kth.sePublications
Change search
Refine search result
43444546474849 2251 - 2300 of 4451
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 2251.
    Kvastad, Linda
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kollotzek, Aaron
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Chang, Chih-Fan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lappalainen, Tuuli
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. New York Genome Ctr, New York, NY USA.;Columbia Univ, Dept Syst Biol, New York, NY USA..
    Spatial transcriptomics data identifies disease-relevant tissue structures from genetically implicated GWAS genes and drug targets2024In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 32, p. 33-33Article in journal (Other academic)
  • 2252.
    Kvastad, Linda
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Mirzazadeh, Reza
    KTH, Centres, Science for Life Laboratory, SciLifeLab. 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. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mollbrink, Annelie
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Shamikh, Alia
    Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden..
    Basmaci, Elisa
    Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden..
    Prochazka, Gabriela
    Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden..
    Diaz De Ståhl, Teresita
    Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden..
    Erickson, Andrew
    Nuffield Department of Surgical Sciences, University of Oxford, UK..
    Lamb, Alastair D
    Nuffield Department of Surgical Sciences, University of Oxford, UK. Department of Urology, Oxford University Hospitals NHS Foundation Trust, UK..
    Nistér, Monica
    Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    The spatial landscape of transcriptomes and genomes in pediatric brain tumorsManuscript (preprint) (Other academic)
    Abstract [en]

    Treatment of pediatric brain tumors is continually being improved; still, there is a great need for new treatment options. Here we explore the spatial transcriptomic and genomic landscape in a cohort of pediatric brain tumors using a new generation of unbiased methodologies. We demonstrate the gene expression patterns of the essential cancer-related gene programs of epithelial-to-mesenchymal transition (EMT), the reverse process mesenchymal-to-epithelial transition (MET), and tumor microenvironment (TME) observations through microglia. Furthermore, we identify the gene expression of SPP1 by microglia in the TME as a potential prognostic mRNA marker - in pediatric brain tumor relapse patients.

  • 2253.
    Kvastad, Linda
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Werne Solnestam, Beata
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Johansson, Elin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nygren, A. O.
    Laddach, N.
    Sahlén, Pelin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vickovic, Sanja
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bendigtsen, S. C.
    Aaserud, M.
    Floer, L.
    Borgen, E.
    Schwind, C.
    Himmelreich, R.
    Latta, D.
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring2015In: Scientific Reports, E-ISSN 2045-2322, Vol. 5, article id 16519Article in journal (Refereed)
    Abstract [en]

    Single cell analysis techniques have great potential in the cancer genomics feld. The detection and characterization of circulating tumour cells are important for identifying metastatic disease at an early stage and monitoring it. This protocol is based on transcript profiling using Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (RT-MLPA), which is a specific method for simultaneous detection of multiple mRNA transcripts. Because of the small amount of (circulating) tumour cells, a pre-amplification reaction is performed after reverse transcription to generate a sufficient number of target molecules for the MLPA reaction. We designed a highly sensitive method for detecting and quantifying a panel of seven genes whose expression patterns are associated with breast cancer, and optimized the method for single cell analysis. For detection we used a fluorescence-dependent semi-quantitative method involving hybridization of unique barcodes to an array. We evaluated the method using three human breast cancer cell lines and identified specific gene expression profiles for each line. Furthermore, we applied the method to single cells and confirmed the heterogeneity of a cell population. Successful gene detection from cancer cells in human blood from metastatic breast cancer patients supports the use of RT-MLPA as a diagnostic tool for cancer genomics.

  • 2254.
    Kvedaraite, Egle
    et al.
    Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden; Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden.
    Jess, David Unnersjö
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Svensson, Mattias
    Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
    et al.,
    Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1752Article in journal (Refereed)
    Abstract [en]

    Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA+CD142−/low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA+CD142−/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures have a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.

  • 2255. Kvedaraite, Egle
    et al.
    Lourda, Magdalini
    Van Acker, Aline
    Jess, David Unnersjö
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Gavhed, Desiree
    Mjosberg, Jenny
    Idestrom, Maja
    Henter, Jan-Inge
    Svensson, Mattias
    Stromal cell - innate immune cell interactions in inflammatory bowel disease patients2017In: Scandinavian Journal of Immunology, ISSN 0300-9475, E-ISSN 1365-3083, Vol. 86, no 4, p. 253-253Article in journal (Other academic)
  • 2256.
    Kviman, Oskar
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Melin, Harald
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Koptagel, Hazal
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Elvira, Victor
    Univ Edinburgh, Edinburgh, Midlothian, Scotland..
    Lagergren, Jens
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations2022In: International Conference on Artificial Intelligence and Statistics, Vol 151 / [ed] Camps-Valls, G Ruiz, FJR Valera, I, ML Research Press , 2022, Vol. 151Conference paper (Refereed)
    Abstract [en]

    In variational inference (VI), the marginal log-likelihood is estimated using the standard evidence lower bound (ELBO), or improved versions as the importance weighted ELBO (IWELBO). We propose the multiple importance sampling ELBO (MISELBO), a versatile yet simple framework. MISELBO is applicable in both amortized and classical VI, and it uses ensembles, e.g., deep ensembles, of independently inferred variational approximations. As far as we are aware, the concept of deep ensembles in amortized VI has not previously been established. We prove that MISELBO provides a tighter bound than the average of standard ELBOs, and demonstrate empirically that it gives tighter bounds than the average of IWELBOs. MISELBO is evaluated in density-estimation experiments that include MNIST and several real-data phylogenetic tree inference problems. First, on the MNIST dataset, MISELBO boosts the density-estimation performances of a state-of-the-art model, nouveau VAE. Second, in the phylogenetic tree inference setting, our framework enhances a state-of-the-art VI algorithm that uses normalizing flows. On top of the technical benefits of MISELBO, it allows to unveil connections between VI and recent advances in the importance sampling literature, paving the way for further methodological advances.

  • 2257.
    Kyriienko, Oleksandr
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm University, Sweden; ITMO University, Russian Federation; University of Exeter, United Kingdom.
    Quantum inverse iteration algorithm for programmable quantum simulators2020In: npj Quantum Information, ISSN 2056-6387, Vol. 6, no 1, article id 7Article in journal (Refereed)
    Abstract [en]

    We propose a quantum inverse iteration algorithm, which can be used to estimate ground state properties of a programmable quantum device. The method relies on the inverse power iteration technique, where the sequential application of the Hamiltonian inverse to an initial state prepares the approximate ground state. To apply the inverse Hamiltonian operation, we write it as a sum of unitary evolution operators using the Fourier approximation approach. This allows to reformulate the protocol as separate measurements for the overlap of initial and propagated wavefunction. The algorithm thus crucially depends on the ability to run Hamiltonian dynamics with an available quantum device, and can be used for analog quantum simulators. We benchmark the performance using paradigmatic examples of quantum chemistry, corresponding to molecular hydrogen and beryllium hydride. Finally, we show its use for studying the ground state properties of relevant material science models, which can be simulated with existing devices, considering an example of the Bose-Hubbard atomic simulator.

  • 2258.
    Kyriienko, Oleksandr
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Kibis, O., V
    Shelykh, I. A.
    Optically induced topological states on the surface of mercury telluride2019In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 99, no 11, article id 115411Article in journal (Refereed)
    Abstract [en]

    We developed the theory which describes the Floquet engineering of surface electronic modes in bulk mercury telluride (HgTe) by a circularly polarized electromagnetic field. The analysis shows that the field results in the appearance of the surface states which arise from the mixing of conduction and valence bands of HgTe. Their branches lie near the center of the Brillouin zone and have the Dirac dispersion characteristic for topological states. Besides them, the irradiation induces the gap between the conduction and valence bands of HgTe. Thus, the irradiation can turn mercury telluride into a topological insulator from a gapless semiconductor. It is demonstrated that the optically induced states differ substantially from the nontopological surface states existing in HgTe without irradiation. The structure of the found states is studied both analytically and numerically in the broad range of their parameters

  • 2259.
    Kyriienko, Oleksandr
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Sigurdsson, H.
    Univ Iceland, Sci Inst, IS-107 Reykjavik, Iceland.;Univ Southampton, Sch Phys & Astron, Southampton SO17 1BJ, Hants, England..
    Liew, T. C. H.
    Nanyang Technol Univ, Sch Phys & Math Sci, Div Phys & Appl Phys, 21 Nanyang Link, Singapore 637371, Singapore..
    Probabilistic solving of NP-hard problems with bistable nonlinear optical networks2019In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 99, no 19, article id 195301Article in journal (Refereed)
    Abstract [en]

    We study theoretically a lattice of locally bistable driven-dissipative nonlinear cavities. The system is found to resemble the classical Ising model and enables its effective simulation. First, we benchmark the performance of driven-dissipative nonlinear cavities for spin-glass problems, and study the scaling of the ground-state-energy deviation and success probability as a function of system size. Next, we show how an effective bias field can be included in an optical model and use it for probabilistic solving of optimization problems. As particular examples we consider NP-hard problems embedded in the Ising model, namely graph partitioning and the knapsack problem. Finally, we confirm that locally bistable polariton networks act as classical optimizers and can potentially provide an improvement within the exponential complexity class.

