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  • 151. Kudrnovsky, J.
    et al.
    Drchal, V.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Rusz, J.
    Turek, I.
    Unified approach to electronic, thermodynamical, and transport properties of Fe3Si and Fe3Al alloys2014Ingår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 90, nr 13, s. 134408-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The electronic, thermodynamical, and transport properties of ordered Fe3X (X = Al, Si) alloys are studied from first principles. We present here a unified approach to the phase stability, the estimate of the Curie temperature, the temperature dependence of sublattice magnetizations, magnon spectra, the spin-stiffnesses, and residual resistivities. An important feature of the present study is that all calculated physical properties are determined in the framework of the same first-principles electronic structure model combined with the effective Ising and Heisenberg Hamiltonians used for study of the thermodynamical properties of alloys. Curie temperatures, spin-stiffnesses, and magnon spectra are determined using the same calculated exchange integrals. Finally, the transport properties are calculated using the linear-response theory. Our theoretical estimates compare well with available experimental data. In particular, calculations predict (in agreement with experiment) the ordered D0(3) phase as the ground-state alloy structure, demonstrate that a correct relation of Curie temperatures of Fe3Al/Fe3Si alloys can be obtained only by going beyond a simple mean-field approximation, provide reasonable estimates of spin-stiffnesses, and give resistivities compatible with structural disorder observed in the experiment. Although the calculated temperature dependences of the Fe magnetization on different sublattices are similar, they nevertheless deviate more than in the experiment, and we discuss a possible origin.

  • 152. Kumar, Ankit
    et al.
    Pan, Fan
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Husain, Sajid
    Akansel, Serkan
    Brucas, Rimantas
    Bergqvist, Lars
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Chaudhary, Sujeet
    Svedlindh, Peter
    Temperature-dependent Gilbert damping of Co2FeAl thin films with different degree of atomic order2017Ingår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 96, nr 22, artikel-id 224425Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Half-metallicity and low magnetic damping are perpetually sought for spintronics materials, and full Heusler compounds in this respect provide outstanding properties. However, it is challenging to obtain the well-ordered half-metallic phase in as-deposited full Heusler compound thin films, and theory has struggled to establish a fundamental understanding of the temperature-dependent Gilbert damping in these systems. Here we present a study of the temperature-dependent Gilbert damping of differently ordered as-deposited Co2FeAl full Heusler compound thin films. The sum of inter-and intraband electron scattering in conjunction with the finite electron lifetime in Bloch states governs the Gilbert damping for the well-ordered phase, in contrast to the damping of partially ordered and disordered phases which is governed by interband electronic scattering alone. These results, especially the ultralow room-temperature intrinsic damping observed for the well-ordered phase, provide fundamental insights into the physical origin of the Gilbert damping in full Heusler compound thin films.

  • 153.
    Käll, Lukas
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Krogh, Anders
    Sonnhammer, Erik L. L.
    Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server2007Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, nr Web Server issue, 1, s. W429-W432Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 154.
    König, Carolin
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Skanberg, Robin
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Hotz, Ingrid
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Ynnerman, Anders
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Norman, P.
    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.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, nr 24, s. 3030-3033Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 155.
    Lambert, Ruth A.
    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.
    Breugem, Wim-Paul
    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.
    Active suspensions in thin films: nutrient uptake and swimmer motion2013Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 733, s. 528-557Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 156. Larsson, Torbjörn
    et al.
    Hammar, Johan
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Barth, Michaela
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Axner, Lilit
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    ENHANCING COMPUTATIONAL AERO-ACOUSTIC PROCESSES FOR GROUNDVEHICLES RESOLVING OPEN SOURCE CFD2018Ingår i: The 13th OpenFOAM Workshop, 2018, s. 1-4Konferensbidrag (Refereegranskat)
  • 157.
    Lashgari, Iman
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Niazi Ardekani, Mehdi
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Banerjee, Indradumna
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Inertial migration of spherical and oblate particles in straight ductsIngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study numerically the inertial migration of a single rigid sphere and an oblate spheroid in straight square and rectangular ducts. A highly accurate interface-resolved numerical algorithm is employed to analyse the entire migration dynamics of the oblate particle and compare it with that of the sphere. Similarly to the inertial focusing of spheres, the oblate particle reaches one of the four face-centred equilibrium positions, however they are vertically aligned with the axis of symmetry in the spanwise direction. In addition, the lateral trajectories of spheres and oblates collapse into an equilibrium manifold before ending at the equilibrium positions, with the equilibrium manifold tangential to lines of constant background shear for both sphere and oblate particles. The differences between the migration of the oblate and sphere are also presented, in particular the oblate may focus on the diagonal symmetry line of the duct cross-section, close to one of the corners, if its diameter is larger than a certain threshold. Moreover, we show that the final orientation and rotation of the oblate exhibit a chaotic behaviour for Reynolds numbers beyond a critical value. Finally, we document that the lateral motion of the oblate particle is less uniform than that of the spherical particle due to its evident tumbling motion throughout the migration. In a square duct, the strong tumbling motion of the oblate in the first stage of the migration results in a lower lateral velocity and consequently longer focusing length with respect to that of the spherical particle. The opposite is true in a rectangular duct where the higher lateral velocity of the oblate in the second stage of the migration, with negligible tumbling, gives rise to shorter focusing lengths.These results can help the design of microfluidic systems for bio-applications.

