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  • 601. Palumbo, M.
    et al.
    Burton, B.
    Costa e Silva, A.
    Fultz, B.
    Grabowski, B.
    Grimvall, Göran
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theory of Materials.
    Hallstedt, B.
    Hellman, O.
    Lindahl, Bonnie
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Computational Thermodynamics.
    Schneider, A.
    Turchi, P. E. A.
    Xiong, W.
    Thermodynamic modelling of crystalline unary phases2014In: Physica status solidi. B, Basic research, ISSN 0370-1972, E-ISSN 1521-3951, Vol. 251, no 1, p. 14-32Article in journal (Refereed)
    Abstract [en]

    Progress in materials science through thermodynamic modelling may rest crucially on access to a database, such as that developed by Scientific Group Thermodata Europe (SGTE) around 1990. It gives the Gibbs energy G(T) of the elements in the form of series as a function of temperature, i.e. essentially a curve fitting to experimental data. In the light of progress in theoretical understanding and first-principles calculation methods, the possibility for an improved database description of the thermodynamics of the elements has become evident. It is the purpose of this paper to provide a framework for such work. Lattice vibrations, which usually give the major contribution to G(T), are treated in some detail with a discussion of neutron scattering studies of anharmonicity in aluminium, first-principles calculations including ab initio molecular dynamics (AIMD), and the strength and weakness of analytic model representations of data. Similarly, electronic contributions to G(T) are treated on the basis of the density of states N(E) for metals, with emphasis on effects at high T. Further, we consider G(T) below 300K, which is not covered by SGTE. Other parts in the paper discuss metastable and dynamically unstable lattices, G(T) in the region of superheated solids and the requirement on a database in the calculation of phase diagrams.

  • 602.
    Patzauer, Maximilian
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Multistability in the Oscillatory Electrodissolution of Silicon2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 603. Paulsen, Peter Aasted
    et al.
    Jurkowski, Wiktor
    Apostolov, Rossen
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Nissen, Poul
    Poulsen, Hanne
    The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology2013In: Molecular membrane biology, ISSN 0968-7688, E-ISSN 1464-5203, Vol. 30, no 2, p. 195-205Article in journal (Refereed)
    Abstract [en]

    The Na,K-ATPase is essential to all animals, since it maintains the electrochemical gradients that energize the plasma membrane. Naturally occurring inhibitors of the pump from plants have been used pharmaceutically in cardiac treatment for centuries. The inhibitors block the pump by binding on its extracellular side and thereby locking it. To explore the possibilities for designing an alternative way of targeting the pump function, we have examined the structural requirements for binding to a pocket that accommodates the two C-terminal residues, YY, in the crystal structures of the pump. To cover the sample space of two residues, we first performed docking studies with the 400 possible dipeptides. For validation of the in silico predictions, pumps with 13 dipeptide sequences replacing the C-terminal YY were expressed in Xenopus laevis oocytes and examined with electrophysiology. Our data show a significant correlation between the docking scores from two different methods and the experimentally determined sodium affinities, which strengthens the previous hypothesis that sodium binding is coupled to docking of the C-terminus. From the dipeptides that dock the best and better than wild-type YY, it may therefore be possible to develop specific drugs targeting a previously unexplored binding pocket in the sodium pump.

  • 604.
    Pawellek, Michael
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Mathematical Physics.
    Semiclassical Strings in AdS(5) X S(5) and Automorphic Functions2011In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 106, no 24, p. 241601-Article in journal (Refereed)
    Abstract [en]

    Using anti-de Sitter-space/conformal-field-theory correspondence we derive from the folded spinning string ordinary differential equations for the anomalous dimension of the dual N = 4 super Yang-Mills theory twist-two operators at strong coupling. We show that for large spin the asymptotic solutions have the Gribov-Lipatov reciprocity property. To obtain this result we use a hidden modular invariance of the energy-spin relation of the folded spinning string. Furthermore, we identify the Moch-Vermaseren-Vogt relations, which were first recognized in plain QCD calculations, as the recurrence relations of the asymptotic series ansatz.

  • 605. Pentcheva, R.
    et al.
    Moritz, W.
    Rundgren, John
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theory of Materials.
    Frank, S.
    Schrupp, D.
    Scheffler, M.
    A combined DFT/LEED-approach for complex oxide surface structure determination: Fe3O4(001)2008In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 602, no 7, p. 1299-1305Article in journal (Refereed)
    Abstract [en]

    A combination of density functional theory (DFT) calculations and low energy electron diffraction (LEED) analysis is used to determine the surface structure of Fe3O4 0 00). We find that the surface is rich in oxygen and the observed (root 2- x root 2-)R45 degrees reconstruction is a result of a Jahn-Teller distortion as established by recent DFT-calculations [R. Pentcheva, F. Wendler, H.L. Meyerheim, W. Moritz, N. Jedrecy, M. Scheffler, Phys. Rev. Lett. 94 (2005) 126101]. The corresponding Pendry reliability factor is 0.34. Furthermore, we investigate the influence of the preparation conditions (temperature, oxygen pressure) on the LEED intensities of natural and synthetic samples. The electron scattering phase shifts used in the analysis of the LEED spectra are derived from two methods, one based on the DFT electron densities and another employing an overlap of atomic potentials with optimized muffin-tin radii. Both approaches lead to similar results.

