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  • 251.
    Parviainen, Pekka
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Farahani, H. S.
    Lagergren, Jens
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Learning bounded tree-width Bayesian networks using integer linear programming2014Ingår i: Journal of machine learning research, ISSN 1532-4435, E-ISSN 1533-7928, Vol. 33, s. 751-759Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In many applications one wants to compute conditional probabilities given a Bayesian network. This inference problem is NP-hard in general but becomes tractable when the network has low tree-width. Since the inference problem is common in many application areas, we provide a practical algorithm for learning bounded tree-width Bayesian networks. We cast this problem as an integer linear program (ILP). The program can be solved by an anytime algorithm which provides upper bounds to assess the quality of the found solutions. A key component of our program is a novel integer linear formulation for bounding tree-width of a graph. Our tests clearly indicate that our approach works in practice, as our implementation was able to find an optimal or nearly optimal network for most of the data sets.

  • 252. Paul, S.
    et al.
    Iuşan, D.
    Thunström, P.
    Kvashnin, Y. O.
    Hellsvik, Johan
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Material- och nanofysik.
    Pereiro, M.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Knut, R.
    Phuyal, D.
    Lindblad, A.
    Karis, O.
    Sanyal, B.
    Eriksson, O.
    Investigation of the spectral properties and magnetism of BiFeO3 by dynamical mean-field theory2018Ingår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 97, nr 12, artikel-id 125120Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Using the local density approximation plus dynamical mean-field theory (LDA+DMFT), we have computed the valence-band photoelectron spectra and magnetic excitation spectra of BiFeO3, one of the most studied multiferroics. Within the DMFT approach, the local impurity problem is tackled by the exact diagonalization solver. The solution of the impurity problem within the LDA+DMFT method for the paramagnetic and magnetically ordered phases produces result in agreement with the experimental data on electronic and magnetic structures. For comparison, we also present results obtained by the LDA+U approach which is commonly used to compute the physical properties of this compound. Our LDA+DMFT derived electronic spectra match adequately with the experimental hard x-ray photoelectron spectroscopy and resonant photoelectron spectroscopy for Fe 3d states, whereas the LDA+U method fails to capture the general features of the measured spectra. This indicates the importance of accurately incorporating the dynamical aspect of electronic correlation among Fe 3d orbitals to reproduce the experimental excitation spectra. Specifically, the LDA+DMFT derived density of states exhibits a significant amount of Fe 3d states at the position of Bi lone pairs, implying that the latter are not alone in the spectral scenario. This fact might modify our interpretation about the origin of ferroelectric polarization in this material. Our study demonstrates that the combination of orbital cross sections for the constituent elements and broadening schemes for the spectral functions are crucial to explain the detailed structures of the experimental electronic spectra. Our magnetic excitation spectra computed from the LDA+DMFT result conform well with the inelastic neutron scattering data.

  • 253.
    Peplinski, Adam
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Global stability and optimal perturbation for a jet in cross-flow2015Ingår i: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 49, s. 438-447Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study the stability of a jet in cross-flow at low values of the jet to cross-flow velocity ratio R using direct numerical simulations (DNS) and global linear stability analysis adopting a time-stepper method. For the simplified setup without a meshed pipe in the simulations we compare results of a fully-spectral code SIMSON with a spectral-element code Nek5000. We find the use of periodic domains, even with the fringe method, unsuitable due to the large sensitivity of the eigenvalues and due to the large spatial growth of the corresponding eigenmodes. However, we observe a similar sensitivity to reflection from the outflow boundary in the inflow/outflow configuration, and therefore we use an extended domain where reflections are minimal. We apply in our studies both modal and non-modal linear analyses investigating transient effects and their asymptotic fate, and we find a transient wavepacket to develop almost identically in both the globally stable and unstable cases. The final results of the global stability analysis for our numerical setup show the critical value of R, at which the first bifurcation occurs, to lie in the range between 1.5 and 1.6.

  • 254.
    Peplinski, Adam
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Investigations of stability and transition of a jet in crossflow using DNS2015Ingår i: Instability and Control of Massively Separated Flows: Proceedings of the International Conference on Instability and Control of Massively Separated Flows, held in Prato, Italy, from 4-6 September 2013, Kluwer Academic Publishers, 2015, Vol. 107, s. 7-18Konferensbidrag (Refereegranskat)
    Abstract [en]

    We study the stability of a jet in crossflow at low values of the jet-tocrossflow velocity ratio R focusing on direct numerical simulations (DNS) and the global linear stability analysis adopting a time-stepper method. For the simplified setup neglecting a meshed pipe in the simulations, we compare results of the fullyspectral code SIMSON with the spectral-element code Nek5000. We find the calculated critical value R for the first bifurcation to be dependent on the numerical method used. This result is related to a large sensitivity of the eigenvalues and to the large spatial growth of the corresponding eigenmodes, making the use of periodic domains, even with the fringe method, difficult. However, we observe a similar sensitivity to reflection from the outflow boundary in the inflow/outflow configuration as well.We apply in our studies both modal and non-modal analyses investigating transient effects and their asymptotic fate, and we find transient wavepacket that develop almost identically in the stable and unstable cases. Finally, we compare these results with the simulation including the pipe in the computational domain finding the latter one to be much more unstable.

  • 255. Peters, Lars
    et al.
    Ghosh, Saurabh
    Sanyal, Biplab
    van Dijk, Chris
    Bowlan, John
    de Heer, Walt
    Delin, Anna
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. Uppsala Universitet, Sweden.
    Di Marco, Igor
    Eriksson, Olle
    Katsnelson, Mikhail I.
    Johansson, Borje
    Kirilyuk, Andrei
    Magnetism and exchange interaction of small rare-earth clusters; Tb as a representative2016Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikel-id 19676Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Here we follow, both experimentally and theoretically, the development of magnetism in Tb clusters from the atomic limit, adding one atom at a time. The exchange interaction is, surprisingly, observed to drastically increase compared to that of bulk, and to exhibit irregular oscillations as a function of the interatomic distance. From electronic structure theory we find that the theoretical magnetic moments oscillate with cluster size in exact agreement with experimental data. Unlike the bulk, the oscillation is not caused by the RKKY mechanism. Instead, the inter-atomic exchange is shown to be driven by a competition between wave-function overlap of the 5d shell and the on-site exchange interaction, which leads to a competition between ferromagnetic double-exchange and antiferromagnetic super-exchange. This understanding opens up new ways to tune the magnetic properties of rare-earth based magnets with nano-sized building blocks.

  • 256. Picano, F.
    et al.
    Costa, P.
    Breugem, W. -P
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Turbulence modulation by dense suspensions in channel flows2017Ingår i: 10th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2017, International Symposium on Turbulence and Shear Flow Phenomena, TSFP10 , 2017, Vol. 1Konferensbidrag (Refereegranskat)
    Abstract [en]

    Dense suspensions are usually investigated in the laminar limit where inertial effects are insignificant. In this regime, the main effect of the suspended phase is to alter the rheological behavior of the flow which always displays higher effective viscosity with respect to the carrier fluid. When the flow rate is high enough, i.e. at high Reynolds number, the flow may become turbulent and the interaction between solid and liquid phase modifies the turbulent dynamics that we know in single-phase fluids. In the present work, we study turbulent channel flows laden with finite-size particles at high volume fraction (F = 0:2) by means of Direct Numerical Simulations. A direct-forcing Immersed Boundary Method has been adopted to couple liquid and solid phases. The two-phase simulations have been performed fixing the bulk Reynolds number at Reb = Ub 2h=n = 12000 (Ub bulk velocity, h channel half-width and n the fluid kinematic viscosity). The particle size is relatively large with respect to the viscous length, i.e. 10 and 20 times, but smaller than large scales. We will present a detailed comparison of the statistical behavior of the particle-laden flow and the corresponding single-phase flow. The presence of the solid phase strongly alters the wall turbulence dynamics and its effect cannot be accounted only considering the higher rheological effective viscosity.

