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  • 351.
    Herrero-Garcia, Juan
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Nebot, M.
    Rius, N.
    Santamaria, A.
    Testing the Zee-Babu model via neutrino data, lepton flavour violation and direct searches at the LHC2016In: Nuclear and Particle Physics Proceedings, ISSN 2405-6014, Vol. 273-275, p. 1678-1684Article in journal (Refereed)
    Abstract [en]

    In this talk we discuss how the Zee-Babu model can be tested combining information from neutrino data, low-energy experiments and direct searches at the LHC. We update previous analysis in the light of the recent measurement of the neutrino mixing angle θ13 [1], the new MEG limits on μ→eγ [2], the lower bounds on doubly-charged scalars coming from LHC data [3, 4], and, of course, the discovery of a 125 GeV Higgs boson by ATLAS and CMS [5, 6]. In particular, we find that the new singly- and doubly-charged scalars are accessible at the second run of the LHC, yielding different signatures depending on the neutrino hierarchy and on the values of the phases. We also discuss in detail the stability of the potential.

  • 352.
    Herrero-Garcia, Juan
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Rius, Nuria
    Santamaria, Arcadi
    Higgs lepton flavour violation: UV completions and connection to neutrino masses2016In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, no 11, article id 084Article in journal (Refereed)
    Abstract [en]

    We study lepton violating Higgs (HLFV) decays, first from the effective field theory (EFT) point of view, and then analysing the different high-energy realizations of the operators of the EFT, highlighting the most promising models. We argue why two Higgs doublet models can have a BR(h -> tau mu) similar to 0:01, and why this rate is suppressed in all other realizations including vector-like leptons. We further discuss HLFV in the context of neutrino mass models: in most cases it is generated at one loop giving always BR (h -> tau mu) < 10(-4) and typically much less, which is beyond experimental reach. However, both the Zee model and extended left-right symmetric models contain extra SU(2) doublets coupled to leptons and could in principle account for the observed excess, with interesting connections between HLFV and neutrino parameters.

  • 353. Heusser, Stephanie A.
    et al.
    Howard, Rebecca J.
    Borghese, Cecilia M.
    Cullins, Madeline A.
    Brömstrup, Torben
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lee, Ui S.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Carlsson, Jens
    Harris, R. Adron
    Functional Validation of Virtual Screening for Novel Agents with General Anesthetic Action at Ligand-Gated Ion Channelss2013In: Molecular Pharmacology, ISSN 0026-895X, E-ISSN 1521-0111, Vol. 84, no 5, p. 670-678Article in journal (Refereed)
    Abstract [en]

    GABA(A) receptors play a crucial role in the actions of general anesthetics. The recently published crystal structure of the general anesthetic propofol bound to Gloeobacter violaceus ligand-gated ion channel (GLIC), a bacterial homolog of GABA(A) receptors, provided an opportunity to explore structure-based ligand discovery for pentameric ligand-gated ion channels (pLGICs). We used molecular docking of 153,000 commercially available compounds to identify molecules that interact with the propofol binding site in GLIC. In total, 29 compounds were selected for functional testing on recombinant GLIC, and 16 of these compounds modulated GLIC function. Active compounds were also tested on recombinant GABA(A) receptors, and point mutations around the presumed binding pocket were introduced into GLIC and GABA(A) receptors to test for binding specificity. The potency of active compounds was only weakly correlated with properties such as lipophilicity or molecular weight. One compound was found to mimic the actions of propofol on GLIC and GABA(A), and to be sensitive to mutations that reduce the action of propofol in both receptors. Mutant receptors also provided insight about the position of the binding sites and the relevance of the receptor's conformation for anesthetic actions. Overall, the findings support the feasibility of the use of virtual screening to discover allosteric modulators of pLGICs, and suggest that GLIC is a valid model system to identify novel GABA(A) receptor ligands.

  • 354. Heusser, Stephanie A.
    et al.
    Howard, Rebecca J.
    Pouya, Iman
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Klement, Göran
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Borghese, Cecilia
    Harris, R. Adron
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholms universitet.
    A Single Mutation in GLIC Reveals Both the Potentiating and the Inhibitory Nature of Propofol2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 3, p. 456A-456AArticle in journal (Other academic)
  • 355.
    Heusser, Stephanie A.
    et al.
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Lycksell, Marie
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Wang, Xueqing
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden.
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Lindahl, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Theoretical Physics. Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden.
    Flexibility of a Transmembrane Helix Underlies Dramatic Reversal of Net Anesthetic Effects in a Pentameric Ligand-Gated Ion Channel2018In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 488A-489AArticle in journal (Other academic)
  • 356. Heusser, Stephanie
    et al.
    Yoluk, Özge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Klement, Goran
    Reiderer, Erika
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Howard, Rebecca
    Functional Characterization of Neurotransmitter Activation and Modulation in a Nematode Model Ligand-gated Ion Channel2016In: Journal of Neurochemistry, ISSN 0022-3042, E-ISSN 1471-4159, Vol. 138, no 2, p. 243-253Article in journal (Refereed)
    Abstract [en]