  • 606.
    Persson, Joakim
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Diagrammatic Monte Carlo Simulation of the Polaron Problem2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 607.
    Persson, Joakim
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Diagrammatic Monte Carlo Simulation of the Polaron Problem2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 608.
    Pettersson, Olov
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Byrnes, Tim
    Light-mediated non-Gaussian entanglement of atomic ensembles2017In: PHYSICAL REVIEW A, ISSN 2469-9926, Vol. 95, no 4, article id 043817Article in journal (Refereed)
    Abstract [en]

    We analyze a similar scheme for producing light-mediated entanglement between atomic ensembles, as first realized by Julsgaard, Kozhekin, and Polzik [Nature (London) 413, 400 (2001)]. In the standard approach to modeling the scheme, a Holstein-Primakoff approximation is made, where the atomic ensembles are treated as bosonic modes, and is only valid for short interaction times. In this paper, we solve the time evolution without this approximation, which extends the region of validity of the interaction time. For short entangling times, we find that this produces a state with characteristics similar to those of a two-mode squeezed state, in agreement with standard predictions. For long entangling times, the state evolves into a non-Gaussian form, and the characteristics of the two-mode squeezed state start to diminish. This is attributed to more exotic types of entangled states being generated. We characterize the states by examining the Fock-state probability distributions, Husimi Q distributions, and nonlocal entanglement between the ensembles. We compare and connect several quantities obtained by using the Holstein-Primakoff approach and our exact time evolution methods.

  • 609. Pollet, L.
    et al.
    Kiselev, M. N.
    Prokof'Ev, Nikolay V
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Svistunov, B. V.
    Grassmannization of classical models2016In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 18, no 11, article id 113025Article in journal (Refereed)
    Abstract [en]

    Applying Feynman diagrammatics to non-fermionic strongly correlated models with local constraints might seem generically impossible for two separate reasons: (i) the necessity to have a Gaussian (non-interacting) limit on top of which the perturbative diagrammatic expansion is generated by Wick's theorem, and (ii) Dyson's collapse argument implying that the expansion in powers of coupling constant is divergent. We show that for arbitrary classical lattice models both problems can be solved/circumvented by reformulating the high-temperature expansion (more generally, any discrete representation of the model) in terms of Grassmann integrals. Discrete variables residing on either links, plaquettes, or sites of the lattice are associated with the Grassmann variables in such a way that the partition function (as well as all correlation functions) of the original system and its Grassmann-field counterpart are identical. The expansion of the latter around its Gaussian point generates Feynman diagrams. Our work paves the way for studying lattice gauge theories by treating bosonic and fermionic degrees of freedom on equal footing. © 2016 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

  • 610.
    Pousaneh, Faezeh
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Edholm, Olle
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Maciolek, Anna
    Molecular dynamics simulation of a binary mixture near the lower critical point2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145, no 1, article id 014501Article in journal (Refereed)
    Abstract [en]

    2,6-lutidine molecules mix with water at high and low temperatures but in a wide intermediate temperature range a 2,6-lutidine/water mixture exhibits a miscibility gap. We constructed and validated an atomistic model for 2,6-lutidine and performed molecular dynamics simulations of 2,6-lutidine/water mixture at different temperatures. We determined the part of demixing curve with the lower critical point. The lower critical point extracted from our data is located close to the experimental one. The estimates for critical exponents obtained from our simulations are in a good agreement with the values corresponding to the 3D Ising universality class.

  • 611.
    Pouya, Iman
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Pronk, Sander
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Rotskoff, Grant
    Kasson, Peter M.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Ligand-Gated Ion Channel Opening and Closing Mechanism from Molecular Simulations2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 271A-271AArticle in journal (Other academic)
  • 612.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Larsson, Per
    Stockholm University.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Bowman, Gregory
    Haque, Imran
    Beauchamp, Kyle
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Pande, Vijay
    Kasson, Peter
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Copernicus: A new paradigm for parallel adaptive molecular dynamics2011In: Proceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, p. 60-Conference paper (Refereed)
    Abstract [en]

    Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring. Copernicus enables execution as single parallel jobs with automatic resource allocation. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. Starting from extended chains we observe structures 0.6 Å from the native state within 30h, and achieve sufficient sampling to predict the native state without a priori knowledge after 80-90h. To match Copernicus'efficiency, a classical simulation would have to exceed 50 microseconds per day, currently infeasible even with custom hardware designed for simulations.

  • 613.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kasson, Peter M.
    Coupled Diffusion in Lipid Bilayers upon Close Approach2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 2, p. 708-714Article in journal (Refereed)
    Abstract [en]

    Biomembrane interfaces create regions of slowed water dynamics in their vicinity. When two lipid bilayers come together, this effect is further accentuated, and the associated slowdown can affect the dynamics of larger-scale processes such as membrane fusion. We have used molecular dynamics simulations to examine how lipid and water dynamics are affected as two lipid bilayers approach each other. These two interacting fluid systems, lipid and water, both slow and become coupled when the lipid membranes are separated by a thin water layer. We show in particular that the water dynamics become glassy, and diffusion of lipids in the apposed leaflets becomes coupled across the water layer, while the outer leaflets remain unaffected. This dynamic coupling between bilayers appears mediated by lipid-water-lipid hydrogen bonding, as it occurs at bilayer separations where water-lipid hydrogen bonds become more common than water-water hydrogen bonds. We further show that such coupling occurs in simulations of vesicle-vesicle fusion prior to the fusion event itself. Such altered dynamics at membrane-membrane interfaces may both stabilize the interfacial contact and slow fusion stalk formation within the interface region.

