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  • 1.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S. P.
    Scott, H. A.
    Interaction of Ultrashort X-ray Pulses with B4C, SiC and Si2008In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 77, no 2, p. 026404-1-026404-8Article in journal (Refereed)
    Abstract [en]

    The interaction of 32.5 and 6 nm ultrashort x-ray pulses with the solid materials B4C, SiC, and Si is simulated with a nonlocal thermodynamic equilibrium radiation transfer code. We study the ionization dynamics as a function of depth in the material and modifications of the opacity during irradiation, and estimate the crater depth. Furthermore, we compare the estimated crater depth with experimental data, for fluences up to 2.2 J/cm(2). Our results show that, at 32.5 nm irradiation, the opacity changes by less than a factor of 2 for B4C and Si and by a factor of 3 for SiC, for fluences up to 200 J/cm(2). At a laser wavelength of 6 nm, the model predicts a dramatic decrease in opacity due to the weak inverse bremsstrahlung, increasing the crater depth for high fluences.

  • 2. Chernodub, Maxim
    et al.
    Hu, Shuangwei
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Topological solitons and folded proteins2010In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 82, no 1, p. 011916-Article in journal (Refereed)
    Abstract [en]

    We argue that protein loops can be described by topological domain-wall solitons that interpolate between ground states which are the alpha helices and beta strands. We present an energy function that realizes loops as soliton solutions to its equation of motion, and apply these solitons to model a number of biologically active proteins including 1VII, 2RB8, and 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to numerically construct soliton solutions that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 1.0 angstrom or less for the central alpha-carbons, i.e., close to the limits of current experimental accuracy.

  • 3. Hau-Riege, S. P.
    et al.
    London, R. A.
    Chapman, H. N.
    Bergh, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Soft-x-ray free-electron-laser interaction with materials2007In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 76, no 4, p. 046403-Article in journal (Refereed)
    Abstract [en]

    Soft-x-ray free-electron lasers have enabled materials studies in which structural information is obtained faster than the relevant probe-induced damage mechanisms. We present a continuum model to describe the damage process based on hot-dense plasma theory, which includes a description of the energy deposition in the samples, the subsequent dynamics of the sample, and the detector signal. We compared the model predictions with experimental data and mostly found reasonable agreement. In view of future free-electron-laser performance, the model was also used to predict damage dynamics of samples and optical elements at shorter wavelengths and larger photon fluences than currently available.

  • 4.
    Hu, Shuangwei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Krokhotin, Andrei
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Peng, Xubiao
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Towards quantitative classification of folded proteins in terms of elementary functions2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 83, no 4, p. 041907-Article in journal (Refereed)
    Abstract [en]

    A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a classification scheme that describes a protein starting from its well-organized secondary structures and often involves direct human involvement, with an atomary-level physics-based approach where a protein is fundamentally nothing more than an ensemble of mutually interacting carbon, hydrogen, oxygen, and nitrogen atoms. In order to bridge these two complementary approaches to proteins, conceptually novel tools need to be introduced. Here we explain how an approach toward geometric characterization of entire folded proteins can be based on a single explicit elementary function that is familiar from nonlinear physical systems where it is known as the kink soliton. Our approach enables the conversion of hierarchical structural information into a quantitative form that allows for a folded protein to be characterized in terms of a small number of global parameters that are in principle computable from atomary-level considerations. As an example we describe in detail how the native fold of the myoglobin 1M6C emerges from a combination of kink solitons with a very high atomary-level accuracy. We also verify that our approach describes longer loops and loops connecting alpha helices with beta strands, with the same overall accuracy.

  • 5. Li, Jiantong
    et al.
    Zhang, Shi-Li
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Conductivity exponents in stick percolation2010In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 81, no 2, p. 021120-Article in journal (Refereed)
    Abstract [en]

    On the basis of Monte Carlo simulations, the present work systematically investigates how conductivity exponents depend on the ratio of stick-stick junction resistance to stick resistance for two-dimensional stick percolation. Simulation results suggest that the critical conductivity exponent extracted from size-dependent conductivities of systems exactly at the percolation threshold is independent of the resistance ratio and has a constant value of 1.280±0.014. In contrast, the apparent conductivity exponent extracted from density-dependent conductivities of systems well above the percolation threshold monotonically varies with the resistance ratio, following an error function, and lies in the vicinity of the critical exponent.