    The superfamily of pentameric ligand-gated ion channels includes neurotransmitter receptors that mediate fast synaptic transmission in vertebrates, and are targets for drugs including alcohols, anesthetics, benzodiazepines and anticonvulsants. However, the mechanisms of ion channel opening, gating and modulation in these receptors leave many open questions, despite their pharmacological importance. Subtle conformational changes in both the extracellular and transmembrane domains are likely to influence channel opening, but have been difficult to characterize given the limited structural data available for human membrane proteins. Recent crystal structures of a modifiedCaenorhabditis elegans glutamate-gated chloride channel (GluCl) in multiple states offer an appealing model system for structure-function studies. However, the pharmacology of the crystallographic GluCl construct is not well established. To establish the functional relevance of this system, we used two-electrode voltage-clamp electrophysiology in Xenopus oocytes to characterize activation of crystallographic and native-like GluCl constructs by L-glutamate and ivermectin. We also tested modulation by ethanol and other anesthetic agents, and used site-directed mutagenesis to explore the role of a region of Loop F which was implicated in ligand gating by molecular dynamics simulations. Our findings indicate that the crystallographic construct functionally models concentration-dependent agonism and allosteric modulation of pharmacologically relevant receptors. Specific substitutions at residue Leu174 in loop F altered direct L-glutamate activation, consistent with computational evidence for this region's role in ligand binding. These insights demonstrate conservation of activation and modulation properties in this receptor family, and establish a framework for GluCl as a model system, including new possibilities for drug discovery.

  • 357.
    Hoglund, Niclas
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Jacobson, Olof
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Bell's Theorem and Inequalities, with Experimental Considerations2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Bell's theorem is an important milestone in the development of quantum mechanics.

    It draws a line between concepts such as realism and locality on the one hand and

    quantum mechanics on the other. Experimentally veried violations of Bell inequalities

    can yield important information about what assumptions can be made about physical

    reality. Experiments have been conducted for over 40 years, but have left loopholes open

    in their executions. It is of great interest to close these loopholes, and in order to do

    so, further experiments are needed. The objective of this project is to investigate the

    underlying, previous work in the eld and to formulate a proposal for a new experiment.

    To do this, the derivations of the original Bell inequality and the CHSH inequality are

    presented along with previously conducted experiments. Also presented is the EPR

    paradox from which sprung the original Bell inequality.

  • 358.
    Holmboe, Michael
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Bourg, Ian C.
    Interlayer diffusion in hydrated smectites - a molecular dynamics study2013In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 245, p. 163-GEOC-Article in journal (Other academic)
  • 359.
    Holmboe, Michael
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Bourg, Ian C.
    Molecular Dynamics Simulations of Water and Sodium Diffusion in Smectite Interlayer Nanopores as a Function of Pore Size and Temperature2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 2, p. 1001-1013Article in journal (Refereed)
    Abstract [en]

    The diffusion coefficients (D) of water and solutes in nanoporous Na-smectite clay barriers have been widely studied because of their importance in high-level radioactive waste (HLRW) management and in the isolation of contaminated sites. However, few measurements have been carried out at the high temperatures that are expected to occur in HLRW repositories. We address this knowledge gap by using molecular dynamics (MD) simulations to predict the temperature dependence of diffusion in clay interlayer nanopores, expressed as a pore scale activation energy of diffusion (E-a). Our sensitivity analysis shows that accurate prediction of pore scale D and E-a values requires careful consideration of the influence of pore size, simulation cell size, and clay structure flexibility on MD simulation results. We find that predicted D values in clay interlayer nanopores are insensitive to the size of the simulation cell (contrary to the behavior observed in simulation of bulk liquid water) but sensitive to the vibrational motions of clay atoms (particularly in the smallest pores investigated here, the one-, two-, and three-layer hydrates). Our predicted D and E-a values are consistent with experimental data. They reveal, for both water and Na+, that E-a increases by similar to 6 kJ mol(-1) with increasing confinement, when going from bulk liquid water to the one-layer hydrate of Na-montmorillonite.

