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  • 201.
    Mahani, Mohammad Reza
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Mirsakiyeva, Amina
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Charge transport via polarons in doped poly(p-phenylene) with impurityManuscript (preprint) (Other academic)
    Abstract [en]

    Polaron charge transport in doped poly(p-phenylene), PPP, in the presence of magnetic and nonmagnetic impurities and an electric field, is studied using the Su-Schrieffer-Heeger (SSH) tight-binding model. In our approach, the electric field is included in the Hamiltonian through the time-dependent vector potential via Peierls substitution of the phase factor. We describe the dynamics of the polarons and identify three distinct regimes: transmission, reflection, and trapping of polarons at the impurity site. The strength of the electric field as well as the impurity potential determine the outcome ofthe scattering.

  • 202.
    Mahmudi, Owais
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sennblad, Bengt
    Arvestad, Lars
    Nowick, Katja
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gene-Pseudogene Evolution: a Probalitistic ApproachManuscript (preprint) (Other academic)
  • 203.
    Mahmudi, Owais
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sjöstrand, Joel
    Sennblad, Bengt
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Genome-wide probabilistic reconciliation analysis across vertebrates2013In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 14, p. S10-Article in journal (Refereed)
    Abstract [en]

    Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertices of a species tree explains where gene duplications have occurred on the species tree. In this study, we sample reconciliations from a posterior over reconciliations, gene trees, edge lengths and other parameters, given a species tree and gene sequences. We employ a Bayesian analysis tool, based on the probabilistic model DLRS that integrates gene duplication, gene loss and sequence evolution under a relaxed molecular clock for substitution rates, to obtain this posterior. By applying these methods, we perform a genome-wide analysis of a nine species dataset, OPTIC, and conclude that for many gene families, the most parsimonious reconciliation (MPR) - a reconciliation that minimizes the number of duplications - is far from the correct explanation of the evolutionary history. For the given dataset, we observe that approximately 19% of the sampled reconciliations are different from MPR. This is in clear contrast with previous estimates, based on simpler models and less realistic assumptions, according to which 98% of the reconciliations can be expected to be identical to MPR. We also generate heatmaps showing where in the species trees duplications have been most frequent during the evolution of these species.

  • 204.
    Malenova, Gabriela
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Motamed, Mohammad
    Department of Mathematics and Statistics, The University of New Mexico, Albuquerque, NM 87131, USA.
    Runborg, Olof
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Regularity of stochastic observables in Gaussian beam superposition of high-frequency waves2017In: Research in mathematical sciences, ISSN 2197-9847Article in journal (Other academic)
    Abstract [en]

    We consider high-frequency waves satisfying the scalar wave equation with highly oscillatory initial data. The wave speed, and the phase and amplitude of the initial data are assumed to be uncertain, described by a finite number of random variables with known probability distributions. We define quantities of interest (QoIs), or observables, as local averages of the squared modulus of the wave solution. We aim to quantify the regularity of these QoIs in terms of the input random parameters, and the wave length, i.e., to estimate the size of their derivatives. The regularity is important for uncertainty quantification methods based on interpolation in the stochastic space. In particular, the size of the derivatives should be bounded independently of the wave length. In this paper, we are able to show that when these QoIs are approximated by Gaussian beam superpositions, they indeed have this property, despite the highly oscillatory character of the waves.

  • 205.
    Malenova, Gabriela
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Stochastic regularity of general quadratic observables of high frequency wavesManuscript (preprint) (Other academic)
    Abstract [en]

    We consider solutions to the wave equation with uncertain initial data and medium, whose wavelength is short compared to thedistance traveled by the wave. We are interested in the statistics of the observables, i.e. functionals of the wave solution. Computation by direct methods gets very expensive or outright non-feasible as the wavelength decreases. To address the difficulties, we proposed a method consisting of the Gaussian beam method to treat the high frequencies and the sparse stochastic collocation method to remedy the curse of dimensionality in the stochastic space. For the latter method to converge, we need the observables to satisfy certain stochastic regularity conditions. The main contribution of this work is to show this regularity for a set of quadratic observables obtained by the Gaussian beam approximation of the wave solution.

  • 206.
    Malm, Johan
    et al.
    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.
    Schlatter, Philipp
    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.
    Fischer, Paul F.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Stabilization of the Spectral Element Method in Convection Dominated Flows by Recovery of Skew-Symmetry2013In: Journal of Scientific Computing, ISSN 0885-7474, E-ISSN 1573-7691, Vol. 57, no 2, p. 254-277Article in journal (Refereed)
    Abstract [en]

    We investigate stability properties of the spectral element method for advection dominated incompressible flows. In particular, properties of the widely used convective form of the nonlinear term are studied. We remark that problems which are usually associated with the nonlinearity of the governing Navier-Stokes equations also arise in linear scalar transport problems, which implicates advection rather than nonlinearity as a source of difficulty. Thus, errors arising from insufficient quadrature of the convective term, commonly referred to as 'aliasing errors', destroy the skew-symmetric properties of the convection operator. Recovery of skew-symmetry can be efficiently achieved by the use of over-integration. Moreover, we demonstrate that the stability problems are not simply connected to underresolution. We combine theory with analysis of the linear advection-diffusion equation in 2D and simulations of the incompressible Navier-Stokes equations in 2D of thin shear layers at a very high Reynolds number and in 3D of turbulent and transitional channel flow at moderate Reynolds number. For the Navier-Stokes equations, where the divergence-free constraint needs to be enforced iteratively to a certain accuracy, small divergence errors can be detrimental to the stability of the method and it is therefore advised to use additional stabilization (e.g. so-called filter-based stabilization, spectral vanishing viscosity or entropy viscosity) in order to assure a stable spectral element method.

  • 207.
    Marin, Oana
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Tornberg, Anna-Karin
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Corrected trapezoidal rules for a class of singular functions2014In: IMA Journal of Numerical Analysis, ISSN 0272-4979, E-ISSN 1464-3642, Vol. 34, no 4, p. 1509-1540Article in journal (Refereed)
    Abstract [en]

    A set of accurate quadrature rules applicable to a class of integrable functions with isolated singularities is designed and analysed theoretically in one and two dimensions. These quadrature rules are based on the trapezoidal rule with corrected quadrature weights for points in the vicinity of the singularity. To compute the correction weights, small-size ill-conditioned systems have to be solved. The convergence of the correction weights is accelerated by the use of compactly supported functions that annihilate boundary errors. Convergence proofs with error estimates for the resulting quadrature rules are given in both one and two dimensions. The tabulated weights are specific for the singularities under consideration, but the methodology extends to a large class of functions with integrable isolated singularities. Furthermore, in one dimension we have obtained a closed form expression based on which the modified weights can be computed directly.