  • 614.
    Pronk, Sander
    et al.
    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.
    Kasson, Peter M.
    Dynamic heterogeneity controls diffusion and viscosity near biological interfaces2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 3034-Article in journal (Refereed)
    Abstract [en]

    At a nanometre scale, the behaviour of biological fluids is largely governed by interfacial physical chemistry. This may manifest as slowed or anomalous diffusion. Here we describe how measures developed for studying glassy systems allow quantitative measurement of interfacial effects on water dynamics, showing that correlated motions of particles near a surface result in a viscosity greater than anticipated from individual particle motions. This effect arises as a fundamental consequence of spatial heterogeneity on nanometre length scales and applies to any fluid near any surface. Increased interfacial viscosity also causes the classic finding that large solutes such as proteins diffuse much more slowly than predicted in bulk water. This has previously been treated via an empirical correction to the solute size: the hydrodynamic radius. Using measurements of quantities from theories of glass dynamics, we can now calculate diffusion constants from molecular details alone, eliminating the empirical correction factor.

  • 615.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pall, Szilard
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schulz, Roland
    Larsson, Per
    Bjelkmar, Pär
    Apostolov, Rossen
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Shirts, Michael R.
    Smith, Jeremy C.
    Kasson, Peter M.
    van der Spoel, David
    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.
    GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit2013In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 29, no 7, p. 845-854Article in journal (Refereed)
    Abstract [en]

    Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

  • 616.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundborg, Magnus
    Rotskoff, Grant
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wesén, Björn
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kasson, Peter M.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 6, p. 2600-2608Article in journal (Refereed)
    Abstract [en]

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

  • 617. Puletti, Valentina Giangreco M.
    et al.
    Månsson, Teresia
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Mathematical Physics.
    The dual string sigma-model of the SUq(3) sector2012In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, Vol. 2012, no 1, p. 1-24Article in journal (Refereed)
    Abstract [en]

    In four-dimensional N = 4 super Yang-Mills (SYM) the SU(3) sub-sector spanned by purely holomorphic fields is isomorphic to the corresponding mixed one spanned by both holomorphic and anti-holomorphic fields. This is no longer the case when one considers the marginally deformed N = 4 SYM. The mixed SU(3) sector marginally deformed by a complex parameter beta, i.e. SUq(3) with q = e(2i pi beta), has been shown to be integrable at one-loop [1], while it is not the case for the corresponding purely holomorphic one. Moreover, the marginally deformed N = 4 SYM also has a gravity dual constructed by Lunin and Maldacena in [2]. However, the mixed SUq(3) sector has not been studied from the supergravity point of view. Hence in this note, for the case of purely imaginary marginal beta-deformations, we compute the superstring SUq (3) sigma-model in the fast spinning string limit and show that, for rational spinning strings, it reproduces the energy computed via Bethe equations.

  • 618.
    Páll, Szilard
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Abraham, Mark James
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kutzner, Carsten
    Hess, Berk
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Biochemistry & Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden .
    Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS2015In: Solving software challenges for exascale, Springer Publishing Company, 2015, p. 3-27Conference paper (Refereed)
    Abstract [en]

    GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.

  • 619.
    Páll, Szilard
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A flexible algorithm for calculating pair interactions on SIMD architectures2013In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 184, no 12, p. 2641-2650Article in journal (Refereed)
    Abstract [en]

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

  • 620.
    Páll, Szilárd
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Poster - 3D Tixels: A highly efficient algorithm for GPU/CPU-acceleration of molecular dynamics on heterogeneous parallel architectures2011In: SC - Proc. High Perform. Comput. Networking, Storage Anal. Companion, Co-located SC, 2011, p. 71-72Conference paper (Refereed)
    Abstract [en]

    Several GPU-based algorithms have been developed to ac-celerate biomolecular simulations, but although they pro-vide benefits over single-core implementations, they have not been able to surpass the performance of state-of-the art SIMD CPU implementations (e.g. GROMACS), not to mention efficient scaling. Here, we present a heteroge-nous parallelization that utilizes both CPU and GPU re-sources efficiently. A novel fixed-particle-number sub-cell algorithm for non-bonded force calculation was developed. The algorithm uses the SIMD width as algorithmic work unit, it is intrinsically future-proof since it can be adapted to future hardware. The CUDA non-bonded kernel imple-mentation achieves up to 60% work-efficiency, 1.5 IPC, and 95% L1 cache utilization. On the CPU OpenMP-parallelized SSE-accelerated code runs overlapping with GPU execution. Fully automated dynamic inter-process as well as CPU-GPU load balancing is employed. We achieve threefold speedup compared to equivalent GROMACS CPU code and show good strong and weak scaling. To the best of our knowledge this the fastest GPU molecular dynamics implementation presented to date.

  • 621.
    Ray, Arjun
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Quality assessment of protein models2012Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins are crucial for all living organisms and they are involved in many different processes. The function of a protein is tightly coupled to its structure, yet to determine the structure experimentally is both non-trivial and expensive. Computational methods that are able to predict the structure are often the only possibility to obtain structural information for a particular protein. Structure prediction has come a long way since its inception. More advanced algorithms, refined mathematics and statistical analysis and use of machine learning techniques have improved this field considerably. Making a large number of protein models is relatively fast. The process of identifying and separating correct from less correct models, from a large set of plausible models, is also known as model quality assessment. Critical Assessment of Techniques for Protein Structure Prediction (CASP) is an international experiment to assess the various methods for structure prediction of proteins. CASP has shown the improvements of these different methods in model quality assessment, structure prediction as well as better model building.

    In the two studies done in this thesis, I have improved the model quality assessment part of this structure prediction problem for globular proteins, as well as trained the first such method dedicated towards membrane proteins. The work has resulted in a much-improved version of our previous model quality assessment program ProQ, and in addition I have also developed the first model quality assessment program specifically tailored for membrane proteins.