  • 360.
    Holmgren, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Properties of superconducting states in s+is and s+d systems2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 361.
    Horemuz, Michal
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    – A study of the Langevin equation in a thermal ratchet model of the myosin V motor protein.2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 362. Howard, Rebecca J.
    et al.
    Heusser, Stephanie A.
    Yoluk, Ozge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Snow, Oliver
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. Stockholm Univ, Sweden.
    Klement, Göran
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. Stockholm Univ, Sweden.
    Mola, Alex R.
    Ruel, Travers M. D.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. Stockholm Univ, Sweden.
    Transmembrane Structural Determinants of Alcohol Binding and Modulation in a Model Ligand-Gated Ion Channel2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 554A-554AArticle in journal (Refereed)
  • 363. Howard, Rebecca J.
    et al.
    Murail, Samuel
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Broemstrup, Torben
    Horani, Suzzane
    Lee, Ui S.
    Ondricek, Kathryn E.
    Corringer, Pierre-Jean
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Bertaccini, Edward J.
    Trudell, James R.
    Harris, R. Adron
    Combined functional-computational approach to characterize sites of anesthetic modulation of ligand-gated ion channels2012In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Article in journal (Other academic)
  • 364.
    Howard, Rebecca J
    et al.
    University of Texas.
    Murail, Samuel
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Ondricek, Kathryn E
    University of Texas.
    Corringer, Pierre-Jean
    Institut Pasteur.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Trudell, James R
    Stanford University.
    Harris, R Adron
    University of Texas.
    Structural basis for alcohol modulation of a pentameric ligand-gated ion channel2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 29, p. 12149-54Article in journal (Refereed)
    Abstract [en]

    Despite its long history of use and abuse in human culture, the molecular basis for alcohol action in the brain is poorly understood. The recent determination of the atomic-scale structure of GLIC, a prokaryotic member of the pentameric ligand-gated ion channel (pLGIC) family, provides a unique opportunity to characterize the structural basis for modulation of these channels, many of which are alcohol targets in brain. We observed that GLIC recapitulates bimodal modulation by n-alcohols, similar to some eukaryotic pLGICs: methanol and ethanol weakly potentiated proton-activated currents in GLIC, whereas n-alcohols larger than ethanol inhibited them. Mapping of residues important to alcohol modulation of ionotropic receptors for glycine, γ-aminobutyric acid, and acetylcholine onto GLIC revealed their proximity to transmembrane cavities that may accommodate one or more alcohol molecules. Site-directed mutations in the pore-lining M2 helix allowed the identification of four residues that influence alcohol potentiation, with the direction of their effects reflecting α-helical structure. At one of the potentiation-enhancing residues, decreased side chain volume converted GLIC into a highly ethanol-sensitive channel, comparable to its eukaryotic relatives. Covalent labeling of M2 positions with an alcohol analog, a methanethiosulfonate reagent, further implicated residues at the extracellular end of the helix in alcohol binding. Molecular dynamics simulations elucidated the structural consequences of a potentiation-enhancing mutation and suggested a structural mechanism for alcohol potentiation via interaction with a transmembrane cavity previously termed the "linking tunnel." These results provide a unique structural model for independent potentiating and inhibitory interactions of n-alcohols with a pLGIC family member.

  • 365. Howard, Rebecca J.
    et al.
    Murail, Samuel
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Ondricek, Kathryn E.
    Corringer, Pierre-Jean
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Trudell, James R.
    Harris, R. Adron
    Structural Basis For Alcohol Modulation of Pentameric Ligand-Gated Ion Channels2012In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, no 3, p. 411A-411AArticle in journal (Other academic)
  • 366. Howard, Rebecca J.
    et al.
    Sauguet, Ludovic
    Brömstrup, Torben
    Swedish e-Science Resarch Centre.
    Murail, Samuel
    Lee, Ui S.
    Horani, Suzzane
    Trudell, James R.
    Corringer, Pierre-Jean
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Delarue, Marc
    Harris, R. Adron
    Alcohol and Anesthetic Binding to Pentameric Ligand-Gated Ion Channels Revealed in a Prokaryotic Model System2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 635A-636AArticle in journal (Other academic)
  • 367.
    Hu Boxi, David
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Von Martens, Dan
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Transmission Properties of an Electron in One Dimensional Crystals with Periodic Potentials2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In 2010, R. Olsen and G. Vignale, published a paper presenting a recursive method for

    calculating electron transmission probability for one dimensional periodic potentials. Based

    on their method, this thesis studies electron transmission in a one dimensional lattice of

    periodic potential barriers both using a classical and quantum mechanical description. The

    transmission is measured by the transmission probability of the system. The transmission

    probabilities are computed with regards to two separate variables, namely the number

    of potential barriers, i.e. the length of the lattice, and the wave number of the incident

    electron. These computations are made using rectangular and Dirac delta potential barriers

    respectively. Lastly, the paper expands on the area of disordered systems of periodic

    potentials by introducing irregularities in potential size and separation.

  • 368.
    Huang, Hao
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Perturbative and non-perturbative aspectsof Chern-Simons2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 369. Huang, L.
    et al.
    Skorodumova, N. V.
    Belonoshko, Anatoly B.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Johansson, Börje
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Carbon in iron phases under high pressure2005In: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 32, no 21Article in journal (Refereed)
    Abstract [en]

    The influence of carbon impurities on the properties of iron phases (bcc, hcp, dhcp, fcc) has been studied using the first-principles projector augmented-wave ( PAW) method for a wide pressure range. It is shown that the presence of similar to 6 at. % of interstitial carbon has a little effect on the calculated structural sequence of the iron phases under high pressure. The bcc ! hcp transition both for pure iron and iron containing carbon takes place around 9 GPa. According to the enthalpies comparison, the solubility of carbon into the iron solid is decreased by high pressure. The coexistence of iron carbide (Fe3C) + pure hcp Fe is most stable phase at high pressure compared with other phases. Based on the analysis of the pressure-density dependences for Fe3C and hcp Fe, we suggest that there might be some fraction of iron carbide present in the core.