  • 2260.
    Käll, Lukas
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Krogh, Anders
    Sonnhammer, Erik L. L.
    Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server2007In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, no Web Server issue, 1, p. W429-W432Article in journal (Refereed)
    Abstract [en]

    When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of all predicted transmembrane topologies overlap. This impairs predictions of 5-10% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius.

  • 2261.
    Käll, Lukas
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vitek, Olga
    Computational Mass Spectrometry-Based Proteomics2011In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 7, no 12, p. e1002277-Article in journal (Refereed)
  • 2262.
    Käller, Max
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ewels, P.
    Krueger, F.
    Andrews, S.
    Cluster Flow: A user-friendly bioinformatics workflow tool2016In: F1000 Research, E-ISSN 2046-1402, Vol. 5, article id 2824Article in journal (Refereed)
    Abstract [en]

    Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.

  • 2263.
    Käpylä, Maarit J.
    et al.
    Aalto Univ, Dept Comp Sci, POB 15400, FI-00076 Aalto, Finland.;Max Planck Inst Solar Syst Res, Justus von Liebig Weg 3, D-37077 Gottingen, Germany.; Nordita SU.
    Vizoso, Javier Alvarez
    Max Planck Inst Solar Syst Res, Justus von Liebig Weg 3, D-37077 Gottingen, Germany..
    Rheinhardt, Matthias
    Aalto Univ, Dept Comp Sci, POB 15400, FI-00076 Aalto, Finland..
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm Univ, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden.;Stockholm Univ, AlbaNova Univ Ctr, Dept Astron, SE-10691 Stockholm, Sweden.;Carnegie Mellon Univ, McWilliams Ctr Cosmol, Pittsburgh, PA 15213 USA.;Carnegie Mellon Univ, Dept Phys, Pittsburgh, PA 15213 USA..
    Singh, Nishant K.
    Max Planck Inst Solar Syst Res, Justus von Liebig Weg 3, D-37077 Gottingen, Germany.;Interuniv Ctr Astron & Astrophys, Post Bag 4, Pune 411007, Maharashtra, India..
    On the Existence of Shear-current Effects in Magnetized Burgulence2020In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 905, no 2, article id 179Article in journal (Refereed)
    Abstract [en]

    The possibility of explaining shear flow dynamos by a magnetic shear-current (MSC) effect is examined via numerical simulations. Our primary diagnostics is the determination of the turbulent magnetic diffusivity tensor eta. In our setup, a negative sign of its component eta(yx) is necessary for coherent dynamo action by the SC effect. To be able to measure turbulent transport coefficients from systems with magnetic background turbulence, we present an extension of the test-field method (TFM) applicable to our setup where the pressure gradient is dropped from the momentum equation: the nonlinear TFM (NLTFM). Our momentum equation is related to Burgers' equation and the resulting flows are referred to as magnetized burgulence. We use both stochastic kinetic and magnetic forcings to mimic cases without and with simultaneous small-scale dynamo action. When we force only kinetically, negative eta(yx) are obtained with exponential growth in both the radial and azimuthal mean magnetic field components. Using magnetokinetic forcing, the field growth is no longer exponential, while NLTFM yields positive eta(yx). By employing an alternative forcing from which wavevectors whose components correspond to the largest scales are removed, the exponential growth is recovered, but the NLTFM results do not change significantly. Analyzing the dynamo excitation conditions for the coherent SC and incoherent alpha and SC effects shows that the incoherent effects are the main drivers of the dynamo in the majority of cases. We find no evidence for MSC-effect-driven dynamos in our simulations.

  • 2264.
    Käpylä, Maarit
    et al.
    Aalto Univ, Dept Comp Sci, POB 15400, FI-00076 Aalto, Finland.;Max Planck Inst Solar Syst Res, Justus von Liebig Weg 3, D-37077 Gottingen, Germany.;Stockholm Univ, NORDITA, Hannes Alfvens Vag 12, SE-10691 Stockholm, Sweden..
    Rheinhardt, Matthias
    Aalto Univ, Dept Comp Sci, POB 15400, FI-00076 Aalto, Finland..
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm Univ, Hannes Alfvens Vag 12, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Astron, Oskar Klein Ctr, AlbaNova, SE-10691 Stockholm, Sweden.;Carnegie Mellon Univ, McWilliams Ctr Cosmol, Pittsburgh, PA 15213 USA.;Carnegie Mellon Univ, Dept Phys, Pittsburgh, PA 15213 USA..
    Compressible Test-field Method and Its Application to Shear Dynamos2022In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 932, no 1, p. 8-, article id 8Article in journal (Refereed)
    Abstract [en]

    In this study, we present a compressible test-field method (CTFM) for computing alpha-effect and turbulent magnetic diffusivity tensors, as well as those relevant for the mean ponderomotive force and mass source, applied to the full MHD equations. We describe the theoretical background of the method and compare it to the quasi-kinematic test-field method and to the previously studied variant working in simplified MHD (SMHD). We present several test cases using velocity and magnetic fields of the Roberts geometry and also compare with the imposed-field method. We show that, for moderate imposed-field strengths, the nonlinear CTFM (nCTFM) gives results in agreement with the imposed-field method. A comparison of different flavors of the nCTFM in the shear dynamo case also yields agreement up to equipartition field strengths. Some deviations between the CTFM and SMHD variants exist. As a relevant physical application, we study nonhelically forced shear flows, which exhibit large-scale dynamo action, and present a reanalysis of low-Reynolds-number, moderate shear systems, where we previously ignored the pressure gradient in the momentum equation and found no coherent shear-current effect. Another key difference is that in the earlier study we used magnetic forcing to mimic small-scale dynamo action, while here it is self-consistently driven by purely kinetic forcing. The kinematic CTFM with general validity forms the core of our analysis. We still find no coherent shear-current effect, but do recover strong large-scale dynamo action that, according to our analysis, is driven by incoherent effects.

  • 2265.
    Käpylä, P. J.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Georg August Univ Gottingen, Inst Astrophys, Friedrich Hund.
    Prandtl number dependence of stellar convection: Flow statistics and convective energy transport2021In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 655, p. A78-, article id A78Article in journal (Refereed)
    Abstract [en]

    Context. The ratio of kinematic viscosity to thermal diffusivity, the Prandtl number, is much smaller than unity in stellar convection zones. Aims. The main goal of this work is to study the statistics of convective flows and energy transport as functions of the Prandtl number. Methods. Three-dimensional numerical simulations of compressible non-rotating hydrodynamic convection in Cartesian geometry are used. The convection zone (CZ) is embedded between two stably stratified layers. The dominant contribution to the diffusion of entropy fluctuations comes in most cases from a subgrid-scale diffusivity whereas the mean radiative energy flux is mediated by a diffusive flux employing Kramers opacity law. Here, we study the statistics and transport properties of up- and downflows separately. Results. The volume-averaged rms velocity increases with decreasing Prandtl number. At the same time, the filling factor of down-flows decreases and leads to, on average, stronger downflows at lower Prandtl numbers. This results in a strong dependence of convective overshooting on the Prandtl number. Velocity power spectra do not show marked changes as a function of Prandtl number except near the base of the convective layer where the dominance of vertical flows is more pronounced. At the highest Reynolds numbers, the velocity power spectra are more compatible with the Bolgiano-Obukhov k(-11/5 )than the Kolmogorov-Obukhov k(-5/3) scaling. The horizontally averaged convected energy flux ((F) over bar (conv)), which is the sum of the enthalpy ((F) over bar (enth)) and kinetic energy fluxes ((F) over bar (kin)), is independent of the Prandtl number within the CZ. However, the absolute values of (F) over bar (enth )and (F) over bar (kin) increase monotonically with decreasing Prandtl number. Furthermore, (F) over bar (enth) and (F) over bar (kin) have opposite signs for downflows and their sum (F) over bar (down arrow)(conv) diminishes with Prandtl number. Thus, the upflows (downflows) are the dominant contribution to the convected flux at low (high) Prandtl numbers. These results are similar to those from Rayleigh-Benard convection in the low Prandtl number regime where convection is vigorously turbulent but inefficient at transporting energy. Conclusions. The current results indicate a strong dependence of convective overshooting and energy flux on the Prandtl number. Numerical simulations of astrophysical convection often use a Prandtl number of unity because it is numerically convenient. The current results suggest that this can lead to misleading results and that the astrophysically relevant low Prandtl number regime is qualitatively different from the parameter regimes explored in typical contemporary simulations.