  • 208.
    Markidis, Stefano
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Henty, David
    Heisey, Katherine
    Fischer, Paul
    OpenACC acceleration of the Nek5000 spectral element code2015In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 29, no 3, p. 311-319Article in journal (Refereed)
    Abstract [en]

    We present a case study of porting NekBone, a skeleton version of the Nek5000 code, to a parallel GPU-accelerated system. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. The original NekBone Fortran source code has been used as the base and enhanced by OpenACC directives. The profiling of NekBone provided an assessment of the suitability of the code for GPU systems, and indicated possible kernel optimizations. To port NekBone to GPU systems required little effort and a small number of additional lines of code (approximately one OpenACC directive per 1000 lines of code). The naïve implementation using OpenACC leads to little performance improvement: on a single node, from 16 Gflops obtained with the version without OpenACC, we reached 20 Gflops with the naïve OpenACC implementation. An optimized NekBone version leads to a 43 Gflop performance on a single node. In addition, we ported and optimized NekBone to parallel GPU systems, reaching a parallel efficiency of 79.9% on 1024 GPUs of the Titan XK7 supercomputer at the Oak Ridge National Laboratory.

  • 209. McIlwain, Sean
    et al.
    Tamura, Kaipo
    Kertesz-Farkas, Attila
    Grant, Charles E.
    Diament, Benjamin
    Frewen, Barbara
    Howbert, J. Jeffry
    Hoopmann, Michael R.
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Eng, Jimmy K.
    MacCoss, Michael J.
    Noble, William Stafford
    Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis2014In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, no 10, p. 4488-4491Article in journal (Refereed)
    Abstract [en]

    Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data.

  • 210.
    Mele, Giampaolo
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    The infinite Lanczos method for symmetric nonlinear eigenvalue problemsManuscript (preprint) (Other academic)
    Abstract [en]

    A new iterative method for solving large scale symmetric nonlineareigenvalue problems is presented. We firstly derive an infinite dimensional symmetric linearization of the nonlinear eigenvalue problem, then we apply the indefinite Lanczos method to this specific linearization, resulting in a short-term recurrence. We show how, under specific assumption on the starting vector, this method can be carried out in finite arithmetic and how the exploitation of the problem structure leads to improvements in terms of computation time. The eigenpair approximations are extracted with the nonlinear Rayleigh–Ritz procedure combined with aspecific choice of the projection space. We illustrate how this extraction technique resolves the instability issues that may occur due to the loss of orthogonality in many standard Lanczos-type methods.

  • 211.
    Mele, Giampaolo
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Jarlebring, Elias
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    On restarting the tensor infinite Arnoldi method2018In: BIT Numerical Mathematics, ISSN 0006-3835, E-ISSN 1572-9125, Vol. 58, no 1, p. 133-162Article in journal (Refereed)
    Abstract [en]

    An efficient and robust restart strategy is important for any Krylov-based method for eigenvalue problems. The tensor infinite Arnoldi method (TIAR) is a Krylov-based method for solving nonlinear eigenvalue problems (NEPs). This method can be interpreted as an Arnoldi method applied to a linear and infinite dimensional eigenvalue problem where the Krylov basis consists of polynomials. We propose new restart techniques for TIAR and analyze efficiency and robustness. More precisely, we consider an extension of TIAR which corresponds to generating the Krylov space using not only polynomials, but also structured functions, which are sums of exponentials and polynomials, while maintaining a memory efficient tensor representation. We propose two restarting strategies, both derived from the specific structure of the infinite dimensional Arnoldi factorization. One restarting strategy, which we call semi-explicit TIAR restart, provides the possibility to carry out locking in a compact way. The other strategy, which we call implicit TIAR restart, is based on the Krylov–Schur restart method for the linear eigenvalue problem and preserves its robustness. Both restarting strategies involve approximations of the tensor structured factorization in order to reduce the complexity and the required memory resources. We bound the error introduced by some of the approximations in the infinite dimensional Arnoldi factorization showing that those approximations do not substantially influence the robustness of the restart approach. We illustrate the effectiveness of the approaches by applying them to solve large scale NEPs that arise from a delay differential equation and a wave propagation problem. The advantages in comparison to other restart methods are also illustrated. 

  • 212. Mikkelsen, R. F.
    et al.
    Sarmast, Sasan
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sørensen, J. N.
    Rotor aerodynamic power limits at low tip speed ratio using CFD2014In: SCIENCE OF MAKING TORQUE FROM WIND 2014 (TORQUE 2014), 2014, Vol. 524, no 1, article id 012099Conference paper (Refereed)
    Abstract [en]

    When investigating limits of rotor aerodynamic models, the Betz limit serves as a solid marker of an upper limit which no model should be able to exceed. A century ago Joukowsky (1912) proposed a rotor aerodynamic model utilizing a rotating actuator disc with a constant circulation. This model has since then been the subject of much controversy as it predicts a power performance that for all tip speed ratios exceeds the Betz limit and which goes to infinity when the tip speed ratio goes to zero. Recently, it was demonstrated that the Joukowsky model is fully consistent with the inviscid Euler equations and that the apparent inconsistency partly can be explained by the lack of viscous effects (Sprensen and van Kuik [4]). However, even including a term to account for the effect of viscosity at small tip speed ratios, the model still predicts a power yield that exceeds the Betz limit. In the present work we study in detail, using a CFD actuator line model, the flow behavior for rotors at small tip speed ratios. It is shown that the excessive swirl appearing towards the rotor center at small tip speed ratios generates vortex breakdown, causing a recirculating zone in the wake that limits the power yield of the rotor. The appearance of vortex breakdown has a similar effect on the flow behavior as the vortex ring state that usually appears at higher tip speed ratios. Limits to where vortex breakdown might occur with tip speed ratio and rotor loading as parameter are investigated and presented in the paper. The limits found correspond to well-known criterion for vortex breakdown onset for swirling flows in general. By applying a criterion for vortex breakdown in combination with the general momentum theory, the power performance always stays below the Betz limit.

  • 213.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Botkina, D.
    Elgammal, Karim
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Ten, Assel
    Hugosson, Håkan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Yu, Valentina
    Experimental and ab initio studies of the novel piperidine-containing acetylene glycolsManuscript (preprint) (Other academic)
  • 214.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre. Kazakh-British Technical University, Kazakhstan.
    Botkina, Darya
    KTH, School of Industrial Engineering and Management (ITM), Production Engineering. Institute of Chemical Sciences, Kazakhstan.
    Elgammal, Karim
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ten, Assel
    Hugosson, Håkan W.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Yu, Valentina
    Experimental and density functional theory studies of some novel piperidine-containing acetylene glycols2016In: ARKIVOC, ISSN 1551-7004, E-ISSN 1551-7012, p. 86-99Article in journal (Refereed)
    Abstract [en]

    Synthesis routes of novel piperidine-containing acetylenes are presented. The new molecules are expected to exhibit plant growth stimulation properties. In particular, the yield in a situation of drought is expected to increase. Our synthesis makes use of the Favorskii reaction between cyclohexanone/piperidone and triple-bond containing alcohols. The structures of the obtained molecules were determined using nuclear magnetic resonance (NMR). The electronic structure and geometries of the molecules were studied theoretically using first-principles calculations based on density functional theory. The calculated geometries agree very well with the experimentally determined ones, and also allow us to determine bond lengths, angles and charge distributions inside the molecules.