  • 158.
    Lashgari, Iman
    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.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. University of Padova, Italy.
    Breugem, W. -P
    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 to Turbulence in the Presence of Finite Size Particles2015Ingår i: Procedia IUTAM, Elsevier, 2015, s. 211-217Konferensbidrag (Refereegranskat)
    Abstract [en]

    We study the transition from laminar to turbulent flow in a channel seeded with finite-size neutrally buoyant particles. A fixed ratio of 10 between the channel height and the particle diameter is considered. The flow is examined in the range of Reynolds numbers 500 ≤ Re ≤; 5000 and the particle volume fractions 0.001 ≤ Φ ≤; 0.3. We report a non-monotonic behavior of the threshold value of the Reynolds number above which the flow becomes turbulent, in agreement with previous experimental studies. The mean square velocity fluctuations and Reynolds shear stress of the fluid phase are reduced by increasing the particle volume fraction at a fixed Re=1500, while the mean square velocities of the solid phase are enhanced monotonically suggesting a transition from fluid to particle dominated dynamics at high volume fraction.

  • 159.
    Lashgari, Iman
    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.
    Picano, Francesco
    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. University of Padova, Italy.
    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.
    Channel flow of rigid sphere suspensions: Particle dynamics in the inertial regime2016Ingår i: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 78, s. 12-24Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider suspensions of neutrally-buoyant finite-size rigid spherical particles in channel flow and investigate the relation between the particle dynamics and the mean bulk behavior of the mixture for Reynolds numbers 500 ≤ Re ≤ 5000 and particle volume fraction 0 ≤ Φ ≤ 0.3, via fully resolved numerical simulations. Analysis of the momentum balance reveals the existence of three different regimes: laminar, turbulent and inertial shear-thickening depending on which of the stress terms, viscous, Reynolds or particle stress, is the major responsible for the momentum transfer across the channel. We show that both Reynolds and particle stress dominated flows fall into the Bagnoldian inertial regime and that the Bagnold number can predict the bulk behavior although this is due to two distinct physical mechanisms. A turbulent flow is characterized by larger particle dispersion and a more uniform particle distribution, whereas the particulate-dominated flows is associated with a significant particle migration towards the channel center where the flow is smooth laminar-like and dispersion low. Interestingly, the collision kernel shows similar values in the different regimes, although the relative particle velocity and clustering clearly vary with inertia and particle concentration.

  • 160.
    Lashgari, Iman
    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.
    Picano, Francesco
    Costa, Pedro
    Breugem, Wim-Paul
    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.
    Turbulent channel flow of a dense binary mixture of rigid particles2017Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 818, s. 623-645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study turbulent channel flow of a binary mixture of finite-sized neutrally buoyant rigid particles by means of interface-resolved direct numerical simulations. We fix the bulk Reynolds number and total solid volume fraction, Re-b = 5600 and Phi = 20 %, and vary the relative fraction of small and large particles. The binary mixture consists of particles of two different sizes, 2h/d(l) = 20 and 2h/d(s) = 30 where h is the half-channel height and d(l) and d(s) the diameters of the large and small particles. While the particulate flow statistics exhibit a significant alteration of the mean velocity profile and turbulent fluctuations with respect to the unladen flow, the differences between the mono-disperse and bi-disperse cases are small. However, we observe a clear segregation of small particles at the wall in binary mixtures, which affects the dynamics of the near-wall region and thus the overall drag. This results in a higher drag in suspensions with a larger number of large particles. As regards bi-disperse effects on the particle dynamics, a non-monotonic variation of the particle dispersion in the spanwise (homogeneous) direction is observed when increasing the percentage of small/large particles. Finally, we note that particles of the same size tend to cluster more at contact whereas the dynamics of the large particles gives the highest collision kernels due to a higher approaching speed.

