheongju 28173, South Korea..
    Jiang, Sheng
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Gothenburg, Dept Phys.
    Frisk, Andreas
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Khademi, Maha
    Shahid Beheshti Univ, Dept Phys, Tehran 1983969411, Iran..
    Khymyn, Roman
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Awad, Ahmad A.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Le, Quang Tuan
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Gothenburg, Dept Phys.
    Mazraati, Hamid
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. NanOsc AB, S-16440 Kista, Sweden..
    Mohseni, Majid
    KTH, School of Engineering Sciences (SCI), Applied Physics. Shahid Beheshti Univ, Dept Phys, Tehran 1983969411, Iran..
    Weigand, Markus
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Bykova, Iuliia
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Gross, Felix
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Goering, Eberhard
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Schutz, Gisela
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Grafe, Joachim
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Gothenburg, Dept Phys.
    Freezing and thawing magnetic droplet solitons2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2462Article in journal (Refereed)
    Abstract [en]

    Magnetic droplets are a type of non-topological magnetic soliton, which are stabilised and sustained by spin-transfer torques for instance. Without this, they would collapse. Here Ahlberg et al show that by decreasing the applied magnetic field, droplets can be frozen, forming a static nanobubble Magnetic droplets are non-topological magnetodynamical solitons displaying a wide range of complex dynamic phenomena with potential for microwave signal generation. Bubbles, on the other hand, are internally static cylindrical magnetic domains, stabilized by external fields and magnetostatic interactions. In its original theory, the droplet was described as an imminently collapsing bubble stabilized by spin transfer torque and, in its zero-frequency limit, as equivalent to a bubble. Without nanoscale lateral confinement, pinning, or an external applied field, such a nanobubble is unstable, and should collapse. Here, we show that we can freeze dynamic droplets into static nanobubbles by decreasing the magnetic field. While the bubble has virtually the same resistance as the droplet, all signs of low-frequency microwave noise disappear. The transition is fully reversible and the bubble can be thawed back into a droplet if the magnetic field is increased under current. Whereas the droplet collapses without a sustaining current, the bubble is highly stable and remains intact for days without external drive. Electrical measurements are complemented by direct observation using scanning transmission x-ray microscopy, which corroborates the analysis and confirms that the bubble is stabilized by pinning.

  • 6.
    Alvez, Maria Bueno
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Edfors, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zwahlen, Martin
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, SE1 9RT, UK.
    Edqvist, Per Henrik
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Sjöblom, Tobias
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Lundin, Emma
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Rameika, Natallia
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Enblad, Gunilla
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Lindman, Henrik
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Höglund, Martin
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Hesselager, Göran
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Stålberg, Karin
    Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden.
    Enblad, Malin
    Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
    Simonson, Oscar E.
    Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
    Häggman, Michael
    Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
    Axelsson, Tomas
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Åberg, Mikael
    Department of Medical Sciences, Clinical Chemistry and SciLifeLab Affinity Proteomics, Uppsala University, Uppsala, Sweden.
    Nordlund, Jessica
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Zhong, Wen
    Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden.
    Karlsson, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gyllensten, Ulf
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Ponten, Fredrik
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Next generation pan-cancer blood proteome profiling using proximity extension assay2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4308Article in journal (Refereed)
    Abstract [en]

    A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.

  • 7.
    Amann-Winkel, Katrin
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.;Johannes Gutenberg Univ Mainz, Max Planck Inst Polymer Res, D-55128 Mainz, Germany..
    Kim, Kyung Hwan
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Giovambattista, Nicolas
    CUNY Brooklyn Coll, Dept Phys, Brooklyn, NY 11210 USA.;CUNY, Grad Ctr, New York, NY 10016 USA..
    Ladd-Parada, Marjorie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Spaeh, Alexander
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Perakis, Fivos
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Pathak, Harshad
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Yang, Cheolhee
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Eklund, Tobias
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Lane, Thomas J.
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    You, Seonju
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Jeong, Sangmin
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Lee, Jae Hyuk
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Eom, Intae
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Kim, Minseok
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Park, Jaeku
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Chun, Sae Hwan
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Poole, Peter H.
    St Francis Xavier Univ, Dept Phys, Antigonish, NS B2G2W5, Canada..
    Nilsson, Anders
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 442Article in journal (Refereed)
    Abstract [en]

    Recent experiments continue to find evidence for a liquid-liquid phase transition (LLPT) in supercooled water, which would unify our understanding of the anomalous properties of liquid water and amorphous ice. These experiments are challenging because the proposed LLPT occurs under extreme metastable conditions where the liquid freezes to a crystal on a very short time scale. Here, we analyze models for the LLPT to show that coexistence of distinct high-density and low-density liquid phases may be observed by subjecting low-density amorphous (LDA) ice to ultrafast heating. We then describe experiments in which we heat LDA ice to near the predicted critical point of the LLPT by an ultrafast infrared laser pulse, following which we measure the structure factor using femtosecond x-ray laser pulses. Consistent with our predictions, we observe a LLPT occurring on a time scale < 100 ns and widely separated from ice formation, which begins at times >1 mu s. Obtaining experimental evidence of a liquid-liquid phase transition in supercooled water is challenging due to the rapid crystallization. Here the authors drive low-density amorphous ice to the conditions of liquid-liquid coexistence using ultrafast laser heating and observe the liquid-liquid phase transition with femtosecond x-ray laser pulses.

  • 8.
    Andersson, Alma
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stenbeck, Linnea
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Salmén, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Hubrecht Inst KNAW Royal Netherlands Acad Arts &, Utrecht, Netherlands.;Univ Med Ctr Utrecht, Canc Genom Netherlands, Utrecht, Netherlands..
    Ehinger, Anna
    Dept Genet & Pathol, Lab Med Reg Sane, Lund, Sweden.;Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Wu, Sunny Z.
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Al-Eryani, Ghamdan
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Roden, Daniel
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Swarbrick, Alex
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Borg, Ake
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Frisen, Jonas
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden..
    Engblom, Camilla
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 6012Article in journal (Refereed)
    Abstract [en]

    In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases. While transcriptomics have enhanced our understanding for cancer, spatial transcriptomics enable the characterisation of cellular interactions. Here, the authors integrate single cell data with spatial information for HER2 + tumours and develop tools for the prediction of interactions between tumour-infiltrating cells.

  • 9. Andersson, Sandra
    et al.
    Sundberg, Marten
    Pristovsek, Nusa
    Ibrahim, Ahmed
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Natl Res Ctr, Egypt.
    Jonsson, Philip
    Katona, Borbala
    Clausson, Carl-Magnus
    Zieba, Agata
    Ramstrom, Margareta
    Soderberg, Ola
    Williams, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Houston, USA; Karolinska Inst, Sweden.
    Asplund, Anna
    Insufficient antibody validation challenges oestrogen receptor beta research2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 15840Article in journal (Refereed)
    Abstract [en]

    The discovery of oestrogen receptor beta (ER beta/ESR2) was a landmark discovery. Its reported expression and homology with breast cancer pharmacological target ER alpha (ESR1) raised hopes for improved endocrine therapies. After 20 years of intense research, this has not materialized. We here perform a rigorous validation of 13 anti-ER beta antibodies, using well-characterized controls and a panel of validation methods. We conclude that only one antibody, the rarely used monoclonal PPZ0506, specifically targets ER beta in immunohistochemistry. Applying this antibody for protein expression profiling in 44 normal and 21 malignant human tissues, we detect ER beta protein in testis, ovary, lymphoid cells, granulosa cell tumours, and a subset of malignant melanoma and thyroid cancers. We do not find evidence of expression in normal or cancerous human breast. This expression pattern aligns well with RNA-seq data, but contradicts a multitude of studies. Our study highlights how inadequately validated antibodies can lead an exciting field astray.

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  • 10. Arabi, A.
    et al.
    Ullah, K.
    Branca, R. M. M.
    Johansson, J.
    Bandarra, D.
    Haneklaus, M.
    Fu, J.
    Ariës, I.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Den Boer, M. L.
    Pokrovskaja, K.
    Grandér, D.
    Xiao, G.
    Rocha, S.
    Lehtiö, J.
    Sangfelt, O.
    Proteomic screen reveals Fbw7 as a modulator of the NF-kappa B pathway2012In: Nature Communications, E-ISSN 2041-1723, Vol. 3, p. 976-Article in journal (Refereed)
    Abstract [en]

    Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-κB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3 2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-κB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-κB2 pathway stimulation.