  • 370. Huber, S. J.
    et al.
    Konstandin, Thomas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Prokopec, T.
    Schmidt, M. G.
    Baryogenesis in the MSSM, nMSSM and NMSSM2007In: Nuclear Physics A, ISSN 0375-9474, E-ISSN 1873-1554, Vol. 785, no 1-2, p. 206C-209CArticle in journal (Refereed)
  • 371. Huber, Stephan J.
    et al.
    Konstandin, Thomas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Production of gravitational waves in the nMSSM2008In: Journal of Cosmology and Astroparticle Physics, ISSN 1475-7516, E-ISSN 1475-7516, no 5, p. 017-Article in journal (Refereed)
    Abstract [en]

    During a strongly first-order phase transition gravitational waves are produced by bubble collisions and turbulent plasma motion. We analyze the relevant characteristics of the electroweak phase transition in the nMSSM to determine the generated gravitational wave signal. Additionally, we comment on correlations between the production of gravitational waves and baryogenesis. We conclude that the gravitational wave relic density in this model is generically too small to be detected in the near future by the LISA experiment. We also consider the case of a 'standard model' with dimension-six Higgs potential, which leads to a slightly stronger signal of gravitational waves.

  • 372. Huber, Stephan J.
    et al.
    Konstandin, Thomas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Prokopec, Tomislav
    Schmidt, Michael G.
    Electroweak phase transition and baryogenesis in the nMSSM2006In: Nuclear Physics B, ISSN 0550-3213, E-ISSN 1873-1562, Vol. 757, no 1-2, p. 172-196Article in journal (Refereed)
    Abstract [en]

    We analyze the nMSSM with CP violation in the singlet sector. We study the static and dynamical properties of the electroweak phase transition. We conclude that electroweak baryogenesis in this model is generic in the sense that if the present limits on the mass spectrum are applied, no severe additional tuning is required to obtain a strong first-order phase transition and to generate a sufficient baryon asymmetry. For this we determine the shape of the nucleating bubbles, including the profiles of CP-violating phases. The baryon asymmetry is calculated using the advanced transport theory to first and second order in gradient expansion presented recently. Still, first and second generation sfermions must be heavy to avoid large electric dipole moments.

  • 373.
    Hultquist, Gunnar
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Graham, M. J.
    Szakalos, P.
    Sproule, G. I.
    Rosengren, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Gråsjö, L..
    Hydrogen gas production during corrosion of copper by water2011In: Corrosion Science, ISSN 0010-938X, E-ISSN 1879-0496, Vol. 53, no 1, p. 310-319Article in journal (Refereed)
    Abstract [en]

    This paper considers the corrosion of copper in water by (1) short term open system weight measurements and (2) long term closed system immersion in distilled water (13 800 h) without O-2 at 21-55 degrees C In the latter experiments the hydrogen gas pressure is measured above the immersed copper and approaches similar to 10(-3) bar at equilibrium This pressure is mostly due to copper corrosion and greatly exceeds that in ambient air Accordingly this measured hydrogen pressure from copper corrosion increases with temperature and has the same dependency as the concentration of OH- in the ion product [OH-] [H+].

  • 374.
    Hultquist, Gunnar
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Corrosion Science.
    Szakalos, P.
    Graham, M. J.
    Belonoshko, A. B.
    Rosengren, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Reply to Lars O. Werme et al.: "Comments on 'Water Corrodes Copper'"2010In: Catalysis Letters, ISSN 1011-372X, E-ISSN 1572-879X, Vol. 135, no 3-4, p. 167-168Article in journal (Refereed)
  • 375.
    Hultquist, Gunnar
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Szakalos, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Graham, M. J.
    Belonoshko, Antoly B.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Sproule, G. I.
    Grasjo, L.
    Dorogokupets, P.
    Danilov, B.
    Aastrup, T.
    Wikmark, G.
    Chuah, G. K.
    Eriksson, Jan Christer
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Rosengren, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Water Corrodes Copper2009In: Catalysis Letters, ISSN 1011-372X, E-ISSN 1572-879X, Vol. 132, no 3-4, p. 311-316Article in journal (Refereed)
    Abstract [en]

    According to a current concept, copper canisters of thickness 0.05 m will be safe for nuclear waste containment for 100,000 years. We show that more than 1 m copper thickness might be required for 100,000 years durability based on water exposures of copper for 20 h, 7 weeks, 15 years, and 333 years. An observed evolution of hydrogen which involves heterogeneous catalysis of molecular hydrogen, first principles simulations, thermodynamic considerations and corrosion product characterization provide further evidence that water corrodes copper resulting in the formation of a copper hydroxide. These findings cast additional doubt on copper for nuclear waste containment and other important applications.