  • 2266.
    Käpylä, P. J.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Georg August Univ Gottingen, Inst Astrophys, Friedrich Hund Pl 1, D-37077 Gottingen, Germany.;KTH Royal Inst Technol, NORDITA, S-10691 Stockholm, Sweden.;Stockholm Univ, S-10691 Stockholm, Sweden..
    Star-in-a-box simulations of fully convective stars2021In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 651, article id A66Article in journal (Refereed)
    Abstract [en]

    Context. Main-sequence late-type stars with masses of less than 0.35 M-circle dot are fully convective.Aims. The goal is to study convection, differential rotation, and dynamos as functions of rotation in fully convective stars.Methods. Three-dimensional hydrodynamic and magnetohydrodynamic numerical simulations with a star-in-a-box model, in which a spherical star is immersed inside of a Cartesian cube, are used. The model corresponds to a 0.2 M-circle dot main-sequence M5 dwarf. A range of rotation periods (P-rot) between 4.3 and 430 d is explored.Results. The slowly rotating model with P-rot=430 days produces anti-solar differential rotation with a slow equator and fast poles, along with predominantly axisymmetric quasi-steady large-scale magnetic fields. For intermediate rotation (P-rot=144 and 43 days) the differential rotation is solar-like (fast equator, slow poles), and the large-scale magnetic fields are mostly axisymmetric and either quasi-stationary or cyclic. The latter occurs in a similar parameter regime as in other numerical studies in spherical shells, and the cycle period is similar to observed cycles in fully convective stars with rotation periods of roughly 100 days. In the rapid rotation regime the differential rotation is weak and the large-scale magnetic fields are increasingly non-axisymmetric with a dominating m=1 mode. This large-scale non-axisymmetric field also exhibits azimuthal dynamo waves.Conclusions. The results of the star-in-a-box models agree with simulations of partially convective late-type stars in spherical shells in that the transitions in differential rotation and dynamo regimes occur at similar rotational regimes in terms of the Coriolis (inverse Rossby) number. This similarity between partially and fully convective stars suggests that the processes generating differential rotation and large-scale magnetism are insensitive to the geometry of the star.

  • 2267.
    Käpylä, P. J.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Georg August Univ Gottingen, Inst Astrophys & Geophys, Friedrich Hund Pl 1, D-37077 Gottingen, Germany.;Stockholm Univ, Hannes Alfvens Vag 12, S-10691 Stockholm, Sweden..
    Transition from anti-solar to solar-like differential rotation: Dependence on Prandtl number2023In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 669, p. A98-, article id A98Article in journal (Refereed)
    Abstract [en]

    Context. Late-type stars such as the Sun rotate differentially due to the interaction of turbulent convection and rotation.Aims. The aim of the study is to investigate the effects of the effective thermal Prandtl number, which is the ratio of kinematic viscosity to thermal diffusivity, on the transition from anti-solar (slow equator, fast poles) to solar-like (fast equator, slow poles) differential rotation.Methods. Three-dimensional hydrodynamic and magnetohydrodynamic simulations in semi-global spherical wedge geometry were used to model the convection zones of solar-like stars.Results. The overall convective velocity amplitude increases as the Prandtl number decreases, in accordance with earlier studies. The transition from anti-solar to solar-like differential rotation is insensitive to the Prandtl number for Prandtl numbers below unity, but for Prandtl numbers greater than unity, solar-like differential rotation becomes significantly harder to excite. Magnetic fields and more turbulent regimes with higher fluid and magnetic Reynolds numbers help to achieve solar-like differential rotation in near-transition cases where anti-solar rotation is found in more laminar simulations. Solar-like differential rotation occurs only in cases with radially outward turbulent angular momentum transport due to the Reynolds stress at the equator. The dominant contribution to this outward transport near the equator is due to prograde propagating thermal Rossby waves.Conclusions. The differential rotation is sensitive to the Prandtl number only for large Prandtl numbers in the parameter regime explored in this study. Magnetic fields have a greater effect on the differential rotation, although the inferred presence of a small-scale dynamo did not lead to drastically different results. The dominance of the thermal Rossby waves in the simulations is puzzling because they are not detected in the Sun. The current simulations are shown to be incompatible with the currently prevailing mean-field theory of differential rotation.

  • 2268. Käpylä, P. J.
    et al.
    Rheinhardt, M.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Käpylä, M. J.
    Turbulent viscosity and magnetic Prandtl number from simulations of isotropically forced turbulence2020In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 636, article id A93Article in journal (Refereed)
    Abstract [en]

    Context. Turbulent diffusion of large-scale flows and magnetic fields plays a major role in many astrophysical systems, such as stellar convection zones and accretion discs. Aims. Our goal is to compute turbulent viscosity and magnetic diffusivity which are relevant for diffusing large-scale flows and magnetic fields, respectively. We also aim to compute their ratio, which is the turbulent magnetic Prandtl number, Pmt, for isotropically forced homogeneous turbulence. Methods. We used simulations of forced turbulence in fully periodic cubes composed of isothermal gas with an imposed large-scale sinusoidal shear flow. Turbulent viscosity was computed either from the resulting Reynolds stress or from the decay rate of the large-scale flow. Turbulent magnetic diffusivity was computed using the test-field method for a microphysical magnetic Prandtl number of unity. The scale dependence of the coefficients was studied by varying the wavenumber of the imposed sinusoidal shear and test fields. Results. We find that turbulent viscosity and magnetic diffusivity are in general of the same order of magnitude. Furthermore, the turbulent viscosity depends on the fluid Reynolds number (Re) and scale separation ratio of turbulence. The scale dependence of the turbulent viscosity is found to be well approximated by a Lorentzian. These results are similar to those obtained earlier for the turbulent magnetic diffusivity. The results for the turbulent transport coefficients appear to converge at sufficiently high values of Re and the scale separation ratio. However, a weak trend is found even at the largest values of Re, suggesting that the turbulence is not in the fully developed regime. The turbulent magnetic Prandtl number converges to a value that is slightly below unity for large Re. For small Re we find values between 0.5 and 0.6 but the data are insufficient to draw conclusions regarding asymptotics. We demonstrate that our results are independent of the correlation time of the forcing function. Conclusions. The turbulent magnetic diffusivity is, in general, consistently higher than the turbulent viscosity, which is in qualitative agreement with analytic theories. However, the actual value of Pmt found from the simulations (≈0.9-0.95) at large Re and large scale separation ratio is higher than any of the analytic predictions (0.4-0.8).

  • 2269.
    Käpylä, Petri
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Magnetic and rotational quenching of the Lambda effect2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 622, article id A195Article in journal (Refereed)
    Abstract [en]

    Context. Differential rotation in stars is driven by the turbulent transport of angular momentum. Aims. Our aim is to measure and parameterize the non-diffusive contribution to the total (Reynolds plus Maxwell) turbulent stress, known as the Lambda effect, and its quenching as a function of rotation and magnetic field. Methods. Simulations of homogeneous, anisotropically forced turbulence in fully periodic cubes are used to extract their associated turbulent Reynolds and Maxwell stresses. The forcing is set up such that the vertical velocity component dominates over the horizontal ones, as in turbulent stellar convection. This choice of the forcing defines the vertical direction. Additional preferred directions are introduced by the imposed rotation and magnetic field vectors. The angle between the rotation vector and the vertical direction is varied such that the latitude range from the north pole to the equator is covered. Magnetic fields are introduced by imposing a uniform large-scale field on the system. Turbulent transport coefficients pertaining to the Lambda effect are obtained by fitting. The results are compared with analytic studies. Results. The numerical and analytic results agree qualitatively at slow rotation and low Reynolds numbers. This means that vertical (horizontal) transport is downward (equatorward). At rapid rotation the latitude dependence of the stress is more complex than predicted by theory. The existence of a significant meridional Lambda effect is confirmed. Large-scale vorticity generation is found at rapid rotation when the Reynolds number exceeds a threshold value. The Lambda effect is severely quenched by large-scale magnetic fields due to the tendency of the Reynolds and Maxwell stresses to cancel each other. Rotational (magnetic) quenching of Lambda occurs at more rapid rotation (at lower field strength) in the simulations than in the analytic studies. Conclusions. The current results largely confirm the earlier theoretical results, and also offer new insights: the non-negligible meridional Lambda effect possibly plays a role in the maintenance of meridional circulation in stars, and the appearance of large-scale vortices raises the question of their effect on the angular momentum transport in rapidly rotating stellar convective envelopes. The results regarding magnetic quenching are consistent with the strong decrease in differential rotation in recent semi-global simulations and highlight the importance of including magnetic effects in differential rotation models.