  • 11. Bagnoud, Alexandre
    et al.
    Chourey, Karuna
    Hettich, Robert L.
    de Bruijn, Ino
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    Leupin, Olivier X.
    Schwyn, Bernhard
    Bernier-Latmani, Rizlan
    Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 12770Article in journal (Refereed)
    Abstract [en]

    The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

  • 12.
    Belonoshko, Anatoly
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Condensed Matter Theory.
    Fu, Jie
    Ningbo Univ, Dept Phys, Fac Sci, Ningbo 315211, Zhejiang, Peoples R China..
    Bryk, Taras
    Natl Acad Sci Ukraine, Inst Condensed Matter Phys, UA-79011 Lvov, Ukraine..
    Simak, Sergei, I
    Linkoping Univ, Dept Phys Chem & Biol IFM, SE-58183 Linkoping, Sweden..
    Mattesini, Maurizio
    Univ Complutense Madrid, Dept Earths Phys & Astrophys, E-28040 Madrid, Spain.;UCM, CSIC, Fac Ciencias Fis, Inst Geociencias, Plaza Ciencias 1, Madrid 28040, Spain..
    Low viscosity of the Earth's inner core2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 2483Article in journal (Refereed)
    Abstract [en]

    The Earth's solid inner core is a highly attenuating medium. It consists mainly of iron. The high attenuation of sound wave propagation in the inner core is at odds with the widely accepted paradigm of hexagonal close-packed phase stability under inner core conditions, because sound waves propagate through the hexagonal iron without energy dissipation. Here we show by first-principles molecular dynamics that the body-centered cubic phase of iron, recently demonstrated to be thermodynamically stable under the inner core conditions, is considerably less elastic than the hexagonal phase. Being a crystalline phase, the body-centered cubic phase of iron possesses the viscosity close to that of a liquid iron. The high attenuation of sound in the inner core is due to the unique diffusion characteristic of the body-centered cubic phase. The low viscosity of iron in the inner core enables the convection and resolves a number of controversies.

  • 13. Belotelov, V. I.
    et al.
    Kreilkamp, L. E.
    Akimov, I. A.
    Kalish, A. N.
    Bykov, D. A.
    Kasture, S.
    Yallapragada, V. J.
    Gopal, Achanta Venu
    Grishin, Alexander M.
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Khartsev, Sergiy I.
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Nur-E-Alam, M.
    Vasiliev, M.
    Doskolovich, L. L.
    Yakovlev, D. R.
    Alameh, K.
    Zvezdin, A. K.
    Bayer, M.
    Plasmon-mediated magneto-optical transparency2013In: Nature Communications, E-ISSN 2041-1723, Vol. 4, p. 2128-Article in journal (Refereed)
    Abstract [en]

    Magnetic field control of light is among the most intriguing methods for modulation of light intensity and polarization on sub-nanosecond timescales. The implementation in nanostructured hybrid materials provides a remarkable increase of magneto-optical effects. However, so far only the enhancement of already known effects has been demonstrated in such materials. Here we postulate a novel magneto-optical phenomenon that originates solely from suitably designed nanostructured metal-dielectric material, the so-called magneto-plasmonic crystal. In this material, an incident light excites coupled plasmonic oscillations and a waveguide mode. An in-plane magnetic field allows excitation of an orthogonally polarized waveguide mode that modifies optical spectrum of the magneto-plasmonic crystal and increases its transparency. The experimentally achieved light intensity modulation reaches 24%. As the effect can potentially exceed 100%, it may have great importance for applied nanophotonics. Further, the effect allows manipulating and exciting waveguide modes by a magnetic field and light of proper polarization.

  • 14.
    Berglund, Emelie
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Maaskola, Jonas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Schultz, Niklas
    Friedrich, Stefanie
    Marklund, Maja
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bergenstråhle, Joseph
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Tarish, Firas
    Tanoglidi, Anna
    Vickovic, Sanja
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Salmén, Fredrik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Ogris, Christoph
    Wallenborg, Karolina
    Lagergren, Jens
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Ståhl, Patrik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Sonnhammer, Erik
    Helleday, Thomas
    Lundeberg, Joakim
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, no 1, article id 2419Article in journal (Refereed)
    Abstract [en]

    Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor micro- environment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.

  • 15.
    Berglund, Jennie
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Mikkelsen, Deidre
    Flanagan, Bernadine M.
    Dhital, Sushil
    Gaunitz, Stefan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Henriksson, Gunnar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Lindström, Mikael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Yakubov, Gleb E.
    Gidley, Michael J.
    Vilaplana, Francisco
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Wood hemicelluloses exert distinct biomechanical contributions to cellulose fibrillar networks2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4692Article in journal (Refereed)
    Abstract [en]

    Hemicelluloses, a family of heterogeneous polysaccharides with complex molecular structures, constitute a fundamental component of lignocellulosic biomass. However, the contribution of each hemicellulose type to the mechanical properties of secondary plant cell walls remains elusive. Here we homogeneously incorporate different combinations of extracted and purified hemicelluloses (xylans and glucomannans) from softwood and hardwood species into self-assembled networks during cellulose biosynthesis in a bacterial model, without altering the morphology and the crystallinity of the cellulose bundles. These composite hydrogels can be therefore envisioned as models of secondary plant cell walls prior to lignification. The incorporated hemicelluloses exhibit both a rigid phase having close interactions with cellulose, together with a flexible phase contributing to the multiscale architecture of the bacterial cellulose hydrogels. The wood hemicelluloses exhibit distinct biomechanical contributions, with glucomannans increasing the elastic modulus in compression, and xylans contributing to a dramatic increase of the elongation at break under tension. These diverging effects cannot be explained solely from the nature of their direct interactions with cellulose, but can be related to the distinct molecular structure of wood xylans and mannans, the multiphase architecture of the hydrogels and the aggregative effects amongst hemicellulose-coated fibrils. Our study contributes to understanding the specific roles of wood xylans and glucomannans in the biomechanical integrity of secondary cell walls in tension and compression and has significance for the development of lignocellulosic materials with controlled assembly and tailored mechanical properties.

  • 16.
    Bian, Qingzhen
    et al.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Ma, Fei
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Chen, Shula
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Wei, Qi
    Univ Macau, Inst Appl Phys & Mat Engn, Macau, Peoples R China..
    Su, Xiaojun
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Buyanova, Irina A.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Chen, Weimin M.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Ponseca, Carlito S.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Karki, Khadga J.
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Yartsev, Arkady
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Inganas, Olle
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Vibronic coherence contributes to photocurrent generation in organic semiconductor heterojunction diodes2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 617Article in journal (Refereed)
    Abstract [en]

    Charge separation dynamics after the absorption of a photon is a fundamental process relevant both for photosynthetic reaction centers and artificial solar conversion devices. It has been proposed that quantum coherence plays a role in the formation of charge carriers in organic photovoltaics, but experimental proofs have been lacking. Here we report experimental evidence of coherence in the charge separation process in organic donor/acceptor heterojunctions, in the form of low frequency oscillatory signature in the kinetics of the transient absorption and nonlinear two-dimensional photocurrent spectroscopy. The coherence plays a decisive role in the initial 200 femtoseconds as we observe distinct experimental signatures of coherent photocurrent generation. This coherent process breaks the energy barrier limitation for charge formation, thus competing with excitation energy transfer. The physics may inspire the design of new photovoltaic materials with high device performance, which explore the quantum effects in the next-generation optoelectronic applications.

  • 17.
    Biltmo, Anders
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Henelius, Patrik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Unreachable glass transition in dilute dipolar magnet2012In: Nature Communications, E-ISSN 2041-1723, Vol. 3, p. 857-Article in journal (Refereed)
    Abstract [en]

    In magnetic systems the combined effects of disorder and frustration may cause the moments to freeze into a disordered state at a spin-glass transition. Recent experiments have shown that the rare earth compound LiHo0.045Y0.955F4 freezes, but that the transition is unreachable because of dynamics that are 10(7) times slower than in ordinary spin-glass materials. This conclusion refutes earlier investigations reporting a speed-up of the dynamics into an exotic anti-glass phase caused by entanglement of quantum dipoles. Here we present a theory, backed by numerical simulations, which describes the material in terms of classical dipoles governed by Glauber dynamics. The dipoles freeze and we find that the ultra-slow dynamics are caused by rare, strongly ordered clusters, which give rise to a previously predicted, but hitherto unobserved, Griffths phase between the paramagnetic and spin-glass phases. In addition, the hyperfine interaction creates a high energy barrier to flipping the electronic spin, resulting in a clear signature in the dynamic correlation function.