  • 376.
    Hutter, Carsten
    et al.
    Stockholm University, Physics.
    Stannigel, Kai
    Stockholm University, Physics.
    Tholén, Erik
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Lidmar, Jack
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Haviland, David
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Josephson junction transmission lines as tunable artificial crystals2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 83, no 1, p. 014511-Article in journal (Refereed)
    Abstract [en]

    We investigate one-dimensional Josephson junction arrays with generalized unit cells, beyond a single junction or SQUID, as a circuit approach to engineer band gaps. Within a specific frequency range, of the order of the single junction plasma frequency, the dispersion relation becomes gapped and the impedance becomes purely imaginary. We derive the parameter dependence of this gap and suggest designs to lower it to microwave frequencies. The gap can be tuned in a wide frequency range by applying external flux, and persists in the presence of small imperfections. These arrays, which can be thought of as tunable artificial crystals, may find use in applications ranging filters to the protection of quantum bits.

  • 377.
    Hällgren, Tomas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Aspects of Dimensional Deconstruction and Neutrino Physics2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The existence of at or curved extra spatial dimensions provides new insights into several of the problems which face the Standard Model of particle physics, including the gauge hierarchy problem, the smallness of neutrino masses, and the dark matter problem. However, higher-dimensional gauge theories are not renormalizable and can only be considered as low-energy effective theories, with limited applicability. Dimensional deconstruction provides a class of manifestly gauge invariant possible ultraviolet completions of higher-dimensional gauge theories, formulated within conventional quantum eld theory. In dimensional deconstruction, the fundamental theory is a four-dimensional quantum eld theory and extra spatial dimensions are generated dynamically at low energies. In this thesis, we study di erent applications of dimensional deconstruction in the contexts of neutrino masses, mixing and oscillations, Kaluza{Klein dark matter, and e ective eld theories for discretized higher-dimensional gravity.

    A different possibility to understand the smallness of neutrino masses is provided by the see-saw mechanism. This is a genuinely four-dimensional mechanism, where the light neutrino masses are induced by the addition of heavy right-handed Majorana neutrinos or by other heavy degrees of freedom, such as scalar SU(2)L triplet elds. It has the attractive feature of simultaneously providing a mechanism for generating the observed baryon asymmetry of the Universe. We study in this context a specific left-right symmetric see-saw model.

  • 378.
    Hällgren, Tomas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Kaluza-klein dark matter from deconstructed universal extra dimensions2007In: SUSY06: 14th International Conference on Supersymmetry and the Unification of Fundamental Interactions, American Institute of Physics (AIP), 2007, p. 652-655Conference paper (Refereed)
    Abstract [en]

    We consider Kaluza-Klein dark matter from deconstructed or latticized universal extra dimensions and study in this model the positron flux from Kaluza-Klein dark matter annihilation in the galactic halo.

  • 379.
    Hällgren, Tomas
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Konstandin, Thomas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Ohlsson, Tommy
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Triplet leptogenesis in left-right symmetric seesaw models2008In: Journal of Cosmology and Astroparticle Physics, ISSN 1475-7516, E-ISSN 1475-7516, Vol. 2008, no 01, p. 014-Article in journal (Refereed)
    Abstract [en]

    We discuss scalar triplet leptogenesis in a specific left-right symmetric seesaw model. We show that the Majorana phases that are present in the model can be effectively used to saturate the existing upper limit on the CP-asymmetry of the triplets. We solve the relevant Boltzmann equations and analyze the viability of triplet leptogenesis. It is known for this kind of scenario that the efficiency of leptogenesis is maximal if there exists a hierarchy between the branching ratios of the triplet decays into leptons and Higgs particles. We show that triplet leptogenesis typically favors branching ratios with not too strong hierarchies, since maximal efficiency can only be obtained at the expense of suppressed CP-asymmetries.

  • 380.
    Hällgren, Tomas
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Ohlsson, Tommy
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Indirect detection of Kaluza-Klein dark matter from latticized universal dimensions2006In: Journal of Cosmology and Astroparticle Physics, ISSN 1475-7516, E-ISSN 1475-7516, Vol. 2006, no 06, p. 014-Article in journal (Refereed)
    Abstract [en]

    We consider Kaluza-Klein dark matter from latticized universal dimensions. We investigate two different lattice models, where the models differ in the choice of boundary conditions. The models reproduce relevant features of the continuum model for Kaluza-Klein dark matter. For the model with simple boundary conditions, this is the case even for a model with only a few lattice sites. We study the effects of the latticization on the differential flux of positrons from annihilation of Kaluza-Klein dark matter in the galactic halo. We find that for different choices of the compactification radius, the differential positron flux rapidly converges to the continuum model results as a function of the number of lattice sites. In addition, we consider the prospects for upcoming space-based experiments such as PAMELA and AMS-02 to probe the latticization effect.