  • 622.
    Ray, Arjun
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wallner, B.
    Improved model quality assessment using ProQ22012In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 13, no 1, p. 224-Article in journal (Refereed)
    Abstract [en]

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

  • 623.
    Ray, Arjun
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Wallner, Björn
    Center for Biomembrane Research, Stockholm, Sweden.
    Evolutionary information and multiple sequence alignments improve protein model guality predictionManuscript (preprint) (Other academic)
  • 624.
    Ray, Arjun
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Wallner, Björn
    Center for Biomembrane Research, Stockholm, Sweden.
    Model quality assessment for membrane proteins2010In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 26, no 24, p. 3067-3074Article in journal (Refereed)
    Abstract [en]

    Motivation: Learning-based model quality assessment programs have been quite successful at discriminating between high-and low-quality protein structures. Here, we show that it is possible to improve this performance significantly by restricting the learning space to a specific context, in this case membrane proteins. Since these are among the most important structures from a pharmaceutical point-of-view, it is particularly interesting to resolve local model quality for regions corresponding, e. g. to binding sites. Results: Our new ProQM method uses a support vector machine with a combination of general and membrane protein-specific features. For the transmembrane region, ProQM clearly outperforms all methods developed for generic proteins, and it does so while maintaining performance for extra-membrane domains; in this region it is only matched by ProQres. The predictor is shown to accurately predict quality both on the global and local level when applied to GPCR models, and clearly outperforms consensus-based scoring. Finally, the combination of ProQM and the Rosetta low-resolution energy function achieve a 7-fold enrichment in selection of near-native structural models, at very limited computational cost.

  • 625. Ray, S. J.
    et al.
    Gibbs, A. S.
    Bending, S. J.
    Curran, P. J.
    Babaev, Egor
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics.
    Baines, C.
    Mackenzie, A. P.
    Lee, S. L.
    Muon-spin rotation measurements of the vortex state in Sr2RuO4: Type-1.5 superconductivity, vortex clustering, and a crossover from a triangular to a square vortex lattice2014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, no 9, p. 094504-Article in journal (Refereed)
    Abstract [en]

    Muon-spin rotation has been used to probe the vortex state in Sr2RuO4. At moderate fields and temperatures a lattice of triangular symmetry is observed, crossing over to a lattice of square symmetry with increasing field and temperature. At lower fields it is found that there are large regions of the sample that are completely free from vortices which grow in volume as the temperature falls. Importantly this is accompanied by increasing vortex density and increasing disorder within the vortex-cluster-containing regions. Both effects are expected to result from the strongly temperature-dependent long-range vortex attractive forces arising from the multiband chiral-order superconductivity.

  • 626. Rehn, M.
    et al.
    Bergkvist, S.
    Rosengren, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Saers, R.
    Zelan, M.
    Lundh, E.
    Kastberg, A.
    One-dimensional phase transitions in a two-dimensional optical lattice2008In: European Physical Journal D: Atomic, Molecular and Optical Physics, ISSN 1434-6060, E-ISSN 1434-6079, Vol. 49, no 2, p. 223-230Article in journal (Refereed)
    Abstract [en]

    A phase transition for bosonic atoms in a two-dimensional anisotropic optical lattice is considered. If the tunnelling rates in two directions are different, the system can undergo a transition between a two-dimensional superfluid and a one-dimensional Mott insulating array of strongly coupled tubes. The connection to other lattice models is exploited in order to better understand the phase transition. Critical properties are obtained using quantum Monte Carlo calculations. These critical properties are related to correlation properties of the bosons and a criterion for commensurate filling is established.

  • 627. Revell, H. M.
    et al.
    Yaraskavitch, L. R.
    Mason, J. D.
    Ross, K. A.
    Noad, H. M. L.
    Dabkowska, H. A.
    Gaulin, B. D.
    Henelius, Patrik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Kycia, J. B.
    Evidence of impurity and boundary effects on magnetic monopole dynamics in spin ice2013In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 9, no 1, p. 34-37Article in journal (Refereed)
    Abstract [en]

    Electrical resistance is a crucial and well-understood property of systems ranging from computer microchips to nerve impulse propagation in the human body. Here we study the motion of magnetic charges in spin ice and find that extra spins inserted in Dy2Ti2O7 trap magnetic monopole excitations and provide the first example of how defects in a spin-ice material obstruct the flow of monopoles-a magnetic version of residual resistance. We measure the time-dependent magnetic relaxation in Dy2Ti2O7 and show that it decays with a stretched exponential followed by a very slow long-time tail. In a Monte Carlo simulation governed by Metropolis dynamics we show that surface effects and a very low level of stuffed spins (0.30%)-magnetic Dy ions substituted for non-magnetic Ti ions-cause these signatures in the relaxation. In addition, we find evidence that the rapidly diverging experimental timescale is due to a temperature-dependent attempt rate proportional to the monopole density.

  • 628.
    Riad, Stella
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Running of Neutrino Parameters in Extra Dimensions2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 629.
    Riad, Stella
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Studies of effective theories beyond the Standard Model2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The vast majority of all experimental results in particle physics can be described by the Standard Model (SM) of particle physics. However, neither the existence of neutrino masses nor the mixing in the leptonic sector, which have been observed, can be described within this model. In fact, the model only describes a fraction of the known energy in the Universe. Thus, we know there must exist a theory beyond the SM. There is a plethora of possible candidates for such a model, such as supersymmetry, extra dimensional theories, and string theory. So far, there are no evidence in favor of these models.

    These theories often reside at high energies, and will therefore be manifest as effective theories at the low energies experienced here on Earth. A first example in extra-dimensional theories. From our four-dimensional point of view, particles which propagate through the extra dimensions will effectivel be perceived as towers of heavy particles. In this thesis we consider an extra-dimensional model with universal extra dimensions, where all SM particles are allowed to propagate through the extra dimensions. Especially, we place a bound on the range of validity for this model. We study the renormalization group running of the leptonic parameters as well as the Higgs self-coupling in this model with the neutrino masses generated by a Weinberg operator.