  • 18.
    Bondarenko, Vasyl
    et al.
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA..
    Wells, Marta M.
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA..
    Chen, Qiang
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA..
    Tillman, Tommy S.
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA..
    Singewald, Kevin
    Univ Pittsburgh, Dept Chem, Pittsburgh, PA 15260 USA..
    Lawless, Matthew J.
    Univ Pittsburgh, Dept Chem, Pittsburgh, PA 15260 USA..
    Caporoso, Joel
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA..
    Brandon, Nicole
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA..
    Coleman, Jonathan A.
    Univ Pittsburgh, Dept Struct Biol, Pittsburgh, PA 15260 USA..
    Saxena, Sunil
    Univ Pittsburgh, Dept Chem, Pittsburgh, PA 15260 USA..
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Xu, Yan
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA.;Univ Pittsburgh, Dept Struct Biol, Pittsburgh, PA 15260 USA.;Univ Pittsburgh, Dept Pharmacol & Chem Biol, Pittsburgh, PA 15260 USA.;Univ Pittsburgh, Dept Phys & Astron, Pittsburgh, PA 15260 USA..
    Tang, Pei
    Univ Pittsburgh, Dept Anesthesiol & Perioperat Med, Pittsburgh, PA 15260 USA.;Univ Pittsburgh, Dept Pharmacol & Chem Biol, Pittsburgh, PA 15260 USA.;Univ Pittsburgh, Dept Computat & Syst Biol, Pittsburgh, PA 15260 USA..
    Structures of highly flexible intracellular domain of human alpha 7 nicotinic acetylcholine receptor2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 793Article in journal (Refereed)
    Abstract [en]

    The intracellular domain (ICD) of Cys-loop receptors mediates diverse functions. To date, no structure of a full-length ICD is available due to challenges stemming from its dynamic nature. Here, combining nuclear magnetic resonance (NMR) and electron spin resonance experiments with Rosetta computations, we determine full-length ICD structures of the human alpha 7 nicotinic acetylcholine receptor in a resting state. We show that similar to 57% of the ICD residues are in highly flexible regions, primarily in a large loop (loop L) with the most mobile segment spanning similar to 50 angstrom from the central channel axis. Loop L is anchored onto the MA helix and virtually forms two smaller loops, thereby increasing its stability. Previously known motifs for cytoplasmic binding, regulation, and signaling are found in both the helices and disordered flexible regions, supporting the essential role of the ICD conformational plasticity in orchestrating a broad range of biological processes.

  • 19. Bonetti, Stefano
    et al.
    Kukreja, R
    Chen, Z
    Macià, F
    Hernàndez, J. M.
    Eklund, Anders
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Backes, D
    Frisch, J
    Katine, J
    Malm, Gunnar
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Urazhdin, S
    Kent, A. D.
    Stöhr, J.
    Ohldag, H.
    Dürr, H. A.
    Direct observation and imaging of a spin-wave soliton with p−like symmetry2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 8889Article in journal (Refereed)
    Abstract [en]

    The prediction and realization of magnetic excitations driven by electrical currents via the spin transfer torque effect, enables novel magnetic nano-devices where spin-waves can be used to process and store information. The functional control of such devices relies on understanding the properties of non-linear spin-wave excitations. It has been demonstrated that spin waves can show both an itinerant character, but also appear as localized solitons. So far, it was assumed that localized solitons have essentially cylindrical, s−like symmetry. Using a newly developed high-sensitivity time-resolved magnetic x-ray microscopy, we instead observe the emergence of a novel localized soliton excitation with a nodal line, i.e. with p−like symmetry. Micromagnetic simulations identify the physical mechanism that controls the transition from s− to p−like solitons. Our results suggest a potential new pathway to design artificial atoms with tunable dynamical states using nanoscale magnetic devices.

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  • 20.
    Borgström, Erik
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Redin, David
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Berglund, Emelie
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Phasing of single DNA molecules by massively parallel barcoding2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 7173Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.

  • 21. Bovo, L.
    et al.
    Twengström, Mikael
    KTH, School of Engineering Sciences (SCI), Physics.
    Petrenko, O. A.
    Fennell, T.
    Gingras, M. J. P.
    Bramwell, S. T.
    Henelius, Patrik
    KTH, School of Engineering Sciences (SCI), Physics.
    Special temperatures in frustrated ferromagnets2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, no 1, article id 1999Article in journal (Refereed)
    Abstract [en]

    The description and detection of unconventional magnetic states, such as spin liquids, is a recurring topic in condensed matter physics. While much of the efforts have traditionally been directed at geometrically frustrated antiferromagnets, recent studies reveal that systems featuring competing antiferromagnetic and ferromagnetic interactions are also promising candidate materials. We find that this competition leads to the notion of special temperatures, analogous to those of gases, at which the competing interactions balance, and the system is quasi-ideal. Although induced by weak perturbing interactions, these special temperatures are surprisingly high and constitute an accessible experimental diagnostic of eventual order or spin-liquid properties. The well characterised Hamiltonian and extended low-temperature susceptibility measurement of the canonical frustrated ferromagnet Dy2Ti2O7 enables us to formulate both a phenomenological and microscopic theory of special temperatures for magnets. Other members of this class of magnets include kapellasite Cu3Zn(OH)6Cl2 and the spinel GeCo2O4.

  • 22. Brasko, Csilla
    et al.
    Smith, Kevin
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Molnar, Csaba
    Farago, Nora
    Hegedus, Lili
    Balind, Arpad
    Balassa, Tamas
    Szkalisity, Abel
    Sukosd, Farkas
    Kocsis, Katalin
    Balint, Balazs
    Paavolainen, Lassi
    Enyedi, Marton Z.
    Nagy, Istvan
    Puskas, Laszlo G.
    Haracska, Lajos
    Tamas, Gabor
    Horvath, Peter
    Intelligent image-based in situ single-cell isolation2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 226Article in journal (Refereed)
    Abstract [en]

    Quantifying heterogeneities within cell populations is important for many fields including cancer research and neurobiology; however, techniques to isolate individual cells are limited. Here, we describe a high-throughput, non-disruptive, and cost-effective isolation method that is capable of capturing individually targeted cells using widely available techniques. Using high-resolution microscopy, laser microcapture microscopy, image analysis, and machine learning, our technology enables scalable molecular genetic analysis of single cells, targetable by morphology or location within the sample.

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    fulltext
  • 23.
    Brotons-Gisbert, Mauro
    et al.
    Heriot Watt Univ, Inst Photon & Quantum Sci, SUPA, Edinburgh EH14 4AS, Midlothian, Scotland..
    Proux, Raphael
    Heriot Watt Univ, Inst Photon & Quantum Sci, SUPA, Edinburgh EH14 4AS, Midlothian, Scotland..
    Picard, Raphael
    Heriot Watt Univ, Inst Photon & Quantum Sci, SUPA, Edinburgh EH14 4AS, Midlothian, Scotland..
    Andres-Penares, Daniel
    Univ Valencia, ICMUV, Inst Ciencia Mat, POB 2208546071, Valencia, Spain..
    Branny, Artur
    KTH, School of Engineering Sciences (SCI), Applied Physics. Heriot Watt Univ, Inst Photon & Quantum Sci, SUPA, Edinburgh EH14 4AS, Midlothian, Scotland..
    Molina-Sanchez, Alejandro
    Univ Valencia, ICMUV, Inst Ciencia Mat, POB 2208546071, Valencia, Spain.;Int Iberian Nanotechnol Lab INL, Av Mestre Jose Veiga, P-4715330 Braga, Portugal..
    Sanchez-Royo, Juan F.
    Univ Valencia, ICMUV, Inst Ciencia Mat, POB 2208546071, Valencia, Spain..
    Gerardot, Brian D.
    Heriot Watt Univ, Inst Photon & Quantum Sci, SUPA, Edinburgh EH14 4AS, Midlothian, Scotland..
    Out-of-plane orientation of luminescent excitons in two-dimensional indium selenide2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 3913Article in journal (Refereed)
    Abstract [en]

    Van der Waals materials offer a wide range of atomic layers with unique properties that can be easily combined to engineer novel electronic and photonic devices. A missing ingredient of the van der Waals platform is a two-dimensional crystal with naturally occurring out-of-plane luminescent dipole orientation. Here we measure the far-field photoluminescence intensity distribution of bulk InSe and two-dimensional InSe, WSe2 and MoSe2. We demonstrate, with the support of ab-initio calculations, that layered InSe flakes sustain luminescent excitons with an intrinsic out-of-plane orientation, in contrast with the in-plane orientation of dipoles we find in two-dimensional WSe2 and MoSe2 at room-temperature. These results, combined with the high tunability of the optical response and outstanding transport properties, position layered InSe as a promising semiconductor for novel optoelectronic devices, in particular for hybrid integrated photonic chips which exploit the out-of-plane dipole orientation.

  • 24.
    Brown, Andrew A.
    et al.
    Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, United Kingdom.
    Hong, Mun-Gwan
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Dale, Matilda
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Schwenk, Jochen M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Solna, SE-171 21, Sweden.
    Viñuela, Ana
    Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, NE1 4EP, United Kingdom.
    et al.,
    Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 5062Article in journal (Refereed)
    Abstract [en]

    We evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant associates with multiple molecular phenotypes over multiple genomic regions. The highest proportion of share genetic regulation is detected between gene expression and proteins (66.6%), with a further median shared genetic associations across 49 different tissues of 78.3% and 62.4% between plasma proteins and gene expression. We represent the genetic and molecular associations in networks including 2828 known GWAS variants, showing that GWAS variants are more often connected to gene expression in trans than other molecular phenotypes in the network. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants using different molecular phenotypes in an accessible tissue.