  • 257.
    Picano, Francesco
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Turbulent channel flow of dense suspensions of neutrally buoyant spheres2015Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 764, s. 463-487Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dense particle suspensions are widely encountered in many applications and in environmental flows. While many previous studies investigate their rheological properties in laminar flows, little is known on the behaviour of these suspensions in the turbulent/inertial regime. The present study aims to fill this gap by investigating the turbulent flow of a Newtonian fluid laden with solid neutrally-buoyant spheres at relatively high volume fractions in a plane channel. Direct numerical simulation (DNS) are performed in the range of volume fractions Phi=0-0.2 with an immersed boundary method (IBM) used to account for the dispersed phase. The results show that the mean velocity profiles are significantly altered by the presence of a solid phase with a decrease of the von Karman constant in the log-law. The overall drag is found to increase with the volume fraction, more than one would expect if just considering the increase of the system viscosity due to the presence of the particles. At the highest volume fraction investigated here, Phi = 0.2, the velocity fluctuation intensities and the Reynolds shear stress are found to decrease. The analysis of the mean momentum balance shows that the particle-induced stresses govern the dynamics at high Phi and are the main responsible of the overall drag increase. In the dense limit, we therefore find a decrease of the turbulence activity and a growth of the particle induced stress, where the latter dominates for the Reynolds numbers considered here.

  • 258.
    Picano, Francesco
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    Mitra, Dhrubaditya
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Shear Thickening in Non-Brownian Suspensions: An Excluded Volume Effect2013Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 111, nr 9, s. 098302-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Shear thickening appears as an increase of the viscosity of a dense suspension with the shear rate, sometimes sudden and violent at high volume fraction. Its origin for noncolloidal suspension with non-negligible inertial effects is still debated. Here we consider a simple shear flow and demonstrate that fluid inertia causes a strong microstructure anisotropy that results in the formation of a shadow region with no relative flux of particles. We show that shear thickening at finite inertia can be explained as an increase of the effective volume fraction when considering the dynamically excluded volume due to these shadow regions.

  • 259. Popovic, Jelena
    et al.
    Runborg, Olof
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.).
    Adaptive fast interface tracking methods2017Ingår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 337, s. 42-61Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this paper, we present a fast time adaptive numerical method for interface tracking. The method uses an explicit multiresolution description of the interface, which is represented by wavelet vectors that correspond to the details of the interface on different scale levels. The complexity of standard numerical methods for interface tracking, where the interface is described by N marker points, is 0 (N/Delta t),when a time step At is used. The methods that we propose in this paper have 0 (TOL-1/P log N + N log N) computational cost, at least for uniformly smooth problems, where TOL is some given tolerance and p is the order of the time stepping method that is used for time advection of the interface. The adaptive method is robust in the sense that it can handle problems with both smooth and piecewise smooth interfaces (e.g. interfaces with corners) while keeping a low computational cost. We show numerical examples that verify these properties.

  • 260.
    Poppi, Stefano
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Energiteknik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Dalarna University, Sweden.
    Bales, Chris
    Techno-Economic Analysis of a Novel Solar Thermal and Air-Source Heat Pump System2016Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    This paper presents a techno-economic analysis of a novel solar thermal and air source heat pump system. The system was designed for relatively high operating temperatures in the space heating circuit and included the use of a heat pump with vapor injection cycle and vacuum insulation on the storage tank. The system model was validated against measurements in laboratory and simulated in TRNSYS 17. Annual simulations were performed for the combination of two climates (Carcassonne and Zurich) and two house standards (SFH45 and SFH100) and the best results were achieved for the boundary conditions the system was designed for. For those conditions (Zurich and SFH100), the novel system showed potential for being cost-effective compared to state of art solar and heat pump system. The “additional investment limit”, i.e. the maximum extra investment cost for the novel system in comparison to a state of art benchmark system that gives a break even result for a period of 10 years, varied between 827 € and 2482 € depending on electricity price. The results of a sensitivity analysis showed that variations in electricity price affected the additional investment limit far more than the other economic parameters.

  • 261.
    Poppi, Stefano
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Energiteknik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Dalarna University, Sweden.
    Sommerfeldt, Nelson
    KTH, Skolan för industriell teknik och management (ITM), Energiteknik.
    Bales, Chris
    Madani, Hatef
    KTH, Skolan för industriell teknik och management (ITM), Energiteknik, Tillämpad termodynamik och kylteknik.
    Lundqvist, Per
    KTH, Skolan för industriell teknik och management (ITM), Energiteknik, Tillämpad termodynamik och kylteknik.
    Techno-economic review of solar heat pump systems for residential heating applications2018Ingår i: Renewable & sustainable energy reviews, ISSN 1364-0321, E-ISSN 1879-0690, Vol. 81, s. 22-32Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Solar heat pump systems (SHPs) have been investigated for several decades and have been proven to increase the share of renewable energy and reduce electric energy demand in residential heating applications. Many review articles have been published on the subject, however literature discussing the techno-economics of different solar technologies (thermal, photovoltaic and hybrid thermal/photovoltaic) in combination with heat pumps is lacking, and thus to directly compare the merits of different SHPs is not an easy task. The objectives of this study are: a) review the different system boundaries and the main performance indicators used for assessing energetic and economic performances; b) review techno-economic studies in the literature and identify which studies give enough information and are compatible enough for making an economic inter-comparison; c) present an economic inter-comparison based on the identified systems. The results show that there is a lack of studies including an economic assessment of solar photovoltaic and heat pump systems. Additionally, there are no consistent boundaries or approaches to the study structures, making comparisons between systems difficult. In conclusion, a standardized or broadly accepted definition of technical and economic performance for SHPs is needed. Despite this, the study has shown that there are clear trends for decreasing payback times for SHPs, both solar thermal (ST) and photovoltaic (PV), with decreasing heating degree-days and with increasing solar resource.

  • 262.
    Pouya, Iman
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Pronk, Sander
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lundborg, M.
    Lindahl, Erik R.
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling2017Ingår i: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 71, s. 18-31Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Compute-intensive applications have gradually changed focus from massively parallel supercomputers to capacity as a resource obtained on-demand. This is particularly true for the large-scale adoption of cloud computing and MapReduce in industry, while it has been difficult for traditional high-performance computing (HPC) usage in scientific and engineering computing to exploit this type of resources. However, with the strong trend of increasing parallelism rather than faster processors, a growing number of applications target parallelism already on the algorithm level with loosely coupled approaches based on sampling and ensembles. While these cannot trivially be formulated as MapReduce, they are highly amenable to throughput computing. There are many general and powerful frameworks, but in particular for sampling-based algorithms in scientific computing there are some clear advantages from having a platform and scheduler that are highly aware of the underlying physical problem. Here, we present how these challenges are addressed with combinations of dataflow programming, peer-to-peer techniques and peer-to-peer networks in the Copernicus platform. This allows automation of sampling-focused workflows, task generation, dependency tracking, and not least distributing these to a diverse set of compute resources ranging from supercomputers to clouds and distributed computing (across firewalls and fragile networks). Workflows are defined from modules using existing programs, which makes them reusable without programming requirements. The system achieves resiliency by handling node failures transparently with minimal loss of computing time due to checkpointing, and a single server can manage hundreds of thousands of cores e.g. for computational chemistry applications.