    Grand unified theories, where the gauge couplings of the SM are unified into a single oe at some high energy scale, are motivated by the electroweak unification. The unification must necessarily take place at energies many orders of magnitude greater than those that ever can be achieved on Earth. In order to make sense of the theoru, ehich is given at the grand unified scale, at the electroweak scale, the symmetry at the grand unified scale is broken down to the SM symmetry. Within these models the SM is considered as an effective field theory. We study renormalization group running of the leptonic parameters in a non-supersymmetric SO(10) model which is broken in two steps via the Pati-Salam group.

    Finally, the discovery of the new boson at the LHC provides a new opportunity to search for physics beyond the SM. We consider an effective model where the magnitudes of the couplings in the Higgs sector are scaled by so-called coupling scale factors. We perform Bayesian parameter inference based on the LHC data. Furthermore, we perform Bayesian model comparison, comparing models where one or several of the Higgs couplings are allowed, to the SM, where the couplings are fixed.

  • 630. Riederer, Erika
    et al.
    Yoluk, Özge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Trudell, James
    Lindahl, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Harris, Adron
    Howard, Rebecca
    Alcohol Modulation of a Eukaryotic Ligand-Gated Ion Channel of Known Structure2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 545A-545AArticle in journal (Other academic)
  • 631.
    Ripellino, Giulia
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Consequences of Violation of Special Relativity and Causality2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 632.
    Rosengren, Anders
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Lundow, Per Håkan
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Balatsky, A. V.
    Isotope effect on superconductivity in Josephson coupled stripes in underdoped cuprates2008In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 77, no 13Article in journal (Refereed)
    Abstract [en]

    Inelastic neutron scattering data for YBaCuO as well as for LaSrCuO indicate incommensurate neutron scattering peaks with an incommensuration delta(x) away from the (pi,pi) point. T-c(x) can be replotted as a linear function of the incommensuration for these materials. This linear relation implies that the constant that relates these two quantities, where one is the incommensuration (momentum) and the other is T-c(x) (energy), has the dimension of velocity, which we denote by v(*): k(B)T(c)(x)=hv(*)delta(x). We argue that this experimentally determined relation can be obtained in a simple model of Josephson coupled stripes. Within this framework, we address the role of the O-16 -> O-18 isotope effect on T-c(x). We assume that the incommensuration is set by the doping of the sample and is not sensitive to the oxygen isotope given the fixed doping. We find therefore that the only parameter that can change with the O isotope substitution in the relation T-c(x)similar to delta(x) is the velocity v(*). We predict an oxygen isotope effect on v(*) and expect it to be similar or equal to 5%.

  • 633.
    Ruban, Andrei V.
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Belonoshko, Anatoly B.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Skorodumova, Natalia V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Impact of magnetism on Fe under Earth's core conditions2013In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 87, no 1, p. 014405-Article in journal (Refereed)
    Abstract [en]

    Using a microscopic phenomenological model for longitudinal spin fluctuations (LSFs) based on density functional theory calculations, we demonstrate that under the Earth's core conditions (P approximate to 360 GPa, T approximate to 6000 K), Fe acquires substantial local magnetic moment, up to 1.3 mu(B), for different crystal structure modifications. We demonstrate that the LSFs produce a substantial effect on the magnetic and thermodynamic properties of iron, in particular, its equilibrium volume under solid Earth's core conditions.

  • 634.
    Rundgren, John
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Elastic electron-atom scattering in amplitude-phase representation with application to electron diffraction and spectroscopy2007In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 76, no 19, p. 195441-Article in journal (Refereed)
    Abstract [en]

    The amplitude-phase representation (APR) [W. E. Milne, Phys. Rev. 35, 863 (1930)] is applied to the relativistic radial Schrodinger equation corresponding to the Dirac equations with central potential. The initial conditions, hitherto unspecified, for the nonlinear second-order amplitude equation at the finite radius of a muffin-tin (MT) sphere are established by a semiconvergent method. This opens the possibility of using APR for the calculation of electron scattering phase shifts with a finite MT radius as well as with a large atomic radius, whereby the first wave node is phase of reference equal to a multiple of pi, adding nothing to the phase shifts. Furthermore, APR is used for benchmarking wave functions obtained by ordinary differential equation integration of the Dirac equations up to high energy and high orbital quantum number. The present APR procedure is discussed with reference to earlier numerical methods. To complete the physical picture, the paper ends with a discussion on exchange-correlation dependent scattering potential in MT spheres of optimized radii, a crystal potential model whose dependence on radii and energy dependent inner potential has recently been corroborated by low energy electron diffraction in oxides with many atoms per unit cell.

  • 635.
    Rundgren, John
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Dong, Qian
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Hultquist, Gunnar
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Concentration-dependent diffusion of hydrogen in vitreous silica2006In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 100, no 10, p. 104902-1-104902-5Article in journal (Refereed)
    Abstract [en]

    We report diffusion experiments where hydrogen permeates through a 1 mm wall of vitreous silica at 550 °C with applied gas pressures of 70, 460, 840, and 1200 mbars. For each pressure, and at steady state, the flux and the amount of hydrogen in the material are measured. Within the experimental accuracy we find that the flux is proportional to the pressure and that the hydrogen amount increases with a falling gradient with respect to pressure. The result is a relationship between flux and mean concentration. A careful evaluation of the flux versus concentration relationship by means of the steady-state diffusion equation shows that the hydrogen diffusivity in the silica wall is concentration dependent and increases linearly with local concentration.