  • 25.
    C. Couto, Rafael
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vaz da Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    F. Guimarães, Freddy
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Föhlisch, Alexander
    Selective gating to vibrational modes through resonant X-ray scattering2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, p. 14165-1-14165-7Article in journal (Refereed)
    Abstract [en]

    The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.

  • 26.
    Carr, Victoria R.
    et al.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Witherden, Elizabeth A.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Lee, Sunjae
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Shoaie, Saeed
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Mullany, Peter
    UCL, Eastman Dent Inst, Microbial Dis, London, England..
    Proctor, Gordon B.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Gomez-Cabrero, David
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England.;Univ Publ Navarra, Translat Bioinformat Unit, NavarraBiomed, Dept Salud, Navarra 31008, Spain.;Karolinska Inst, Unit Computat Med, Karolinska Univ Hosp SE, L8 05, SE-17176 Stockholm, Sweden..
    Moyes, David L.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Abundance and diversity of resistomes differ between healthy human oral cavities and gut2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1Article in journal (Refereed)
    Abstract [en]

    The global threat of antimicrobial resistance has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the resistome, in microbial populations. The human oral cavity contains a poorly explored reservoir of these genes. Here we analyse and compare the resistome profiles of 788 oral cavities worldwide with paired stool metagenomes. We find country and body site-specific differences in the prevalence of antimicrobial resistance genes, classes and mechanisms in oral and stool samples. Within individuals, the highest abundances of antimicrobial resistance genes are found in the oral cavity, but the oral cavity contains a lower diversity of resistance genes compared to the gut. Additionally, co-occurrence analysis shows contrasting ARG-species associations between saliva and stool samples. Maintenance and persistence of antimicrobial resistance is likely to vary across different body sites. Thus, we highlight the importance of characterising the resistome across body sites to uncover the antimicrobial resistance potential in the human body. Antimicrobial resistance (AMR) represents a global health threat. Here, the authors analyse the oral and gut resistomes from metagenomes of diverse populations and find that the oral resistome harbours higher abundance but lower diversity of antimicrobial resistance genes than the gut resistome.

  • 27. Carreras-Puigvert, J.
    et al.
    Zitnik, M.
    Jemth, A. -S
    Carter, M.
    Unterlass, J. E.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Loseva, O.
    Karem, Z.
    Calderón-Montanõ, J. M.
    Lindskog, C.
    Edqvist, P. -H
    Matuszewski, D. J.
    Ait Blal, Hammou
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Berntsson, R. P. A.
    Häggblad, M.
    Martens, U.
    Studham, M.
    Lundgren, B.
    Wählby, C.
    Sonnhammer, E. L. L.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stenmark, P.
    Zupan, B.
    Helleday, T.
    A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, no 1, article id 1541Article in journal (Refereed)
    Abstract [en]

    The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.

  • 28. Chang, J.
    et al.
    Månsson, Martin
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Pailhes, S.
    Claesson, Thomas
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Lipscombe, O. J.
    Hayden, S. M.
    Patthey, L.
    Tjernberg, Oscar
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Mesot, J.
    Anisotropic breakdown of Fermi liquid quasiparticle excitations in overdoped La2-xSrxCuO42013In: Nature Communications, E-ISSN 2041-1723, Vol. 4, p. 2559-Article in journal (Refereed)
    Abstract [en]

    High-temperature superconductivity emerges from an un-conventional metallic state. This has stimulated strong efforts to understand exactly how Fermi liquids breakdown and evolve into an un-conventional metal. A fundamental question is how Fermi liquid quasiparticle excitations break down in momentum space. Here we show, using angle-resolved photoemission spectroscopy, that the Fermi liquid quasiparticle excitations of the overdoped superconducting cuprate La1.77Sr0.23CuO4 is highly anisotropic in momentum space. The quasiparticle scattering and residue behave differently along the Fermi surface and hence the Kadowaki-Wood's relation is not obeyed. This kind of Fermi liquid breakdown may apply to a wide range of strongly correlated metal systems where spin fluctuations are present.

  • 29.
    Chang, Shu-Chieh
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan..
    Kao, Mu-Rong
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan.
    Saldivar, Rebecka Karmakar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan..
    Diaz-Moreno, Sara M
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Xing, Xiaohui
    Agr & Agrifood Canada, Lethbridge Res & Dev Ctr, Lethbridge, AB T1J 4B1, Canada.
    Furlanetto, Valentina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Yayo, Johannes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Vilaplana, Francisco
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Abbott, D. Wade
    Agr & Agrifood Canada, Lethbridge Res & Dev Ctr, Lethbridge, AB T1J 4B1, Canada.
    Hsieh, Yves S. Y.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan..
    The Gram-positive bacterium Romboutsia ilealis harbors a polysaccharide synthase that can produce (1,3;1,4)-β-D-glucans2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1Article in journal (Refereed)
    Abstract [en]

    (1,3;1,4)-β-D-Glucans are widely distributed in the cell walls of grasses (family Poaceae) and closely related families, as well as some other vascular plants. Additionally, they have been found in other organisms, including fungi, lichens, brown algae, charophycean green algae, and the bacterium Sinorhizobium meliloti. Only three members of the Cellulose Synthase-Like (CSL) genes in the families CSLF, CSLH, and CSLJ are implicated in (1,3;1,4)-β-D-glucan biosynthesis in grasses. Little is known about the enzymes responsible for synthesizing (1,3;1,4)-β-D-glucans outside the grasses. In the present study, we report the presence of (1,3;1,4)-β-D-glucans in the exopolysaccharides of the Gram-positive bacterium Romboutsia ilealis CRIBT. We also report that RiGT2 is the candidate gene of R. ilealis that encodes (1,3;1,4)-β-D-glucan synthase. RiGT2 has conserved glycosyltransferase family 2 (GT2) motifs, including D, D, D, QXXRW, and a C-terminal PilZ domain that resembles the C-terminal domain of bacteria cellulose synthase, BcsA. Using a direct gain-of-function approach, we insert RiGT2 into Saccharomyces cerevisiae, and (1,3;1,4)-β-D-glucans are produced with structures similar to those of the (1,3;1,4)-β-D-glucans of the lichen Cetraria islandica. Phylogenetic analysis reveals that putative (1,3;1,4)-β-D-glucan synthase candidate genes in several other bacterial species support the finding of (1,3;1,4)-β-D-glucans in these species.

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  • 30. Chen, Gefei
    et al.
    Abelein, Axel
    Nilsson, Harriet E.
    KTH, School of Technology and Health (STH), Medical Engineering, Structural Biotechnology.
    Leppert, Axel
    Andrade-Talavera, Yuniesky
    Tambaro, Simone
    Hemmingsson, Lovisa
    Roshan, Firoz
    Landreh, Michael
    Biverstal, Henrik
    Koeck, Philip J. B.
    KTH, School of Technology and Health (STH), Medical Engineering, Structural Biotechnology.
    Presto, Jenny
    Hebert, Hans
    Fisahn, Andre
    Johansson, Jan
    Bri2 BRICHOS client specificity and chaperone activity are governed by assembly state2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 2081Article in journal (Refereed)
    Abstract [en]

    . Protein misfolding and aggregation is increasingly being recognized as a cause of disease. In Alzheimer's disease the amyloid-beta peptide (A beta) misfolds into neurotoxic oligomers and assembles into amyloid fibrils. The Bri2 protein associated with Familial British and Danish dementias contains a BRICHOS domain, which reduces A beta fibrillization as well as neurotoxicity in vitro and in a Drosophila model, but also rescues proteins from irreversible nonfibrillar aggregation. How these different activities are mediated is not known. Here we show that Bri2 BRICHOS monomers potently prevent neuronal network toxicity of A beta, while dimers strongly suppress A beta fibril formation. The dimers assemble into high-molecular-weight oligomers with an apparent two-fold symmetry, which are efficient inhibitors of non-fibrillar protein aggregation. These results indicate that Bri2 BRICHOS affects qualitatively different aspects of protein misfolding and toxicity via different quaternary structures, suggesting a means to generate molecular chaperone diversity.

  • 31.
    Chen, Qiao
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Electromagnetic Engineering.
    Horsley, Simon A. R.
    Univ Exeter, Dept Phys & Astron, Stocker Rd, Exeter EX4 4QL, Devon, England..
    Fonseca, Nelson J. G.
    European Space Agcy, Antenna & Sub Millimetre Waves Sect, NL-2200 AG Noordwijk, Netherlands..
    Tyc, Tomas
    Masaryk Univ, Fac Sci, Inst Theoret Phys & Astrophys, Kotlarska 2, Brno 61137, Czech Republic..
    Quevedo-Teruel, Oscar
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Electromagnetic Engineering.
    Double-layer geodesic and gradient-index lenses2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2354Article in journal (Refereed)
    Abstract [en]

    A double-layer lens consists of a first gradient-index/geodesic profile in an upper waveguide, partially surrounded by a mirror that reflects the wave into a lower guide where there is a second profile. Here, we derive a new family of rotational-symmetric inhomogeneous index profiles and equivalent geodesic lens shapes by solving an inverse problem of pre-specified focal points. We find an equivalence where single-layer lenses have a different functionality as double-layer lenses with the same profiles. As an example, we propose, manufacture, and experimentally validate a practical implementation of a geodesic double-layer lens that is engineered for a low-profile antenna with a compact footprint in the millimeter wave band. Its unique double-layer configuration allows for two-dimensional beam scanning using the same footprint as an extension of the presented design. These lenses may find applications in future wireless communication systems and sensing instruments in microwave, sub-terahertz, and optical domains. A double-layer lens consists of a first gradient-index/geodesic profile in an upper waveguide, partially surrounded by a mirror that reflects the wave into a lower guide where there is a second profile. A family of such lens profiles are derived.