  • 263.
    Pronk, Sander
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Pouya, Iman
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lundborg, Magnus
    Rotskoff, Grant
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Wesén, Björn
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Kasson, Peter M.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 6, s. 2600-2608Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide mote processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  • 264.
    Páll, Szilard
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    A flexible algorithm for calculating pair interactions on SIMD architectures2013Ingår i: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 184, nr 12, s. 2641-2650Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have traditionally worked well, especially since compilers usually do a good job of unrolling the inner loop. In order to reach high performance on modern CPU and accelerator architectures, single-instruction multiple-data (SIMD) parallelization has become essential. Avoiding memory bottlenecks is also increasingly important and requires reducing the ratio of memory to arithmetic operations. Moreover, when pairs only interact within a certain cut-off distance, good SIMD utilization can only be achieved by reordering input and output data, which quickly becomes a limiting factor. Here we present an algorithm for SIMD parallelization based on grouping a fixed number of particles, e.g. 2, 4, or 8, into spatial clusters. Calculating all interactions between particles in a pair of such clusters improves data reuse compared to the traditional scheme and results in a more efficient SIMD parallelization. Adjusting the cluster size allows the algorithm to map to SIMD units of various widths. This flexibility not only enables fast and efficient implementation on current CPUs and accelerator architectures like GPUs or Intel MIC, but it also makes the algorithm future-proof. We present the algorithm with an application to molecular dynamics simulations, where we can also make use of the effective buffering the method introduces.

  • 265.
    Quaranta, Hugo Umberto
    et al.
    Airbus Helicopters, Aerodynamics Department, Marignane, France.
    Brynjell-Rahkola, Mattias
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Leweke, Thomas
    CNRS, Aix-Marseille Universit ́e, Centrale Marseille, IRPHE, Marseille, France.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Long-wave instabilities of two interlaced helical vortices2017Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    We investigate theoretically and experimentally the stability of two interlaced helical vortices with respect to displacement perturbations having wavelengths that are large compared to the size of the vortex cores. First, existing theoretical results are recalled and applied to the present configuration. Various modes of unstable perturbations, involving different phase relationships between the two vortices, are identified and their growth rates are calculated. They lead to a local pairing of neighbouring helix loops, or to a uniform pairing with one helix expanding and the other one contracting. A relation is established between this instability and the three-dimensional pairing of arrays of straight parallel vortices, and a striking quantitative agreement concerning the growth rates is found, showing that the local pairing of vortices is the driving mechanism behind the instability of the helix system. Second, an experimental study designed to observe these instabilities in a real flow is presented. Two helical vortices are generated by a two-bladed rotor in a water channel and characterised through dye visualisations and PIV measurements. Unstable displacement modes are triggered individually, either by varying the rotation frequency of the rotor, or by imposing a small rotor eccentricity. The observed unstable mode structure, and the corresponding growth rates obtained from advanced processing of visualisation sequences, are in good agreement with theoretical predictions. The non-linear late stages of the instability are also documented experimentally. Whereas local pairing leads to strong deformations and subsequent break-up of the vortices, uniform pairing results in a leapfrogging phenomenon, which intermittently restores the initial double-helix geometry, in agreement with recent observations from numerical simulations.

  • 266.
    Rasam, Amin
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Farkost och flyg.
    Wallin, Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brethouwer, Gert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Johansson, Arne V.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Large-eddy simulation using the explicit algebraic subgrid model in complex geometries2013Ingår i: International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2013, TSFP-8 , 2013Konferensbidrag (Refereegranskat)
    Abstract [en]

    In Rasam et al. (2011) we compared the performance of the explicit algebraic subgrid-scale (SGS) model (EASSM) (Marstorp et al., 2009) with that of the conventional dynamic Smagorinsky model (DSM) in large eddy simulation (LES) of channel flow using a pseudo-spectral Navier-Stokes solver. We showed that, due to the better prediction of the individual SGS stresses in a wide range of grid resolutions and due to the nonlinear SGS stress contribution by the model, the EASSM predictions were less resolution dependent and more accurate than those of the DSM. As the first step in this study towards LES in complex geometries, we extend our previous study and perform LES of turbulent channel flow at Ret = 590 using the EASSM and the code Saturne, which is an unstructured finite volume solver suitable for LES in complex geometries. The results are compared to those of the DSM and show that the EASSM predictions of the wall shear and the Reynolds stresses are more accurate. LES results using the EASSM obtained from the code Saturne are also compared to those obtained using the pseudo-spectral solver obtained in our previous study (Rasam et al., 2013). As the next step, we are performing LES of flow over periodic hill using the EASSM and the code Saturne. The results will be compared with those of the DSM and the reference LES and will be presented at the conference.

  • 267.
    Ray, Arjun
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Wallner, B.
    Improved model quality assessment using ProQ22012Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 13, nr 1, s. 224-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Employing methods to assess the quality of modeled protein structures is now standard practice in bioinformatics. In a broad sense, the techniques can be divided into methods relying on consensus prediction on the one hand, and single-model methods on the other. Consensus methods frequently perform very well when there is a clear consensus, but this is not always the case. In particular, they frequently fail in selecting the best possible model in the hard cases (lacking consensus) or in the easy cases where models are very similar. In contrast, single-model methods do not suffer from these drawbacks and could potentially be applied on any protein of interest to assess quality or as a scoring function for sampling-based refinement.Results: Here, we present a new single-model method, ProQ2, based on ideas from its predecessor, ProQ. ProQ2 is a model quality assessment algorithm that uses support vector machines to predict local as well as global quality of protein models. Improved performance is obtained by combining previously used features with updated structural and predicted features. The most important contribution can be attributed to the use of profile weighting of the residue specific features and the use features averaged over the whole model even though the prediction is still local.Conclusions: ProQ2 is significantly better than its predecessors at detecting high quality models, improving the sum of Z-scores for the selected first-ranked models by 20% and 32% compared to the second-best single-model method in CASP8 and CASP9, respectively. The absolute quality assessment of the models at both local and global level is also improved. The Pearson's correlation between the correct and local predicted score is improved from 0.59 to 0.70 on CASP8 and from 0.62 to 0.68 on CASP9; for global score to the correct GDT_TS from 0.75 to 0.80 and from 0.77 to 0.80 again compared to the second-best single methods in CASP8 and CASP9, respectively. ProQ2 is available at http://proq2.wallnerlab.org.