  • 636.
    Runsö, Andreas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    – A study of the Langevin equation in a thermal ratchet model of the myosin V motor protein2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 637.
    Sandalov, Igor
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Lundin, U
    Eriksson, O
    Theory of strongly correlated electron systems. I. Intersite coulomb interaction and the approximation of renormalized fermions in total energy calculations2005In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 102, no 6, p. 1019-1045Article in journal (Refereed)
    Abstract [en]

    The diagrammatic strong-coupling perturbation theory (SCPT) for correlated electron systems is developed for intersite Coulomb interaction and for a nonorthogonal basis set. The construction is based on iterations of exact closed equations for many - electron Green functions (GFs) for Hubbard operators in terms of functional derivatives with respect to external sources. The graphs, which do not contain the contributions from the fluctuations of the local population numbers of the ion states, play a special role: a one-to-one correspondence is found between the subset of such graphs for the many - electron GFs and the complete set of Feynman graphs of weak-coupling perturbation theory (WCPT) for single-electron GFs. This fact is used for formulation of the approximation of renormalized Fermions (ARF) in which the many-electron quasi-particles behave analogously to normal Fermions. Then, by analyzing: (a) Sham's equation, which connects the self-energy and the exchange- correlation potential in density functional theory (DFT); and (b) the Galitskii and Migdal expressions for the total energy, written within WCPT and within ARF SCPT, a way we suggest a method to improve the description of the systems with correlated electrons within the local density approximation (LDA) to DFT. The formulation, in terms of renormalized Fermions LIDA (RF LDA), is obtained by introducing the spectral weights of the many electron GFs into the definitions of the charge density, the overlap matrices, effective mixing and hopping matrix elements, into existing electronic structure codes, whereas the weights themselves have to be found from an additional set of equations. Compared with LDA+U and self-interaction correction (SIC) methods, RF LDA has the advantage of taking into account the transfer of spectral weights, and, when formulated in terms of GFs, also allows for consideration of excitations and nonzero temperature. Going beyond the ARF SCPT, as well as RF LIDA, and taking into account the fluctuations of ion population numbers would require writing completely new codes for ab initio calculations. The application of RF LDA for ab initio band structure calculations for rare earth metals is presented in part 11 of this study (this issue).

  • 638.
    Sandalov, Igor
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Nazmitdinov, R. G.
    Nonlinear transport at the strong intra-dot Coulomb interaction2006In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 18, no 5, p. L55-L61Article in journal (Refereed)
    Abstract [en]

    Nonlinear transport is studied in the limit of weak and strong intra-dot Coulomb interaction. The nonequilibrium self-consistent mean-field equations for one-electron transition energies of an open dot and their spectral weights are derived at the strong Coulomb interaction. In this limit populations of states involved in tunnelling equalize upon the increase of the bias-voltage window even at low temperature. This results in a simple analytical relation between the heights of the current steps and the degeneracy of a spectrum in a two-dimensional parabolic dot in a magnetic field.

  • 639.
    Sandalov, Igor
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Nazmitdinov, R. G.
    Shell effects in nonlinear magnetotransport through small quantum dots2007In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 75, no 7, p. 075315-Article in journal (Refereed)
    Abstract [en]

    Nonlinear transport through a quantum dot attached to two metallic contacts is studied in the limit of a weak and a strong intradot Coulomb interaction. The nonequilibrium self-consistent mean-field equations for the energies and spectral weights of one-electron transitions are formulated in the strong-interaction regime. The self-consistent solutions result in a decrease of bias voltage threshold for nonzero current, contrary to the weak case. With an increase of the bias voltage window, the solutions lead to a significant deviation from the Gibbs statistics: the populations of states involved in tunneling are equalizing even at low temperatures. For a symmetric dot-contact coupling we obtain simple analytical relations between the heights of the current steps and degeneracies of a spectrum of a circular dot in a perpendicular magnetic field, in both regimes.

  • 640.
    Sandalov, Igor
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Padyukov, L.
    Genetic Vectors Approach in a Study of Fine Structure of Interaction Between Risk Haplotype of HTR2A and HLA-DRB1 Shared Epitope Alleles in Rheumatoid Arthritis2013In: Between the Lines of Genetic Code: Genetic Interactions in Understanding Disease and Complex Phenotypes, Elsevier, 2013, p. 151-174Chapter in book (Refereed)
    Abstract [en]

    We introduce new quantitative characteristics of the population using an analogy to the system of multi-spin molecules: the disease fields, which may depend on interactions, and the susceptibility to disease as derivative of genetic vector's (GV's) frequency of cases with respect to these fields. The genetic vector's approach (GVA) is applied to statistical analysis of the interaction of two SNP haplotype of HTR2A and shared epitope (SE) alleles in relation to development of rheumatoid arthritis (RA). The analysis is performed for two independent cohorts, EIRA and NARAC, and based on the evaluation of double- and triple genotype-genotype versus SE alleles correlations. The Gibbs-like parametrization of GV frequencies makes analysis transparent and easy interpretable. We find that the main contribution into association to RA comes from GVs containing double SE. GVA may resolve an opposite role in risk/protection from different pairs of genetic variations and reveal an association to RA whereas the univariate analysis does not show significant association.

  • 641.
    Schwaiger, Christine S.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Dynamics of the voltage-sensor domain in voltage-gated ion channels: Studies on helical content and hydrophobic barriers within voltage-sensor domains2011Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Voltage-gated ion channels play fundamental roles in neural excitability and thus dysfunctional channels can cause disease. Understanding how the voltage-sensor of these channels activate and inactivate could potentially be useful in future drug design of compounds targeting neuronal excitability.

    The opening and closing of the pore in voltage-gated ion channels is caused by the arginine-rich S4 helix of the voltage sensor domain (VSD) moving in response to an external potential. Exactly how this movement is accomplished is not yet fully known and an area of hot debate. In this thesis I study how the opening and closing in voltage-gated potassium (Kv) channels occurs.