  • 161.
    Lashgari, Iman
    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.
    Tammisola, Outi
    Department of Engineering, University of Cambridge, Cambridge, UK.
    Citro, Vincenzo
    DIIN, University of Salerno, Fisciano, Italy.
    Juniper, Matthew P.
    Department of Engineering, Univerisyt of Cambridge, Cambridge, UK.
    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.
    The planar X-junction flow: stability analysis and control2014Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 753, s. 1-28Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The bifurcations and control of the flow in a planar X-junction are studied via linear stability analysis and direct numerical simulations. This study reveals the instability mechanisms in a symmetric channel junction and shows how these can be stabilized or destabilized by boundary modification. We observe two bifurcations as the Reynolds number increases. They both scale with the inlet speed of the two side channels and are almost independent of the inlet speed of the main channel. Equivalently, both bifurcations appear when the recirculation zones reach a critical length. A two-dimensional stationary global mode becomes unstable first, changing the flow from a steady symmetric state to a steady asymmetric state via a pitchfork bifurcation. The core of this instability, whether defined by the structural sensitivity or by the disturbance energy production, is at the edges of the recirculation bubbles, which are located symmetrically along the walls of the downstream channel. The energy analysis shows that the first bifurcation is due to a lift-up mechanism. We develop an adjustable control strategy for the first bifurcation with distributed suction or blowing at the walls. The linearly optimal wall-normal velocity distribution is computed through a sensitivity analysis and is shown to delay the first bifurcation from Re = 82.5 to Re = 150. This stabilizing effect arises because blowing at the walls weakens the wall-normal gradient of the streamwise velocity around the recirculation zone and hinders the lift-up. At the second bifurcation, a three-dimensional stationary global mode with a spanwise wavenumber of order unity becomes unstable around the asymmetric steady state. Nonlinear three-dimensional simulations at the second bifurcation display transition to a nonlinear cycle involving growth of a three-dimensional steady structure, time-periodic secondary instability and nonlinear breakdown restoring a two-dimensional flow. Finally, we show that the sensitivity to wall suction at the second bifurcation is as large as it is at the first bifurcation, providing a possible mechanism for destabilization.

  • 162.
    Laure, Erwin
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Holmgren, Sverker
    Preface2013Ingår i: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, nr 8, s. 2115-2116Artikel i tidskrift (Refereegranskat)
  • 163.
    Lazeroms, Werner
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brethouwer, Gert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Wallin, Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Johansson, Arne V.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Nonlinear features in explicit algebraic models for turbulent flows with active scalars2015Ingår i: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Konferensbidrag (Refereegranskat)
    Abstract [en]

    A detailed discussion of explicit algebraic turbulence models in the case of active scalars is given. In particular, we discuss the appearance of nonlinearities in the models and the need for explicit solutions of the resulting nonlinear equations. Focussing on a recently published model for two-dimensional stratified flows, we present an intuitive way of approximating the solution of a sixth-order polynomial equation for the production-to-dissipation ratio (p + g)/e of turbulent kinetic energy K. This formulation is shown to be consistent for turbulent channel flow with stable and unstable stratification. The result is important for obtaining a robust model with a correct behaviour of the turbulence production in different limits of shear and buoyancy. The results have recently been published in Lazeroms et al. (2015).

  • 164. Lehtio, J.
    et al.
    Branca, M.
    Johansson, H.
    Orre, M.
    Granholm, Viktor
    KTH.
    Forshed, J.
    Perez-Bercoff, M.
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Genome Wide Proteomics Using Peptide High Resolution Isoelectric Focusing Hirief-Ms Allows Detection New Human Gene Models2012Ingår i: Annals of Oncology, ISSN 0923-7534, E-ISSN 1569-8041, Vol. 23, s. 33-34Artikel i tidskrift (Övrigt vetenskapligt)
  • 165.
    Li, Xin
    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.
    Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics2014Ingår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, nr 11, s. 5833-5840Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To promote a more comprehensive understanding of the influence of metal-adsorbate interaction for molecules at metallo surfaces or metallo nanoparticles in solvent environments on their electronic circular dichroism (ECD) spectra, we evaluate the application of a recently derived quantum mechanics capacitance molecular mechanics (QMCMM) model for ECD. Using helicene absorbed on gold surfaces in protic and aprotic solvents as illustration, we elucidate the detailed effects on excitation energies, transition moments, rotatory strengths, orientation dependence of ECD spectra, and the different roles of aprotic and protic solvents and the induced charge distribution patterns on the surface. These changes are decomposed in terms of surface alone, solvent alone, and combined surface solvent influence, and furthermore into the indirect contributions by the surface-induced restructuring of the helicene. Much of the salient changes of the ECD can be rationalized to the substantial redistribution of charge at the gold surface induced by the presence of the helicene. The study indicates that through the QMCMNI model the effects of a metallic surface on the circular dichroism spectra of adsorbed organic molecules can be tackled by extended QM calculations coupled to polarizability-capacitance force fields for large metallic clusters representing surfaces or nanoparticles.