  • 2270.
    Käpylä, Petri
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Aalto University, Finland.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm University, Sweden.
    Kleeorin, Nathan
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Ben-Gurion University of the Negev, Israel.
    Kapyla, M. J.
    Rogachevskii, Igor
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Ben-Gurion University of the Negev, Israel.
    Magnetic flux concentrations from turbulent stratified convection2016In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 588, article id A150Article in journal (Refereed)
    Abstract [en]

    Context. The formation of magnetic flux concentrations within the solar convection zone leading to sunspot formation is unexplained. Aims. We study the self-organization of initially uniform sub-equipartition magnetic fields by highly stratified turbulent convection. Methods. We perform simulations of magnetoconvection in Cartesian domains representing the uppermost 8 : 5 24 Mm of the solar convection zone with the horizontal size of the domain varying between 34 and 96 Mm. The density contrast in the 24 Mm deep models is more than 3 x 10(3) or eight density scale heights, corresponding to a little over 12 pressure scale heights. We impose either a vertical or a horizontal uniform magnetic field in a convection-driven turbulent flow in set-ups where no small-scale dynamos are present. In the most highly stratified cases we employ the reduced sound speed method to relax the time step constraint arising from the high sound speed in the deep layers. We model radiation via the diffusion approximation and neglect detailed radiative transfer in order to concentrate on purely magnetohydrodynamic effects. Results. We find that super-equipartition magnetic flux concentrations are formed near the surface in cases with moderate and high density stratification, corresponding to domain depths of 12 : 5 and 24 Mm. The size of the concentrations increases as the box size increases and the largest structures (20 Mm horizontally near the surface) are obtained in the models that are 24 Mm deep. The field strength in the concentrations is in the range of 3-5 kG, almost independent of the magnitude of the imposed field. The amplitude of the concentrations grows approximately linearly in time. The effective magnetic pressure measured in the simulations is positive near the surface and negative in the bulk of the convection zone. Its derivative with respect to the mean magnetic field, however, is positive in most of the domain, which is unfavourable for the operation of the negative effective magnetic pressure instability (NEMPI). Simulations in which a passive vector field is evolved do not show a noticeable difference from magnetohydrodynamic runs in terms of the growth of the structures. Furthermore, we find that magnetic flux is concentrated in regions of converging flow corresponding to large-scale supergranulation convection pattern. Conclusions. The linear growth of large-scale flux concentrations implies that their dominant formation process is a tangling of the large-scale field rather than an instability. One plausible mechanism that can explain both the linear growth and the concentration of the flux in the regions of converging flow pattern is flux expulsion. A possible reason for the absence of NEMPI is that the derivative of the effective magnetic pressure with respect to the mean magnetic field has an unfavourable sign. Furthermore, there may not be sufficient scale separation, which is required for NEMPI to work.

  • 2271.
    Käpylä, Petri
    et al.
    Georg August Univ Gottingen, Inst Astrophys, Gottingen, Germany.;Leibniz Inst Astrophys, Potsdam, Germany.;ReSoLVE Ctr Excellence, Dept Comp Sci, Aalto, Finland.;Max Planck Inst Sonnensyst Forsch, Gottingen, Germany.;KTH Royal Inst Technol, NORDITA, Stockholm, Sweden.;Stockholm Univ, Stockholm, Sweden..
    Gent, F. A.
    ReSoLVE Ctr Excellence, Dept Comp Sci, Aalto, Finland..
    Olspert, N.
    ReSoLVE Ctr Excellence, Dept Comp Sci, Aalto, Finland..
    Kaepylae, M. J.
    ReSoLVE Ctr Excellence, Dept Comp Sci, Aalto, Finland.;Max Planck Inst Sonnensyst Forsch, Gottingen, Germany..
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm Univ, Stockholm, Sweden.;Stockholm Univ, AlbaNova Univ Ctr, Dept Astron, Stockholm, Sweden.;Univ Colorado, JILA, Boulder, CO 80309 USA.;Univ Colorado, Dept Astrophys & Planetary Sci, Boulder, CO 80309 USA.;Lab Atmospher & Space Phys, Boulder, CO USA..
    Sensitivity to luminosity, centrifugal force, and boundary conditions in spherical shell convection2020In: Geophysical and Astrophysical Fluid Dynamics, ISSN 0309-1929, E-ISSN 1029-0419, Vol. 114, no 1-2, p. 8-34Article in journal (Refereed)
    Abstract [en]

    We test the sensitivity of hydrodynamic and magnetohydrodynamic turbulent convection simulations with respect to Mach number, thermal and magnetic boundary conditions, and the centrifugal force. We find that varying the luminosity, which also controls the Mach number, has only a minor effect on the large-scale dynamics. A similar conclusion can also be drawn from the comparison of two formulations of the lower magnetic boundary condition with either vanishing electric field or current density. The centrifugal force has an effect on the solutions, but only if its magnitude with respect to acceleration due to gravity is by two orders of magnitude greater than in the Sun. Finally, we find that the parameterisation of the photospheric physics, either by an explicit cooling term or enhanced radiative diffusion, is more important than the thermal boundary condition. In particular, runs with cooling tend to lead to more anisotropic convection and stronger deviations from the Taylor-Proudman state. In summary, the fully compressible approach taken here with the Pencil Code is found to be valid, while still allowing the disparate timescales to be taken into account.

  • 2272.
    Käpylä, Petri J.
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Kleeorin, Nathan
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Mantere, M. J.
    Rogachevskii, Igor
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Flux concentrations in turbulent convection2012In: Proceedings of the International Astronomical Union, Cambridge University Press, 2012, no S294, p. 283-288Conference paper (Refereed)
    Abstract [en]

    We present preliminary results from high resolution magneto-convection simulations where we find the formation of flux concentrations from an initially uniform magnetic field. The structures appear in roughly ten convective turnover times and live close to a turbulent diffusion time. The time scales are compatible with the negative effective magnetic pressure instability (NEMPI), although structure formation is not restricted to regions where the effective magnetic pressure is negative.

  • 2273.
    Käpylä, Petri J.
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Käpylä, M. J.
    Olspert, N.
    Warnecke, J.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Convection-driven spherical shell dynamos at varying Prandtl numbers2017In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 599, article id A4Article in journal (Refereed)
    Abstract [en]

    Context. Stellar convection zones are characterized by vigorous high-Reynolds number turbulence at low Prandtl numbers. Aims. We study the dynamo and differential rotation regimes at varying levels of viscous, thermal, and magnetic diffusion. Methods. We perform three-dimensional simulations of stratified fully compressible magnetohydrodynamic convection in rotating spherical wedges at various thermal and magnetic Prandtl numbers (from 0.25 to 2 and from 0.25 to 5, respectively). Differential rotation and large-scale magnetic fields are produced self-consistently. Results. We find that for high thermal diffusivity, the rotation profiles show a monotonically increasing angular velocity from the bottom of the convection zone to the top and from the poles toward the equator. For sufficiently rapid rotation, a region of negative radial shear develops at mid-latitudes as the thermal diffusivity is decreased, corresponding to an increase of the Prandtl number. This coincides with and results in a change of the dynamo mode from poleward propagating activity belts to equatorward propagating ones. Furthermore, the clearly cyclic solutions disappear at the highest magnetic Reynolds numbers and give way to irregular sign changes or quasi-stationary states. The total (mean and fluctuating) magnetic energy increases as a function of the magnetic Reynolds number in the range studied here (5-151), but the energies of the mean magnetic fields level off at high magnetic Reynolds numbers. The differential rotation is strongly affected by the magnetic fields and almost vanishes at the highest magnetic Reynolds numbers. In some of our most turbulent cases, however, we find that two regimes are possible, where either differential rotation is strong and mean magnetic fields are relatively weak, or vice versa. Conclusions. Our simulations indicate a strong nonlinear feedback of magnetic fields on differential rotation, leading to qualitative changes in the behaviors of large-scale dynamos at high magnetic Reynolds numbers. Furthermore, we do not find indications of the simulations approaching an asymptotic regime where the results would be independent of diffusion coefficients in the parameter range studied here.