  • 32.
    Chen, Shula
    et al.
    Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
    Huang, Yuqing
    Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
    Visser, Dennis
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Anand, Srinivasan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Photonics.
    Buyanova, Irina A.
    Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
    Chen, Weimin M.
    Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
    Room-temperature polarized spin-photon interface based on a semiconductor nanodisk-in-nanopillar structure driven by few defects2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 3575Article in journal (Refereed)
    Abstract [en]

    Owing to their superior optical properties, semiconductor nanopillars/nanowires in one-dimensional (1D) geometry are building blocks for nano-photonics. They also hold potential for efficient polarized spin-light conversion in future spin nano-photonics. Unfortunately, spin generation in 1D systems so far remains inefficient at room temperature. Here we propose an approach that can significantly enhance the radiative efficiency of the electrons with the desired spin while suppressing that with the unwanted spin, which simultaneously ensures strong spin and light polarization. We demonstrate high optical polarization of 20%, inferring high electron spin polarization up to 60% at room temperature in a 1D system based on a GaNAs nanodisk-in-GaAs nanopillar structure, facilitated by spin-dependent recombination via merely 2-3 defects in each nanodisk. Our approach points to a promising direction for realization of an interface for efficient spin-photon quantum information transfer at room temperature-a key element for future spin-photonic applications.

  • 33. Chen, X.
    et al.
    Zhao, W.
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Steigerwald, M. L.
    Gu, J.
    Zhou, Y.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zou, Q.
    Chen, W.
    Zhu, L.
    Engineering stable radicals using photochromic triggers2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 945Article in journal (Refereed)
    Abstract [en]

    Long-standing radical species have raised noteworthy concerns in organic functional chemistry and materials. However, there remains a substantial challenge to produce long-standing radicals by light, because of the structural dilemmas between photoproduction and stabilization. Herein, we present a pyrrole and chloride assisted photochromic structure to address this issue. In this well-selected system, production and stabilization of a radical species were simultaneously found accompanied by a photochemical process in chloroform. Theoretical study and mechanism construction indicate that the designed π-system provides a superior spin-delocalization effect and a large steric effect, mostly avoiding possible consumptions and making the radical stable for hours even under an oxygen-saturated condition. Moreover, this radical system can be applied for a visualized and quantitative detection towards peroxides, such as 2,2,6,6-tetramethylpiperidine-1-oxyl, hydrogen peroxide, and ozone. As the detection relies on a radical capturing mechanism, a higher sensing rate was achieved compared to traditional redox techniques for peroxide detection.

  • 34. Cherifi-Hertel, S.
    et al.
    Bulou, H.
    Hertel, R.
    Taupier, G.
    Dorkenoo, K. D. H.
    Andreas, C.
    Guyonnet, J.
    Gaponenko, I.
    Gallo, Katia
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
    Paruch, P.
    Non-Ising and chiral ferroelectric domain walls revealed by nonlinear optical microscopy2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 15768Article in journal (Refereed)
    Abstract [en]

    The properties of ferroelectric domain walls can significantly differ from those of their parent material. Elucidating their internal structure is essential for the design of advanced devices exploiting nanoscale ferroicity and such localized functional properties. Here, we probe the internal structure of 180° ferroelectric domain walls in lead zirconate titanate (PZT) thin films and lithium tantalate bulk crystals by means of second-harmonic generation microscopy. In both systems, we detect a pronounced second-harmonic signal at the walls. Local polarimetry analysis of this signal combined with numerical modelling reveals the existence of a planar polarization within the walls, with Néel and Bloch-like configurations in PZT and lithium tantalate, respectively. Moreover, we find domain wall chirality reversal at line defects crossing lithium tantalate crystals. Our results demonstrate a clear deviation from the ideal Ising configuration that is traditionally expected in uniaxial ferroelectrics, corroborating recent theoretical predictions of a more complex, often chiral structure.

  • 35.
    Chi, Gamma
    et al.
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England..
    Liang, Qiansheng
    Thomas Jefferson Univ, Dept Neurosci & Vickie, Sidney Kimmel Med Coll, Philadelphia, PA 19107 USA.;Thomas Jefferson Univ, Jack Farber Inst Neurosci, Sidney Kimmel Med Coll, Philadelphia, PA 19107 USA..
    Sridhar, Akshay
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Cowgill, John
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Sader, Kasim
    Thermo Fisher Sci, Mat & Struct Anal, Achtseweg Noord 5, NL-5651 GG Eindhoven, Netherlands..
    Radjainia, Mazdak
    Thermo Fisher Sci, Mat & Struct Anal, Achtseweg Noord 5, NL-5651 GG Eindhoven, Netherlands..
    Qian, Pu
    Thermo Fisher Sci, Mat & Struct Anal, Achtseweg Noord 5, NL-5651 GG Eindhoven, Netherlands..
    Castro-Hartmann, Pablo
    Thermo Fisher Sci, Mat & Struct Anal, Achtseweg Noord 5, NL-5651 GG Eindhoven, Netherlands..
    Venkaya, Shayla
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England.;Exscientia Ltd, Schrodinger Bldg,Heatley Rd,Oxford Sci Pk, Oxford OX4 4GE, England..
    Singh, Nanki Kaur
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England..
    McKinley, Gavin
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England..
    Fernandez-Cid, Alejandra
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England.;Exact Sci Ltd, Sherard Bldg,Edmund Halley Rd,Oxford Sci Pk, Oxford OX4 4DQ, England..
    Mukhopadhyay, Shubhashish M. M.
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England.;Exscientia Ltd, Schrodinger Bldg,Heatley Rd,Oxford Sci Pk, Oxford OX4 4GE, England..
    Burgess-Brown, Nicola A.
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England.;Exact Sci Ltd, Sherard Bldg,Edmund Halley Rd,Oxford Sci Pk, Oxford OX4 4DQ, England..
    Delemotte, Lucie
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Sci Life Lab, Dept Appl Phys, Solna, Sweden..
    Covarrubias, Manuel
    Thomas Jefferson Univ, Dept Neurosci & Vickie, Sidney Kimmel Med Coll, Philadelphia, PA 19107 USA.;Thomas Jefferson Univ, Jack Farber Inst Neurosci, Sidney Kimmel Med Coll, Philadelphia, PA 19107 USA..
    Durr, Katharina L.
    Univ Oxford, Ctr Med Discovery, Nuffield Dept Med, Roosevelt Dr, Oxford OX3 7DQ, England.;Univ Oxford, Nuffield Dept Med, Struct Genom Consortium, Roosevelt Dr, Oxford OX3 7DQ, England.;OMass Therapeut Ltd, Schrddinger Bldg,Heatley Rd,Oxford Sci Pk, Oxford OX4 4GE, England..
    Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4087Article in journal (Refereed)
    Abstract [en]

    Kv3 channels have distinctive gating kinetics tailored for rapid repolarization in fast-spiking neurons. Malfunction of this process due to genetic variants in the KCNC1 gene causes severe epileptic disorders, yet the structural determinants for the unusual gating properties remain elusive. Here, we present cryo-electron microscopy structures of the human Kv3.1a channel, revealing a unique arrangement of the cytoplasmic tetramerization domain T1 which facilitates interactions with C-terminal axonal targeting motif and key components of the gating machinery. Additional interactions between S1/S2 linker and turret domain strengthen the interface between voltage sensor and pore domain. Supported by molecular dynamics simulations, electrophysiological and mutational analyses, we identify several residues in the S4/S5 linker which influence the gating kinetics and an electrostatic interaction between acidic residues in alpha 6 of T1 and R449 in the pore-flanking S6T helices. These findings provide insights into gating control and disease mechanisms and may guide strategies for the design of pharmaceutical drugs targeting Kv3 channels. Here, Chi et al. report cryo-EM structures of the human Kv3.1a channel, revealing a unique arrangement of the cytoplasmic T1 domain, which allows the interactions with the C-terminal axonal targeting motif and key components of the gating machinery. These findings provide insights into the functional relevance of previously unknown interdomain interactions in Kv3 channels and may guide the design of new pharmaceutical drugs.

