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  • 1.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca Stella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobicrajski, R.
    Tolcikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    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.
    Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, no 1, p. 016403-Article in journal (Refereed)
    Abstract [en]

    Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 1017 W/cm2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 1016 W/cm2. This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.

  • 2.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    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.
    Model for the Dynamics of a Water Cluster in an X-ray Free Electron Laser Beam2004In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 70, no 5:1, p. 051904-Article in journal (Refereed)
    Abstract [en]

    A microscopic sample placed into a focused x-ray free electron laser beam will explode due to strong ionization on a femtosecond time scale. The dynamics of this Coulomb explosion has been modeled by Neutze et al. [Nature (London) 406, 752 (2000)] for a protein, using computer simulations. The results suggest that by using ultrashort exposures, structural information may be collected before the sample is destroyed due to radiation damage. In this paper a method is presented to include the effect of screening by free electrons in the sample in a molecular dynamics simulation. The electrons are approximated by a classical gas, and the electron distribution is calculated iteratively from the Poisson-Boltzmann equation. Test simulations of water clusters reveal the details of the explosion dynamics, as well as the evolution of the free electron gas during the beam exposure. We find that inclusion of the electron gas in the model slows down the Coulomb explosion. The hydrogen atoms leave the sample faster than the oxygen atoms, leading to a double layer of positive ions. A considerable electron density is located between these two layers. The fact that the hydrogens are found to explode much faster than the oxygens means that the diffracting part of the sample stays intact somewhat longer than the sample as a whole.

  • 3.
    Borlenghi, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Gauge invariance and geometric phase in nonequilibrium thermodynamics2016In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 93, no 1, article id 012133Article in journal (Refereed)
    Abstract [en]

    We show the link between U(1) lattice gauge theories and the off-equilibrium thermodynamics of a large class of nonlinear oscillators networks. The coupling between the oscillators plays the role of a gauge field, or connection, on the network. The thermodynamical forces that drive energy flows are expressed in terms of the curvature of the connection, analogous to a geometric phase. The model, which holds both close and far from equilibrium, predicts the existence of persistent energy and particle currents circulating in closed loops through the network. The predictions are confirmed by numerical simulations. Possible extension of the theory and experimental applications to nanoscale devices are briefly discussed.

  • 4.
    Borlenghi, Simone
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Iubini, Stefano
    Lepri, Stefano
    Bergqvist, Lars
    Delin, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Fransson, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Coherent energy transport in classical nonlinear oscillators: An analogy with the Josephson effect2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 91, no 4, article id 040102Article in journal (Refereed)
    Abstract [en]

    By means of a simple theoretical model and numerical simulations, we demonstrate the presence of persistent energy currents in a lattice of classical nonlinear oscillators with uniform temperature and chemical potential. In analogy with the well-known Josephson effect, the currents are proportional to the sine of the phase differences between the oscillators. Our results elucidate general aspects of nonequilibrium thermodynamics and point towards a way to practically control transport phenomena in a large class of systems. We apply the model to describe the phase-controlled spin-wave current in a bilayer nanopillar.

  • 5.
    Borlenghi, Simone
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Iubini, Stefano
    Lepri, Stefano
    Chico, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Bergqvist, Lars
    Delin, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Fransson, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Energy and magnetization transport in nonequilibrium macrospin systems2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, no 1, article id 012116Article in journal (Refereed)
    Abstract [en]

    We investigate numerically the magnetization dynamics of an array of nanodisks interacting through the magnetodipolar coupling. In the presence of a temperature gradient, the chain reaches a nonequilibrium steady state where energy and magnetization currents propagate. This effect can be described as the flow of energy and particle currents in an off-equilibrium discrete nonlinear Schrodinger (DNLS) equation. This model makes transparent the transport properties of the system and allows for a precise definition of temperature and chemical potential for a precessing spin. The present study proposes a setup for the spin-Seebeck effect, and shows that its qualitative features can be captured by a general oscillator-chain model.

  • 6.
    Bottinelli, Arianna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Applied Mathematics.
    Bassetti, B.
    Lagomarsino, M. C.
    Gherardi, M.
    Influence of homology and node age on the growth of protein-protein interaction networks2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, no 4, p. 041919-Article in journal (Refereed)
    Abstract [en]

    Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so the dynamics of the two objects are intrinsically linked. Here we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions through the definition of three different node wiring or divergence schemes. A comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition and topology observables.