  • 381.
    Hällgren, Tomas
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Mathematical Physics.
    Ohlsson, Tommy
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Seidl, Gerhart
    Department of Physics, Oklahoma State University.
    Neutrino oscillations in deconstructed dimensions2005In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, Vol. 2005, no 02, p. 049-Article in journal (Refereed)
    Abstract [en]

    We present a model for neutrino oscillations in the presence of a deconstructed non-gravitational large extra dimension compactified on the boundary of a two-dimensional disk. In the deconstructed phase, sub-mm lattice spacings are generated from the hierarchy of energy scales between similar to 1 TeV and the usual B - L breaking scale similar to 10(15) GeV. Here, short-distance cutoffs down to similar to 1eV are motivated by the strong coupling behavior of gravity in local discrete extra dimensions. This could make it possible to probe the discretization of extra dimensions and non-trivial field configurations in theory spaces which have only a few sites, i.e., for coarse latticizations. Thus, the model has relevance to present and future precision neutrino oscillation experiments.

  • 382. Jackson, A D
    et al.
    Kavoulakis, G M
    Lundh, Emil
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Stability of the solutions of the Gross-Pitaevskii equation2005In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 72, no 5, p. 053617-Article in journal (Refereed)
    Abstract [en]

    We examine the static and dynamic stability of the solutions of the Gross-Pitaevskii equation and demonstrate the intimate connection between them. All salient features related to dynamic stability are reflected systematically in static properties. We find, for example, the obvious result that static stability always implies dynamic stability and present a simple explanation of the fact that dynamic stability can exist even in the presence of static instability.

  • 383.
    Janmark, Jonatan
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Quantum Search on Strongly Regular Graphs2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 384. Jiang, X.
    et al.
    Andersson, Magnus
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Chau, B. T.
    Wong, L. Y.
    Villafuerte, M. K. R.
    Kaback, H. R.
    Role of Conserved Gly-Gly Pairs on the Periplasmic Side of LacY2016In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 55, no 31, p. 4326-4332Article in journal (Refereed)
    Abstract [en]

    On the periplasmic side of LacY, two conserved Gly-Gly pairs in helices II and XI (Gly46 and Gly370, respectively) and helices V and VIII (Gly159 and Gly262, respectively) allow close packing of each helix pair in the outward (periplasmic)-closed conformation. Previous studies demonstrate that replacing one Gly residue in each Gly-Gly pair with Trp leads to opening of the periplasmic cavity with abrogation of transport activity, but an increased rate of galactoside binding. To further investigate the role of the Gly-Gly pairs, 11 double-replacement mutants were constructed for each pair at positions 46 (helix II) and 262 (helix VIII). Replacement with Ala or Ser results in decreased but significant transport activity, while replacements with Thr, Val, Leu, Asn, Gln, Tyr, Trp, Glu, or Lys exhibit very little or no transport. Remarkably, however, the double mutants bind galactoside with affinities 10-20-fold higher than that of the pseudo-WT or WT LacY. Moreover, site-directed alkylation of a periplasmic Cys replacement indicates that the periplasmic cavity becomes readily accessible in the double-replacement mutants. Molecular dynamics simulations with the WT and double-Leu mutant in the inward-open/outward-closed conformation provide support for this interpretation. 

  • 385.
    Johansson, Petter
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Carlson, Andreas
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Water-substrate physico-chemistry in wetting dynamics2015In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 781, p. 695-711Article in journal (Refereed)
    Abstract [en]

    We consider the wetting of water droplets on substrates with different chemical composition and molecular spacing, but with an identical equilibrium contact angle. A combined approach of large-scale molecular dynamics simulations and a continuum phase field model allows us to identify and quantify the influence of the microscopic physics at the contact line on the macroscopic droplet dynamics. We show that the substrate physico-chemistry, in particular hydrogen bonding, can significantly alter the flow. Since the material parameters are systematically derived from the atomistic simulations, our continuum model has only one adjustable parameter, which appears as a friction factor at the contact line. The continuum model approaches the atomistic wetting rate only when we adjust this contact line friction factor. However, the flow appears to he qualitatively different when comparing the atomistic and continuum models, highlighting that non-trivial continuum effects can come into play near the interface of the wetting front.