  • 2274.
    Käpylä, Petri J.
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Mantere, M. J.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Oscillatory large-scale dynamos from Cartesian convection simulations2013In: Geophysical and Astrophysical Fluid Dynamics, ISSN 0309-1929, E-ISSN 1029-0419, Vol. 107, no 1-2, p. 244-257Article in journal (Refereed)
    Abstract [en]

    We present results from compressible Cartesian convection simulations with and without imposed shear. In the former case the dynamo is expected to be of 2 type, which is generally expected to be relevant for the Sun, whereas the latter case refers to 2 dynamos that are more likely to occur in more rapidly rotating stars whose differential rotation is small. We perform a parameter study where the shear flow and the rotational influence are varied to probe the relative importance of both types of dynamos. Oscillatory solutions are preferred both in the kinematic and saturated regimes when the negative ratio of shear to rotation rates, qS/, is between 1.5 and 2, i.e. when shear and rotation are of comparable strengths. Other regions of oscillatory solutions are found with small values of q, i.e. when shear is weak in comparison to rotation, and in the regime of large negative qs, when shear is very strong in comparison to rotation. However, exceptions to these rules also appear so that for a given ratio of shear to rotation, solutions are non-oscillatory for small and large shear, but oscillatory in the intermediate range. Changing the boundary conditions from vertical field to perfect conductor ones changes the dynamo mode from oscillatory to quasi-steady. Furthermore, in many cases an oscillatory solution exists only in the kinematic regime whereas in the nonlinear stage the mean fields are stationary. However, the cases with rotation and no shear are always oscillatory in the parameter range studied here and the dynamo mode does not depend on the magnetic boundary conditions. The strengths of total and large-scale components of the magnetic field in the saturated state, however, are sensitive to the chosen boundary conditions.

  • 2275. Käpylä, Petri J.
    et al.
    Mantere, Maarit J.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Cyclic magnetic activity due to turbulent convection in spherical wedge geometry2012In: Astrophysical Journal Letters, ISSN 2041-8205, Vol. 755, no 1, p. L22-Article in journal (Refereed)
    Abstract [en]

    We report on simulations of turbulent, rotating, stratified, magnetohydrodynamic convection in spherical wedge geometry. An initially small-scale, random, weak-amplitude magnetic field is amplified by several orders of magnitude in the course of the simulation to form oscillatory large-scale fields in the saturated state of the dynamo. The differential rotation is solar-like (fast equator), but neither coherent meridional poleward circulation nor near-surface shear layer develop in these runs. In addition to a poleward branch of magnetic activity beyond 50 degrees latitude, we find for the first time a pronounced equatorward branch at around 20 degrees latitude, reminiscent of the solar cycle.

  • 2276.
    Käpylä, Petri J.
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Mantere, Maarit J.
    Cole, Elizabeth
    Warnecke, Jörn
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Brandenburg, Axel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Effects of enhanced stratification on equatorward dynamo wave propagation2013In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 778, no 1, p. 41-Article in journal (Refereed)
    Abstract [en]

    We present results from simulations of rotating magnetized turbulent convection in spherical wedge geometry representing parts of the latitudinal and longitudinal extents of a star. Here we consider a set of runs for which the density stratification is varied, keeping the Reynolds and Coriolis numbers at similar values. In the case of weak stratification, we find quasi-steady dynamo solutions for moderate rotation and oscillatory ones with poleward migration of activity belts for more rapid rotation. For stronger stratification, the growth rate tends to become smaller. Furthermore, a transition from quasi-steady to oscillatory dynamos is found as the Coriolis number is increased, but now there is an equatorward migrating branch near the equator. The breakpoint where this happens corresponds to a rotation rate that is about three to seven times the solar value. The phase relation of the magnetic field is such that the toroidal field lags behind the radial field by about pi/2, which can be explained by an oscillatory alpha(2) dynamo caused by the sign change of the alpha-effect about the equator. We test the domain size dependence of our results for a rapidly rotating run with equatorward migration by varying the longitudinal extent of our wedge. The energy of the axisymmetric mean magnetic field decreases as the domain size increases and we find that an m = 1 mode is excited for a full 2 pi azimuthal extent, reminiscent of the field configurations deduced from observations of rapidly rotating late-type stars.

  • 2277.
    König, Carolin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Skanberg, Robin
    Linköpings Univ, Dept Media & Informat Technol, Norrköping, Sweden..
    Hotz, Ingrid
    Linköpings Univ, Dept Media & Informat Technol, Norrköping, Sweden..
    Ynnerman, Anders
    Linköpings Univ, Dept Media & Informat Technol, Norrköping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 24, p. 3030-3033Article in journal (Refereed)
    Abstract [en]

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  • 2278. Könnig, F.
    et al.
    Nersisyan, H.
    Akrami, Y.
    Amendola, L.
    Zumalacárregui, Miguel
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    A spectre is haunting the cosmos: quantum stability of massive gravity with ghosts2016In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, Vol. 2016, no 11, article id 118Article in journal (Refereed)
    Abstract [en]

    Many theories of modified gravity with higher order derivatives are usually ignored because of serious problems that appear due to an additional ghost degree of freedom. Most dangerously, it causes an immediate decay of the vacuum. However, breaking Lorentz invariance can cure such abominable behavior. By analyzing a model that describes a massive graviton together with a remaining Boulware-Deser ghost mode we show that even ghostly theories of modified gravity can yield models that are viable at both classical and quantum levels and, therefore, they should not generally be ruled out. Furthermore, we identify the most dangerous quantum scattering process that has the main impact on the decay time and find differences to simple theories that only describe an ordinary scalar field and a ghost. Additionally, constraints on the parameters of the theory including some upper bounds on the Lorentz-breaking cutoff scale are presented. In particular, for a simple theory of massive gravity we find that a breaking of Lorentz invariance is allowed to happen even at scales above the Planck mass. Finally, we discuss the relevance to other theories of modified gravity.

  • 2279.
    Kördel, Mikael
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Fogelqvist, Emelie
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Carannante, Valentina
    Department of Microbiology, Karolinska Institutet.
    Önfelt, Björn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Reddy, Hemanth K. N.
    Department of Cell and Molecular Biology, Uppsala University.
    Okamoto, Kenta
    Department of Cell and Molecular Biology, Uppsala University.
    Svenda, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Sellberg, Jonas A.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Hertz, Hans
    KTH, School of Engineering Sciences (SCI), Physics. KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Biological Laboratory X-ray Microscopy2018In: Microscopy and Microanalysis, ISSN 1431-9276, E-ISSN 1435-8115, Vol. 24, no S2, p. 346-347Article in journal (Refereed)
  • 2280. Kümmel, F.
    et al.
    ten Hagen, B.
    Wittkowski, R.
    Takagi, D.
    Buttinoni, I.
    Eichhorn, Ralf
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Volpe, G.
    Löwen, H.
    Bechinger, C.
    Comment on "Circular Motion of Asymmetric Self-Propelling Particles" Reply2014In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 113, no 2, p. 029802-Article in journal (Refereed)
  • 2281. Kümmel, Felix
    et al.
    ten Hagen, Borge
    Wittkowski, Raphael
    Buttinoni, Ivo
    Eichhorn, Ralf
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Volpe, Giovanni
    Loewen, Hartmut
    Bechinger, Clemens
    Circular Motion of Asymmetric Self-Propelling Particles2013In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 110, no 19, p. 198302-Article in journal (Refereed)
    Abstract [en]

    Micron-sized self-propelled (active) particles can be considered as model systems for characterizing more complex biological organisms like swimming bacteria or motile cells. We produce asymmetric microswimmers by soft lithography and study their circular motion on a substrate and near channel boundaries. Our experimental observations are in full agreement with a theory of Brownian dynamics for asymmetric self-propelled particles, which couples their translational and orientational motion.

  • 2282.
    Kürten, Charlotte
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    On Catalytic Mechanisms for Rational Enzyme Design Strategies2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Enzymes enable life by promoting chemical reactions that govern the metabolism of all living organisms. As green catalysts, they have been extensively used in industry. However, to reach their full potential, engineering is often required, which can benefit from a detailed understanding of the underlying reaction mechanism.

    In Paper I, we screened for an esterase with promiscuous amidase activity capitalizing on a key hydrogen bond acceptor that is able to stabilize the rate limiting nitrogen inversion. In silicoanalyses revealed the esterase patatin as promising target that indeed catalyzed amide hydrolysis when tested in vitro. While key transition state stabilizers for amide hydrolysis are known, we were interested in increasing our fundamental understanding of terpene cyclase catalysis (Paper II-V). In Paper II, kinetic studies in D2O-enriched buffers using a soluble diterpene cyclase suggested that hydrogen tunneling is part of the rate-limiting protonation step. In Paper III, we performed intense computational analyses on a bacterial triterpene cyclase to show the influence of water flow on catalysis. Water movement in the active site and in specific water channels, influencing transition state formation, was detected using streamline analysis. In Paper IV and V, we focused on the human membrane-bound triterpene cyclase oxidosqualene cyclase. We first established a bacterial expression and purification protocol in Paper IV, before performing detailed in vitroand in silicoanalyses in Paper V. Our analyses showed an entropy-driven reaction mechanism and the existence of a tunnel network in the structure of the human enzyme. The influence of water network rearrangements on the thermodynamics of the transition state formation were confirmed. Introducing mutations in the tunnel lining residues severely affected the temperature dependence of the reaction by changing the water flow and network rearrangements in the tunnels and concomitant the active site.