  • 6. Li, Jiantong
    et al.
    Zhang, Shi-Li
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Finite-size scaling in stick percolation2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 4, p. 040104-Article in journal (Refereed)
    Abstract [en]

    This work presents the generalization of the concept of universal finite-size scaling functions to continuum percolation. A high-efficiency algorithm for Monte Carlo simulations is developed to investigate, with extensive realizations, the finite-size scaling behavior of stick percolation in large-size systems. The percolation threshold of high precision is determined for isotropic widthless stick systems as Ncl2=5.637 26±0.000 02, with Nc as the critical density and l as the stick length. Simulation results indicate that by introducing a nonuniversal metric factor A=0.106 910±0.000 009, the spanning probability of stick percolation on square systems with free boundary conditions falls on the same universal scaling function as that for lattice percolation.

  • 7.
    Lindén, Martin
    et al.
    Theoretical Physics, Royal Institute of Technology, AlbaNova, 10691 Stockholm, Sweden.
    Tuohimaa, Tomi
    Jonsson, Ann-Beth
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Wallin, Mats
    Force generation in small ensembles of Brownian motors2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 74, no 2, p. 021908-1-021908-8Article in journal (Refereed)
    Abstract [en]

    The motility of certain gram-negative bacteria is mediated by retraction of type IV pili surface filaments, which are essential for infectivity. The retraction is powered by a strong molecular motor protein, PilT, producing very high forces that can exceed 150 pN. The molecular details of the motor mechanism are still largely unknown, while other features have been identified, such as the ring-shaped protein structure of the PilT motor. The surprisingly high forces generated by the PilT system motivate a model investigation of the generation of large forces in molecular motors. We propose a simple model, involving a small ensemble of motor subunits interacting through the deformations on a circular backbone with finite stiffness. The model describes the motor subunits in terms of diffusing particles in an asymmetric, time-dependent binding potential (flashing ratchet potential), roughly corresponding to the ATP hydrolysis cycle. We compute force-velocity relations in a subset of the parameter space and explore how the maximum force (stall force) is determined by stiffness, binding strength, ensemble size, and degree of asymmetry. We identify two qualitatively different regimes of operation depending on the relation between ensemble size and asymmetry. In the transition between these two regimes, the stall force depends nonlinearly on the number of motor subunits. Compared to its constituents without interactions, we find higher efficiency and qualitatively different force-velocity relations. The model captures several of the qualitative features obtained in experiments on pilus retraction forces, such as roughly constant velocity at low applied forces and insensitivity in the stall force to changes in the ATP concentration.

  • 8.
    Maia, Filipe R. N. C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structural variability and the incoherent addition of scattered intensities in single-particle diffraction2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 3, p. 031905-Article in journal (Refereed)
    Abstract [en]

    X-ray lasers may allow structural studies on single particles and biomolecules without crystalline periodicity in the samples. We examine here the effect of sample dynamics as a source of structural heterogeneity on the resolution of the reconstructed image of a small protein molecule. Structures from molecular-dynamics simulations of lysozyme were sampled and aligned. These structures were then used to calculate diffraction patterns corresponding to different dynamic states. The patterns were incoherently summed and the resulting data set was phased using the oversampling method. Reconstructed images of hydrated and dehydrated lysozyme gave resolutions of 3.7 angstrom and 7.6 angstrom, respectively. These are significantly worse than the root-mean-square deviation of the hydrated (2.7 angstrom for all atoms and 1.45 angstrom for C-alpha positions) or dehydrated (3.7 angstrom for all atoms and 2.5 angstrom for C-alpha positions) structures. The noise introduced by structural dynamics and incoherent addition of dissimilar structures restricts the maximum resolution to be expected from direct image reconstruction of dynamic systems. A way of potentially reducing this effect is by grouping dynamic structures into distinct structural substates and solving them separately.

  • 9.
    Michaud, Jérôme
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Sociology. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Szilva, Attila
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Social influence with recurrent mobility and multiple options2018In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 97, no 6, article id 062313Article in journal (Refereed)
    Abstract [en]

    In this paper, we discuss the possible generalizations of the Social Influence with Recurrent Mobility (SIRM) model developed in Phys. Rev. Lett. 112, 158701 (2014). Although the SIRM model worked approximately satisfying when US election was modelled, it has its limits: it has been developed only for two-party systems and can lead to unphysical behaviour when one of the parties has extreme vote share close to 0 or 1. We propose here generalizations to the SIRM model by its extension for multi-party systems that are mathematically well-posed in case of extreme vote shares, too, by handling the noise term in a different way. In addition, we show that our method opens new applications for the study of elections by using a new calibration procedure, and makes possible to analyse the influence of the "free will" (creating a new party) and other local effects for different commuting network topologies.