  • 268. Ren, J.
    et al.
    Fu, S.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish Defence Research Agency.
    Stabilization of the hypersonic boundary layer by finite-amplitude streaks2016Ingår i: 54th AIAA Aerospace Sciences Meeting, 2016Konferensbidrag (Refereegranskat)
    Abstract [en]

    Stabilization of two-dimensional disturbances in hypersonic boundary layer flows by finite-amplitude streaks is investigated using nonlinear parabolized stability equations. The boundary-layer flows at Mach numbers 4.5 and 6.0 are studied in which both the first-and second modes are supported. The streaks considered here are driven either by the so-called optimal perturbations (Klebanoff-type) or the centrifugal instability (Görtler-type). When the streak amplitude is in an appropriate range, i.e., large enough to modulate the laminar boundary layer but low enough to not trigger secondary instability, both the first-and second modes can effectively be suppressed.

  • 269. Ren, Jie
    et al.
    Fu, Song
    Hanifi, Ardeshir
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. Swedish Def Res Agcy FOI, Stockholm, Sweden.
    Stabilization of the hypersonic boundary layer by finite-amplitude streaks2016Ingår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 28, nr 2, artikel-id 024110Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Stabilization of two-dimensional disturbances in hypersonic boundary layer flows by finite-amplitude streaks is investigated using nonlinear parabolized stability equations. The boundary-layer flows at Mach numbers 4.5 and 6.0 are studied in which both first and second modes are supported. The streaks considered here are driven either by the so-called optimal perturbations (Klebanoff-type) or the centrifugal instability (Gortler-type). When the streak amplitude is in an appropriate range, i.e., large enough to modulate the laminar boundary layer but low enough to not trigger secondary instability, both first and second modes can effectively be suppressed. (C) 2016 AIP Publishing LLC.

  • 270. Rezaeiravesh, S.
    et al.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Liefvendahl, M.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Assessment of uncertainties in hot-wire anemometry and oil-film interferometry measurements for wall-bounded turbulent flows2018Ingår i: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 72, s. 57-73Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study, the sources of uncertainty of hot-wire anemometry (HWA) and oil-film interferometry (OFI) measurements are assessed. Both statistical and classical methods are used for the forward and inverse problems, so that the contributions to the overall uncertainty of the measured quantities can be evaluated. The correlations between the parameters are taken into account through the Bayesian inference with error-in-variable (EiV) model. In the forward problem, very small differences were found when using Monte Carlo (MC), Polynomial Chaos Expansion (PCE) and linear perturbation methods. In flow velocity measurements with HWA, the results indicate that the estimated uncertainty is lower when the correlations among parameters are considered, than when they are not taken into account. Moreover, global sensitivity analyses with Sobol indices showed that the HWA measurements are most sensitive to the wire voltage, and in the case of OFI the most sensitive factor is the calculation of fringe velocity. The relative errors in wall-shear stress, friction velocity and viscous length are 0.44%, 0.23% and0.22%, respectively. Note that these values are lower than the ones reported in other wall-bounded turbulence studies. Note that in most studies of wall-bounded turbulence the correlations among parameters are not considered, and the uncertainties from the various parameters are directly added when determining the overall uncertainty of the measured quantity. In the present analysis we account for these correlations, which may lead to a lower overall uncertainty estimate due to error cancellation Furthermore, our results also indicate that the crucial aspect when obtaining accurate inner-scaled velocity measurements is the wind-tunnel flow quality, which is more critical than the accuracy in wall-shear stress measurements.

  • 271.
    Rinaldi, Enrico
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Patel, A.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Pecnik, R.
    Linear stability of buffer layer streaks in turbulent channels with variable density and viscosity2017Ingår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 2, nr 11, artikel-id 113903Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We investigate the stability of streaks in the buffer layer of turbulent channel flows with temperature-dependent density and viscosity by means of linear theory. The adopted framework consists of an extended set of the Orr-Sommerfeld-Squire equations that accounts for density and viscosity nonuniformity in the direction normal to the walls. The base flow profiles for density, viscosity, and velocity are averaged from direct numerical simulations (DNSs) of fully developed turbulent channel flows. We find that the inner scaling based on semilocal quantities provides an effective parametrization of the effect of variable properties on the linearized flow. The spanwise spacing of optimal buffer layer streaks scales to λz,opt≈90 for all cases considered and the maximum energy amplification decreases, compared to the one for a flow with constant properties, if the semilocal Reynolds number Reτ increases away from the walls, consistently with less energetic streaks observed in DNSs of turbulent channels. A secondary stability analysis of the two-dimensional velocity profile formed by the mean turbulent velocity and the nonlinearly saturated optimal streaks predicts a streamwise instability mode with wavelength λx,cr≈230 in semilocal units, regardless of the fluid property distribution across the channel. The threshold for the onset of the secondary instability is reduced, compared to a constant property flow, if Reτ increases away from the walls, which explains the more intense ejection events reported in DNSs. The opposite behavior is predicted by the linear theory for decreasing Reτ, in accord with DNS observations. We finally show that the phase velocity of the critical mode of secondary instability agrees well with the convection velocity calculated by DNSs in the near-wall region for both constant and variable viscosity flows.

  • 272.
    Rinaldi, Enrico
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Bagheri, Shervin
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Edge state modulation by mean viscosity gradients2018Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 838, s. 379-403Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Motivated by the relevance of edge state solutions as mediators of transition, we use direct numerical simulations to study the effect of spatially non-uniform viscosity on their energy and stability in minimal channel flows. What we seek is a theoretical support rooted in a fully nonlinear framework that explains the modified threshold for transition to turbulence in flows with temperature-dependent viscosity. Consistently over a range of subcritical Reynolds numbers, we find that decreasing viscosity away from the walls weakens the streamwise streaks and the vortical structures responsible for their regeneration. The entire self-sustained cycle of the edge state is maintained on a lower kinetic energy level with a smaller driving force, compared to a flow with constant viscosity. Increasing viscosity away from the walls has the opposite effect. In both cases, the effect is proportional to the strength of the viscosity gradient. The results presented highlight a local shift in the state space of the position of the edge state relative to the laminar attractor with the consequent modulation of its basin of attraction in the proximity of the edge state and of the surrounding manifold. The implication is that the threshold for transition is reduced for perturbations evolving in the neighbourhood of the edge state in the case that viscosity decreases away from the walls, and vice versa.

  • 273.
    Rinkevicius, Zilvinas
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rosal Sandberg, Jaime Axel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Mikkelsen, Kurt V.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments2014Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 3, s. 989-1003Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

  • 274.
    Rinkevicius, Zilvinas
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rosal Sandberg, Jaime Axel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Non-linear optical properties of molecules in heterogeneous environments: a quadratic density functional/molecular mechanics response theory2014Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 19, s. 8981-8989Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We generalize a density functional theory/molecular mechanics approach for heterogeneous environments with an implementation of quadratic response theory. The updated methodology allows us to address a variety of non-linear optical, magnetic and mixed properties of molecular species in complex environments, such as combined metallic, solvent and confined organic environments. Illustrating calculations of para-nitroaniline on gold surfaces and in solution reveals a number of aspects that come into play when analyzing second harmonic generation of such systems - such as surface charge flow, coupled surface-solvent dynamics and induced geometric and electronic structure effects of the adsorbate. Some ramifications of the methodology for applied studies are discussed.