    Download full text (pdf)
    On Catalytic Mechanisms for Rational Enzyme Design Strategies
  • 2283.
    Kürten, Charlotte
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Coating Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Eriksson, Adam
    Maddalo, Gianluca
    Edfors, Fredrik
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Syrén, Per-Olof
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Engineering of water networks in class II terpene cyclases underscores the importance of amino acid hydration and entropy in biocatalysis and enzyme designManuscript (preprint) (Other academic)
  • 2284.
    Kürten, Charlotte
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Syren, Per-Olof
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes2016In: Journal of Visualized Experiments, E-ISSN 1940-087X, no 107, article id e53168Article in journal (Refereed)
    Abstract [en]

    Enzyme catalysis evolved in an aqueous environment. The influence of solvent dynamics on catalysis is, however, currently poorly understood and usually neglected. The study of water dynamics in enzymes and the associated thermodynamical consequences is highly complex and has involved computer simulations, nuclear magnetic resonance (NMR) experiments, and calorimetry. Water tunnels that connect the active site with the surrounding solvent are key to solvent displacement and dynamics. The protocol herein allows for the engineering of these motifs for water transport, which affects specificity, activity and thermodynamics. By providing a biophysical framework founded on theory and experiments, the method presented herein can be used by researchers without previous expertise in computer modeling or biophysical chemistry. The method will advance our understanding of enzyme catalysis on the molecular level by measuring the enthalpic and entropic changes associated with catalysis by enzyme variants with obstructed water tunnels. The protocol can be used for the study of membrane-bound enzymes and other complex systems. This will enhance our understanding of the importance of solvent reorganization in catalysis as well as provide new catalytic strategies in protein design and engineering.

  • 2285. Küçükdoğru, R.
    et al.
    Türkez, H.
    Arslan, M. E.
    Tozlu, Ö.Ö.
    Sönmez, E.
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Cacciatore, I.
    Di Stefano, A.
    Neuroprotective effects of boron nitride nanoparticles in the experimental Parkinson’s disease model against MPP+ induced apoptosis2020In: Metabolic brain disease, ISSN 0885-7490, E-ISSN 1573-7365Article in journal (Refereed)
    Abstract [en]

    Parkinson’s disease (PD) is one of the most aggressive neurodegenerative diseases and characterized by the loss of dopamine-sensitive neurons in the substantia nigra region of the brain. There is no any definitive treatment to completely cure PD and existing treatments can only ease the symptoms of the disease. Boron nitride nanoparticles have been extensively studied in nano-biological studies and researches showed that it can be a promising candidate for PD treatment with its biologically active unique properties. In the present study, it was aimed to investigate ameliorative effects of hexagonal boron nitride nanoparticles (hBNs) against toxicity of 1-methyl-4-phenylpyridinium (MPP+) in experimental PD model. Experimental PD model was constituted by application of MPP+ to differentiated pluripotent human embryonal carcinoma cell (Ntera-2, NT-2) culture in wide range of concentrations (0.62 to 2 mM). Neuroprotective activity of hBNs against MPP+ toxicity was determined by cell viability assays including MTT and LDH release. Oxidative alterations by hBNs application in PD cell culture model were investigated using total antioxidant capacity (TAC) and total oxidant status (TOS) tests. The impacts of hBNs and MPP+ on nuclear integrity were analyzed by Hoechst 33258 fluorescent staining method. Acetylcholinesterase (AChE) enzyme activities were determined by a colorimetric assay towards to hBNs treatment. Cell death mechanisms caused by hBNs and MPP+ exposure was investigated by flow cytometry analysis. Experimental results showed that application of hBNs increased cell viability in PD model against MPP+ application. TAS and TOS analysis were determined that antioxidant capacity elevated after hBNs applications while oxidant levels were reduced. Furthermore, flow cytometric analysis executed that MPP+ induced apoptosis was prevented significantly (p < 0.05) after application with hBNs. In a conclusion, the obtained results indicated that hBNs have a huge potential against MPP+ toxicity and can be used in PD treatment as novel neuroprotective agent and drug delivery system.

  • 2286.
    La Martina, Thomas
    et al.
    Univ North Florida, Dept Phys, Jacksonville, FL 32224 USA..
    Zhu, Jian-Xin
    Los Alamos Natl Lab, Theoret Div, Los Alamos, NM 87545 USA.;Los Alamos Natl Lab, Ctr Integrated Nanotechnol, Los Alamos, NM 87545 USA..
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Los Alamos Natl Lab, Inst Mat Sci, Los Alamos, NM 87545 USA..
    Haraldsen, Jason T.
    Univ North Florida, Dept Phys, Jacksonville, FL 32224 USA..
    Dirac Nodes and Magnetic Order in M2X2 Transition-Metal Chalcogenides2018In: Physica Status Solidi. Rapid Research Letters, ISSN 1862-6254, E-ISSN 1862-6270, Vol. 12, no 11, article id 1800181Article in journal (Refereed)
    Abstract [en]

    In this study, we perform a computational analysis of the M2X2 transition-metal chalcogenides (TMCs). Using density functional theory with a spin-polarized generalized gradient approximation, we examine the magnetic and electronic properties for the antiferromagnetic and ferromagnetic states with M = Cr, Mn, and Fe and X = S and Se. After optimizing the geometric structure for stability, we examine the spin-polarized electronic structure, density of states, and Mulliken population. It is discovered that these materials are quasi-two-dimensional honeycomb lattices with metallic antiferromagnetic ground states. The structures consist of a distorted tetrahedral crystal-field symmetry that has a distinct magnetic moment. An analysis of the electronic structure shows the presence of nodal points that resemble Dirac nodes for all cases, which leads to the possibility of the realization of magnetic Dirac materials.

  • 2287.
    Lacis, Ugis
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Johansson, Petter
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fullana, Tomas
    Sorbonne Université.
    Hess, Berk
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI).
    Amberg, Gustav
    KTH, Superseded Departments (pre-2005), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Södertorn University, Stockholm, Sweden.
    Bagheri, Shervin
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Zaleski, Stephane
    Sorbonne Université.
    Steady moving contact line of water over a no-slip substrateManuscript (preprint) (Other academic)
    Abstract [en]

    The movement of the triple contact line plays a crucial role inmany applications such as ink-jet printing, liquid coating and drainage(imbibition) in porous media. To design accurate computational toolsfor these applications, predictive models of the moving contact line areneeded. However, the basic mechanisms responsible for movement ofthe triple contact line are not well understood but still debated. We investigatethe movement of the contact line between water, vapour anda silica-like solid surface under steady conditions in low capillary numberregime. We use molecular dynamics (MD) with an atomistic watermodel to simulate a nanoscopic drop between two moving plates. Weinclude hydrogen bonding between the water molecules and the solidsubstrate, which leads to a sub-molecular slip length. We benchmarktwo continuum methods, the Cahn{Hilliard phase-eld (PF) model anda volume-of-uid (VOF) model, against MD results.We show that bothcontinuum models reproduce the statistical measures obtained fromMD reasonably well, with a trade-o in accuracy. We demonstrate theimportance of the phase-eld mobility parameter and the local sliplength in accurately modelling the moving contact line.

  • 2288.
    Lacis, Ugis
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Johansson, Petter
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fullana, Tomas
    Sorbonne Univ, Paris, France.;CNRS, Paris, France..
    Hess, Berk
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Amberg, Gustav
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics. Södertörn Univ, Stockholm, Sweden..
    Bagheri, Shervin
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Zaleski, Stephane
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Sorbonne Univ, Paris, France.;CNRS, Paris, France..
    Steady moving contact line of water over a no-slip substrate Challenges in benchmarking phase-field and volume-of-fluid methods against molecular dynamics simulations2020In: The European Physical Journal Special Topics, ISSN 1951-6355, E-ISSN 1951-6401, Vol. 229, no 10, p. 1897-1921Article in journal (Refereed)
    Abstract [en]

    The movement of the triple contact line plays a crucial role in many applications such as ink-jet printing, liquid coating and drainage (imbibition) in porous media. To design accurate computational tools for these applications, predictive models of the moving contact line are needed. However, the basic mechanisms responsible for movement of the triple contact line are not well understood but still debated. We investigate the movement of the contact line between water, vapour and a silica-like solid surface under steady conditions in low capillary number regime. We use molecular dynamics (MD) with an atomistic water model to simulate a nanoscopic drop between two moving plates. We include hydrogen bonding between the water molecules and the solid substrate, which leads to a sub-molecular slip length. We benchmark two continuum methods, the Cahn-Hilliard phase-field (PF) model and a volume-of-fluid (VOF) model, against MD results. We show that both continuum models reproduce the statistical measures obtained from MD reasonably well, with a trade-off in accuracy. We demonstrate the importance of the phase-field mobility parameter and the local slip length in accurately modelling the moving contact line.