  • 7.
    Carstensen, Hauke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Kapaklis, Vassilios
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Wolff, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Phase formation in colloidal systems with tunable interaction2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, no 1, article id 012303Article in journal (Refereed)
    Abstract [en]

    Self-assembly is one of the most fascinating phenomena in nature and is one key component in the formation of hierarchical structures. The formation of structures depends critically on the interaction between the different constituents, and therefore the link between these interactions and the resulting structure is fundamental for the understanding of materials. We have realized a two-dimensional system of colloidal particles with tunable magnetic dipole forces. The phase formation is studied by transmission optical microscopy and a phase diagram is constructed. We report a phase transition from hexagonal to random and square arrangements when the magnetic interaction between the individual particles is tuned from antiferromagnetic to ferrimagnetic.

  • 8. Chernodub, M.N.
    et al.
    Lundgren, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Elastic Energy and Phase Structure in a Continuous Spin Ising Chain with Applications to the Protein Folding Problem2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, no 1Article in journal (Refereed)
    Abstract [en]

    We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three known nontrivial phases of polymers: At low temperatures the model is in a collapsed phase, at medium temperatures it is in a random walk phase, and at high temperatures it enters the self-avoiding random walk phase. By investigating the temperature dependence of the specific energy we confirm that the transition between the collapsed phase and the random walk phase is a phase transition, while the random walk phase and self-avoiding random walk phase are separated from each other by a cross-over transition. We also compare the predictions of the model to a phenomenological elastic energy formula, proposed by Huang and Lei to describe folded proteins.

  • 9.
    Engblom, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lötstedt, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Meinecke, Lina
    Mesoscopic modeling of random walk and reactions in crowded media2018In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 98, p. 033304:1-16, article id 033304Article in journal (Refereed)
  • 10.
    Fedotov, Alexei
    et al.
    Brookhaven national laboratory.
    Gålnander, Björn
    Uppsala University, The Svedberg Laboratory.
    Litvinenko, Vladimir
    Brookhaven national laboratory.
    Lofnes, Tor
    Uppsala University, The Svedberg Laboratory.
    Sidorin, Anantoly
    JINR, Dubna.
    Smirnov, Alexander
    JINR, Dubna.
    Ziemann, Volker
    Uppsala University, The Svedberg Laboratory.
    Experimental studies of the magnetized friction force2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 74, no 6, article id 066503Article in journal (Refereed)
    Abstract [en]

    High-energy electron cooling, presently considered as an essential tool for several applications in high-energy and nuclear physics, requires an accurate description of the friction force which ions experience by passing through an electron beam. Present low-energy electron coolers can be used for a detailed study of the friction force. In addition, parameters of a low-energy cooler can be chosen in a manner, to reproduce regimes expected in future high-energy operation. Here, we report a set of dedicated experiments in CELSIUS aimed at a detailed study of the magnetized friction force. Some results of the accurate comparison of experimental data with the friction force formulas are presented.

  • 11. Hellander, Stefan
    et al.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Petzold, Linda
    Reaction rates for mesoscopic reaction-diffusion kinetics2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 91, p. 023312:1-12, article id 023312Article in journal (Refereed)
  • 12.
    Hellander, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Hellander, Andreas
    Petzold, Linda
    Reaction-diffusion master equation in the microscopic limit2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, p. 042901:1-5Article in journal (Refereed)
  • 13.
    Krokhotin, Andrei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Univ Tours, Lab Math & Phys Theor, CNRS, UMR 6083, F-37200 Tours, France.
    Peng, Xubiao
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Soliton concepts and protein structure2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, no 3, article id 031906Article in journal (Refereed)
    Abstract [en]

    Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.

  • 14.
    Krokhotin, Andrey
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Lundgren, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Solitons and collapse in the lambda-repressor protein2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, no 2, p. 021923-Article in journal (Refereed)
    Abstract [en]

    The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding lambda-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability, and folding pathways of the lambda-repressor protein, which controls the transition from the lysogenic to the lytic state. We first investigate the supersecondary helix-loop helix composition of its backbone. We use a discrete Frenet framing to resolve the backbone spectrum in terms of bond and torsion angles. Instead of four, there appears to be seven individual loops. We model the putative loops using an explicit soliton Ansatz. It is based on the standard soliton profile of the continuum nonlinear Schrodinger equation. The accuracy of the Ansatz far exceeds the B-factor fluctuation distance accuracy of the experimentally determined protein configuration. We then investigate the folding pathways and dynamics of the lambda-repressor protein. We introduce a coarse-grained energy function to model the backbone in terms of the C-alpha atoms and the side chains in terms of the relative orientation of the C-beta atoms. We describe the folding dynamics in terms of relaxation dynamics and find that the folded configuration can be reached from a very generic initial configuration. We conclude that folding is dominated by the temporal ordering of soliton formation. In particular, the third soliton should appear before the first and second. Otherwise, the DNA binding turn does not acquire its correct structure. We confirm the stability of the folded configuration by repeated heating and cooling simulations.

