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Sökning: L773:1367 2630 > Umeå universitet

  • Resultat 1-10 av 30
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1.
  • Ahlberg, Sebastian, et al. (författare)
  • Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA
  • 2015
  • Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 17
  • Tidskriftsartikel (refereegranskat)abstract
    • 30% of the DNA in E. coli bacteria is covered by proteins. Such a high degree of crowding affects the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc) in ways that are not yet fully understood. In this paper, we theoretically address the diffusion constant of a tracer particle in a one-dimensional system surrounded by impenetrable crowder particles. While the tracer particle always stays on the lattice, crowder particles may unbind to a surrounding bulk and rebind at another, or the same, location. In this scenario we determine how the long time diffusion constant D (after many unbinding events) depends on (i) the unbinding rate of crowder particles k(off), and (ii) crowder particle line density rho, from simulations (using the Gillespie algorithm) and analytical calculations. For small k(off), we find D similar to k(off)/rho(2) when crowder particles do not diffuse on the line, and D similar to root Dk(off)/rho when they are diffusing; D is the free particle diffusion constant. For large k(off), we find agreement with mean-field results which do not depend on k(off). From literature values of k(off) and D, we show that the small k(off) -limit is relevant for in vivo protein diffusion on crowded DNA. Our results apply to single-molecule tracking experiments.
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2.
  • Burza, Matthias, et al. (författare)
  • Hollow microspheres as targets for staged laser-driven proton acceleration
  • 2011
  • Ingår i: New Journal of Physics. - : Institute of Physics Publishing (IOPP). - 1367-2630. ; 13, s. 013030-
  • Tidskriftsartikel (refereegranskat)abstract
    • A coated hollow core microsphere is introduced as a novel targetin ultra-intense laser–matter interaction experiments. In particular, it facilitates staged laser-driven proton acceleration by combining conventional target normal sheath acceleration (TNSA), power recycling of hot laterally spreading electrons and staging in a very simple and cheap target geometry. During TNSA of protons from one area of the sphere surface, laterally spreading hot electrons form a charge wave. Due to the spherical geometry, this wave refocuses on the opposite side of the sphere, where an opening has been laser micromachined.This leads to a strong transient charge separation field being set up there, which can post-accelerate those TNSA protons passing through the hole at the right time. Experimentally, the feasibility of using such targets is demonstrated. A redistribution is encountered in the experimental proton energy spectra, as predicted by particle-in-cell simulations and attributed to transient fields set up by oscillating currents on the sphere surface.
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3.
  • Eliasson, Bengt, et al. (författare)
  • Laser acceleration of monoenergetic protons via a double layer emerging from an ultra-thin foil
  • 2009
  • Ingår i: New Journal of Physics. - : IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. - 1367-2630. ; 11, s. 073006-073025
  • Tidskriftsartikel (refereegranskat)abstract
    • We present theoretical and numerical studies of the acceleration of monoenergetic protons in a double layer formed by the laser irradiation of an ultra-thin film. The ponderomotive force of the laser light pushes the electrons forward, and the induced space charge electric field pulls the ions and makes the thin foil accelerate as a whole. The ions trapped by the combined electric field and inertial force in the accelerated frame, together with the electrons trapped in the well of the ponderomotive and ion electric field, form a stable double layer. The trapped ions are accelerated to monoenergetic energies up to 100 MeV and beyond, making them suitable for cancer treatment. We present an analytic theory for the laser-accelerated ion energy and for the amount of trapped ions as functions of the laser intensity, foil thickness and the plasma number density. We also discuss the underlying physics of the trapped and untrapped ions in a double layer. The analytical results are compared with those obtained from direct Vlasov simulations of the fully nonlinear electron and ion dynamics that is controlled by the laser light.
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4.