    Recently, both experimental and computational results have pointed to the possibility of a secondary structure transition from α- to 3(10)-helix in S4 being an important part of the gating. First, I show that the 3(10)-helix structure in the S4 helix of a Kv1.2-2.1 chimera protein is significantly more favorable compared to the α-helix in terms of a lower free energy barrier during the gating motion. Additional I suggest a new gating model for S4, moving as sliding 310-helix. Interestingly, the single most conserved residue in voltage- gated ion channels is a phenylalanine located in the hydrophobic core and directly facing S4 causing a barrier for the gating charges.

    In a second study, I address the problem of the energy barrier and show that mutations of the phenylalanine directly alter the free energy barrier of the open to closed transition for S4. Mutations can either facilitate the relaxation of the voltage-sensor or increase the free energy barrier, depending on the size of the mutant. These results are confirmed by new experimental data that supports that a rigid, cyclic ring at the phenylalanine position is the determining rate-limiting factor for the voltage sensor gating process.

  • 642.
    Schwaiger, Christine S
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Voltage sensor activation and modulation in ion channels2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Voltage-gated ion channels play fundamental roles in neural excitability, they are for instance responsible for every single heart beat in our bodies, and dysfunctional channels cause disease that can be even lethal. Understanding how the voltage sensor of these channels function is critical for drug design of compounds targeting neuronal excitability.

    The opening and closing of the pore in voltage-gated potassium (Kv) channels is caused by the arginine-rich S4 helix of the voltage sensor domain (VSD) moving in response to an external potential. In fact, VSDs are remarkably efficient at turning membrane potential into conformational changes, which likely makes them the smallest existing biological engines. Exactly how this is accomplished is not yet fully known and an area of hot debate, especially due to the lack of structures of the resting and intermediate states along the activation pathway. In this thesis I study how the VSD activation works and show how toxic compounds modulate channel gating through direct interaction with these quite unexplored drug targets.

    First, I show that a secondary structure transition from alpha- to 3(10)-helix in the S4 helix is an important part of the gating as this helix type is significantly more favorable compared to the -helix in terms of a lower free energy barrier. Second, I present new models for intermediate states along the whole voltage sensor cycle from closed to open and suggest a new gating model for S4, where it moves as a sliding 3(10)-helix. Interestingly, this 3(10)-helix is formed in the region of the single most conserved residue in Kv channels, the phenylalanine F233. Located in the hydrophobic core, it directly faces S4 and creates a structural barrier for the gating charges. Substituting this residue alters the deactivation free energy barrier and can either facilitate the relaxation of the voltage sensor or increase the free energy barrier, depending on the size of the mutant. These results are confirmed by new experimental data that supports that a rigid ring at the phenylalanine position is the rate-limiting factor for the deactivation gating process, while the activation is unaffected. Finally, we study how the activation can be modulated for pharmaceutical reasons. Neurotoxins such as hanatoxin and stromatoxin push S3b towards S4 helix limiting S4's flexibility. This makes it harder for the VSD to activate and might explain the stronger binding affinities in resting state.

    All these results are highly important both for the general topic of biological macromolecules undergoing functionally critical conformational transitions, as well as the particular case of voltage-gated ion channels where understanding of the gating process is probably the key step to explain the effects of mutations or drug interactions.

  • 643.
    Schwaiger, Christine S.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Bjelkmar, Pär
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    310-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State2011In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 6, p. 1446-1454Article in journal (Refereed)
    Abstract [en]

    The activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models propose combinations of translation, rotation, and tilt to reach the resting state. Recently, experiments and simulations have independently observed occurrence of 3(10)-helix in S4. This suggests S4 might make a transition from alpha- to 3(10)-helix in the gating process. Here, we show 3(10)-helix structure between 01 and R3 in the S4 segment of a voltage sensor appears to facilitate the early stage of the motion toward a down state. We use multiple microsecond-steered molecular simulations to calculate the work required for translating S4 both as a-helix and transformed to 3(10)-helix. The barrier appears to be caused by salt-bridge reformation simultaneous to R4 passing the F233 hydrophobic lock, and it is almost a factor-two lower with 3(10)-helix. The latter facilitates translation because R2/R3 line up to face E183/E226, which reduces the requirement to rotate S4. This is also reflected in a lower root mean-square deviation distortion of the rest of the voltage sensor. This supports the 3(10) hypothesis, and could explain some of the differences between the open-inactivated- versus activated-states.

  • 644.
    Schwaiger, Christine S
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Börjesson, Sara I
    Carlsson, Jens
    Elinder, Fredrik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Modulation of the voltage sensor resting state through Hanatoxin and StromatoxinManuscript (preprint) (Other academic)
  • 645.
    Schwaiger, Christine S.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Börjesson, Sara I.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Elinder, Fredrik
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Phe233 in the Voltage-Sensor is Rate Limiting for Channel Closure but not for the Opening2012In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, no 3, p. 13A-13AArticle in journal (Other academic)
  • 646.
    Schwaiger, Christine S.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Börjesson, Sara I.
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Cell Biology, Linköping, Sweden.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Wallner, Björn
    The voltage sensor deactivation barrier is altered by substitutions in the hydrophobic coreManuscript (preprint) (Other academic)
    Abstract [en]

    The gating of voltage-gated ion channels is caused by the arginine-rich S4 helix of the voltage sensor moving in response to an external potential. Exactly how this is accomplished is not yet fully known, but several studies now indicate S4 transiently adopts 310-conformation to facilitate the process. Here, we combine modeling of intermediate states based on experimental constraints with systematic in silico mutagenesis and free energy calculations to identify metastable states and characterize the energetics when moving between them. We show that states very close to the X-ray structure can be obtained with steered simulations starting from the intermediate state, and that several residues in the narrow hydrophobic band in the middle of the voltage sensor contribute to the free energy between the activated and intermediate states. The single most important is the structural barrier caused by the aromatic ring of F233. Substitution for smaller amino acids reduces the translation cost signi cantly, while introduction of a larger ring increases it, both con rming experimental activation shift results. In fact, the rigid ring appears to determine the barrier for the voltage sensor gating process, with a close interaction between the ring rotation and the arginine barrier crossing.