  • 166.
    Li, Xin
    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.
    Two-Photon Absorption of Metal-Assisted Chromophores2014Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 12, s. 5630-5639Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aiming to understand the effect of a metal surface on nonlinear optical properties and the combined effects of surface and solvent environments on such properties, we present a multiscale response theory study, integrated with dynamics of the two-photon absorption of 4-nitro-4'-amino-trans-stilbene physisorbed on noble metal surfaces, considering two such surfaces, Ag(111) and Au(111), and two solvents, cyclohexane and water, as cases for demonstration. A few conclusions of general character could be drawn: While the geometrical change of the chromophore induced by the environment was found to notably alter (diminish) the two-photon absorption cross section in the polar medium, the effects of the metal surface and solvent on the electronic structure of the chromophore surpasses the geometrical effects and leads to a considerably enhanced two-photon absorption cross section in the polar solvent. This enhancement of two-photon absorption arises essentially from the metal charge image induced enlargement of the difference between the dipole moment of the excited state and the ground state. The orientation-dependence of the two-photon absorption is found to connect with the lateral rotation of the chromophore, where the two-photon absorption reaches its maximum when the polarization of the incident light coincides with the long-axis of the chromophore. Our results demonstrate a distinct enhancement of the two-photon absorption by a metal surface and a polar medium and envisage the employment of metal-chromophore composite materials for future development of nonlinear optical materials with desirable properties.

  • 167. Liin, Sara
    et al.
    Gabrielsson, Anders
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elinder, Fredrik
    Lindahl, Erik
    The Molecular Mechanism of the Dual Spider Toxin Effect on Voltage Gated K+ Channels2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 3, s. 107A-107AArtikel i tidskrift (Övrigt vetenskapligt)
  • 168.
    Linares, Mathieu
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sun, Haofan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. East China Univ Sci & Technol, Shanghai Key Lab Funct Mat Chem, Dept Chem & Mol Engn, Shanghai 200237, Peoples R China.
    Biler, Michal
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Andreasson, Joakim
    Chalmers Univ Technol, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Norman, P.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra2019Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 7, s. 3637-3643Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.

  • 169.
    Lindahl, V.
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Lidmar, Jack
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Riemann metric approach to optimal sampling of multidimensional free-energy landscapes2018Ingår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, nr 2, artikel-id 023312Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g., large molecules or spin glasses. In simulations this usually requires sampling conformational transitions or phase transitions, but efficient sampling is often difficult to attain due to the roughness of the energy landscape. For Boltzmann distributions, crossing rates decrease exponentially with free-energy barrier heights. Thus, exponential acceleration can be achieved in simulations by applying an artificial bias along λ tuned such that a flat target distribution is obtained. A flat distribution is, however, an ambiguous concept unless a proper metric is used and is generally suboptimal. Here we propose a multidimensional Riemann metric, which takes the local diffusion into account, and redefine uniform sampling such that it is invariant under nonlinear coordinate transformations. We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by the metric. We demonstrate that for complex problems, such as molecular dynamics simulations of DNA base-pair opening, sampling uniformly according to the metric, which can be calculated without significant computational overhead, improves sampling efficiency by 50%-70%.

  • 170.
    Lindahl, Viveca
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gourdon, Pontus
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function2018Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikel-id 2995Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.

  • 171.
    Lindahl, Viveca
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Villa, Alessandra
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sequence dependency of canonical base pair opening in the DNA double helix2017Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, nr 4, artikel-id e1005463Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.