  • 36.
    Chung, Sunjae
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. Univ Gothenburg, Sweden.
    Eklund, Anders
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Iacocca, Ezio
    Mohseni, Seyed Majid
    Redjai Sani, Sohrab
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Bookman, Lake
    Hoefer, Mark A.
    Dumas, Randy K.
    Åkerman, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. Univ Gothenburg, Sweden.
    Magnetic droplet nucleation boundary in orthogonal spin-torque nano-oscillators2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 11209Article in journal (Refereed)
    Abstract [en]

    Static and dynamic magnetic solitons play a critical role in applied nanomagnetism. Magnetic droplets, a type of non-topological dissipative soliton, can be nucleated and sustained in nanocontact spin-torque oscillators with perpendicular magnetic anisotropy free layers. Here, we perform a detailed experimental determination of the full droplet nucleation boundary in the current-field plane for a wide range of nanocontact sizes and demonstrate its excellent agreement with an analytical expression originating from a stability analysis. Our results reconcile recent contradicting reports of the field dependence of the droplet nucleation. Furthermore, our analytical model both highlights the relation between the fixed layer material and the droplet nucleation current magnitude, and provides an accurate method to experimentally determine the spin transfer torque asymmetry of each device.

  • 37. Coucheron, David A.
    et al.
    Fokine, Michael
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Patil, Nilesh
    Breiby, Dag Werner
    Buset, Ole Tore
    Healy, Noel
    Peacock, Anna C.
    Hawkins, Thomas
    Jones, Max
    Ballato, John
    Gibson, Ursula J.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Laser recrystallization and inscription of compositional microstructures in crystalline SiGe-core fibres2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 13265Article in journal (Refereed)
    Abstract [en]

    Glass fibres with silicon cores have emerged as a versatile platform for all-optical processing, sensing and microscale optoelectronic devices. Using SiGe in the core extends the accessible wavelength range and potential optical functionality because the bandgap and optical properties can be tuned by changing the composition. However, silicon and germanium segregate unevenly during non-equilibrium solidification, presenting new fabrication challenges, and requiring detailed studies of the alloy crystallization dynamics in the fibre geometry. We report the fabrication of SiGe-core optical fibres, and the use of CO2 laser irradiation to heat the glass cladding and recrystallize the core, improving optical transmission. We observe the ramifications of the classic models of solidification at the microscale, and demonstrate suppression of constitutional undercooling at high solidification velocities. Tailoring the recrystallization conditions allows formation of long single crystals with uniform composition, as well as fabrication of compositional microstructures, such as gratings, within the fibre core.

  • 38.
    Coughlin, Michael W.
    et al.
    Univ Minnesota, Sch Phys & Astron, Minneapolis, MN 55455 USA.;CALTECH, Div Phys Math & Astron, Pasadena, CA 91125 USA..
    Antier, Sarah
    APC, UMR 7164, 10 Rue Alice Domon & Leonie Duquet, F-75205 Paris, France..
    Dietrich, Tim
    Univ Potsdam, Inst Phys & Astron, Haus 28,Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Nikhef, Sci Pk 105, NL-1098 XG Amsterdam, Netherlands..
    Foley, Ryan J.
    Univ Calif Santa Cruz, Dept Astron & Astrophys, Santa Cruz, CA 95064 USA..
    Heinzel, Jack
    Univ Cote dAzur, Artemis, Observ Cote dAzur, CNRS, CS 34229, F-06304 Nice 4, France.;Carleton Coll, Phys & Astron, Northfield, MN 55057 USA..
    Bulla, Mattia
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm Univ, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden..
    Christensen, Nelson
    Univ Cote dAzur, Artemis, Observ Cote dAzur, CNRS, CS 34229, F-06304 Nice 4, France.;Carleton Coll, Phys & Astron, Northfield, MN 55057 USA..
    Coulter, David A.
    Univ Calif Santa Cruz, Dept Astron & Astrophys, Santa Cruz, CA 95064 USA..
    Issa, Lina
    Stockholm Univ, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden.;Univ Paris Saclay, Dept Phys, ENS Paris Saclay, F-91190 Gif Sur Yvette, France.;Nordita SU.
    Khetan, Nandita
    Gran Sasso Sci Inst GSSI, I-67100 Laquila, Italy..
    Measuring the Hubble constant with a sample of kilonovae2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4129Article in journal (Refereed)
    Abstract [en]

    Kilonovae produced by the coalescence of compact binaries with at least one neutron star are promising standard sirens for an independent measurement of the Hubble constant (H-0). Through their detection via follow-up of gravitational-wave (GW), short gamma-ray bursts (sGRBs) or optical surveys, a large sample of kilonovae (even without GW data) can be used for H-0 contraints. Here, we show measurement of H-0 using light curves associated with four sGRBs, assuming these are attributable to kilonovae, combined with GW170817. Including a systematic uncertainty on the models that is as large as the statistical ones, we find H0=73.8-5.8+6.3</mml:msubsup><mml:mspace width="0.33em"></mml:mspace>km<mml:mspace width="0.33em"></mml:mspace>s-1<mml:mspace width="0.33em"></mml:mspace>Mpc-1 and <mml:msub>H0=71.2-3.1+3.2<mml:mspace width="0.33em"></mml:mspace>km<mml:mspace width="0.33em"></mml:mspace>s-1<mml:mspace width="0.33em"></mml:mspace>Mpc-1 for two different kilonova models that are consistent with the local and inverse-distance ladder measurements. For a given model, this measurement is about a factor of 2-3 more precise than the standard-siren measurement for GW170817 using only GWs. Kilonovae observations can be used to out constraints on the Hubble constant (H0). Here, the authors show H0 measurements by combining light curves of four short gamma-ray burts with GW170817 are about a factor of 2-3 more precise than the standard-siren measurements using only gravitational-waves.

  • 39.
    da Cruz, Vinicius Vaz
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Lab Nonlinear Opt & Spect, Krasnoyarsk 660041, Russia.
    Eckert, Sebastian
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Iannuzzi, Marcella
    Univ Zurich, Phys Chem Inst, CH-8057 Zurich, Switzerland..
    Ertan, Emelie
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Niskanen, Johannes
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Turku, Dept Phys & Astron, FI-20014 Turunyliopisto, Finland..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Dantz, Marcus
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Schmitt, Thorsten
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Lu, Xingye
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    McNally, Daniel
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Jay, Raphael M.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Kimberg, Victor
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Odelius, Michael
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 1013Article in journal (Refereed)
    Abstract [en]

    Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.

  • 40. Das, Tanmoy
    et al.
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Engineering three-dimensional topological insulators in Rashba-type spin-orbit coupled heterostructures2013In: Nature Communications, E-ISSN 2041-1723, Vol. 4, p. 1972-Article in journal (Refereed)
    Abstract [en]

    Topological insulators represent a new class of quantum phase defined by invariant symmetries and spin-orbit coupling that guarantees metallic Dirac excitations at its surface. The discoveries of these states have sparked the hope of realizing non-trivial excitations and novel effects such as a magnetoelectric effect and topological Majorana excitations. Here we develop a theoretical formalism to show that a three-dimensional topological insulator can be designed artificially via stacking bilayers of two-dimensional Fermi gases with opposite Rashba-type spin-orbit coupling on adjacent layers, and with interlayer quantum tunneling. We demonstrate that in the stack of bilayers grown along a (001)-direction, a non-trivial topological phase transition occurs above a critical number of Rashba bilayers. In the topological phase, we find the formation of a single spin-polarized Dirac cone at the G-point. This approach offers an accessible way to design artificial topological insulators in a set up that takes full advantage of the atomic layer deposition approach. This design principle is tunable and also allows us to bypass limitations imposed by bulk crystal geometry.

  • 41.
    de Thonel, Aurelie
    et al.
    Univ Paris, CNRS, Epigenet & Cell Fate, F-75013 Paris, France..
    Vihervaara, Anniina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Abo Akad Univ, Fac Sci & Engn, Cell Biol, Turku, Finland.;Univ Turku, Turku Biosci Ctr, Turku, Finland..
    Mezger, Valerie
    Univ Paris, CNRS, Epigenet & Cell Fate, F-75013 Paris, France..
    et al.,
    CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 7002Article in journal (Refereed)
    Abstract [en]

    Rubinstein-Taybi syndrome (RSTS) is a neurodevelopmental disorder with unclear underlying mechanisms. Here, the authors unravel the contribution of a stress-responsive pathway to RSTS where impaired HSF2 acetylation, due to RSTS-associated CBP/EP300 mutations, alters the expression of neurodevelopmental players, in keeping with hallmarks of cell-cell adhesion defects. Patients carrying autosomal dominant mutations in the histone/lysine acetyl transferases CBP or EP300 develop a neurodevelopmental disorder: Rubinstein-Taybi syndrome (RSTS). The biological pathways underlying these neurodevelopmental defects remain elusive. Here, we unravel the contribution of a stress-responsive pathway to RSTS. We characterize the structural and functional interaction between CBP/EP300 and heat-shock factor 2 (HSF2), a tuner of brain cortical development and major player in prenatal stress responses in the neocortex: CBP/EP300 acetylates HSF2, leading to the stabilization of the HSF2 protein. Consequently, RSTS patient-derived primary cells show decreased levels of HSF2 and HSF2-dependent alteration in their repertoire of molecular chaperones and stress response. Moreover, we unravel a CBP/EP300-HSF2-N-cadherin cascade that is also active in neurodevelopmental contexts, and show that its deregulation disturbs neuroepithelial integrity in 2D and 3D organoid models of cerebral development, generated from RSTS patient-derived iPSC cells, providing a molecular reading key for this complex pathology.