  • 275.
    Rinkevicius, Zilvinas
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sandberg, Jaime A. R.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Linares, Mathieu
    Norman, Patrick
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hybrid Complex Polarization Propagator/Molecular Mechanics Method for Heterogeneous Environments2016Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, nr 6, s. 2661-2667Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We introduce a hybrid complex polarization propagator/molecular mechanics method for the calculation of near-resonant and resonant response properties of molecules in heterogeneous environments, which consist of a metallic surface, or nanoparticle, and a solvent. The applicability and performance of the method is demonstrated by computations of linear absorption spectra of p-nitroaniline physisorbed at a gold/dimethyl sulfoxide interface in the UV/vis and near carbon-K-edge regions of the spectrum. It is shown that the shift of absorption cross-section induced by the heterogeneous environment varies significantly depending on the nature,of the excited states encountered in the targeted frequency region as' well as on the actual size of the resonant frequencies, and that the solvent component of the heterogeneous environment is responsible for the major part of the environmental shift, especially in the higher frequency range of the carbon K-edge region.

  • 276.
    Rolland, Nicolas
    et al.
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Franco-Gonzalez, Juan Felipe
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Volpi, Riccardo
    Linkoping Univ, Dept Phys Chem & Biol IFM, SE-58183 Linkoping 3, Sweden.;RIST, Machine Learning & Optimizat Grp, Cluj Napoca, Romania..
    Linares, Mathieu
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Zozoulenko, Igor, V
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Understanding morphology-mobility dependence in PEDOT:Tos2018Ingår i: Physical Review Materials, ISSN 2475-9953, Vol. 2, nr 4, artikel-id 045605Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The potential of conjugated polymers to compete with inorganic materials in the field of semiconductor is conditional on fine-tuning of the charge carriers mobility. The latter is closely related to the material morphology, and various studies have shown that the bottleneck for charge transport is the connectivity between well-ordered crystallites, with a high degree of pi-pi stacking, dispersed into a disordered matrix. However, at this time there is a lack of theoretical descriptions accounting for this link between morphology and mobility, hindering the development of systematic material designs. Here we propose a computational model to predict charge carriers mobility in conducting polymer PEDOT depending on the physicochemical properties of the system. We start by calculating the morphology using molecular dynamics simulations. Based on the calculated morphology we perform quantum mechanical calculation of the transfer integrals between states in polymer chains and calculate corresponding hopping rates using the Miller-Abrahams formalism. We then construct a transport resistive network, calculate the mobility using a mean-field approach, and analyze the calculated mobility in terms of transfer integrals distributions and percolation thresholds. Our results provide theoretical support for the recent study [Noriega et al., Nat Mater 12, 1038 (2013)] explaining why the mobility in polymers rapidly increases as the chain length is increased and then saturates for sufficiently long chains. Our study also provides the answer to the long-standing question whether the enhancement of the crystallinity is the key to designing high-mobility polymers. We demonstrate, that it is the effective pi-pi stacking, not the long-range order that is essential for the material design for the enhanced electrical performance. This generic model can compare the mobility of a polymer thin film with different solvent contents, solvent additives, dopant species or polymer characteristics, providing a general framework to design new high mobility conjugated polymer materials.

  • 277.
    Rosal Sandberg, Jaime Axel
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    New recurrence relations for analytic evaluationof two-electron repulsion integrals over highly contracted gaussian-type orbitalsManuskript (preprint) (Övrigt vetenskapligt)
  • 278.
    Rosal Sandberg, Jaime Axel
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Efficient time dependent density functional theory calculations using general contraction basis setsManuskript (preprint) (Övrigt vetenskapligt)
  • 279.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Banaei, Arash Alizad
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Mazzino, Andrea
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Flexible Fiber Reveals the Two-Point Statistical Properties of Turbulence2018Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 121, nr 4, artikel-id 044501Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study the dynamics of a flexible fiber freely moving in a three-dimensional fully developed turbulent field and present a phenomenological theory to describe the interaction between the fiber elasticity and the turbulent flow. This theory leads to the identification of two distinct regimes of flapping, which we validate against direct numerical simulations fully resolving the fiber dynamics. The main result of our analysis is the identification of a flapping regime where the fiber, despite its elasticity, is slaved to the turbulent fluctuations. In this regime the fiber can be used to measure two-point statistical observables of turbulence, including scaling exponents of velocity structure functions, the sign of the energy cascade and the energy flux of turbulence, as well as the characteristic times of the eddies within the inertial range of scales. Our results are expected to have a deep impact on the experimental turbulence research as a new way, accurate and efficient, to measure two-point, and more generally multipoint, statistics of turbulence.

  • 280.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Suspensions of deformable particles in a Couette flow2018Ingår i: Journal of Non-Newtonian Fluid Mechanics, ISSN 0377-0257, E-ISSN 1873-2631, Vol. 262, s. 3-11Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider suspensions of deformable particles in a Newtonian fluid by means of fully Eulerian numerical simulations with a one-continuum formulation. We study the rheology of the visco-elastic suspension in plane Couette flow in the limit of vanishing inertia and examine the dependency of the effective viscosity mu on the solid volume-fraction Phi, the capillary number Ca, and the solid to fluid viscosity ratio K. The suspension viscosity decreases with deformation and applied shear (shear-thinning) while still increasing with volume fraction. We show that mu collapses to an universal function, mu(Phi(e)), with an effective volume fraction Phi(e), lower than the nominal one owing to the particle deformation. This universal function is well described by the Eilers fit, which well approximate the rheology of suspension of rigid spheres at all O. We provide a closure for the effective volume fraction Phi(e) as function of volume fraction Phi and capillary number Ca and demonstrate it also applies to data in literature for suspensions of capsules and red-blood cells. In addition, we show that the normal stress differences exhibit a non-linear behavior, with a similar trend as in polymer and filament suspensions. The total stress budgets reveals that the particle-induced stress contribution increases with the volume fraction Phi and decreases with deformability.

  • 281.
    Rosti, Marco E.
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Mitra, Dhrubaditya
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Rheology of suspensions of viscoelastic spheres: Deformability as an effective volume fraction2018Ingår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, nr 1, artikel-id 012301Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study suspensions of deformable (viscoelastic) spheres in a Newtonian solvent in planeCouette geometry, by means of direct numerical simulations. We find that in the limit of vanishing inertia, the effective viscosity mu of the suspension increases as the volume fraction occupied by the spheres Phi increases and decreases as the elastic modulus of the spheres G decreases; the function mu(Phi,G) collapses to a universal function mu(Phi(e)) with a reduced effective volume fraction Phi(e)(Phi,G). Remarkably, the function mu(Phi(e)) is the well- known Eilers fit that describes the rheology of suspension of rigid spheres at all Phi. Our results suggest different ways to interpret the macrorheology of blood.

  • 282.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Pinelli, Alfredo
    Turbulent channel flow over an anisotropic porous wall - drag increase and reduction2018Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 842, s. 381-394Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The effect of the variations of the permeability tensor on the close-to-the-wall behaviour of a turbulent channel flow bounded by porous walls is explored using a set of direct numerical simulations. It is found that the total drag can be either reduced or increased by more than 20% by adjusting the permeability directional properties. Drag reduction is achieved for the case of materials with permeability in the vertical direction lower than the one in the wall-parallel planes. This configuration limits the wall-normal velocity at the interface while promoting an increase of the tangential slip velocity leading to an almost 'one-component' turbulence where the low- and high-speed streak coherence is strongly enhanced. On the other hand, strong drag increase is found when high wall-normal and low wall-parallel permeabilities are prescribed. In this condition, the enhancement of the wall-normal fluctuations due to the reduced wall-blocking effect triggers the onset of structures which are strongly correlated in the spanwise direction, a phenomenon observed by other authors in flows over isotropic porous layers or over ribletted walls with large protrusion heights. The use of anisotropic porous walls for drag reduction is particularly attractive since equal gains can be achieved at different Reynolds numbers by rescaling the magnitude of the permeability only.