  • 15.
    Liberman, Michael A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Kiverin, A. D.
    Ivanov, M. F.
    Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, no 5, p. 056312-Article in journal (Refereed)
    Abstract [en]

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  • 16. Lindén, Martin
    Decay times in turnover statistics of single enzymes2008In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 78, no 1 Pt 1, p. 010901-Article in journal (Refereed)
    Abstract [en]

    The first passage times for enzymatic turnovers in nonequilibrium steady state display a statistical symmetry property related to nonequilibrium fluctuation theorems, which makes it possible to extract the chemical driving force from single molecule trajectories in nonequilibrium steady state. Below, we show that the number of decay constants needed to describe the first passage time distribution of this system is not equal to the number of states in the first passage problem, as one would generally expect. Instead, the structure of the kinetic mechanism makes half of the decay times vanish identically from the turnover time distribution. The terms that cancel out correspond to the eigenvalues of a certain submatrix of the master equation matrix for the first exit time problem. We discuss how these results make modeling and data analysis easier for such systems, and how the turnovers can be measured.

  • 17.
    Liu, Jing
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Engblom, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Assessing uncertainties in x-ray single-particle three-dimensional reconstruction2018In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 98, p. 013303:1-12, article id 013303Article in journal (Refereed)
  • 18.
    Lundgren, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Krokhotin, Andrey
    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, Theoretical Physics.
    Topology and structural self-organization in folded proteins2013In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 88, no 4, p. 042709-Article in journal (Refereed)
    Abstract [en]

    Topological methods are indispensable in theoretical studies of particle physics, condensed matter physics, and gravity. These powerful techniques have also been applied to biological physics. For example, knowledge of DNA topology is pivotal to the understanding as to how living cells function. Here, the biophysical repertoire of topological methods is extended, with the aim to understand and characterize the global structure of a folded protein. For this, the elementary concept of winding number of a vector field on a plane is utilized to introduce a topological quantity called the folding index of a crystallographic protein. It is observed that in the case of high resolution protein crystals, the folding index, when evaluated over the entire length of the crystallized protein backbone, has a very clear and strong propensity towards integer values. The observation proposes that the way how a protein folds into its biologically active conformation is a structural self-organization process with a topological facet that relates to the concept of solitons. It is proposed that the folding index has a potential to become a useful tool for the global, topological characterization of the folding pathways.

  • 19.
    Lundgren, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Correlation between protein secondary structure, backbone bond angles, and side-chain orientations2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, no 2, p. 021904-Article in journal (Refereed)
    Abstract [en]

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C-alpha carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C-beta carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C-alpha-C-beta structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 angstrom in root-mean-square distance from the experimental x-ray structure.

  • 20.
    Lundgren, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Niemi, Antti
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Sha, Fan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Protein loops, solitons and side-chain visualization with applications to the left-handed helix region2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, no 6, p. 061909-Article in journal (Refereed)
    Abstract [en]

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha helices and beta strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C-alpha atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C-beta carbons on the two-sphere. We show that the residue independent localization extends to C gamma and C-delta carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed beta turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  • 21.
    Nicolis, Stamatios C.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Applied Mathematics.
    Information flow and information production in a population system2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 84, no 1, p. 011110-Article in journal (Refereed)
    Abstract [en]

    An approach aiming to quantify the dynamics of information within a population is developed based on the mapping of the processes underlying the system's evolution into a birth and death type stochastic process and the derivation of a balance equation for the information entropy. Information entropy flux and information entropy production are identified and their time-dependent properties, as well as their dependence on the parameters present in the problem, are analyzed. States of minimum information entropy production are shown to exist for appropriate parameter values. Furthermore, uncertainty and information production are transiently intensified when the population traverses the inflexion point stage of the logisticlike growth process.

  • 22. Niklasson, Anders M. N.
    et al.
    Cawkwell, Marc J.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Canonical density matrix perturbation theory2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, p. 063301:1-8, article id 063301Article in journal (Refereed)
  • 23.
    Romenskyy, Maksym
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Lobaskin, Vladimir
    Ihle, Thomas
    Tricritical points in a Vicsek model of self-propelled particles with bounded confidence2014In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 90, no 6, article id 063315Article 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.