  • 386.
    Johansson, Petter
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Khartsev, Sergiy
    KTH, School of Information and Communication Technology (ICT), Material Physics, Material Physics, MF.
    Grishin, Alexander M.
    KTH, School of Information and Communication Technology (ICT), Material Physics.
    Comparison of Bi3Fe5O12 film giant Faraday rotators grown on (111) and (001) Gd3Ga5O12 single crystals2006In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 515, no 2, p. 477-480Article in journal (Refereed)
    Abstract [en]

    Bismuth iron garnet (Bi3Fe5O12, BIG) epitaxial thin films were grown on single crystal (Gd3Ga5O12, GGG) (111) and (001) substrates by rf-magnetron sputtering technique. Processing parameters have been optimized to obtain high deposition rate (2.74 mu m/h) and the surface rms roughness less than 10 nm. X-ray diffraction reveals films epitaxial quality: exclusive (111) or (00 1) orientation with narrow rocking curves and strong in-plane texture. Films possess low optical loss and magneto-optical Faraday rotation (FR) as high as 5 deg/mu m at 677 nm wavelength. Comparative analysis of films grown on (111) and (001) substrates clearly shows significant superiority of BIG/GGG(001) film. For this film, the coercive field similar to 100 Oe appears to be 2.5 times lower while the optical transmission to be 10% higher than that for BIG/GGG(111) film. Enhanced magneto-optical performance of BIG/GGG(001) films relies upon better accommodation of the film-to-substrate mismatch strain through the tetragonal BIG lattice distortions compared to the rhombohedral one in BIG/GGG(111) films.

  • 387.
    Jägrell, Linus
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Geometry of the Lunin-Maldacena metric2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 388.
    Kahl, Sören
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Grishin, Alexander M.
    KTH, Superseded Departments, Microelectronics and Information Technology, IMIT.
    Enhanced Faraday rotation in all-garnet magneto-optical photonic crystal2004In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 84, no 9, p. 1438-1440Article in journal (Refereed)
    Abstract [en]

    Research on magneto-optical photonic crystals has so far been focused on theoretical investigations, because suitable multilayers of iron garnet, the most promising material, have not been readily available. We report the preparation and characterization of a one-dimensional magneto-optical photonic crystal composed of 17 heteroepitaxial layers of bismuth iron garnet and yttrium iron garnet. The magneto-optical Faraday rotation was increased by 140% while transmission decreased by just 16% at the design wavelength of 750 nm as compared with a single-layer bismuth iron garnet film of equivalent thickness. The sample is free of cracks, and good agreement of simulated and experimental spectra of optical transmission and Faraday rotation indicate high quality of the sample and robustness of the preparation technique.

  • 389.
    Kalkitsas, Nikolaos
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Jäderlund, Thom
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Simulation of Dark Matter Using micrOMEGAs2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Weakly interactive massive particles (WIMPs) are one of the most popular dark matter candidates and in our study we have decided on a WIMP based model due to its accurate predictions of the dark matter (DM) relic density. To determine a possible WIMP, we have used the minimal supersymmetric model (MSSM), an extension of superymmetry (SUSY). Using micrOMEGAs we have made predictions of the direct and indirect detection for two different sets of parameters for a MSSM model considering the neutralino as the lightest supersymmetric particle (LSP). The results showed a discrete difference for the two sets of parameters in order of magnitude and the energy range, experimental data can rule in favour of one of the sets accordingly. We also found that it was preferable to have indirect detectors aimed at the Sun rather than the Earth.

  • 390.
    Karis, Klas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    The Free Energy of Vesicular Transmembrane Lipid Transfer Studied With Molecular Dynamics Simulations2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 391.
    Karis, Klas
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Merzan, Deborah
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Wärnhjelm, Jacob
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Electron Propagation in Periodic Potentials2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In this bachelor thesis we study the propagation of electrons in crystals. The crystalline

    structure is modeled as a one dimensional periodic potential primarily composed of delta

    function potential barriers.

    We use two different models to describe how a particle behaves in such a periodic

    structure. The first model is the Kronig Penney model described by S. Gasiorowicz in

    [

    1]. The second model is described by Olsen and Vignale in the article "The Quantum

    mechanics of electric conduction in crystals" [

    3]. We show that there exists certain ranges

    of energy for which electron propagation can occur, namely the allowed energy bands separeted

    by regions of forbidden energies. In addition, we solve the Schrödinger equation

    numerically for some simple cases and reproduce some of the results seen from the two

    mentioned models.

  • 392.
    Kasimova, Marina
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Yazici, Aysenur
    Granata, Daniele
    Rohacs, Tibor
    Carnevale, Vincenzo
    Dynamic Solvation of Protein Cavities Underlies TRPV1 Gating2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 466A-466AArticle in journal (Refereed)
  • 393. Kasson, Peter M.
    et al.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions2013In: Chemistry and Physics of Lipids, ISSN 0009-3084, E-ISSN 1873-2941, Vol. 169, p. 106-112Article in journal (Refereed)
    Abstract [en]

    Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations.