  • 215.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Hugosson, Håkan W.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. Univ Gävle, Sweden.
    Crispin, Xavier
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Quantum Molecular Dynamical Calculations of PEDOT 12-Oligomer and its Selenium and Tellurium Derivatives2017In: Journal of Electronic Materials, ISSN 0361-5235, E-ISSN 1543-186X, Vol. 46, no 5, p. 3071-3075Article in journal (Refereed)
    Abstract [en]

    We present simulation results, computed with the Car-Parrinello molecular dynamics method, at zero and ambient temperature (300 K) for poly(3,4-ethylenedioxythiophene) [PEDOT] and its selenium and tellurium derivatives PEDOS and PEDOTe, represented as 12-oligomer chains. In particular, we focus on structural parameters such as the dihedral rotation angle distribution, as well as how the charge distribution is affected by temperature. We find that for PEDOT, the dihedral angle distribution shows two distinct local maxima whereas for PEDOS and PEDOTe, the distributions only have one clear maximum. The twisting stiffness at ambient temperature appears to be larger the lighter the heteroatom (S, Se, Te) is, in contrast to the case at 0 K. As regards point charge distributions, they suggest that aromaticity increases with temperature, and also that aromaticity becomes more pronounced the lighter the heteroatom is, both at 0 K and ambient temperature. Our results agree well with previous results, where available. The bond lengths are consistent with substantial aromatic character both at 0 K and at ambient temperature. Our calculations also reproduce the expected trend of diminishing gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital with increasing atomic number of the heteroatom.

  • 216.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Hugosson, Håkan W.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics. 5)Department of Physics and Astronomy, Materials Theory Division, Uppsala University.
    Temperature dependence of band gaps and conformational disorder in PEDOT and its selenium and tellurium derivatives: density functional calculations2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690Article in journal (Refereed)
    Abstract [en]

    The conducting polymer poly(3,4-ethylenedioxythiophene), or PEDOT, is an attractive material for flexibleelectronics. We present combined molecular dynamics and quantum chemical calculations, based on den-sity functional theory, of EDOT oligomers and isoelectronic selenium and tellurium derivatives (EDOS andEDOTe) to address the effect of temperature on the geometrical and electronic properties of these systems.With finite size scaling, we also extrapolate our results to the infinite polymers, i.e. PEDOT, PEDOS and PEDOTe. Our computations indicate that the most favourable oligomer conformations at finite temperature are conformations around the flat trans-conformation and a non-flat conformation around 45 from the cis-conformation. Also, the dihedral stiffness increases with the atomic number of the heteroatom. We find excellent agreement with experimentally measured gaps for PEDOT and PEDOS. For PEDOT, the gap does not increase with temperature where as this is the case for its derivatives. The conformational disorder as well as the choice of basis set both significantly affect the calculated gaps.

  • 217.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Optical properties of Naphthobischalcogenadiazoles from density functional perspectiveManuscript (preprint) (Other academic)
    Abstract [en]

    In the present work the density functional calculations of two naphthobischalcogenadiazole (NXz) oligomers are shown. The oxygen- and sulphur-containing NXz trimers were optimized in a form of a neutral oligomer and a radical cation in order to investigate structural changes resulting from the polaron formation. The influence of polaron on band gaps is determined and supported with densities of states analysis together with absorption spectra. This manuscript used B3LYP and ωB97XD functionals in combination with 6-31+G(d) basis set.

  • 218.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Polaron formation and optical absorption in PEDOT and its selenium and tellurium derivatives: density functional calculationsManuscript (preprint) (Other academic)
    Abstract [en]

    We present a density functional theory (DFT) study on polaron formation and optical properties of PEDOT and its selenium and tellurium derivatives. Comparing a number of combinations of basis set and approximations to the exchange-correlation functional, we find that the ωB97XD functional is an overall good choice giving well-localized polarons and optical spectra in good agreement with experiment. This functional has the correct long-range  asymptotic behavior, and also includes some short-range Hartree-Fock exchange. Despite the  long-range Hartree-Fock exchange part present in this functional, the spin contamination remains relatively limited and it also stably produces results that are virtually independent of the basis set used.

  • 219. Mohammad, Dara K.
    et al.
    Ali, Raja H.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Computer Science and Communication (CSC).
    Turunen, Janne J.
    Nore, Beston F.
    Smith, C. I. Edvard
    B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA Processing2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 8, article id e0160255Article in journal (Refereed)
    Abstract [en]

    Protein kinase B (AKT) phosphorylates numerous substrates on the consensus motif RXRXXpS/T, a docking site for 14-3-3 interactions. To identify novel AKT-induced phosphorylation events following B cell receptor (BCR) activation, we performed proteomics, biochemical and bioinformatics analyses. Phosphorylated consensus motif-specific antibody enrichment, followed by tandem mass spectrometry, identified 446 proteins, containing 186 novel phosphorylation events. Moreover, we found 85 proteins with up regulated phosphorylation, while in 277 it was down regulated following stimulation. Up regulation was mainly in proteins involved in ribosomal and translational regulation, DNA binding and transcription regulation. Conversely, down regulation was preferentially in RNA binding, mRNA splicing and mRNP export proteins. Immunoblotting of two identified RNA regulatory proteins, RBM25 and MEF-2D, confirmed the proteomics data. Consistent with these findings, the AKT-inhibitor (MK-2206) dramatically reduced, while the mTORC-inhibitor PP242 totally blocked phosphorylation on the RXRXXpS/T motif. This demonstrates that this motif, previously suggested as an AKT target sequence, also is a substrate for mTORC1/2. Proteins with PDZ, PH and/or SH3 domains contained the consensus motif, whereas in those with an HMG-box, H15 domains and/or NF-X1-zinc-fingers, the motif was absent. Proteins carrying the consensus motif were found in all eukaryotic clades indicating that they regulate a phylogenetically conserved set of proteins.