  • Nyberg, Markus, et al. (författare)
  • A simple method to calculate first-passage time densities with arbitrary initial conditions
  • 2016
  • Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 18:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Numerous applications all the way from biology and physics to economics depend on the density of first crossings over a boundary. Motivated by the lack of general purpose analytical tools for computing first-passage time densities (FPTDs) for complex problems, we propose a new simple method based on the independent interval approximation (IIA). We generalise previous formulations of the IIA to include arbitrary initial conditions as well as to deal with discrete time and non-smooth continuous time processes. We derive a closed form expression for the FPTD in z and Laplace-transform space to a boundary in one dimension. Two classes of problems are analysed in detail: discrete time symmetric random walks (Markovian) and continuous time Gaussian stationary processes (Markovian and non-Markovian). Our results are in good agreement with Langevin dynamics simulations.
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5.
  • Sanders, Lloyd, et al. (författare)
  • Severe slowing-down and universality of the dynamics in disordered interacting many-body systems : ageing and ultraslow diffusion
  • 2014
  • Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 16, s. 113050-
  • Tidskriftsartikel (refereegranskat)abstract
    • Low-dimensional, many-body systems are often characterized by ultraslow dynamics. We study a labelled particle in a generic system of identical particles with hard-core interactions in a strongly disordered environment. The disorder is manifested through intermittent motion with scale-free sticking times at the single particle level. While for a non-interacting particle we find anomalous diffusion of the power-law form < x(2)(t)> similar or equal to t(alpha) of the mean squared displacement with 0 < alpha < 1, we demonstrate here that the combination of the disordered environment with the many-body interactions leads to an ultraslow, logarithmic dynamics < x(2)(t)> similar or equal to log(1/2)t with a universal 1/2 exponent. Even when a characteristic sticking time exists but the fluctuations of sticking times diverge we observe the mean squared displacement < x(2)(t)> similar or equal to t(gamma) with 0 < gamma < 1/2, that is slower than the famed Harris law < x(2)(t)> similar or equal to t(1/2) without disorder. We rationalize the results in terms of a subordination to a counting process, in which each transition is dominated by the forward waiting time of an ageing continuous time process.
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6.
  • Hedström, Lucas, et al. (författare)
  • Modelling chromosome-wide target search
  • 2023
  • Ingår i: New Journal of Physics. - : Institute of Physics (IOP). - 1367-2630. ; 25:3
  • Tidskriftsartikel (refereegranskat)abstract
    • The most common gene regulation mechanism is when a transcription factor (TF) protein binds to a regulatory sequence to increase or decrease RNA transcription. However, TFs face two main challenges when searching for these sequences. First, the sequences are vanishingly short relative to the genome length. Second, there are many nearly identical sequences scattered across the genome, causing proteins to suspend the search. But as pointed out in a computational study of LacI regulation in Escherichia coli, such almost-targets may lower search times if considering DNA looping. In this paper, we explore if this also occurs over chromosome-wide distances. To this end, we developed a cross-scale computational framework that combines established facilitated-diffusion models for basepair-level search and a network model capturing chromosome-wide leaps. To make our model realistic, we used Hi-C data sets as a proxy for 3D proximity between long-ranged DNA segments and binding profiles for more than 100 TFs. Using our cross-scale model, we found that median search times to individual targets critically depend on a network metric combining node strength (sum of link weights) and local dissociation rates. Also, by randomizing these rates, we found that some actual 3D target configurations stand out as considerably faster or slower than their random counterparts. This finding hints that chromosomes’ 3D structure funnels essential TFs to relevant DNA regions.
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7.
  • Abou-Hamad, Edy, et al. (författare)
  • Electronic properties of Cs-intercalated single-walled carbon nanotubes derived from nuclear magnetic resonance
  • 2011
  • Ingår i: New Journal of Physics. - : IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. - 1367-2630. ; 13, s. 053045 (1)-(9)
  • Tidskriftsartikel (refereegranskat)abstract
    • We report on the electronic properties of Cs-intercalated singlewalled carbon nanotubes (SWNTs). A detailed analysis of the 13C and133Cs nuclear magnetic resonance (NMR) spectra reveals an increased metallization of the pristine SWNTs under Cs intercalation. The ‘metallization’ of CsxC materials where x =0–0.144 is evidenced from the increased local electronic density of states (DOS) n(EF)at the Fermi level of the SWNTs as determined from spin–lattice relaxation measurements. In particular, there are two distinct electronic phases called α and β and the transition between these occurs around x = 0.05. The electronic DOS at the Fermi level increases monotonically at low intercalation levels x <0.05 (α-phase), whereas it reaches a plateau in the range 0.05 < x < 0.143 at high intercalation levels (β-phase). The new β-phase is accompanied by a hybridization of Cs(6s) orbitals with C(sp2)orbitals of the SWNTs. In both phases, two types of metallic nanotubes are found with a low and a high local n(EF), corresponding to different local electronic band structures of the SWNTs.