  • 172.
    Lindvall, Jenny
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Bolin Ctr Climate Res, Dept Meteorol, Stockholm, Sweden..
    Svensson, Gunilla
    KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Bolin Ctr Climate Res, Dept Meteorol, Stockholm, Sweden.
    Caballero, Rodrigo
    KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Bolin Ctr Climate Res, Dept Meteorol, Stockholm, Sweden.
    The impact of changes in parameterizations of surface drag and vertical diffusion on the large-scale circulation in the Community Atmosphere Model (CAM5)2017Ingår i: Climate Dynamics, ISSN 0930-7575, E-ISSN 1432-0894, Vol. 48, nr 11, s. 3741-3758Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Simulations with the Community Atmosphere Model version 5 (CAM5) are used to analyze the sensitivity of the large-scale circulation to changes in parameterizations of orographic surface drag and vertical diffusion. Many GCMs and NWP models use enhanced turbulent mixing in stable conditions to improve simulations, while CAM5 cuts off all turbulence at high stabilities and instead employs a strong orographic surface stress parameterization, known as turbulent mountain stress (TMS). TMS completely dominates the surface stress over land and reduces the near-surface wind speeds compared to simulations without TMS. It is found that TMS is generally beneficial for the large-scale circulation as it improves zonal wind speeds, Arctic sea level pressure and zonal anomalies of the 500-hPa stream function, compared to ERA-Interim. It also alleviates atmospheric blocking frequency biases in the Northern Hemisphere. Using a scheme that instead allows for a modest increase of turbulent diffusion at higher stabilities only in the planetary boundary layer (PBL) appears to in some aspects have a similar, although much smaller, beneficial effect as TMS. Enhanced mixing throughout the atmospheric column, however, degrades the CAM5 simulation. Evaluating the simulations in comparison with detailed measurements at two locations reveals that TMS is detrimental for the PBL at the flat grassland ARM Southern Great Plains site, giving too strong wind turning and too deep PBLs. At the Sodankyla forest site, the effect of TMS is smaller due to the larger local vegetation roughness. At both sites, all simulations substantially overestimate the boundary layer ageostrophic flow.

  • 173. Liu, H.
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tanushev, N. M.
    Sobolev and max norm error estimates for Gaussian beam superpositions2016Ingår i: Communications in Mathematical Sciences, ISSN 1539-6746, E-ISSN 1945-0796, Vol. 14, nr 7, s. 2037-2072Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This work is concerned with the accuracy of Gaussian beam superpositions, which are asymptotically valid high frequency solutions to linear hyperbolic partial differential equations and the Schrödinger equation. We derive Sobolev and max norms estimates for the difference between an exact solution and the corresponding Gaussian beam approximation, in terms of the short wavelength e. The estimates are performed for the scalar wave equation and the Schrödinger equation. Our result demonstrates that a Gaussian beam superposition with kth order beams converges to the exact solution as O(εk/2-s) in order s Sobolev norms. This result is valid in any number of spatial dimensions and it is unaffected by the presence of caustics in the solution. In max norm, we show that away from caustics the convergence rate is O(ε⌈k/2⌉) and away from the essential support of the solution, the convergence is spectral in ε. However, in the neighborhood of a caustic point we are only able to show the slower, and dimensional dependent, rate O(ε(k-n)/2) in n spatial dimensions.

  • 174. Liu, Hailiang
    et al.
    Ralston, James
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tanushev, Nicolay M.
    Gaussian beam methods for the helmholtz equation2014Ingår i: SIAM Journal on Applied Mathematics, ISSN 0036-1399, E-ISSN 1095-712X, Vol. 74, nr 3, s. 771-793Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work we construct Gaussian beam approximations to solutions of the high frequency Helmholtz equation with a localized source. Under the assumption of nontrapping rays we show error estimates between the exact outgoing solution and Gaussian beams in terms of the wave number k, both for single beams and superposition of beams. The main result is that the relative local L-2 error in the beam approximations decay as k(-N/2) independent of dimension and presence of caustics for Nth order beams.

  • 175. Liu, Hailiang
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tanushev, Nicolay M.
    Error estimates for Gaussian beam superpositions2013Ingår i: Mathematics of Computation, ISSN 0025-5718, E-ISSN 1088-6842, Vol. 82, nr 282, s. 919-952Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Gaussian beams are asymptotically valid high frequency solutions to hyperbolic partial differential equations, concentrated on a single curve through the physical domain. They can also be extended to some dispersive wave equations, such as the Schrodinger equation. Superpositions of Gaussian beams provide a powerful tool to generate more general high frequency solutions that are not necessarily concentrated on a single curve. This work is concerned with the accuracy of Gaussian beam superpositions in terms of the wavelength epsilon. We present a systematic construction of Gaussian beam superpositions for all strictly hyperbolic and Schrodinger equations subject to highly oscillatory initial data of the form Ae(i Phi/) (epsilon). Through a careful estimate of an oscillatory integral operator, we prove that the k-th order Gaussian beam superposition converges to the original wave field at a rate proportional to epsilon(k/2) in the appropriate norm dictated by the well-posedness estimate. In particular, we prove that the Gaussian beam superposition converges at this rate for the acoustic wave equation in the standard, epsilon-scaled, energy norm and for the Schrodinger equation in the L-2 norm. The obtained results are valid for any number of spatial dimensions and are unaffected by the presence of caustics. We present a numerical study of convergence for the constant coefficient acoustic wave equation in R-2 to analyze the sharpness of the theoretical results.