  • 42.
    Dellantonio, Luca
    et al.
    Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark.;Univ Copenhagen, Niels Bohr Inst, Ctr Hybrid Quantum Networks Hy Q, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark..
    Kyriienko, Oleksandr
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark..
    Marquardt, Florian
    Univ Erlangen Nurnberg, Inst Theoret Phys, Staudstr 7, D-91058 Erlangen, Germany.;Max Planck Inst Sci Light, Gunther Scharowsky Str 1, D-91058 Erlangen, Germany..
    Sorensen, Anders S.
    Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark.;Univ Copenhagen, Niels Bohr Inst, Ctr Hybrid Quantum Networks Hy Q, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark..
    Quantum nondemolition measurement of mechanical motion quanta2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 3621Article in journal (Refereed)
    Abstract [en]

    The fields of optomechanics and electromechanics have facilitated numerous advances in the areas of precision measurement and sensing, ultimately driving the studies of mechanical systems into the quantum regime. To date, however, the quantization of the mechanical motion and the associated quantum jumps between phonon states remains elusive. For optomechanical systems, the coupling to the environment was shown to make the detection of the mechanical mode occupation difficult, typically requiring the single-photon strong coupling regime. Here, we propose and analyse an electromechanical setup, which allows us to overcome this limitation and resolve the energy levels of a mechanical oscillator. We found that the heating of the membrane, caused by the interaction with the environment and unwanted couplings, can be suppressed for carefully designed electromechanical systems. The results suggest that phonon number measurement is within reach for modern electromechanical setups.

  • 43.
    Dereli-Begue, Husne
    et al.
    Bar Ilan Univ, Dept Phys, IL-52900 Ramat Gan, Israel..
    Pe'er, Asaf
    Bar Ilan Univ, Dept Phys, IL-52900 Ramat Gan, Israel..
    Ryde, Felix
    KTH, School of Engineering Sciences (SCI), Physics. Oskar Klein Ctr, SE-10691 Stockholm, Sweden..
    Oates, Samantha R.
    Univ Birmingham, Sch Phys & Astron, Birmingham B15 2TT, W Midlands, England.;Univ Birmingham, Inst Gravitat Wave Astron, Birmingham B15 2TT, W Midlands, England..
    Zhang, Bing
    Univ Nevada, Nevada Ctr Astrophys, Las Vegas, NV 89154 USA.;Univ Nevada, Dept Phys & Astron, Las Vegas, NV 89154 USA..
    Dainotti, Maria G.
    Natl Astron Observ Japan, 2-21-1 Osawa, Mitaka, Tokyo 1818588, Japan.;SOKENDAI, Grad Univ Adv Studies, Miura Dist, Kanagawa 2400193, Japan.;Space Sci Inst, Boulder, CO 80301 USA..
    A wind environment and Lorentz factors of tens explain gamma-ray bursts X-ray plateau2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 5611Article in journal (Refereed)
    Abstract [en]

    The origin of the plateau observed in the early X-ray light curves of gamma ray bursts (GRBs) is debated. Here, the authors show that the observed plateau can be explained within the classical GRB model by considering expanding shell with initial Lorentz factor of a few tens. Gamma-ray bursts (GRBs) are known to have the most relativistic jets, with initial Lorentz factors in the order of a few hundreds. Many GRBs display an early X-ray light-curve plateau, which was not theoretically expected and therefore puzzled the community for many years. Here, we show that this observed signal is naturally obtained within the classical GRB fireball model, provided that the initial Lorentz factor is rather a few tens, and the expansion occurs into a medium-low density wind. The range of Lorentz factors in GRB jets is thus much wider than previously thought and bridges an observational gap between mildly relativistic jets inferred in active galactic nuclei, to highly relativistic jets deduced in few extreme GRBs. Furthermore, long GRB progenitors are either not Wolf-Rayet stars, or the wind properties during the final stellar evolution phase are different than at earlier times. Our model has predictions that can be tested to verify or reject it in the future, such as lack of GeV emission, lack of strong thermal component and long (few seconds) variability during the prompt phase characterizing plateau bursts.

  • 44.
    Dobryden, Illia
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science. Luleå Univ Technol, Dept Engn Sci & Math, Div Mat Sci, Expt Phys, SE-97187 Luleå, Sweden..
    Korolkov, Vladimir V.
    Pk Syst UK Ltd, MediCity Nottingham, Thane Rd, Nottingham NG90 6BH, England..
    Lemaur, Vincent
    Univ Mons, Lab Chem Novel Mat, Pl Parc 20, B-7000 Mons, Belgium..
    Waldrip, Matthew
    Wake Forest Univ, Dept Phys, Winston Salem, NC 27109 USA.;Wake Forest Univ, Ctr Funct Mat, Winston Salem, NC 27109 USA..
    Un, Hio-Ieng
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England..
    Simatos, Dimitrios
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England..
    Spalek, Leszek J.
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England..
    Jurchescu, Oana D.
    Wake Forest Univ, Dept Phys, Winston Salem, NC 27109 USA.;Wake Forest Univ, Ctr Funct Mat, Winston Salem, NC 27109 USA..
    Olivier, Yoann
    Univ Namur, Namur Inst Struct Matter, Lab Computat Modelling Funct Mat, Rue Bruxelles 61, B-5000 Namur, Belgium..
    Claesson, Per M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science.
    Venkateshvaran, Deepak
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England..
    Dynamic self-stabilization in the electronic and nanomechanical properties of an organic polymer semiconductor2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 3076Article in journal (Refereed)
    Abstract [en]

    The field of organic electronics has profited from the discovery of new conjugated semiconducting polymers that have molecular backbones which exhibit resilience to conformational fluctuations, accompanied by charge carrier mobilities that routinely cross the 1 cm(2)/Vs benchmark. One such polymer is indacenodithiophene-co-benzothiadiazole. Previously understood to be lacking in microstructural order, we show here direct evidence of nanosized domains of high order in its thin films. We also demonstrate that its device-based high-performance electrical and thermoelectric properties are not intrinsic but undergo rapid stabilization following a burst of ambient air exposure. The polymer's nanomechanical properties equilibrate on longer timescales owing to an orthogonal mechanism; the gradual sweating-out of residual low molecular weight solvent molecules from its surface. We snapshot the quasistatic temporal evolution of the electrical, thermoelectric and nanomechanical properties of this prototypical organic semiconductor and investigate the subtleties which play on competing timescales. Our study documents the untold and often overlooked story of a polymer device's dynamic evolution toward stability. Organic polymer nanomechanics has been explored through precise nanometre-scale stiffness measurements in a high-mobility semiconducting polymer. Higher eigen-mode atomic force microscopy is used to measure nanomechnical variations in the film texture, as well as the nanoscale order in the material.

  • 45.
    Dong, Shuo
    et al.
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
    Beaulieu, Samuel
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany; Université de Bordeaux - CNRS - CEA, CELIA, UMR5107, F33405, Talence, France.
    Selig, Malte
    Nichtlineare Optik und Quantenelektronik, Institut für Theoretische Physik, Technische Universität Berlin, 10623, Berlin, Germany.
    Rosenzweig, Philipp
    Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany.
    Christiansen, Dominik
    Nichtlineare Optik und Quantenelektronik, Institut für Theoretische Physik, Technische Universität Berlin, 10623, Berlin, Germany.
    Pincelli, Tommaso
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
    Dendzik, Maciej
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
    Ziegler, Jonas D.
    Institute of Applied Physics and Würzburg-Dresden Cluster of Excellence ct.qmat, Technische Universität Dresden, 01062, Dresden, Germany; Photonics Laboratory, ETH Zürich, 8093, Zürich, Switzerland.
    Maklar, Julian
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
    Xian, R. Patrick
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany; Department of Statistical Sciences, University of Toronto, 700 University Avenue, Toronto, ON, M5G 1Z5, Canada.
    Neef, Alexander
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
    Mohammed, Avaise
    Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany.
    Schulz, Armin
    Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany.
    Stadler, Mona
    Institute of Semiconductor Optics and Functional Interfaces, Research Center SCoPE and IQST, University of Stuttgart, 70569, Stuttgart, Germany.
    Jetter, Michael
    Institute of Semiconductor Optics and Functional Interfaces, Research Center SCoPE and IQST, University of Stuttgart, 70569, Stuttgart, Germany.
    Michler, Peter
    Institute of Semiconductor Optics and Functional Interfaces, Research Center SCoPE and IQST, University of Stuttgart, 70569, Stuttgart, Germany.
    Taniguchi, Takashi
    International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan.
    Watanabe, Kenji
    Research Center for Electronic and Optical Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan.
    Takagi, Hidenori
    Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany; Department of Physics, University of Tokyo, 113-0033, Tokyo, Japan; Institute for Functional Matter and Quantum Technologies, University of Stuttgart, 70569, Stuttgart, Germany.
    Starke, Ulrich
    Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany.
    Chernikov, Alexey
    Institute of Applied Physics and Würzburg-Dresden Cluster of Excellence ct.qmat, Technische Universität Dresden, 01062, Dresden, Germany.
    Wolf, Martin
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
    Nakamura, Hiro
    Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany; Department of Physics, University of Arkansas, Fayetteville, AR, 72701, USA.
    Knorr, Andreas
    Nichtlineare Optik und Quantenelektronik, Institut für Theoretische Physik, Technische Universität Berlin, 10623, Berlin, Germany.
    Rettig, Laurenz
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
    Ernstorfer, Ralph
    Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany; Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623, Berlin, Germany.
    Observation of ultrafast interfacial Meitner-Auger energy transfer in a Van der Waals heterostructure2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 5057Article in journal (Refereed)
    Abstract [en]