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  • 10. Muller, Hans-Peter
    et al.
    Kimmich, Rainer
    Weis, Jan
    NMR flow velocity mapping in random percolation model objects: Evidence for a power-law dependence of the volume-averaged velocity on the probe-radius1996In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. E54, p. 5278-5285Article in journal (Refereed)
  • 11. Muller, Hans-Peter
    et al.
    Weis, Jan
    Computer simulation and six-dimensional spin density/velocity NMR microimaging of lacunar systems. A comparative analysis of percolation properties1995In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 52, no 5, p. 5195-5204Article in journal (Refereed)
  • 12. Müller,
    et al.
    Kimmich,
    Weis,
    NMR flow velocity mapping in random percolation model objects: Evidence for a power-law dependence of the volume-averaged velocity on the probe-volume radius.1996In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 54, no 5, p. 5278-5285Article in journal (Refereed)
  • 13. Müller,
    et al.
    Weis,
    Kimmich,
    Computer simulation and six-dimensional spin density and velocity NMR microimaging of lacunar systems: A comparative analysis of percolation properties.1995In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 52, no 5, p. 5195-5204Article in journal (Refereed)
  • 14. Nicolis, C
    et al.
    Nicolis, S. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Propagation of extremes in space2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 2, p. 026201-Article in journal (Refereed)
    Abstract [en]

    The propagation of extreme events in space is analyzed for a class of dynamical systems giving rise to spatiotemporal chaos. It is shown that this process can be mapped into a generalized random walk, whereby the mean square displacement increases linearly in time and there is a nonvanishing probability for jumps beyond first neighbors. The relative roles of the local dynamics and of the spatial coupling are identified.

  • 15.
    Nicolis, S. C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Nicolis, C.
    Extreme events in bimodal systems2008In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 78, no 3, p. 036222-Article in journal (Refereed)
    Abstract [en]

    The extreme value statistics of systems possessing a two-hump probability density of the relevant variable, in which the left peak is more pronounced than the right one, is studied. It is shown that systems of this type display a nontrivial transient behavior in the form of anomalous fluctuations around the mean, for certain (finite) ranges of observational time windows. The results are illustrated on independent identically distributed random variables, systems possessing two locally stable states and subjected to additive white noise, and dynamical systems in the regime of deterministic chaos.

  • 16.
    Romensky, Maksym
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Lobaskin, Vladimir
    University College Dublin.
    Ihle, Thomas
    North Dakota State University.
    Tricritical points in a Vicsek model of self-propelled particles with bounded confidence2014In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787Article in journal (Refereed)
    Abstract [en]

    We study the orientational ordering in systems of self-propelled particles with selective interactions. To introduce the selectivity we augment the standard Vicsek model with a bounded-confidence collision rule: a given particle only aligns to neighbors who have directions quite similar to its own. Neighbors whose directions deviate more than a fixed restriction angle α are ignored. The collective dynamics of this system is studied by agent-based simulations and kinetic mean-field theory. We demonstrate that the reduction of the restriction angle leads to a critical noise amplitude decreasing monotonically with that angle, turning into a power law with exponent 32 for small angles. Moreover, for small system sizes we show that upon decreasing the restriction angle, the kind of the transition to polar collective motion changes from continuous to discontinuous. Thus, an apparent tricritical point with different scaling laws is identified and calculated analytically. We investigate the shifting and vanishing of this point due to the formation of density bands as the system size is increased. Agent-based simulations in small systems with large particle velocities show excellent agreement with the kinetic theory predictions. We also find that at very small interaction angles, the polar ordered phase becomes unstable with respect to the apolar phase. We derive analytical expressions for the dependence of the threshold noise on the restriction angle. We show that the mean-field kinetic theory also permits stationary nematic states below a restriction angle of 0.681π. We calculate the critical noise, at which the disordered state bifurcates to a nematic state, and find that it is always smaller than the threshold noise for the transition from disorder to polar order. The disordered-nematic transition features two tricritical points: At low and high restriction angle, the transition is discontinuous but continuous at intermediate α. We generalize our results to systems that show fragmentation into more than two groups and obtain scaling laws for the transition lines and the corresponding tricritical points. A numerical method to evaluate the nonlinear Fredholm integral equation for the stationary distribution function is also presented. This method is shown to give excellent agreement with agent-based simulations, even in strongly ordered systems at noise values close to zero.

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