  • 176.
    Lizarraga, Raquel
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Pan, Fan
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Bergqvist, Lars
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Holmstrom, Erik
    Gercsi, Zsolt
    Vitos, Levente
    First Principles Theory of the hcp-fcc Phase Transition in Cobalt2017Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikel-id 3778Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Identifying the forces that drive a phase transition is always challenging. The hcp-fcc phase transition that occurs in cobalt at similar to 700 K has not yet been fully understood, although early theoretical studies have suggested that magnetism plays a main role in the stabilization of the fcc phase at high temperatures. Here, we perform a first principles study of the free energies of these two phases, which we break into contributions arising from the vibration of the lattice, electronic and magnetic systems and volume expansion. Our analysis of the energy of the phases shows that magnetic effects alone cannot drive the fcc-hcp transition in Co and that the largest contribution to the stabilization of the fcc phase comes from the vibration of the ionic lattice. By including all the contributions to the free energy considered here we obtain a theoretical transition temperature of 825 K.

  • 177. Locht, I. L. M.
    et al.
    Di Marco, I.
    Garnerone, S.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Battiato, M.
    Ultrafast magnetization dynamics: Microscopic electronic configurations and ultrafast spectroscopy2015Ingår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, nr 6, artikel-id 064403Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We provide an approach for the identification of the electronic and magnetic configurations of ferromagnetic Fe after an ultrafast decrease or increase of the magnetization. The model is based on the well-grounded assumption that, after an ultrafast variation of the magnetization, the system achieves a partial thermal equilibrium. With statistical arguments we show that the magnetic configurations are qualitatively different in the case of reduced or increased magnetization. The predicted magnetic configurations are then used to compute the dielectric response at the 3p (M) absorption edge, which is directly related to the changes observed in the experimental T-MOKE data. The good qualitative agreement between theory and experiment offers a substantial support for the validity of the model, and to the very existence of an ultrafast increase of the magnetization.

  • 178. Locht, I. L. M.
    et al.
    Kvashnin, Y. O.
    Rodrigues, D. C. M.
    Pereiro, M.
    Bergman, A.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lichtenstein, A. I.
    Katsnelson, M. I.
    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.
    Klautau, A. B.
    Johansson, Börje
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Uppsala University, Sweden.
    Di Marco, I.
    Eriksson, O.
    Standard model of the rare earths analyzed from the Hubbard I approximation2016Ingår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 94, nr 8, artikel-id 085137Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work we examine critically the electronic structure of the rare-earth elements by use of the so-called Hubbard I approximation. From the theoretical side all measured features of both occupied and unoccupied states are reproduced, without significant deviations between observations and theory. We also examine cohesive properties like the equilibrium volume and bulk modulus, where we find, in general, a good agreement between theory andmeasurements. In addition, we have reproduced the spin and orbital moments of these elements as they are reflected from measurements of the saturation moment. We have also employed the Hubbard I approximation to extract the interatomic exchange parameters of an effective spin Hamiltonian for the heavy rare earths. We show that the Hubbard I approximation gives results which are consistent with calculations where 4f electrons are treated as core states for Gd. The latter approach was also used to address the series of the heavy/late rare earths. Via Monte Carlo simulations we obtained ordering temperatures which reproduce measurements within about 20%. We have further illustrated the accuracy of these exchange parameters by comparing measured and calculated magnetic configurations for the heavy rare earths and the magnon dispersion for Gd. The Hubbard I approximation is compared to other theories of the electronic structure, and we argue that it is superior. We discuss the relevance of our results in general and how this makes it possible to treat the electronic structure of materials containing rare-earth elements, such as permanent magnets, magnetostrictive compounds, photovoltaics, optical fibers, topological insulators, and molecular magnets.

  • 179.
    Lundborg, Magnus
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Apostolov, Rossen
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Spångberg, Daniel
    Gärdenäs, Anders
    van der Spoel, David
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations2014Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, nr 3, s. 260-269Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes.