  • 283.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    De Vita, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Numerical simulations of emulsions in shear flows2019Ingår i: Acta Mechanica, ISSN 0001-5970, E-ISSN 1619-6937, Vol. 230, nr 2, s. 667-682Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a modification of a recently developed volume of fluid method for multiphase problems (Ii et al. in J Comput Phys 231(5):2328-2358, 2012), so that it can be used in conjunction with a fractional-step method and fast Poisson solver, and validate it with standard benchmark problems. We then consider emulsions of two-fluid systems and study their rheology in a plane Couette flow in the limit of vanishing inertia. We examine the dependency of the effective viscosity on the volume fraction phi (from 10 to 30%) and the Capillary number Ca (from 0.1 to 0.4) for the case of density and viscosity ratio 1. We show that the effective viscosity decreases with the deformation and the applied shear (shear-thinning) while exhibiting a non-monotonic behavior with respect to the volume fraction. We report the appearance of a maximum in the effective viscosity curve and compare the results with those of suspensions of rigid and deformable particles and capsules. We show that the flow in the solvent is mostly a shear flow, while it is mostly rotational in the suspended phase; moreover, this behavior tends to reverse as the volume fraction increases. Finally, we evaluate the contributions to the total shear stress of the viscous stresses in the two fluids and of the interfacial force between them.

  • 284.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Izbassarov, Daulet
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Tammisola, Outi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hormozi, Sarah
    Ohio Univ, Dept Mech Engn, Athens, OH 45701 USA..
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Turbulent channel flow of an elastoviscoplastic fluid2018Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 853, s. 488-514Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present numerical simulations of laminar and turbulent channel flow of an elastoviscoplastic fluid. The non-Newtonian flow is simulated by solving the full incompressible Navier-Stokes equations coupled with the evolution equation for the elastoviscoplastic stress tensor. The laminar simulations are carried out for a wide range of Reynolds numbers, Bingham numbers and ratios of the fluid and total viscosity, while the turbulent flow simulations are performed at a fixed bulk Reynolds number equal to 2800 and weak elasticity. We show that in the laminar flow regime the friction factor increases monotonically with the Bingham number (yield stress) and decreases with the viscosity ratio, while in the turbulent regime the friction factor is almost independent of the viscosity ratio and decreases with the Bingham number, until the flow eventually returns to a fully laminar condition for large enough yield stresses. Three main regimes are found in the turbulent case, depending on the Bingham number: for low values, the friction Reynolds number and the turbulent flow statistics only slightly differ from those of a Newtonian fluid; for intermediate values of the Bingham number, the fluctuations increase and the inertial equilibrium range is lost. Finally, for higher values the flow completely laminarizes. These different behaviours are associated with a progressive increases of the volume where the fluid is not yielded, growing from the centreline towards the walls as the Bingham number increases. The unyielded region interacts with the near-wall structures, forming preferentially above the high-speed streaks. In particular, the near-wall streaks and the associated quasi-streamwise vortices are strongly enhanced in an highly elastoviscoplastic fluid and the flow becomes more correlated in the streamwise direction.

  • 285.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    The effect of elastic walls on suspension flow2018Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114Artikel i tidskrift (Övrigt vetenskapligt)
  • 286.
    Rosti, Marco E.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Omidyeganeh, Mohammad
    City Univ London, Sch Math Comp Sci & Engn, London EC1V 0HB, England..
    Pinelli, Alfredo
    City Univ London, Sch Math Comp Sci & Engn, London EC1V 0HB, England..
    Numerical Simulation of a Passive Control of the Flow Around an Aerofoil Using a Flexible, Self Adaptive Flaplet2018Ingår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 100, nr 4, s. 1111-1143Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Self-activated feathers are used by almost all birds to adapt their wing characteristics to delay stall or to moderate its adverse effects (e.g., during landing or sudden increase in angle of attack due to gusts). Some of the feathers are believed to pop up as a consequence of flow separation and to interact with the flow and produce beneficial modifications of the unsteady vorticity field. The use of self adaptive flaplets in aircrafts, inspired by birds feathers, requires the understanding of the physical mechanisms leading to the mentioned aerodynamic benefits and the determination of the characteristics of optimal flaps including their size, positioning and ideal fabrication material. In this framework, this numerical study is divided in two parts. Firstly, in a simplified scenario, we determine the main characteristics that render a flap mounted on an aerofoil at high angle of attack able to deliver increased lift and improved aerodynamic efficiency, by varying its length, position and its natural frequency. Later on, a detailed direct numerical simulation analysis is used to understand the origin of the aerodynamic benefits introduced by the flaplet movement induced by the interaction with the flow field. The parametric study that has been carried out, reveals that an optimal flap can deliver a mean lift increase of about 20% on a NACA0020 aerofoil at an incidence of 20 (o) degrees. The results obtained from the direct numerical simulation of the flow field around the aerofoil equipped with the optimal flap at a chord Reynolds number of 2 x 10(4) shows that the flaplet movement is mainly induced by a cyclic passage of a large recirculation bubble on the aerofoil suction side. In turns, when the flap is pushed downward, the induced plane jet displaces the trailing edge vortices further downstream, away from the wing, moderating the downforce generated by those vortices and regularising the shedding cycle that appears to be much more organised when the optimal flaplet configuration is selected.

  • 287.
    Rosti, Marco Edoardo
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Effect of elastic walls on suspension flow2019Ingår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 4, nr 6, artikel-id 062301Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study suspensions of rigid particles in a plane Couette flow with deformable elastic walls. We find that, in the limit of vanishing inertia, the elastic walls induce shear thinning of the suspension flow such that the effective viscosity decreases as the wall deformability increases. This shear-thinning behavior originates from the interactions between rigid particles, soft walls, and carrier fluids; an asymmetric wall deformation induces a net lift force acting on the particles which therefore migrate towards the bulk of the channel. Based on our observations, we provide a closure for the suspension viscosity which can be used to model the rheology of suspensions with arbitrary volume fraction in elastic channels.