  • 2289.
    Lade, Steven J.
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Niiranen, Susa
    Hentati-Sundberg, Jonas
    Blenckner, Thorsten
    Boonstra, Wiebren J.
    Orach, Kirill
    Quaas, Martin F.
    Oesterblom, Henrik
    Schlueter, Maja
    An empirical model of the Baltic Sea reveals the importance of social dynamics for ecological regime shifts2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 35, p. 11120-11125Article in journal (Refereed)
    Abstract [en]

    Regime shifts triggered by human activities and environmental changes have led to significant ecological and socioeconomic consequences in marine and terrestrial ecosystems worldwide. Ecological processes and feedbacks associated with regime shifts have received considerable attention, but human individual and collective behavior is rarely treated as an integrated component of such shifts. Here, we used generalized modeling to develop a coupled social-ecological model that integrated rich social and ecological data to investigate the role of social dynamics in the 1980s Baltic Sea cod boom and collapse. We showed that psychological, economic, and regulatory aspects of fisher decision making, in addition to ecological interactions, contributed both to the temporary persistence of the cod boom and to its subsequent collapse. These features of the social-ecological system also would have limited the effectiveness of stronger fishery regulations. Our results provide quantitative, empirical evidence that incorporating social dynamics into models of natural resources is critical for understanding how resources can be managed sustainably. We also show that generalized modeling, which is well-suited to collaborative model development and does not require detailed specification of causal relationships between system variables, can help tackle the complexities involved in creating and analyzing social-ecological models.

  • 2290. Lagae, L.
    et al.
    Liu, C. X.
    Latta, D.
    Henry, O.
    O'Sullivan, C.
    Roeser, T.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kvastad, Linda
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Riley, I.
    Borgen, E.
    Lab-on-chip tracing circulating tumour cells2013In: European Journal of Cancer, ISSN 0959-8049, E-ISSN 1879-0852, Vol. 49, p. S74-S74Article in journal (Other academic)
  • 2291.
    Lagman, David
    et al.
    Uppsala Univ, Sci Life Lab, Dept Med Cell Biol, Biomed Ctr, Uppsala, Sweden..
    Haines, Helen J.
    Uppsala Univ, Sci Life Lab, Dept Med Cell Biol, Biomed Ctr, Uppsala, Sweden..
    Abalo, Xesús M
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Sci Life Lab, Dept Med Cell Biol, Biomed Ctr, Uppsala, Sweden..
    Larhammar, Dan
    Uppsala Univ, Sci Life Lab, Dept Med Cell Biol, Biomed Ctr, Uppsala, Sweden..
    Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before reexpansion by whole genome duplications in vertebrates2022In: PLOS ONE, E-ISSN 1932-6203, Vol. 17, no 12, article id e0279548Article in journal (Refereed)
    Abstract [en]

    Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in metazoans and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.

  • 2292. Lahtvee, Petri-Jaan
    et al.
    Kumar, Rahul
    Hallström, Björn M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Chalmers University of Technology, Sweden.
    Adaptation to different types of stress converge on mitochondrial metabolism2016In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 27, no 15, p. 2505-2514Article in journal (Refereed)
    Abstract [en]

    Yeast cell factories encounter physical and chemical stresses when used for industrial production of fuels and chemicals. These stresses reduce productivity and increase bioprocess costs. Understanding the mechanisms of the stress response is essential for improving cellular robustness in platform strains. We investigated the three most commonly encountered industrial stresses for yeast (ethanol, salt, and temperature) to identify the mechanisms of general and stress-specific responses under chemostat conditions in which specific growth rate-dependent changes are eliminated. By applying systems-level analysis, we found that most stress responses converge on mitochondrial processes. Our analysis revealed that stress-specific factors differ between applied stresses; however, they are underpinned by an increased ATP demand. We found that when ATP demand increases to high levels, respiration cannot provide sufficient ATP, leading to onset of respirofermentative metabolism. Although stress-specific factors increase ATP demand for cellular growth under stressful conditions, increased ATP demand for cellular maintenance underpins a general stress response and is responsible for the onset of overflow metabolism.

  • 2293.
    Lakshmanan, Ramnath
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Sanchez-Dominguez, Margarita
    Centro de Investigacion en Materials Avanzados (CIMAV) S.C., Mexico.
    Matutes-Aquino, Jose
    Centro de Investigacion en Materials Avanzados (CIMAV) S.C., Mexico.
    Wennmalm, Stefan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kuttuva Rajarao, Gunaratna
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Removal of total organic carbon from sewage wastewater using poly(ethylenimine)-functionalized magnetic nanoparticles2014In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 30, no 4, p. 1036-1044Article in journal (Refereed)
    Abstract [en]

    The increased levels of organic carbon in sewage wastewater during recent years impose a great challenge to the existing wastewater treatment process (WWTP). Technological innovations are therefore sought that can reduce the release of organic carbon into lakes and seas. In the present study, magnetic nanoparticles (NPs) were synthesized, functionalized with poly(ethylenimine) (PEI), and characterized using TEM (transmission electron microscopy), X-ray diffraction (XRD), FTIR (Fourier transform infrared spectroscopy), CCS (confocal correlation spectroscopy), SICS (scattering interference correlation spectroscopy), magnetism studies, and thermogravimetric analysis (TGA). The removal of total organic carbon (TOC) and other contaminants using PEI-coated magnetic nanoparticles (PEI-NPs) was tested in wastewater obtained from the Hammarby Sjöstadsverk sewage plant, Sweden. The synthesized NPs were about 12 nm in diameter and showed a homogeneous particle size distribution in dispersion by TEM and CCS analyses, respectively. The magnetization curve reveals superparamagnetic behavior, and the NPs do not reach saturation because of surface anisotropy effects. A 50% reduction in TOC was obtained in 60 min when using 20 mg/L PEI-NPs in 0.5 L of wastewater. Along with TOC, other contaminants such as turbidity (89%), color (86%), total nitrogen (24%), and microbial content (90%) were also removed without significant changes in the mineral ion composition of wastewater. We conclude that the application of PEI-NPs has the potential to reduce the processing time, complexity, sludge production, and use of additional chemicals in the WWTP.

  • 2294.
    Lakshmikanth, Tadepally
    et al.
    Karolinska Inst, Dept Womens & Childrens Hlth, Sci Life Lab, Karolinska, Solna, Sweden..
    Muhammad, Sayyed Auwn
    Karolinska Inst, Dept Womens & Childrens Hlth, Sci Life Lab, Karolinska, Solna, Sweden..
    Olin, Axel
    Karolinska Inst, Dept Womens & Childrens Hlth, Sci Life Lab, Karolinska, Solna, Sweden..
    Chen, Yang
    Karolinska Inst, Dept Womens & Childrens Hlth, Sci Life Lab, Karolinska, Solna, Sweden..
    Mikes, Jaromir
    Karolinska Inst, Dept Womens & Childrens Hlth, Sci Life Lab, Karolinska, Solna, Sweden..
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gummesson, Anders
    Univ Gothenburg, Inst Med, Dept Mol & Clin Med, Wallenberg Lab, Gothenburg, Sweden.;Sahlgrens Univ Hosp, Dept Physiol, Gothenburg, Sweden..
    Bergström, Göran
    Univ Gothenburg, Inst Med, Dept Mol & Clin Med, Wallenberg Lab, Gothenburg, Sweden.;Sahlgrens Univ Hosp, Dept Physiol, Gothenburg, Sweden..
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brodin, Petter
    Karolinska Inst, Dept Womens & Childrens Hlth, Sci Life Lab, Karolinska, Solna, Sweden.;Karolinska Univ Hosp, Dept Pediat Rheumatol, Karolinska, Solna, Sweden..
    Human Immune System Variation during 1 Year2020In: Cell Reports, E-ISSN 2211-1247, Vol. 32, no 3, article id 107923Article in journal (Refereed)
    Abstract [en]

    The human immune system varies extensively between individuals, but variation within individuals over time has not been well characterized. Systems-level analyses allow for simultaneous quantification of many interacting immune system components and the inference of global regulatory principles. Here, we present a longitudinal, systems-level analysis in 99 healthy adults 50 to 65 years of age and sampled every third month for 1 year. We describe the structure of interindividual variation and characterize extreme phenotypes along a principal cum. From coordinated measurement fluctuations, we infer relationships between 115 immune cell populations and 750 plasma proteins constituting the blood immune system. While most individuals have stable immune systems, the degree of longitudinal variability is an individual feature. The most variable individuals, in the absence of overt infections, exhibited differences in markers of metabolic health suggestive of a possible link between metabolic and immunologic homeostatic regulation.