  • 180.
    Lundborg, Magnus
    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. Center for Biomembrane Research, Stockholm University, Sweden .
    Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations2015Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 3, s. 810-823Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.

  • 181.
    Lundborg, Magnus
    et al.
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Narangifard, Ali
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden.;Karolinska Inst, Dept Med, Solna MedS, Solna, Sweden..
    Wennberg, Christian L.
    KTH, Skolan för teknikvetenskap (SCI), Fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.
    Daneholt, Bertil
    Karolinska Inst, Dept Cell & Mol Biol CMB, Stockholm, Sweden..
    Norlén, Lars
    Karolinska Inst, Dept Cell & Mol Biol CMB, Stockholm, Sweden.;Karolinska Univ Hosp, Dermatol Clin, Stockholm, Sweden..
    Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation2018Ingår i: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 203, nr 2, s. 149-161Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems.

  • 182.
    Lundborg, Magnus
    et al.
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Wennberg, Christian L.
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Narangifard, Ali
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden.;Karolinska Inst, Solna MedS, Dept Med, Solna, Sweden..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.
    Norlén, Lars
    Karolinska Inst, Dept Cell & Mol Biol CMB, Solna, Sweden.;Karolinska Univ Hosp, Dermatol Clin, Solna, Sweden..
    Predicting drug permeability through skin using molecular dynamics simulation2018Ingår i: Journal of Controlled Release, ISSN 0168-3659, E-ISSN 1873-4995, Vol. 283, s. 269-279Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Understanding and predicting permeability of compounds through skin is of interest for transdermal delivery of drugs and for toxicity predictions of chemicals. We show, using a new atomistic molecular dynamics model of the skin's barrier structure, itself validated against near-native cryo-electron microscopy data from human skin, that skin permeability to the reference compounds benzene, DMSO (dimethyl sulfoxide), ethanol, codeine, naproxen, nicotine, testosterone and water can be predicted. The permeability results were validated against skin permeability data in the literature. We have investigated the relation between skin barrier molecular organization and permeability using atomistic molecular dynamics simulation. Furthermore, it is shown that the calculated mechanism of action differs between the five skin penetration enhancers Azone, DMSO, oleic acid, stearic acid and water. The permeability enhancing effect of a given penetration enhancer depends on the permeating compound and on the concentration of penetration enhancer inside the skin's barrier structure. The presented method may open the door for computer based screening of the permeation of drugs and toxic compounds through skin.

  • 183.
    Löytynoja, Tuomas
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Oulu, Finland.
    Niskanen, J.
    Jankala, K.
    Vahtras, Olav
    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.
    Quantum Mechanics/Molecular Mechanics Modeling of Photoelectron Spectra: The Carbon 1s Core-Electron Binding Energies of Ethanol-Water Solutions2014Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 46, s. 13217-13225Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Using ethanolwater solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solutesolvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics modelelectrostatic, polarization, and van der Waalswith atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  • 184.
    Mahani, Mohammad Reza
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Mirsakiyeva, Amina
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Breakdown of Polarons in Conducting Polymers at Device Field Strengths2017Ingår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 121, nr 19, s. 10317-10324Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Conducting polymers have become standard engineering materials used in many electronic devices. Despite this, there is a lack of understanding of the microscopic origin of the conducting properties, especially at realistic device field strengths. We present simulations of doped poly(p-phenylene) (PPP) using a Su-Schrieffer-Heeger (SSH) tight-binding model, with the electric field included in the Hamiltonian through a time-dependent vector potential via Peierls substitution of the phase factor. We find that polarons typically break down within less than a picosecond after the field has been switched on, already for electric fields as low as around 1.6 mV/angstrom. This is a field strength common in many flexible organic electronic devices. Our results challenge the relevance of the polaron as charge carrier in conducting polymers for a wide range of applications.