  • 288.
    Rubio-Magnieto, Jenifer
    et al.
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium.;Univ Jaume 1, Dept Quim Inorgan & Organ, Bioinspired Supramol Chem & Mat Grp, Avda Sos Baynat S-N, E-12071 Castellon de La Plana, Spain..
    Kajouj, Sofia
    Univ Libre Bruxelles, Chim Organ & Photochim CP160 08, 50 Ave FD Roosevelt, B-1050 Brussels, Belgium..
    Di Meo, Florent
    Univ Limoges, Sch Pharm, INSERM, U1248,IPPRITT, 2 Rue Dr Marcland, F-87025 Limoges, France..
    Fossepre, Mathieu
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium..
    Trouillas, Patrick
    Univ Limoges, Sch Pharm, INSERM, U1248,IPPRITT, 2 Rue Dr Marcland, F-87025 Limoges, France.;Palacky Univ, Fac Sci, RCPTM, Slechtitelu 27, Olomouc 78371, Czech Republic..
    Norman, Patrick
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Linares, Mathieu
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Moucheron, Cecile
    Univ Libre Bruxelles, Chim Organ & Photochim CP160 08, 50 Ave FD Roosevelt, B-1050 Brussels, Belgium..
    Surin, Mathieu
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium..
    Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G-Quadruplexes2018Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, nr 58, s. 15577-15588Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Metal complexes constitute an important class of DNA binders. In particular, a few ruthenium polyazaaromatic complexes are attractive as light switches because of their strong luminescence enhancement upon DNA binding. In this paper, a comprehensive study on the binding modes of several mononuclear and binuclear ruthenium complexes to human telomeric sequences, made of repeats of the d(TTAGGG) fragment is reported. These DNA sequences form G-quadruplexes (G4s) at the ends of chromosomes and constitute a relevant biomolecular target in cancer research. By combining spectroscopy experiments and molecular modelling simulations, several key properties are deciphered: the binding modes, the stabilization of G4 upon binding, and the selectivity of these complexes towards G4 versus double-stranded DNA. These results are rationalized by assessing the possible deformation of G4 and the binding free energies of several binding modes via modelling approaches. Altogether, this comparative study provides fundamental insights into the molecular recognition properties and selectivity of Ru complexes towards this important class of DNA G4s.

  • 289.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Analysis of high order fast interface tracking methods2014Ingår i: Numerische Mathematik, ISSN 0029-599X, E-ISSN 0945-3245, Vol. 128, nr 2, s. 339-375Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fast high order methods for the propagation of an interface in a velocity field are constructed and analyzed. The methods are generalizations of the fast interface tracking method proposed in Runborg (Commun Math Sci 7:365-398, 2009). They are based on high order subdivision to make a multiresolution decomposition of the interface. Instead of tracking marker points on the interface the related wavelet vectors are tracked. Like the markers they satisfy ordinary differential equations (ODEs), but fine scale wavelets can be tracked with longer timesteps than coarse scale wavelets. This leads to methods with a computational cost of rather than for markers and reference timestep . These methods are proved to still have the same order of accuracy as the underlying direct ODE solver under a stability condition in terms of the order of the subdivision, the order of the ODE solver and the time step ratio between wavelet levels. In particular it is shown that with a suitable high order subdivision scheme any explicit Runge-Kutta method can be used. Numerical examples supporting the theory are also presented.

  • 290. Ryzhenkov, V.
    et al.
    Ivashchenko, V.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mullyadzhanov, R.
    Simulation of heat and mass transfer in turbulent channel flow using the spectral-element method: Effect of spatial resolution2016Ingår i: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 754, nr 6, artikel-id 062009Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We use the open-source code nek5000 to assess the accuracy of high-order spectral element large-eddy simulations (LES) of a turbulent channel flow depending on the spatial resolution compared to the direct numerical simulation (DNS). The Reynolds number Re = 6800 is considered based on the bulk velocity and half-width of the channel. The filtered governing equations are closed with the dynamic Smagorinsky model for subgrid stresses and heat flux. The results show very good agreement between LES and DNS for time-averaged velocity and temperature profiles and their fluctuations. Even the coarse LES grid which contains around 30 times less points than the DNS one provided predictions of the friction velocity within 2.0% accuracy interval. © Published under licence by IOP Publishing Ltd.

  • 291. Ryzhenkov, V.
    et al.
    Ivashchenko, V.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mullyadzhanov, R.
    Spectral-element simulations of variable-density turbulent flow in a plane channel2017Ingår i: EPJ Web of Conferences, EDP Sciences, 2017, Vol. 159, artikel-id 0041Konferensbidrag (Refereegranskat)
    Abstract [en]

    We perform Large-eddy simulations (LES) of the turbulent flow in a channel with isothermal heated walls with the temperature ratio equal to 2. The variable properties of the fluid are accounted for by using the low Mach number approximation. The Reynolds number based on the bulk velocity, half-width of the channel, density and dynamic viscosity near the cold wall is 6800. We study the effect of spatial resolution on the accuracy of Large-eddy simulations with dynamic Smagorinsky model. The very good agreement of LES results is shown even for the coarse meshes which is attributed to the high accuracy of the spectral method.

  • 292.
    Råsander, Mikael
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Electronic structure and lattice dynamics in the FeSb3 skutterudite from density functional theory2015Ingår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 91, nr 1, artikel-id 014303Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have performed density functional calculations of the electronic structure and lattice dynamics of the binary skutterudite FeSb3. We find that the ground state of FeSb3 is a near half-metallic ferromagnet with T-c = 175 K. Furthermore, we find that FeSb3 is softer than CoSb3 based on an analysis of the relation of the elastic constants and the shape of the phonon density of states in the two systems, which is in agreement with experimental observation. Based on these observations we find it plausible that FeSb3 will have a lower thermal conductivity than CoSb3. Additionally, our calculations indicate that FeSb3 may be stable towards decomposition into FeSb2 and Sb. Furthermore, for ferromagnetic FeSb3 we obtain real-valued phonon frequencies and also a c44 greater than zero, indicating that the system is mechanically as well as dynamically stable.

  • 293.
    Råsander, Mikael
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. Imperial College London, United Kingdom.
    Hugosson, Håkan W.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Density functional study of carbon vacancies in titanium carbide2018Ingår i: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 30, nr 1, artikel-id 015702Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It is well established that TiC contains carbon vacancies not only in carbon-deficient environments but also in carbon-rich environments. We have performed density functional calculations of the vacancy formation energy in TiC for C-as well as Ti-rich conditions using several different approximations to the exchange-correlation functional, and also carefully considering the nature and thermodynamics of the carbon reference state, as well as the effect of varying growth conditions. We find that the formation of carbon vacancies is clearly favorable under Ti-rich conditions, whereas it is slightly energetically unfavorable under C-rich conditions. Furthermore, we find that the relaxations of the atoms close to the vacancy site are rather long-ranged, and that these relaxations contribute significantly to the stabilization of the vacancy. Since carbon vacancies in TiC are also experimentally observed in carbon-rich environments, we conclude that kinetics may play an important role. This conclusion is consistent with the experimentally observed high activation energies and sluggish diffusion of vacancies in TiC, effectively causing a freezing in of the vacancies.

  • 294.
    Saglietti, Clio
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Wadbro, Eddie
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Berggren, Martin
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Henningson, Dan S.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Topology optimization of heat sinks in a square differentially heated cavity2018Ingår i: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 74, s. 36-52Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Innovative designs of heat sinks are generated in the present paper through numerical optimization, by applying a material distribution topology optimization approach. The potential of the method is demonstrated in a two-dimensional differentially heated cavity, in which the heat transfer is increased by means of introducing a solid structure that acts as a heat sink. We simulate the heat transfer in the whole system by performing direct numerical simulations of the conjugated problem, i.e. temperature diffusion and convection in the entire domain and momentum conservation in the fluid surrounding the solid. The flow is driven by the buoyancy force, under the Boussinesq approximation, and we describe the presence of solid material as the action of a Brinkman friction force in the Navier–Stokes equations. To obtain a design with a given length scale, we apply regularization techniques by filtering the material distribution. Two different types of filters are applied and compared for obtaining the most realistic solution. Given the large scale of the problem, the optimization is solved with a gradient based method that relies on adjoint sensitivity analysis. The results show the applicability of the method by presenting innovative geometries that are increasing the heat flux. Moreover, the effect of various factors is studied: We investigate the impact of boundary conditions, initial designs, and Rayleigh number. Complex tree-like structures are favored when a horizontal temperature gradient is imposed on the boundary and when we limit the amount of solid volume in the cavity. The choice of the initial design affects the final topology of the generated solid structures, but not their performance for the studied cases. Additionally, when the Rayleigh number increases, the topology of the heat exchanger is able to substantially enhance the convection contribution to the heat transfer. 