  • 220.
    Monokrousos, Antonios
    et al.
    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.
    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.
    Mavriplis, Catherine
    Henningson, Dan S.
    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.
    Optimal disturbances above and upstream of a flat plate with an elliptic-type leading edge2014In: Theoretical and Computational Fluid Dynamics, ISSN 0935-4964, E-ISSN 1432-2250, Vol. 28, no 2, p. 147-157Article in journal (Refereed)
    Abstract [en]

    Adjoint-based iterative methods are employed to compute linear optimal disturbances in a spatially growing boundary layer around an elliptic leading edge. The Lagrangian approach is used where an objective function is chosen and constraints are assigned. The optimisation problem is solved using power iterations combined with a matrix-free formulation, where the state is marched forward in time with a standard direct numerical simulation solver and backward with the adjoint solver until a chosen convergence criterion is fulfilled. We consider the global and, more relevant to receptivity studies, the upstream localised optimal initial condition leading to the largest possible energy amplification at time T. We find that the two-dimensional initial condition with the largest potential for growth is a Tollmien-Schlichting-like wave packet that includes the Orr mechanism and is located inside the boundary layer downstream of the leading edge. Three-dimensional optimal disturbances induce streaks by the lift-up mechanism. Requiring the optimal initial condition to be localised upstream of the plate enables us to better study the effects of the leading edge on the boundary layer receptivity mechanisms. Two-dimensional upstream disturbances are inefficient at triggering unstable eigenmodes, whereas three-dimensional disturbances induce streamwise streaks with significant growth.

  • 221. Moruz, Luminita
    et al.
    Hoopmann, Michael R.
    Rosenlund, Magnus
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Granholm, Viktor
    Moritz, Robert L.
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Mass Fingerprinting of Complex Mixtures: Protein Inference from High-Resolution Peptide Masses and Predicted Retention Times2013In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 12, no 12, p. 5730-5741Article in journal (Refereed)
    Abstract [en]

    In typical shotgun experiments, the mass spectrometer records the masses of a large set of ionized analytes but fragments only a fraction of them. In the subsequent analyses, normally only the fragmented ions are used to compile a set of peptide identifications, while the unfragmented ones are disregarded. In this work, we show how the unfragmented ions, here denoted MS1-features, can be used to increase the confidence of the proteins identified in shotgun experiments. Specifically, we propose the usage of in silico mass tags, where the observed MS1-features are matched against de novo predicted masses and retention times for all peptides derived from a sequence database. We present a statistical model to assign protein-level probabilities based on the MS1-features and combine this data with the fragmentation spectra. Our approach was evaluated for two triplicate data sets from yeast and human, respectively, leading to up to 7% more protein identifications at a fixed protein-level false discovery rate of 1%. The additional protein identifications were validated both in the context of the mass spectrometry data and by examining their estimated transcript levels generated using RNA-Seq. The proposed method is reproducible, straightforward to apply, and can even be used to reanalyze and increase the yield of existing data sets.

  • 222. Moruz, Luminita
    et al.
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    GradientOptimizer: An open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography2014In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 14, no 12, p. 1464-1466Article in journal (Refereed)
    Abstract [en]

    We here present GradientOptimizer, an intuitive, lightweight graphical user interface to design nonlinear gradients for separation of peptides by reversed-phase liquid chromatography. The software allows to calculate three types of nonlinear gradients, each of them optimizing a certain retention time distribution of interest. GradientOptimizer is straightforward to use, requires minimum processing of the input files, and is supported under Windows, Linux, and OS X platforms. The software is open-source and can be downloaded under an Apache 2.0 license at https://github.com/statisticalbiotechnology/NonlinearGradientsUI.

  • 223. Moruz, Luminita
    et al.
    Pichler, Peter
    Stranzl, Thomas
    Mechtler, Karl
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Optimized Nonlinear Gradients for Reversed-Phase Liquid Chromatography in Shotgun Proteomics2013In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 85, no 16, p. 7777-7785Article in journal (Refereed)
    Abstract [en]

    Reversed-phase liquid chromatography has become the preferred method for separating peptides in most of the mass spectrometry-based proteomics workflows of today. In the way the technique is typically applied, the peptides are released from the chromatography column by the gradual addition of an organic buffer according to a linear function. However, when applied to complex peptide mixtures, this approach leads to unequal spreads of the peptides over the chromatography time. To address this, we investigated the use of nonlinear gradients, customized for each setup at hand. We developed an algorithm to generate optimized gradient functions for shotgun proteomics experiments and evaluated it for two data sets consisting each of four replicate runs of a human complex sample. Our results show that the optimized gradients produce a more even spread of the peptides over the chromatography run, while leading to increased numbers of confident peptide identifications. In addition, the list of peptides identified using nonlinear gradients differed considerably from those found with the linear ones, suggesting that such gradients can be a valuable tool for increasing the proteome coverage of mass spectrometry-based experiments.

  • 224. Motamed, M.
    et al.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    A wavefront-based Gaussian beam method for computing high frequency wave propagation problems2015In: Computers and Mathematics with Applications, ISSN 0898-1221, E-ISSN 1873-7668, Vol. 69, no 9, p. 949-963Article in journal (Refereed)
    Abstract [en]

    We present a novel wavefront method based on Gaussian beams for computing high frequency wave propagation problems. Unlike standard geometrical optics, Gaussian beams compute the correct solution of the wave field also at caustics. The method tracks a front of two canonical beams with two particular initial values for width and curvature. In a fast post-processing step, from the canonical solutions we recreate any other Gaussian beam with arbitrary initial data on the initial front. This provides a simple mechanism to include a variety of optimization processes, including error minimization and beam width minimization, for a posteriori selection of optimal beam initial parameters. The performance of the method is illustrated with two numerical examples.

  • 225.
    Muhle, Franz
    et al.
    Norwegian Univ Life Sci, Fac Environm Sci & Nat Resource Management, As, Norway..
    Schottler, Jannik
    Carl von Ossietzky Univ Oldenburg, ForWind Ctr Wind Energy, Inst Phys, Oldenburg, Germany..
    Bartl, Jan
    Norwegian Univ Sci & Technol, Dept Energy & Proc Engn, Trondheim, Norway..
    Futrzynski, Romain
    Siemens PLM Software, London, England..
    Evans, Steve
    Siemens PLM Software, London, England..
    Bernini, Luca
    Politecn Milan, Dept Mech Engn, Milan, Italy..
    Schito, Paolo
    Politecn Milan, Dept Mech Engn, Milan, Italy..
    Draper, Martin
    Univ Republica, Fac Ingn, Montevideo, Uruguay..
    Guggeri, Andres
    Univ Republica, Fac Ingn, Montevideo, Uruguay..
    Kleusberg, Elektra
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Holling, Michael
    Carl von Ossietzky Univ Oldenburg, ForWind Ctr Wind Energy, Inst Phys, Oldenburg, Germany..
    Peinke, Joachim
    Carl von Ossietzky Univ Oldenburg, ForWind Ctr Wind Energy, Inst Phys, Oldenburg, Germany.;Fraunhofer IWES, Oldenburg, Germany..
    Adaramola, Muyiwa S.
    Norwegian Univ Life Sci, Fac Environm Sci & Nat Resource Management, As, Norway..
    Saetran, Lars
    Norwegian Univ Sci & Technol, Dept Energy & Proc Engn, Trondheim, Norway..
    Blind test comparison on the wake behind a yawed wind turbine2018In: Wind Energy Science, ISSN 2213-3968, E-ISSN 2366-7443, Vol. 3, no 2, p. 883-903Article in journal (Refereed)
    Abstract [en]