  • 2295. Lal, S.
    et al.
    Nguyen, L.
    Tezone, R.
    Pontén, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Odeberg, J.
    Li, A.
    dos Remedios, C.
    Tissue microarray profiling in human heart failure2016In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861Article in journal (Refereed)
    Abstract [en]

    Tissue MicroArrays (TMAs) are a versatile tool for high-throughput protein screening, allowing qualitative analysis of a large number of samples on a single slide. We have developed a customizable TMA system that uniquely utilizes cryopreserved human cardiac samples from both heart failure and donor patients to produce formalin-fixed paraffin-embedded sections. Confirmatory upstream or downstream molecular studies can then be performed on the same (biobanked) cryopreserved tissue. In a pilot study, we applied our TMAs to screen for the expression of four-and-a-half LIM-domain 2 (FHL2), a member of the four-and-a-half LIM family. This protein has been implicated in the pathogenesis of heart failure in a variety of animal models. While FHL2 is abundant in the heart, not much is known about its expression in human heart failure. For this purpose, we generated an affinity-purified rabbit polyclonal anti-human FHL2 antibody. Our TMAs allowed high-throughput profiling of FHL2 protein using qualitative and semiquantitative immunohistochemistry that proved complementary to Western blot analysis. We demonstrated a significant relative reduction in FHL2 protein expression across different forms of human heart failure.

  • 2296.
    Lam, Simon
    et al.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Arif, Muhammad
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Song, Xiya
    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.
    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.;.
    Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological Diseases2022In: Frontiers in Molecular Neuroscience, ISSN 1662-5099, Vol. 15, article id 889728Article in journal (Refereed)
    Abstract [en]

    It is critical to identify biomarkers for neurological diseases (NLDs) to accelerate drug discovery for effective treatment of patients of diseases that currently lack such treatments. In this work, we retrieved genotyping and clinical data from 1,223 UK Biobank participants to identify genetic and clinical biomarkers for NLDs, including Alzheimer's disease (AD), Parkinson's disease (PD), motor neuron disease (MND), and myasthenia gravis (MG). Using a machine learning modeling approach with Monte Carlo randomization, we identified a panel of informative diagnostic biomarkers for predicting AD, PD, MND, and MG, including classical liver disease markers such as alanine aminotransferase, alkaline phosphatase, and bilirubin. A multinomial model trained on accessible clinical markers could correctly predict an NLD diagnosis with an accuracy of 88.3%. We also explored genetic biomarkers. In a genome-wide association study of AD, PD, MND, and MG patients, we identified single nucleotide polymorphisms (SNPs) implicated in several craniofacial disorders such as apnoea and branchiootic syndrome. We found evidence for shared genetic risk loci among NLDs, including SNPs in cancer-related genes and SNPs known to be associated with non-brain cancers such as Wilms tumor, leukemia, and colon cancer. This indicates overlapping genetic characterizations among NLDs which challenges current clinical definitions of the neurological disorders. Taken together, this work demonstrates the value of data-driven approaches to identify novel biomarkers in the absence of any known or promising biomarkers.

  • 2297.
    Lam, Simon
    et al.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Bayraktar, Abdulahad
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Zhang, Cheng
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Turkez, Hasan
    Ataturk Univ, Fac Med, Dept Med Biol, TR-25240 Erzurum, Turkey..
    Nielsen, Jens
    Chalmers Univ Technol, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden..
    Boren, Jan
    Univ Gothenburg, Sahlgrenska Univ Hosp, Dept Mol & Clin Med, Wallenberg Lab, SE-41345 Gothenburg, Sweden..
    Shoaie, Saeed
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England.
    A systems biology approach for studying neurodegenerative diseases2020In: Drug Discovery Today, ISSN 1359-6446, E-ISSN 1878-5832, Vol. 25, no 7, p. 1146-1159Article, review/survey (Refereed)
    Abstract [en]

    Neurodegenerative diseases (NDDs), such as Alzheimer's (AD) and Parkinson's (PD), are among the leading causes of lost years of healthy life and exert a great strain on public healthcare systems. Despite being first described more than a century ago, no effective cure exists for AD or PD. Although extensively characterised at the molecular level, traditional neurodegeneration research remains marred by narrow-sense approaches surrounding amyloid beta (A beta), tau, and alpha-synuclein (alpha-syn). A systems biology approach enables the integration of multi-omics data and informs discovery of biomarkers, drug targets, and treatment strategies. Here, we present a comprehensive timeline of high-throughput data collection, and associated biotechnological advancements and computational analysis related to AD and PD. We hereby propose that a philosophical change in the definitions of AD and PD is now needed.

  • 2298.
    Lam, Simon
    et al.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Doran, Stephen
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Yüksel, Hatice Hilal
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Altay, Özlem
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Turkez, Hasan
    Ataturk Univ, Fac Med, Dept Med Biol, TR-25240 Erzurum, Turkey..
    Nielsen, Jens
    Chalmers Univ Technol, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden..
    Boren, Jan
    Univ Gothenburg, Sahlgrenska Univ Hosp, Dept Mol & Clin Med, Wallenberg Lab, Gothenburg, Sweden..
    Uhlén, Mathias
    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. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England.;KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden..
    Addressing the heterogeneity in liver diseases using biological networks2021In: Briefings in Bioinformatics, ISSN 1467-5463, E-ISSN 1477-4054, Vol. 22, no 2, p. 1751-1766Article, review/survey (Refereed)
    Abstract [en]

    The abnormalities in human metabolism have been implicated in the progression of several complex human diseases, including certain cancers. Hence, deciphering the underlying molecular mechanisms associated with metabolic reprogramming in a disease state can greatly assist in elucidating the disease aetiology. An invaluable tool for establishing connections between global metabolic reprogramming and disease development is the genome-scale metabolic model (GEM). Here, we review recent work on the reconstruction of cell/tissue-type and cancer-specific GEMs and their use in identifying metabolic changes occurring in response to liver disease development, stratification of the heterogeneous disease population and discovery of novel drug targets and biomarkers. We also discuss how GEMs can be integrated with other biological networks for generating more comprehensive cell/tissue models. In addition, we review the various biological network analyses that have been employed for the development of efficient treatment strategies. Finally, we present three case studies in which independent studies converged on conclusions underlying liver disease.

  • 2299.
    Lam, Simon
    et al.
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, London SE1 9RT, England..
    Hartmann, Nils
    Leibniz Inst Aging Fritz Lipmann Inst, D-07745 Jena, Germany.;Univ Med Ctr, Inst Pathol, D-55131 Mainz, Germany..
    Benfeitas, Rui
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Natl Bioinformat Infrastruct Sweden NBIS, SE-17121 Stockholm, Sweden..
    Zhang, Cheng
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Arif, Muhammad
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Turkez, Hasan
    Ataturk Univ, Fac Med, Dept Med Biol, TR-25240 Erzurum, Turkey..
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Englert, Christoph
    Leibniz Inst Aging Fritz Lipmann Inst, D-07745 Jena, Germany.;Freidrich Schiller Univ Jena, Inst Biochem & Biophys, D-07745 Jena, Germany..
    Knight, Robert
    Kings Coll London, Fac Dent Oral & Craniofacial Sci, London SE1 9RT, England..
    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, London SE1 9RT, England..
    Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases2021In: Biomedicines, E-ISSN 2227-9059, Vol. 9, no 10, article id 1310Article in journal (Refereed)
    Abstract [en]

    Neurodegenerative diseases, including Alzheimer's (AD) and Parkinson's diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analysed transcriptomic data from AD and PD patients, and stratified these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identified retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrated that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.

  • 2300.
    Lambert, Ruth A.
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Picano, Francesco
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Active suspensions in thin films: nutrient uptake and swimmer motion2013In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 733, p. 528-557Article in journal (Refereed)
    Abstract [en]

    A numerical study of swimming particle motion and nutrient transport is conducted for a semidilute to dense suspension in a thin film. The steady squirmer model is used to represent the motion of living cells in suspension with the nutrient uptake by swimming particles modelled using a first-order kinetic equation representing the absorption process that occurs locally at the particle surface. An analysis of the dynamics of the neutral squirmers inside the film shows that the vertical motion is reduced significantly. The mean nutrient uptake for both isolated and populations of swimmers decreases for increasing swimming speeds when nutrient advection becomes relevant as less time is left for the nutrient to diffuse to the surface. This finding is in contrast to the case where the uptake is modelled by imposing a constant nutrient concentration at the cell surface and the mass flux results to be an increasing monotonic function of the swimming speed. In comparison to non-motile particles, the cell motion has a negligible influence on nutrient uptake at lower particle absorption rates since the process is rate limited. At higher absorption rates, the swimming motion results in a large increase in the nutrient uptake that is attributed to the movement of particles and increased mixing in the fluid. As the volume fraction of swimming particles increases, the squirmers consume slightly less nutrients and require more power for the same swimming motion. Despite this increase in energy consumption, the results clearly demonstrate that the gain in nutrient uptake make swimming a winning strategy for micro-organism survival also in relatively dense suspensions.

43444546474849 2251 - 2300 of 4451
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf