Tobias Ambjornsson

Publications (4)4.34 Total impact

• Article: Non-renewal counting processes in systems with ageing waiting times: microscopic origin of logarithmic time evolution

  Michael A. Lomholt, Tobias Ambjornsson, Ludvig Lizana, Ralf Metzler
  [show abstract] [hide abstract]
  ABSTRACT: We study a generic counting process for systems governed by ageing waiting times. In contrast to renewal continuous time random walks with independent waiting times, we consider the case when each state is characterized by its own internal waiting time process, having been initiated at time t=0. Therefore each transition from state n to n+1 is triggered by psi_1, the forward waiting time density, instead of the regular waiting time density psi. For states characterized by heavy-tailed forms of psi we obtain an asymptotically logarithmic evolution of the counting dynamics n(t), whose fluctuations vanish relatively to the mean. The counting process introduced here describes the dynamics of crack propagation, the counting of on-off transitions in ensembles of blinking quantum dots, or, more generally, the dynamics in complex systems such as glasses or biological cells.
  08/2012;
• Source

  Available from: ArXiv

  Article: Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

  Tomas Novotny, Jonas Nyvold Pedersen, Tobias Ambjornsson, Mikael Sonne Hansen, Ralf Metzler
  [show abstract] [hide abstract]
  ABSTRACT: We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.
  EPL (Europhysics Letters) 11/2006; · 2.17 Impact Factor
• Source

  Available from: arxiv.org

  Article: Stochastic approach to DNA breathing dynamics

  Suman Kumar Banik, Tobias Ambjornsson, Ralf Metzler
  [show abstract] [hide abstract]
  ABSTRACT: We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups. Comment: 7 pages, 6 figures, epl.cls
  EPL (Europhysics Letters) 06/2005; · 2.17 Impact Factor
• Source

  Available from: ArXiv

  Article: Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins

  Tobias Ambjornsson, Ralf Metzler
  [show abstract] [hide abstract]
  ABSTRACT: We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can drive the system from undisturbed bubble fluctuations to full, binding protein-induced denaturation. We determine the effective free energy landscape of the DNA-bubble and explore its relaxation modes.
  12/2004;