    This article summarizes the results of the "Blind test 5" workshop, which was held in Visby, Sweden, in May 2017. This study compares the numerical predictions of the wake flow behind a model wind turbine operated in yaw to experimental wind tunnel results. Prior to the workshop, research groups were invited to predict the turbine performance and wake flow properties using computational fluid dynamics (CFD) methods. For this purpose, the power, thrust, and yaw moments for a 30 degrees yawed model turbine, as well as the wake's mean and turbulent streamwise and vertical flow components, were measured in the wind tunnel at the Norwegian University of Science and Technology (NTNU). In order to increase the complexity, a non-yawed downstream turbine was added in a second test case, while a third test case challenged the modelers with a new rotor and turbine geometry. Four participants submitted predictions using different flow solvers, three of which were based on large eddy simulations (LES) while another one used an improved delayed detached eddy simulation (IDDES) model. The performance of a single yawed turbine was fairly well predicted by all simulations, both in the first and third test cases. The scatter in the downstream turbine performance predictions in the second test case, however, was found to be significantly larger. The complex asymmetric shape of the mean streamwise and vertical velocities was generally well predicted by all the simulations for all test cases. The largest improvement with respect to previous blind tests is the good prediction of the levels of TKE in the wake, even for the complex case of yaw misalignment. These very promising results confirm the mature development stage of LES/DES simulations for wind turbine wake modeling, while competitive advantages might be obtained by faster computational methods.

  • 226.
    Murail, Samuel
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Howard, Rebecca J.
    Trudell, James R.
    Bertaccini, Edward
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Tracing the Closing of a Ligand-Gated Ion Channel in Atomic Detail: An Unconstrained Four-Microsecond Simulation of GLIC Leads to a Closed State Remarkably Similar to ELIC2012In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, no 3, p. 113A-114AArticle in journal (Other academic)
  • 227.
    Murail, Samuel
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wallner, Björn
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Trudell, James R.
    Bertaccini, Edward
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Microsecond Simulations Indicate that Ethanol Binds between Subunits and Could Stabilize an Open-State Model of a Glycine Receptor2011In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 7, p. 1642-1650Article in journal (Refereed)
    Abstract [en]

    Cys-loop receptors constitute a superfamily of ion channels gated by ligands such as acetylcholine, serotonin, glycine, and gamma-aminobutyric acid. All of these receptors are thought to share structural characteristics, but due to high sequence variation and limited structure availability, our knowledge about allosteric binding sites is still limited. These sites are frequent targets of anesthetic and alcohol molecules, and are of high pharmacological importance. We used molecular simulations to study ethanol binding and equilibrium exchange for the homomeric alpha 1 glycine receptor (GlyR alpha 1), modeled on the structure of the Gloeobacter violaceus pentameric ligand-gated channel. Ethanol has a well-known potentiating effect and can be used in high concentrations. By performing two microsecond-scale simulations of GlyR with/without ethanol, we were able to observe spontaneous binding in cavities and equilibrium ligand exchange. Of interest, it appears that there are ethanol-binding sites both between and within the GlyR transmembrane subunits, with the intersubunit site having the highest occupancy and slowest exchange (similar to 200 ns). This model site involves several residues that were previously identified via mutations as being crucial for potentiation. Finally, ethanol appears to stabilize the GlyR model built on a presumably open form of the ligand-gated channel. This stabilization could help explain the effects of allosteric ligand binding in Cys-loop receptors.

  • 228.
    Nakane, Takanori
    et al.
    MRC Lab Mol Biol, Cambridge, England..
    Kimanius, Dari
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics.
    Scheres, Sjors H. W.
    MRC Lab Mol Biol, Cambridge, England..
    Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION2018In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e36861Article in journal (Refereed)
    Abstract [en]

    Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.

  • 229.
    Narangifard, A.
    et al.
    KI, Dept Med, Solna MedS, Stockholm, Sweden.;ERCO Pharma AB, Sci Life Lab, Stockholm, Sweden..
    den Hollander, L.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Wennberg, Christian L.
    KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundborg, M.
    ERCO Pharma AB, Sci Life Lab, Stockholm, Sweden..
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Iwai, I.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Han, H.
    Max Planck Inst Mol Physiol, Syst Cell Biol, Dortmund, Germany..
    Masich, S.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Daneholt, B.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Norlen, L.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden.;Karolinska Univ Hosp, Dermatol Clin, Stockholm, Sweden..
    Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation2018In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 366, no 2, p. 139-151Article in journal (Refereed)
    Abstract [en]

    The skin's permeability barrier consists of stacked lipid sheets of splayed ceramides, cholesterol and free fatty acids, positioned intercellularly in the stratum corneum. We report here on the early stage of skin barrier formation taking place inside the tubuloreticular system in the secretory cells of the topmost viable epidermis and in the intercellular space between viable epidermis and stratum corneum. The barrier formation process was analysed in situ in its near-native state, using cryo-EM combined with molecular dynamics modeling and EM simulation. Stacks of lamellae appear towards the periphery of the tubuloreticular system and they are closely associated with granular regions. Only models based on a bicontinuous cubic phase organization proved compatible with the granular cryo-EM patterns. Only models based on a dehydrated lamellar phase organization agreed with the lamellar cryo-EM patterns. The data support that human skin barrier formation takes place via a cubic to lamellar lipid phase transition.

  • 230. Nason, F.
    et al.
    Zhu, Lailai
    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.
    Dubini, G.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics, Physicochemical Fluid Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Numerical simulation of a deformable cell in microchannels2013In: Computational Methods for Coupled Problems in Science and Engineering V: A Conference Celebrating the 60th Birthday of Eugenio Onate, COUPLED PROBLEMS 2013, 2013, p. 685-695Conference paper (Refereed)
    Abstract [en]

    The main goal of this work is to numerically investigate the behavior of a cell flowing in a microfluidic system. In particular, we want to model flow-induced deformations of an isolated cell to quantitatively evaluate the cell response when subjected to a representative range of flow rates in a realistic geometry, with specific interest in the case of cell trapping. This research will help optimize operating conditions as well as the design of cell manipulation/culture micro-devices, so as to guarantee cell viability and ultimately improve high-throughput performance.