  • 185.
    Mahani, Mohammad Reza
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Mirsakiyeva, Amina
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Charge transport via polarons in doped poly(p-phenylene) with impurityManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

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

  • 186.
    Mahmudi, Owais
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sennblad, Bengt
    Arvestad, Lars
    Nowick, Katja
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Gene-Pseudogene Evolution: a Probalitistic ApproachManuskript (preprint) (Övrigt vetenskapligt)
  • 187.
    Mahmudi, Owais
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sjöstrand, Joel
    Sennblad, Bengt
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Genome-wide probabilistic reconciliation analysis across vertebrates2013Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 14, s. S10-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 188.
    Malenova, Gabriela
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Motamed, M.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Stochastic regularity of a quadratic observable of high-frequency waves2017Ingår i: RESEARCH IN THE MATHEMATICAL SCIENCES, ISSN 2197-9847, Vol. 4, artikel-id UNSP 3Artikel i tidskrift (Refereegranskat)
  • 189.
    Malenova, Gabriela
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Motamed, Mohammad
    Department of Mathematics and Statistics, The University of New Mexico, Albuquerque, NM 87131, USA.
    Runborg, Olof
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
    Regularity of stochastic observables in Gaussian beam superposition of high-frequency waves2017Ingår i: Research in mathematical sciences, ISSN 2197-9847Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

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

  • 190.
    Malenova, Gabriela
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Stochastic regularity of general quadratic observables of high frequency wavesManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

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

  • 191.
    Malm, Johan
    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.
    Fischer, Paul F.
    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.
    Stabilization of the Spectral Element Method in Convection Dominated Flows by Recovery of Skew-Symmetry2013Ingår i: Journal of Scientific Computing, ISSN 0885-7474, E-ISSN 1573-7691, Vol. 57, nr 2, s. 254-277Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 192.
    Marin, Oana
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tornberg, Anna-Karin
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Corrected trapezoidal rules for a class of singular functions2014Ingår i: IMA Journal of Numerical Analysis, ISSN 0272-4979, E-ISSN 1464-3642, Vol. 34, nr 4, s. 1509-1540Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 193.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Henty, David
    Heisey, Katherine
    Fischer, Paul
    OpenACC acceleration of the Nek5000 spectral element code2015Ingår i: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 29, nr 3, s. 311-319Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 194. McIlwain, Sean
    et al.
    Tamura, Kaipo
    Kertesz-Farkas, Attila
    Grant, Charles E.
    Diament, Benjamin
    Frewen, Barbara
    Howbert, J. Jeffry
    Hoopmann, Michael R.
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Eng, Jimmy K.
    MacCoss, Michael J.
    Noble, William Stafford
    Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis2014Ingår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, nr 10, s. 4488-4491Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 195.
    Mele, Giampaolo
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Jarlebring, Elias
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    On restarting the tensor infinite Arnoldi method2018Ingår i: BIT Numerical Mathematics, ISSN 0006-3835, E-ISSN 1572-9125, Vol. 58, nr 1, s. 133-162Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 196. Mikkelsen, R. F.
    et al.
    Sarmast, Sasan
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sørensen, J. N.
    Rotor aerodynamic power limits at low tip speed ratio using CFD2014Ingår i: SCIENCE OF MAKING TORQUE FROM WIND 2014 (TORQUE 2014), 2014, Vol. 524, nr 1, artikel-id 012099Konferensbidrag (Refereegranskat)
    Abstract [en]

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

  • 197.
    Mirsakiyeva, Amina
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Botkina, D.
    Elgammal, Karim
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Ten, Assel
    Hugosson, Håkan
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Yu, Valentina
    Experimental and ab initio studies of the novel piperidine-containing acetylene glycolsManuskript (preprint) (Övrigt vetenskapligt)
  • 198.
    Mirsakiyeva, Amina
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Kazakh-British Technical University, Kazakhstan.
    Botkina, Darya
    KTH, Skolan för industriell teknik och management (ITM), Industriell produktion. Institute of Chemical Sciences, Kazakhstan.
    Elgammal, Karim
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ten, Assel
    Hugosson, Håkan W.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik.
    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.
    Yu, Valentina
    Experimental and density functional theory studies of some novel piperidine-containing acetylene glycols2016Ingår i: ARKIVOC, ISSN 1551-7004, E-ISSN 1551-7012, s. 86-99Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 199.
    Mirsakiyeva, Amina
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik.
    Hugosson, Håkan W.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. Univ Gävle, Sweden.
    Crispin, Xavier
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Quantum Molecular Dynamical Calculations of PEDOT 12-Oligomer and its Selenium and Tellurium Derivatives2017Ingår i: Journal of Electronic Materials, ISSN 0361-5235, E-ISSN 1543-186X, Vol. 46, nr 5, s. 3071-3075Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 200.
    Mirsakiyeva, Amina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Hugosson, Håkan W.
    Linares, Mathieu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. 5)Department of Physics and Astronomy, Materials Theory Division, Uppsala University.
    Temperature dependence of band gaps and conformational disorder in PEDOT and its selenium and tellurium derivatives: density functional calculations2017Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

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