    Atomically thin layered van der Waals heterostructures feature exotic and emergent optoelectronic properties. With growing interest in these novel quantum materials, the microscopic understanding of fundamental interfacial coupling mechanisms is of capital importance. Here, using multidimensional photoemission spectroscopy, we provide a layer- and momentum-resolved view on ultrafast interlayer electron and energy transfer in a monolayer-WSe2/graphene heterostructure. Depending on the nature of the optically prepared state, we find the different dominating transfer mechanisms: while electron injection from graphene to WSe2 is observed after photoexcitation of quasi-free hot carriers in the graphene layer, we establish an interfacial Meitner-Auger energy transfer process following the excitation of excitons in WSe2. By analysing the time-energy-momentum distributions of excited-state carriers with a rate-equation model, we distinguish these two types of interfacial dynamics and identify the ultrafast conversion of excitons in WSe2 to valence band transitions in graphene. Microscopic calculations find interfacial dipole-monopole coupling underlying the Meitner-Auger energy transfer to dominate over conventional Förster- and Dexter-type interactions, in agreement with the experimental observations. The energy transfer mechanism revealed here might enable new hot-carrier-based device concepts with van der Waals heterostructures.

  • 46.
    Dreier, Jes
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Castello, Marco
    Ist Italiano Tecnol, Mol Microscopy & Spect, Via Morego 30, I-16136 Genoa, Italy..
    Coceano, Giovanna
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Caceres, Rodrigo
    PSL Res Univ, CNRS, Inst Curie, Lab Phys Chim Curie, F-75005 Paris, France.;Sorbonne Univ, F-75005 Paris, France.;Univ Paris 05, F-75005 Paris, France..
    Plastino, Julie
    PSL Res Univ, CNRS, Inst Curie, Lab Phys Chim Curie, F-75005 Paris, France.;Sorbonne Univ, F-75005 Paris, France..
    Vicidomini, Giuseppe
    Ist Italiano Tecnol, Mol Microscopy & Spect, Via Morego 30, I-16136 Genoa, Italy..
    Testa, Ilaria
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Smart scanning for low-illumination and fast RESOLFT nanoscopy in vivo2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 556Article in journal (Refereed)
    Abstract [en]

    RESOLFT fluorescence nanoscopy can nowadays image details far beyond the diffraction limit. However, signal to noise ratio (SNR) and temporal resolution are still a concern, especially deep inside living cells and organisms. In this work, we developed a non-deterministic scanning approach based on a real-time feedback system which speeds up the acquisition up to 6-fold and decreases the light dose by 70-90% for in vivo imaging. Also, we extended the information content of the images by acquiring the complete temporal evolution of the fluorescence generated by reversible switchable fluorescent proteins. This generates a series of images with different spatial resolution and SNR, from conventional to RESOLFT images, which combined through a multi-image deconvolution algorithm further enhances the effective resolution. We reported nanoscale imaging of organelles up to 35 Hz and actin dynamics during an invasion process at a depth of 20-30 mu m inside a living Caenorhabditis elegans worm.

  • 47.
    Dubois, Valentin J.
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Raja, Shyamprasad Natarajan
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Gehring, Pascal
    Delft Univ Technol, Kavli Inst Nanosci, Lorentzweg 1, NL-2628 CJ Delft, Netherlands..
    Caneva, Sabina
    Delft Univ Technol, Kavli Inst Nanosci, Lorentzweg 1, NL-2628 CJ Delft, Netherlands..
    van der Zant, Herre S. J.
    Delft Univ Technol, Kavli Inst Nanosci, Lorentzweg 1, NL-2628 CJ Delft, Netherlands..
    Niklaus, Frank
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Massively parallel fabrication of crack-defined gold break junctions featuring sub-3 nm gaps for molecular devices2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 3433Article in journal (Refereed)
    Abstract [en]

    Break junctions provide tip-shaped contact electrodes that are fundamental components of nano and molecular electronics. However, the fabrication of break junctions remains notoriously time-consuming and difficult to parallelize. Here we demonstrate true parallel fabrication of gold break junctions featuring sub-3 nm gaps on the wafer-scale, by relying on a novel self-breaking mechanism based on controlled crack formation in notched bridge structures. We achieve fabrication densities as high as 7 million junctions per cm(2), with fabrication yields of around 7% for obtaining crack-defined break junctions with sub-3 nm gaps of fixed gap width that exhibit electron tunneling. We also form molecular junctions using dithiol-terminated oligo(phenylene ethynylene) (OPE3) to demonstrate the feasibility of our approach for electrical probing of molecules down to liquid helium temperatures. Our technology opens a whole new range of experimental opportunities for nano and molecular electronics applications, by enabling very large-scale fabrication of solid-state break junctions.

  • 48.
    Edfors, Fredrik
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hober, Andreas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Linderbäck, Klas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Maddalo, Gianluca
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Azimi, Alireza
    Karolinska Inst, Karolinska Univ Hosp, Dept Oncol Pathol, SE-17177 Stockholm, Sweden..
    Sivertsson, Åsa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tegel, Hanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hober, Sophia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Al-Khalili Szigyarto, Cristina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fagerberg, Linn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oksvold, Per
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindskog, Cecilia
    Uppsala Univ, Dept Immunol Genet & Pathol, SE-75185 Uppsala, Sweden..
    Forsström, Björn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab. Biosustainabil, DK-2970 Horsholm, Denmark..
    Enhanced validation of antibodies for research applications2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 4130Article in journal (Refereed)
    Abstract [en]

    There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.

  • 49.
    Elshaari, Ali W.
    et al.
    KTH, School of Electrical Engineering (EES).
    Zadeh, Iman Esmaeil
    Fognini, Andreas
    Reimer, Michael E.
    Dalacu, Dan
    Poole, Philip J.
    Zwiller, Val
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Electrical Engineering (EES).
    Jöns, Klaus D.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Nano Photonics.
    On-chip single photon filtering and multiplexing in hybrid quantum photonic circuits2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 379Article in journal (Refereed)
    Abstract [en]

    Quantum light plays a pivotal role in modern science and future photonic applications. Since the advent of integrated quantum nanophotonics different material platforms based on III-V nanostructures-, colour centers-, and nonlinear waveguides as on-chip light sources have been investigated. Each platform has unique advantages and limitations; however, all implementations face major challenges with filtering of individual quantum states, scalable integration, deterministic multiplexing of selected quantum emitters, and on-chip excitation suppression. Here we overcome all of these challenges with a hybrid and scalable approach, where single III-V quantum emitters are positioned and deterministically integrated in a complementary metal-oxide-semiconductor-compatible photonic circuit. We demonstrate reconfigurable on-chip single-photon filtering and wavelength division multiplexing with a foot print one million times smaller than similar table-top approaches, while offering excitation suppression of more than 95 dB and efficient routing of single photons over a bandwidth of 40 nm. Our work marks an important step to harvest quantum optical technologies' full potential.

  • 50.
    Englund, Elias
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). Joint BioEnergy Institute, Emeryville, CA, USA.
    Schmidt, Matthias
    Joint BioEnergy Institute, Emeryville, CA, USA; Institute of Applied Microbiology, Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA.
    Nava, Alberto A.
    Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
    Klass, Sarah
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
    Keiser, Leah
    Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
    Dan, Qingyun
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA.
    Katz, Leonard
    Joint BioEnergy Institute, Emeryville, CA, USA; QB3, University of California, Berkeley, Berkeley, CA, USA.
    Yuzawa, Satoshi
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan; Graduate school of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan.
    Keasling, Jay D.
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA; QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Center for Biosustainability, Danish Technical University, Lyngby, Denmark; Center for Synthetic biochemistry, Institute for Synthetic biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
    Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4871Article in journal (Refereed)
    Abstract [en]

    Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

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