  • 231.
    Negi, Prabal
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Boundary layers over wing sections2017Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The understanding of developing boundary layers over wings is an important topic from the perspective of industrial applications. An increased understanding would be consequential not only for achieving higher fuel efficiency but also in the design of aircraft control strategies. With these aims in mind, the current work aims to further the understanding of developing boundary layer over wingsections. The study is performed with two particular perspectives in mind -unsteady aerodynamic effects in a pitching airfoil and turbulent boundary layerstructure in non-equilibrium boundary layers over a stationary airfoil.The boundary layer evolution in unsteady natural laminar flow airfoils undergoing small-amplitude pitch-oscillations is investigated. For high Reynolds numbers the origins of the non-linear unsteady aerodynamic response of laminar airfoils is explained on the basis of quasi-steady assumptions. Temporal nonlinearitiesin aerodynamic forces are shown to be inherently linked to thenon-linearities of static aerodynamic force coefficients and that a simple phaselagconcept can model the observed non-linear unsteady response. On the other hand at lower Reynolds numbers, when there exists an unstable leading edgelaminar separation bubble, the unsteady response is dynamically rich and changes in boundary layer characteristics can be abrupt. Such quasi-steadyphase-lag concepts are no longer appropriate to explain the unsteady flow physics in such a case. For the case of stationary airfoils, flow statistics for flow around an airfoil at two different Reynolds numbers are compared to assess Reynolds number effects in non-equilibrium flows. Pressure gradient effects found to be stronger at low Reynolds numbers, leading to higher energy in the larger structures present  in the outer part of the turbulent boundary layer.

  • 232.
    Negi, Prabal
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Stability and transition in pitching wings2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The aeroelastic stability of airplanes is one of the most important aspects of airplane design. Flutter or divergence instabilities arising out of the interaction of fluid forces and structural elasticity must be avoided by design or through the limitation of the flight envelope. Classical unsteady theories have been established since the 1930s however, recent investigations with laminar wings and in transitional flows have found the theories to be unreliable in these regimes. The current work investigates the flow around unsteady airfoils in these flow regimes. A linear framework for the stability analysis of fluid-structure-interaction (FSI) problems is derived and validated. The derived formulation is then used to investigate the changes in the structural sensitivity of an eigenvalue for an oscillating cylinder, which is found to change significantly when the fluid and structural systems are close to resonance. The linear stability analysis is then applied to investigate the aeroelastic stability of a NACA0012 airfoil with a free pitch-deegree-of-freedom at transitional Reynolds numbers. The stability results of the coupled FSI system are found to be in good agreement with previously performed experimental results and were able to predict the onset of aeroelastic pitch-oscillations. The boundary layer evolution for a natural laminar flow airfoil undergoing forced small-amplitude pitch-oscillations is investigated at Rec = 7.5×105. Large changes in laminar-to-turbulent transition location are found throughout the pitch cycle which cause a non-linear aerodynamic force response. The origins of the non-linear unsteady aerodynamic response is explained on the basis of the phase-lagged quasi-steady evolution of the boundary layer. A simple empirical model is developed using the phase-lag concept to model the unsteady aerodynamic forces which fits the experimental data very well. On the other hand, the forced pitching investigation at Rec = 1.0×105 for the same airfoil found abrupt changes in transition during the pitch-cycle. A local stability analysis in the reverse flow region indicates that the stability characteristics of the LSB change character from convective to absolute, and it is conjectured that this change in stability characteristics may be the cause of abrupt changes inboundary-layertransition.

  • 233.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    Dynamic response of laminar flow airfoils2017Report (Other academic)
  • 234.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Linear and non-linear response of a laminar airfoil subject to small amplitude pitch-oscillationsManuscript (preprint) (Other academic)
  • 235.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics. Swedish e-Science Research Center (SeRC).
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics. Swedish e-Science Research Center (SeRC).
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Global Stability of rigid-body-motion fluid-structure-interaction problems2019Report (Other academic)
    Abstract [en]

    A rigorous derivation and validation for linear fluid-structure-interaction (FSI) equations for a rigid-body-motion problem is performed in an Eulerian framework. We show that the “added-stiffness” terms arising in the formulation of Fanion et al. (2000) vanish at the FSI interface in a first-order approximation. Several numerical tests with rigid-body motion are performed to show the validity of the derived formulation by comparing the time evolution between the linear and non-linear equations when the base flow is perturbed by identical small-amplitude perturbations. In all cases both the growth rate and angular frequency of the instability matches within 0.1% accuracy. The derived formulation is used to investigate the phenomenon of symmetry breaking for a rotating cylinder with an attached splitter-plate. The results show that the onset of symmetry breaking can be explained by the existence of a zero-frequency linearly unstable mode of the coupled fluid-structure-interaction system. Finally, the structural sensitivity of the least stable eigenvalue is studied for an oscillating cylinder, which is found to change significantly when the fluid and structural frequencies are close to resonance.

  • 236.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    On the onset of aeroelastic pitch-oscillations of aNACA0012 wing at transitional Reynolds numbersManuscript (preprint) (Other academic)
  • 237.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    A re-examination of filter-based stabilization for spectral-element methods2017Report (Other academic)
  • 238.
    Negi, Prabal Singh
    et al.
    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.
    Hanifi, Ardeshir
    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.
    Henningson, Dan S.
    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.
    LES of the unsteady response of a natural laminar flow airfoil2018In: 2018 Applied Aerodynamics Conference, American Institute of Aeronautics and Astronautics, 2018Conference paper (Refereed)
    Abstract [en]

    Large-eddy simulations are performed to investigate the dynamic response of a natural laminar flow airfoil undergoing harmonic pitch oscillations at a chord based Reynolds number of Rec= 750, 000. Large changes in the transition location are observed throughout the pitch cycles which leads to a non-linear response of the aerodynamic force coefficients. Preliminary results show that the evolution of the boundary layer over the airfoil can be modeled by using a simple phase-lag concept which implies that the boundary-layer evolution is quasi-steady in nature. A simple empirical model is developed based on this quasi-steady, phase-lag assumption which fits very well with the measured experimental data.

  • 239.
    Negi, Prabal Singh
    et al.
    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.
    Mishra, Maneesh
    Nanyang Technol Univ, Sch Mech & Aerosp Engn, Singapore 639798, Singapore..
    Schlatter, Philipp
    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.
    Skote, Martin
    Cranfield Univ, Sch Aerosp Transport & Mfg, Cranfield MK43 OAL, Beds, England..
    Bypass transition delay using oscillations of spanwise wall velocity2019In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 4, no 6, article id 063904Article in journal (Refereed)
    Abstract [en]

    Large eddy simulations are performed to investigate the possibility of bypass transition delay in spatially developing boundary layers. An open loop wall control mechanism is employed which consists of either spatial or temporal oscillations of the spanwise wall velocity. Both spatial and temporal oscillations show a delay in the sharp rise in skin friction coefficient which is characteristic of laminar-turbulent transition. An insight into the mechanism is offered based on a secondary filtering of the continuous Orr-Sommerfeld-Squire (OSQ) modes provided by the Stokes layer, and it is shown that the control mechanism selectively affects the low-frequency penetrating modes of the OSQ spectrum. This perspective clarifies the limitations of the mechanism's capability to create transition delay. Furthermore, we extend the two-mode model of bypass transition proposed by T. Zaki and P. Durbin [j Fluid Mech. 531, 85 (2005)] to cases with wall control and illustrate the selective action of the wall oscillations on the penetrating mode in this simplified case.