  • 394.
    Kasson, Peter M.
    et al.
    University of Virginia, USA.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. Stockholm University, Sweden.
    Pande, Vijay S.
    Stanford University, United States .
    Water Ordering at Membrane Interfaces Controls Fusion Dynamics2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 11, p. 3812-3815Article in journal (Refereed)
    Abstract [en]

    Membrane interfaces are critical to many cellular functions, yet the vast array of molecular components involved make the fundamental physics of interaction difficult to define. Water has been shown to play an important role in the dynamics of small biological systems, for example when trapped in hydrophobic regions, but the molecular details of water have generally been thought dispensable when considering large membrane interfaces. Nevertheless, spectroscopic data indicate that water has distinct, ordered behavior near membrane surfaces. While coarse-grained simulations have achieved success recently in aiding understanding the dynamics of membrane assemblies, it is natural to ask, does the missing chemical nature of water play an important role? We have therefore performed atomic-resolution simulations of vesicle fusion to understand the role of chemical detail, particularly the molecular structure of water, in membrane fusion and at membrane interfaces more generally. These membrane interfaces present a form of hydrophilic confinement, yielding surprising, non-bulk-like water behavior.

  • 395.
    Khartsev, Sergiy
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Grishin, Alexander
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    New garnet films for magneto-optical photonic crystals2005In: Magneto-Optical Materials For Photonics and Recording / [ed] Ando, K; Challener, W; Gambino, R; Levy, M, WARRENDALE: MATERIALS RESEARCH SOCIETY , 2005, Vol. 834, p. 47-52Conference paper (Refereed)
    Abstract [en]

    Epitaxial La3Ga5O12 (LGG) garnet films and Bi3Fe5O12/La3Ga5O12 (BIG/LGG) heteroepitaxial structures have been synthesized on Gd3Ga5O12(GGG,111) single crystal. LGG films were grown by Pulsed Laser Deposition (PLD) technique whereas rf-magnetron sputtering was used to grow BIG films. We demonstrate LGG is a promising material to be integrated with a giant Faraday rotator Bi3Fe5O12 in magneto-optical photonic crystals. LGG has a lattice constant 12.772 angstrom that is bigger than that in GGG (12.384 angstrom) and closer to that in BIG (12.626 angstrom). Heteroepitaxial Bi3Fe5O12(2 mu m)/La3Ga5O12(300nm) structures grown on the GGG(111) single crystal show the Faraday rotation as high as 5.74 deg/mu m compared to 5.46 deg/mu m in BIG/GGG at lambda = 655 nm. Fitting LGG reflectivity spectra to Fresnel formulas yields LGG refractive index n = 1.981 compared to 1.963 in GGG at 655 nm. Dispersion of LGG refraction index follows Sellmeier formula n(2) = 1 + 2.78/[1 - (138nm/lambda)(2)] in the range from 400 nm to 1000 nm.

  • 396. Kimanius, Dari
    et al.
    Forsberg, Bjorn O.
    Scheres, Sjors H. W.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm University, Sweden.
    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-22016In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e18722Article in journal (Refereed)
    Abstract [en]

    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

  • 397. Kimanius, Dari
    et al.
    Pettersson, Ingrid
    Schluckebier, Gerd
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm University, Sweden.
    Andersson, Magnus
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    SAXS-Guided Metadynamics2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 7, p. 3491-3498Article in journal (Refereed)
    Abstract [en]

    The small-angle X-ray scattering (SAXS) methodology enables structural characterization of biological macromolecules in solution. However, because SAXS provides low-dimensional information, several potential structural configurations can reproduce the experimental scattering profile, which severely complicates the structural refinement process. Here, we present a bias-exchange metadynamics refinement protocol that incorporates SAXS data as collective variables and therefore tags all possible configurations with their corresponding free energies, which allows identification of a unique structural solution. The method has been implemented in PLUMED and combined with the GROMACS simulation package, and as a proof of principle, we explore the Trp-cage protein folding landscape.

  • 398.
    Kimanos, Farhad
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    SAXS-Guided Metadynamics2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 399. King, Stephen F.
    et al.
    Merle, Alexander
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Warm Dark Matter from keVins2012In: Journal of Cosmology and Astroparticle Physics, ISSN 1475-7516, E-ISSN 1475-7516, no 8, p. 016-Article in journal (Refereed)
    Abstract [en]

    We propose a simple model for Warm Dark Matte (WDM) in which two femions are added to the Standard,Model: (quasi-) stable "keVins" (keV inert fermions) which account for WDM and their unstable brothers, the "GeVins" (GeV inert fermions), both of which carry zero electric charge and zero lepton number, and are (approximately) "inert", in the sense that their only interactions are via suppressed couplings to the Z. We consider scenarios in which stable keVins are thermally produced and their abundance is subsequently diluted by entropy production from the decays of the heavier unstable GeVins. This mechanism could be implemented in a wide variety of models, including E-6 inspired supersymmetric models or models involving sterile neutrinos.

  • 400. Klement, Goran
    et al.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Yoluk, Özge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Howard, Rebecca
    Lindahl, Erik
    Ligand-Gated Ion Channel Gating Kinetics and the Opening/Closing Mechanism are Sensitive to Mutations Altering the Hydrophobicity of the Ion Conduction Pore2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 343A-343AArticle in journal (Other academic)
567891011 351 - 400 of 764
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