  • 24.
    Sieradzan, Adam K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Niemi, Antti
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Peng, Xubiao
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Peierls-Nabarro barrier and protein loop propagation2014In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 90, no 6, p. 062717-Article in journal (Refereed)
    Abstract [en]

    When a self-localized quasiparticle excitation propagates along a discrete one-dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy no longer enables the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the C-alpha backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink that solves a variant of the discrete nonlinear Schrodinger equation. We study the propagation of such a kink in the case of the protein G related albumin-binding domain, using the united residue coarse-grained molecular-dynamics force field. We estimate the height of the energy barriers that the kink needs to cross over in order to propagate along the backbone lattice. We analyze how these barriers give rise to both stresses and reliefs, which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone toward the native location. We observe that the dissipative forces that are exerted on the kink by the various energy barriers have a pivotal role in determining how a protein folds toward its native state.

  • 25.
    Sinelnikova, A.
    et al.
    Moscow MV Lomonosov State Univ, Inst Theoret Problems Microphys, Moscow 119899, Russia..
    Niemi, Antti J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Univ Tours, CNRS, UMR 6083, Lab Math & Phys Theor,Federat Denis Poisson, F-37200 Tours, France.;Beijing Inst Technol, Dept Phys, Beijing 100081, Peoples R China..
    Ulybyshev, M.
    Moscow MV Lomonosov State Univ, Inst Theoret Problems Microphys, Moscow 119899, Russia.;Univ Regensburg, Inst Theoret Phys, D-93053 Regensburg, Germany.;ITEP, Moscow 117218, Russia..
    Phase diagram and the pseudogap state in a linear chiral homopolymer model2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, no 3, article id 032602Article in journal (Refereed)
    Abstract [en]

    The phase structure of a single self-interacting homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the chain in the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence of a short-range attractive interaction between monomers, at various ambient temperature values. In the high-temperature limit the homopolymer chain is in the self-avoiding random walk phase. At very low temperatures two different phases are possible: When short-range attractive interactions dominate over chirality, the chain collapses into a space-filling conformation. But when the attractive interactions weaken, there is a low-temperature unfolding transition and the chain becomes like a straight rod. Between the high- and low-temperature limits, several intermediate states are observed, including the theta regime and pseudogap state, which is a novel form of phase state in the context of polymer chains. Applications to polymers and proteins, in particular collagen, are suggested.

  • 26.
    Siretskiy, Alexey
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Elvingson, Christer
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Vorontsov-Velyaminov, Pavel
    Saint-Petersburg State University, Physical Faculty.
    Khan, Malek
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Method for sampling compact configurations for semistiff  polymers2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 84, no 1, p. 016702-Article in journal (Refereed)
    Abstract [en]

    The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.

  • 27. Tsygankov, Denis
    et al.
    Lindén, Martin
    Fisher, Michael E
    Back-stepping, hidden substeps, and conditional dwell times in molecular motors2007In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 75, no 2 Pt 1, p. 021909-Article in journal (Refereed)
    Abstract [en]

    Processive molecular motors take more-or-less uniformly sized steps, along spatially periodic tracks, mostly forwards but increasingly backwards under loads. Experimentally, the major steps can be resolved clearly within the noise but one knows biochemically that one or more mechanochemical substeps remain hidden in each enzymatic cycle. In order to properly interpret experimental data for back-to-forward step ratios, mean conditional step-to-step dwell times, etc., a first-passage analysis has been developed that takes account of hidden substeps in N -state sequential models. The explicit, general results differ significantly from previous treatments that identify the observed steps with complete mechanochemical cycles; e.g., the mean dwell times tau(+) and tau(-) prior to forward and back steps, respectively, are normally unequal although the dwell times tau(++) and tau(--) between successive forward and back steps are equal. Illustrative (N=2) -state examples display a wide range of behavior. The formulation extends to the case of two or more detectable transitions in a multistate cycle with hidden substeps.

  • 28. Wang, F
    et al.
    Weckert, E
    Ziaja, B
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Van der spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, p. 031907-1-031907-5Article in journal (Refereed)
    Abstract [en]

    Coherent diffractive imaging using x-ray free-electron lasers (XFELs) may provide a unique opportunity for high-resolution structural analysis of single particles sprayed from an aqueous solution into the laser beam. As a result, diffraction images are measured from randomly oriented objects covered by a water layer. We analyze theoretically how the thickness of the covering water layer influences the structural and orientational information contained in the recorded diffraction images. This study has implications for planned experiments on single-particle imaging with XFELs.

1 - 28 of 28
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