  • 240.
    Negi, Prabal Singh
    et al.
    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.
    Vinuesa, Ricardo
    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.
    Hanifi, Ardeshir
    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.
    Schlatter, Philipp
    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.
    Henningson, Dan S.
    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.
    Unsteady aerodynamic effects in small-amplitude pitch oscillations of an airfoil2018In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 71, p. 378-391Article in journal (Refereed)
    Abstract [en]

    High-fidelity wall-resolved large-eddy simulations (LES) are utilized to investigate the flow-physics of small-amplitude pitch oscillations of an airfoil at Rec=100,000. The investigation of the unsteady phenomenon is done in the context of natural laminar flow airfoils, which can display sensitive dependence of the aerodynamic forces on the angle of attack in certain “off-design” conditions. The dynamic range of the pitch oscillations is chosen to be in this sensitive region. Large variations of the transition point on the suction-side of the airfoil are observed throughout the pitch cycle resulting in a dynamically rich flow response. Changes in the stability characteristics of a leading-edge laminar separation bubble has a dominating influence on the boundary layer dynamics and causes an abrupt change in the transition location over the airfoil. The LES procedure is based on a relaxation-term which models the dissipation of the smallest unresolved scales. The validation of the procedure is provided for channel flows and for a stationary wing at Rec=400,000.

  • 241.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Philipp, Schlatter
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center (SeRC).
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Unsteady aerodynamic effects in small-amplitude pitch oscillations of an airfoilManuscript (preprint) (Other academic)
  • 242.
    Negi, Prabal
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Unsteady aerodynamic effects in small-amplitude pitch oscillations of anairfoil2018In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 71, p. 378-391Article in journal (Refereed)
  • 243.
    Niazi Ardekani, Mehdi
    et al.
    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.
    Abouali, Omid
    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. School of Mechanical Engineering, Shiraz University.
    Picano, Francesco
    University of Padova, Department of Industrial Engineering.
    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.
    Heat transfer in laminar Couette flow laden with rigid spherical particles2018In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 834, p. 308-334Article in journal (Refereed)
    Abstract [en]

    We study heat transfer in plane Couette flow laden with rigid spherical particles by means of direct numerical simulations. In the simulations we use a direct-forcing immersed boundary method to account for the dispersed phase together with a volume-of-fluid approach to solve the temperature field inside and outside the particles. We focus on the variation of the heat transfer with the particle Reynolds number, total volume fraction (number of particles) and the ratio between the particle and fluid thermal diffusivity, quantified in terms of an effective suspension diffusivity. We show that, when inertia at the particle scale is negligible, the heat transfer increases with respect to the unladen case following an empirical correlation recently proposed in the literature. In addition, an average composite diffusivity can be used to approximate the effective diffusivity of the suspension in the inertialess regime when varying the molecular diffusion in the two phases. At finite particle inertia, however, the heat transfer increase is significantly larger, smoothly saturating at higher volume fractions. By phase-ensemble-averaging we identify the different mechanisms contributing to the total heat transfer and show that the increase of the effective conductivity observed at finite inertia is due to the increase of the transport associated with fluid and particle velocity. We also show that the contribution of the heat conduction in the solid phase to the total wall-normal heat flux reduces when increasing the particle Reynolds number, so that particles of low thermal diffusivity weakly alter the total heat flux in the suspension at finite particle Reynolds numbers. On the other hand, a higher particle thermal diffusivity significantly increases the total heat transfer.

  • 244.
    Niazi Ardekani, Mehdi
    et al.
    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.
    Asmar, L. A.
    Picano, F.
    Brandt, L.uca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Numerical study of heat transfer in laminar and turbulent pipe flow with finite-size spherical particles2018In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 71, p. 189-199Article in journal (Refereed)
    Abstract [en]

    Controlling heat and mass transfer in particulate suspensions has many applications in fuel combustion, food industry, pollution control and life science. We perform direct numerical simulations (DNS) to study the heat transfer within a suspension of neutrally buoyant, finite-size spherical particles in laminar and turbulent pipe flows, using the immersed boundary method (IBM) to account for the solid fluid interactions and a volume of fluid (VoF) method to resolve the temperature equation both inside and outside the particles. Particle volume fractions up to 40% are simulated for different pipe to particle diameter ratios. We show that a considerable heat transfer enhancement (up to 330%) can be achieved in the laminar regime by adding spherical particles. The heat transfer is observed to increase significantly as the pipe to particle diameter ratio decreases for the parameter range considered here. Larger particles are found to have a greater impact on the heat transfer enhancement than on the wall-drag increase. In the turbulent regime, however, only a transient increase in the heat transfer is observed and the process decelerates in time below the values in single-phase flows as high volume fractions of particles laminarize the core region of the pipe. A heat transfer enhancement, measured with respect to the single phase flow, is only achieved at volume fractions as low as 5% in a turbulent flow.

  • 245.
    Niazi Ardekani, Mehdi
    et al.
    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.
    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.
    Turbulence modulation in channel flow of finite-size spheroidal particles2018In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 859, p. 887-901Article in journal (Refereed)
    Abstract [en]

    Finite-size particles modulate wall-bounded turbulence, leading, for the case of spherical particles, to increased drag also owing to the formation of a particle wall layer. Here, we study the effect of particle shape on the turbulence in suspensions of spheroidal particles at volume fraction phi = 10 % and show how the near-wall particle dynamics deeply changes with the particle aspect ratio and how this affects the global suspension behaviour. Direct numerical simulations are performed using a direct-forcing immersed boundary method to account for the dispersed phase, combined with a soft-sphere collision model and lubrication corrections for short-range particle-particle and particle-wall interactions. The turbulence reduces with the aspect ratio of oblate particles, leading to drag reduction with respect to the single-phase flow for particles with aspect ratio AR <= 1/3, when the significant reduction in Reynolds shear stress is more than the compensation by the additional stresses, induced by the solid phase. Oblate particles are found to avoid the region close to the wall, travelling parallel to it with small angular velocities, while preferentially sampling high-speed fluid in the wall region. Prolate particles also tend to orient parallel to the wall and avoid its vicinity. Their reluctance to rotate around the spanwise axis reduces the wall-normal velocity fluctuation of the flow and therefore the turbulence Reynolds stress, similar to oblates; however, they undergo rotations in wall-parallel planes which increase the additional solid stresses due to their relatively larger angular velocities compared to the oblates. These larger additional stresses compensate for the reduction in turbulence activity and lead to a wall drag similar to that of single-phase flows. Spheres on the other hand, form a layer close to the wall with large angular velocities in the spanwise direction, which increases the turbulence activity in addition to exerting the largest solid stresses on the suspension, in comparison to the other studied shapes. Spherical particles therefore increase the wall drag with respect to the single-phase flow.