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8.
  • Asenjo, Felipe A., et al. (författare)
  • Semi-relativistic effects in spin-1/2 quantum plasmas
  • 2012
  • Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 14, s. 073042-
  • Tidskriftsartikel (refereegranskat)abstract
    • Emerging possibilities for creating and studying novel plasma regimes, e. g. relativistic plasmas and dense systems, in a controlled laboratory environment also require new modeling tools for such systems. This motivates theoretical studies of the kinetic theory governing the dynamics of plasmas for which both relativistic and quantum effects occur simultaneously. Here, we investigate relativistic corrections to the Pauli Hamiltonian in the context of a scalar kinetic theory for spin-1/2 quantum plasmas. In particular, we formulate a quantum kinetic theory for the collective motion of electrons that takes into account effects such as spin-orbit coupling and Zitterbewegung. We discuss the implications and possible applications of our findings.
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9.
  • Baek, Seung Ki, et al. (författare)
  • The Ten Thousand Kims
  • 2011
  • Ingår i: New Journal of Physics. - : Institute of Physics. - 1367-2630. ; 13, s. 073036-
  • Tidskriftsartikel (refereegranskat)abstract
    • In the Korean culture the family members are recorded in special familybooks. This makes it possible to follow the distribution of Korean familynames far back in history. It is here shown that these name distributionsare well described by a simple null model, the random group formation (RGF)model. This model makes it possible to predict how the name distributionschange and these predictions are shown to be borne out. In particular, theRGF model predicts that, for married women entering a collection of familybooks in a certain year, the occurrence of the most common family name``Kim'' should be directly proportional the total number of married womenwith the same proportionality constant for all the years. This prediction isalso borne out to high degree. We speculate that it reflects some inherentsocial stability in the Korean culture. In addition, we obtain an estimate ofthe total population of the Korean culture down to year 500 AD, based on theRGF model and find about ten thousand Kims.
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10.
  • Baek, Seung Ki, et al. (författare)
  • Zipf's law unzipped
  • 2011
  • Ingår i: New Journal of Physics. - : IoP. - 1367-2630. ; 13, s. 043004-
  • Tidskriftsartikel (refereegranskat)abstract
    • Why does Zipf's law give a good description of data from seemingly completely unrelated phenomena? Here it is argued that the reason is that they can all be described as outcomes of a ubiquitous random group division: the elements can be citizens of a country and the groups family names, or the elements can be all the words making up a novel and the groups the unique words, or the elements could be inhabitants and the groups the cities in a country, and so on. A Random Group Formation (RGF) is presented from which a Bayesian estimate is obtained based on minimal information: it provides the best prediction for the number of groups with $k$ elements, given the total number of elements, groups, and the number of elements in the largest group. For each specification of these three values, the RGF predicts a unique group distribution $N(k)\propto \exp(-bk)/k^{\gamma}$, where the power-law index $\gamma$ is a unique function of the same three values. The universality of the result is made possible by the fact that no system specific assumptions are made about the mechanism responsible for the group division. The direct relation between $\gamma$ and the total number of elements, groups, and the number of elements in the largest group, is calculated. The predictive power of the RGF model is demonstrated by direct comparison with data from a variety of systems. It is shown that $\gamma$ usually takes values in the interval $1\leq\gamma\leq 2$ and that the value for a given phenomena depends in a systematic way on the total size of the data set. The results are put in the context of earlier discussions on Zipf's and Gibrat's laws, $N(k)\propto k^{-2}$ and the connection between growth models and RGF is elucidated.
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