  • 295.
    Sahlin, Kristoffer
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Frånberg, M.
    Arvestad, Lars
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm University, Sweden.
    Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias2017Ingår i: Journal of Computational Biology, ISSN 1066-5277, E-ISSN 1557-8666, Vol. 24, nr 6, s. 581-589Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning read pairs to the reference, read pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model limits statistical analysis of identifying variants and propose a new model by adapting a model we have previously introduced for contig scaffolding, which agrees with data. From this model, we derive an improved null hypothesis that when applied in the variant caller CLEVER, reduces the number of false positives and corrects a bias that contributes to more deletion calls than insertion calls. We advise developers of variant callers with statistical fragment length-based methods to adapt the concepts in our proposed model and null hypothesis.

  • 296.
    Samanta, Arghya
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lashgari, Iman
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Enhanced secondary motion of the turbulent flow through a porous square duct2015Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 784, s. 681-693Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Direct numerical simulations of the fully developed turbulent flow through a porous square duct are performed to study the effect of the permeable wall on the secondary cross-stream flow. The volume-averaged Navier-Stokes equations are used to describe the flow in the porous phase, a packed bed with porosity epsilon(c) = 0.95. The porous square duct is computed at Re-b similar or equal to 5000 and compared with the numerical simulations of a turbulent duct with four solid walls. The two boundary layers on the top wall and porous interface merge close to the centre of the duct, as opposed to the channel, because the sidewall boundary layers inhibit the growth of the shear layer over the porous interface. The most relevant feature in the porous duct is the enhanced magnitude of the secondary flow, which exceeds that of a regular duct by a factor of four. This is related to the increased vertical velocity, and the different interaction between the ejections from the sidewalls and the porous medium. We also report a significant decrease in the streamwise turbulence intensity over the porous wall of the duct (which is also observed in a porous channel), and the appearance of short spanwise rollers in the buffer layer, replacing the streaky structures of wall-bounded turbulence. These spanwise rollers most probably result from a Kelvin-Helmholtz type of instability, and their width is limited by the presence of the sidewalls.

  • 297. Sardina, G.
    et al.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Transition Delay and its Implications for Drag Reduction in Particle-laden Channel Flow2015Ingår i: International Conference of Computational Methods in Sciences and Engineering (ICCMSE),, American Institute of Physics (AIP), 2015, artikel-id 180009Konferensbidrag (Refereegranskat)
    Abstract [en]

    Direct numerical simulations of a two-way coupled particle-laden channel flow are performed in the transitional and turbulent regime. Our aim is to investigate whether particles, assumed solid, spherical and heavy delay transition and diminish drag in wall bounded flows. We consider that the only interaction between the carrier and dispersed phase is due to the Stokes drag. The simulations have been performed with a pseudo-spectral solver for the incompressible Navier-Stokes equations while the particle equations are solved in a Lagrangian formulation. In the transitional regime, we study the evolution of disturbances added to a plane Poiseuille base flow with Reynolds number 2000, based on the channel half-height and centerline velocity. By fixing the Reynolds number, the only two free parameters are the particle Stokes number St and the particle mass fraction f. Two different scenarios are considered depending on the initial condition of the velocity field. The first scenario consists of counter-rotating streamwise vortices and one three-dimensional mode while the second is a nonlinear interaction of two symmetric oblique waves. The effects of the particles on the flow transition depend on the particle mass fraction. In particular, at lower concentrations, the transition is facilitated by the presence of the particles, conversely at higher mass fractions the particles tend to stabilize the flow. The results indicate that the particle can play an important role by influencing secondary instabilities and streaks breakdown. These effects can be linked to the reduced drag observed in turbulent channel flow laden with heavy particles and specific simulations in the turbulent regime have been performed.

  • 298.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    An Efficient-high Performance Code for Particle Transport in Homogeneous Turbulence2016Ingår i: Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2016 (ICCMSE-2016), American Institute of Physics (AIP), 2016, artikel-id UNSP 090004Konferensbidrag (Refereegranskat)
    Abstract [en]

    We have developed a fully parallel fortran/MPI code for tracking particles in homogeneous turbulent flows. The fluid is discretized in a uniform Eulerian grid while the particles are evolved via a Lagrangian tracking framework. The code is pseudo-spectral and employs the libraries FFTw, time integration has a third or fourth-order accuracy. The carrier phase can transport several equations for active/passive scalars that can act like a source of mass/energy transfer to the particles. We were able to simulate a fully-turbulent flow in an Eulerian grid of about 10(10) points and to track in a Lagrangian framework at least 10(9) point particles. The code is fully modular, can be easily extended or modified and available upon request.

  • 299. Sardina, Gaetano
    et al.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Processteknisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Processteknisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Caballero, Rodrigo
    Continuous Growth of Droplet Size Variance due to Condensation in Turbulent Clouds2015Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 115, nr 18, artikel-id 184501Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We use a stochastic model and direct numerical simulation to study the impact of turbulence on cloud droplet growth by condensation. We show that the variance of the droplet size distribution increases in time as t(1/2), with growth rate proportional to the large-to-small turbulent scale separation and to the turbulence integral scales but independent of the mean turbulent dissipation. Direct numerical simulations confirm this result and produce realistically broad droplet size spectra over time intervals of 20 min, comparable with the time of rain formation.

  • 300.
    Sardina, Gaetano
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Casciola, C. M.
    Statistics of Particle Accumulation in Spatially Developing Turbulent Boundary Layers2014Ingår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 92, nr 1-2, s. 27-40Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present the results of a Direct Numerical Simulation of a particle-laden spatially developing turbulent boundary layer up to Re (theta) = 2500. Two main features differentiate the behavior of inertial particles in a zero-pressure-gradient turbulent boundary layer from the more commonly studied case of a parallel channel flow. The first is the variation along the streamwise direction of the local dimensionless parameters defining the fluid-particle interactions. The second is the coexistence of an irrotational free-stream and a near-wall rotational turbulent flow. As concerns the first issue, an inner and an outer Stokes number can be defined using inner and outer flow units. The inner Stokes number governs the near-wall behavior similarly to the case of channel flow. To understand the effect of a laminar-turbulent interface, we examine the behavior of particles initially released in the free stream and show that they present a distinct behavior with respect to those directly injected inside the boundary layer. A region of minimum concentration occurs inside the turbulent boundary layer at about one displacement thickness from the wall. Its formation is due to the competition between two transport mechanisms: a relatively slow turbulent diffusion towards the buffer layer and a fast turbophoretic drift towards the wall.

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