  • 246.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Costa, Pedro
    Breugem, Wim Paul
    Picano, Francesco
    University of Padova, Department of Industrial Engineering.
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Drag reduction in turbulent channel flow laden with finite-size oblate spheroids2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 816, p. 43-70Article in journal (Refereed)
    Abstract [en]

    We study suspensions of oblate rigid particles in a viscous fluid for different values of the particle volume fractions.Direct numerical simulations have been performed using a direct-forcing immersed boundary method to account for the dispersed phase, combined with a soft-sphere collision model and lubrication corrections for short-range particle-particle and particle-wall interactions. With respect to the single phase flow, we show that in flows laden with oblate spheroids the drag is reduced and the turbulent fluctuations attenuated.In particular, the turbulence activity decreases to lower values than those obtained by only accounting for the effective suspension viscosity.To explain the observed drag reduction we consider the particle dynamics and the interactions of the particles with the turbulent velocity field and show that the particle wall layer, previously observed and found to be responsible for the increased dissipation in suspensions of spheres, disappears in the case of oblate particles.These rotate significantly slower than spheres near the wall and tend to stay with their major axes parallel to the wall, which leads to a decrease of the Reynolds stresses and turbulence production and so to the overall drag reduction.

  • 247.
    Niazi Ardekani, Mehdi
    et al.
    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.
    Rosti, Marco E.
    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.
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics.
    Turbulent  flow of finite-size spherical particles with viscous hyper-elastic walls2018In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Article in journal (Other academic)
  • 248.
    Niazi Ardekani, Mehdi
    et al.
    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.
    Rosti, Marco Edoardo
    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.
    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.
    Turbulent flow of finite-size spherical particles in channels with viscous hyper-elastic walls2019In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 873, p. 410-440, article id PII S0022112019004130Article in journal (Refereed)
    Abstract [en]

    We study single-phase and particle-laden turbulent channel flows bounded by two incompressible hyper-elastic walls with different deformability at bulk Reynolds number $5600$ . The solid volume fraction of finite-size neutrally buoyant rigid spherical particles considered is $10\,\%$ . The elastic walls are assumed to be of a neo-Hookean material. A fully Eulerian formulation is employed to model the elastic walls together with a direct-forcing immersed boundary method for the coupling between the fluid and the particles. The data show a significant drag increase and the enhancement of the turbulence activity with growing wall elasticity for both the single-phase and particle-laden flows when compared with the single-phase flow over rigid walls. Drag reduction and turbulence attenuation is obtained, on the other hand, with highly elastic walls when comparing the particle-laden flow with the single-phase flow for the same wall properties; the opposite effect, drag increase, is observed upon adding particles to the flow over less elastic walls. This is explained by investigating the near-wall turbulence, where the strong asymmetry in the magnitude of the wall-normal velocity fluctuations (favouring positive $v<^>{\prime }$ ), is found to push the particles towards the channel centre. The particle layer close to the wall contributes to turbulence production by increasing the wall-normal velocity fluctuations, so that in the absence of this layer, smaller wall deformations and in turn turbulence attenuation is observed. For a moderate wall elasticity, we increase the particle volume fraction up to $20\,\%$ and find that particle migration away from the wall is the cause of turbulence attenuation with respect to the flow over rigid walls. However, for this higher volume fractions, the particle induced stress compensates for the decreasing Reynolds shear stress, resulting in a higher overall drag for the case with elastic walls. The effect of the wall elasticity on the overall drag reduces significantly with increasing particle volume fraction.

  • 249.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Sardina, Gaetano
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Karp-Boss, Lee
    School of Marine Sciences, University of Maine.
    Bearon, Rachel
    Department of Mathematical Sciences, University of Liverpool.
    Variano, Evan
    Department of Civil and Environmental Engineering, University of California.
    Sedimentation of inertia-less prolate spheroids in homogenous isotropic turbulence with application to non-motile phytoplankton2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 831, p. 655-674Article in journal (Refereed)
    Abstract [en]

    Phytoplankton are the foundation of aquatic food webs. Through photosynthesis, phytoplankton draw down $CO_2$ at magnitudes equivalent to forests and other terrestrial plants and convert it to organic material that is then consumed by other organisms of phytoplankton in higher trophic levels. Mechanisms that affect local concentrations and velocities are of primary significance to many encounter-based processes in the plankton including prey-predator interactions, fertilization and aggregate formation. We report results from simulations of sinking phytoplankton, considered as elongated spheroids, in homogenous isotropic turbulence to answer the question of whether trajectories and velocities of sinking phytoplankton are altered by turbulence. We show in particular that settling spheroids with physical characteristics similar to those of diatoms weakly cluster and preferentially sample regions of down-welling flow, corresponding to an increase of the mean settling speed with respect to the mean settling speed in quiescent fluid.  We explain how different parameters can affect the settling speed and what underlying mechanisms might be involved.  Interestingly, we observe that the increase in the aspect ratio of the prolate spheroids can affect the clustering and the average settling speed of particles by two mechanisms: first is the effect of aspect ratio on the rotation rate of the particles, which saturates faster than the second mechanism of increasing drag anisotropy.   

  • 250. Nogueira, P. A. S.
    et al.
    Cavalieri, A. V. G.
    Hanifi, Ardeshir
    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.
    Henningson, Dan S.
    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.
    Resolvent-based control of streaks in boundary layers2018In: 31st Congress of the International Council of the Aeronautical Sciences, ICAS 2018, International Council of the Aeronautical Sciences , 2018Conference paper (Refereed)
    Abstract [en]

    In the present work, we investigate efficient placement of sensors and actuators for closed-loop control of boundary-layer flows. The focus of this work is on the transitional flow cases where perturbation field is dominated by streaks. This is done using a reduced-order model based on resolvent analysis, an approach that also allows us to analyse the sensitivity of the flow response to control. A numerical sensitivity analysis was performed in this first approach, leading to conclusions about best choices of velocity components to be sensed and directions to be forced. Afterwards, we compared the performance between gaussian and shear sensors at the wall, focusing on the damping of the first resolvent gain using these devices. We close the work with the analysis of a plasma actuator, a configuration closer to standard choices for this kind of problem in both simulations and experiments. 

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