     

  • 647.
    Schwaiger, Christine S.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Börjesson, Sara I.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wallner, Björn
    Elinder, Fredrik
    Linköping University, Linköping, Sweden.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain.2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 10, p. e45880-Article in journal (Refereed)
    Abstract [en]

    The gating of voltage-gated ion channels is controlled by the arginine-rich S4 helix of the voltage-sensor domain moving in response to an external potential. Recent studies have suggested that S4 moves in three to four steps to open the conducting pore, thus visiting several intermediate conformations during gating. However, the exact conformational changes are not known in detail. For instance, it has been suggested that there is a local rotation in the helix corresponding to short segments of a 3-helix moving along S4 during opening and closing. Here, we have explored the energetics of the transition between the fully open state (based on the X-ray structure) and the first intermediate state towards channel closing (C), modeled from experimental constraints. We show that conformations within 3 Å of the X-ray structure are obtained in simulations starting from the C model, and directly observe the previously suggested sliding 3-helix region in S4. Through systematic free energy calculations, we show that the C state is a stable intermediate conformation and determine free energy profiles for moving between the states without constraints. Mutations indicate several residues in a narrow hydrophobic band in the voltage sensor contribute to the barrier between the open and C states, with F233 in the S2 helix having the largest influence. Substitution for smaller amino acids reduces the transition cost, while introduction of a larger ring increases it, largely confirming experimental activation shift results. There is a systematic correlation between the local aromatic ring rotation, the arginine barrier crossing, and the corresponding relative free energy. In particular, it appears to be more advantageous for the F233 side chain to rotate towards the extracellular side when arginines cross the hydrophobic region.

  • 648.
    Schwaiger, Christine S.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Liin, Sara I.
    Elinder, Fredrik
    Linköping University.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    The conserved phenylalanine in the K+ channel voltage-sensor domain creates a barrier with unidirectional effects2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 1, p. 75-84Article in journal (Refereed)
    Abstract [en]

    Voltage-gated ion channels are crucial for regulation of electric activity of excitable tissues such as nerve cells, and play important roles in many diseases. During activation, the charged S4 segment in the voltage sensor domain translates across a hydrophobic core forming a barrier for the gating charges. This barrier is critical for channel function, and a conserved phenylalanine in segment S2 has previously been identified to be highly sensitive to substitutions. Here, we have studied the kinetics of Kv1-type potassium channels (Shaker and Kv1.2/2.1 chimera) through site-directed mutagenesis, electrophysiology, and molecular simulations. The F290L mutation in Shaker (F233L in Kv1.2/2.1) accelerates channel closure by at least a factor 50, although opening is unaffected. Free energy profiles with the hydrophobic neighbors of F233 mutated to alanine indicate that the open state with the fourth arginine in S4 above the hydrophobic core is destabilized by ∼17 kJ/mol compared to the first closed intermediate. This significantly lowers the barrier of the first deactivation step, although the last step of activation is unaffected. Simulations of wild-type F233 show that the phenyl ring always rotates toward the extracellular side both for activation and deactivation, which appears to help stabilize a well-defined open state.

  • 649. Scott, Pat
    et al.
    Sivertsson, Sofia
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Gamma Rays from Ultracompact Primordial Dark Matter Minihalos2009In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 103, no 21, p. 211301-1-211301-4Article in journal (Refereed)
    Abstract [en]

    Ultracompact minihalos have been proposed as a new class of dark matter structure. They would be produced by phase transitions in the early Universe or features in the inflaton potential, and constitute nonbaryonic massive compact halo objects today. We examine the prospects of detecting these minihalos in gamma rays if dark matter can self-annihilate. We compute present-day fluxes from minihalos produced in the e(+)e(-) annihilation epoch and the QCD and electroweak phase transitions. Even at a distance of 4 kpc, minihalos from the e(+)e(-) epoch would be eminently detectable today by the Fermi satellite or air Ccerenkov telescopes, or even in archival EGRET data. Within 2 kpc, they would appear as extended sources to Fermi. At 4 kpc, minihalos from the QCD transition have similar predicted fluxes to dwarf spheroidal galaxies, so might also be detectable by present or upcoming experiments.

  • 650.
    Sellin, Karl
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics.
    Phase transitions and vortex structures in multicomponent superconductors2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Theoretical aspects of multicomponent superconductivity and systemswith competing interactions are studied using Monte Carlo techniques.Motivated by recent experimental and theoretical results of complex struc-ture formation of vortices in multicomponent systems, possible vortex struc-ture formations due to vortex interactions that are not purely attractive orrepulsive are considered. Vortex structures such as clusters, superclusters,hierarchical structure formation, stripes, gossamer patters, glassy phases, aswell as checkerboard lattices and loops are demonstrated to be possible.The order of the superconducting phase transition is considered for multi-component lattice London superconductors. The phase transition is demon-strated to be either rst-order or continuous depending on the strength of asymmetry-breaking Josephson intercomponent interaction. It is argued thatthe rst-order phase transition is caused by a vortex phase separation due toa uctuation-induced attractive interaction between vortex lines.

10111213141516 601 - 650 of 764
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