@article{AbdolvahabMetzlerEjtehadi2011,
  author    = {Abdolvahab, Rouhollah Haji and Metzler, Ralf and Ejtehadi, Mohammad Reza},
  title     = {First passage time distribution of chaperone driven polymer translocation through a nanopore homopolymer and heteropolymer cases},
  series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  volume    = {135},
  journal   = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  number    = {24},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0021-9606},
  doi       = {10.1063/1.3669427},
  pages     = {8},
  year      = {2011},
  abstract  = {Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Peclet number, a dimensionless parameter comparing drift strength and diffusivity. Moreover it is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chaperone concentration, and the chain length, is also effectively determined by the Peclet number. We investigate the effect of the chaperone size on the translocation process. In particular, for large chaperone size, the translocation progress and the mean waiting time as function of the reaction coordinate exhibit pronounced sawtooth-shapes. The effects of a heterogeneous polymer sequence on the translocation dynamics is studied in terms of the translocation velocity, the probability distribution for the translocation progress, and the monomer waiting times. (C) 2011 American Institute of Physics.},
  language  = {en}
}
@article{AdamcikJeonKarczewskietal.2012,
  author    = {Adamcik, Jozef and Jeon, Jae-Hyung and Karczewski, Konrad J. and Metzler, Ralf and Dietler, Giovanni},
  title     = {Quantifying supercoiling-induced denaturation bubbles in DNA},
  series = {Soft matter},
  volume    = {8},
  journal   = {Soft matter},
  number    = {33},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1744-683X},
  doi       = {10.1039/c2sm26089a},
  pages     = {8651 -- 8658},
  year      = {2012},
  abstract  = {In both eukaryotic and prokaryotic DNA sequences of 30-100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive single DNA plasmid imaging. We demonstrate that long-lived single-stranded denaturation bubbles exist in negatively supercoiled DNA, at the expense of partial twist release. Remarkably, we observe a linear relation between the degree of supercoiling and the bubble size, in excellent agreement with statistical modelling. Furthermore, we obtain the full distribution of bubble sizes and the opening probabilities at varying salt and temperature conditions. The results presented herein underline the important role of denaturation bubbles in negatively supercoiled DNA for biological processes such as transcription and replication initiation in vivo.},
  language  = {en}
}
@article{AkimotoCherstvyMetzler2018,
  author    = {Akimoto, Takuma and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Ergodicity, rejuvenation, enhancement, and slow relaxation of diffusion in biased continuous-time random walks},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {98},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {2},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {2470-0045},
  doi       = {10.1103/PhysRevE.98.022105},
  pages     = {6},
  year      = {2018},
  abstract  = {Bias plays an important role in the enhancement of diffusion in periodic potentials. Using the continuous-time random walk in the presence of a bias, we report on an interesting phenomenon for the enhancement of diffusion by the start of the measurement in a random energy landscape. When the variance of the waiting time diverges, in contrast to the bias-free case, the dynamics with bias becomes superdiffusive. In the superdiffusive regime, we find a distinct initial ensemble dependence of the diffusivity. Moreover, the diffusivity can be increased by the aging time when the initial ensemble is not in equilibrium. We show that the time-averaged variance converges to the corresponding ensemble-averaged variance; i.e., ergodicity is preserved. However, trajectory-to-trajectory fluctuations of the time-averaged variance decay unexpectedly slowly. Our findings provide a rejuvenation phenomenon in the superdiffusive regime, that is, the diffusivity for a nonequilibrium initial ensemble gradually increases to that for an equilibrium ensemble when the start of the measurement is delayed.},
  language  = {en}
}
@article{AwadMetzler2020,
  author    = {Awad, Emad and Metzler, Ralf},
  title     = {Crossover dynamics from superdiffusion to subdiffusion},
  series = {Fractional calculus and applied analysis : an international journal for theory and applications},
  volume    = {23},
  journal   = {Fractional calculus and applied analysis : an international journal for theory and applications},
  number    = {1},
  publisher = {De Gruyter},
  address   = {Berlin ; Boston},
  issn      = {1311-0454},
  doi       = {10.1515/fca-2020-0003},
  pages     = {55 -- 102},
  year      = {2020},
  abstract  = {The Cattaneo or telegrapher's equation describes the crossover from initial ballistic to normal diffusion. Here we study and survey time-fractional generalisations of this equation that are shown to produce the crossover of the mean squared displacement from superdiffusion to subdiffusion. Conditional solutions are derived in terms of Fox H-functions and the dth-order moments as well as the diffusive flux of the different models are derived. Moreover, the concept of the distribution-like is proposed as an alternative to the probability density function.},
  language  = {en}
}
@article{AwadMetzler2022,
  author    = {Awad, Emad and Metzler, Ralf},
  title     = {Closed-form multi-dimensional solutions and asymptotic behaviours for subdiffusive processes with crossovers: II. Accelerating case},
  series = {Journal of physics : A, Mathematical and theoretical},
  volume    = {55},
  journal   = {Journal of physics : A, Mathematical and theoretical},
  number    = {20},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1751-8113},
  doi       = {10.1088/1751-8121/ac5a90},
  pages     = {29},
  year      = {2022},
  abstract  = {Anomalous diffusion with a power-law time dependence vertical bar R vertical bar(2)(t) similar or equal to t(alpha i) of the mean squared displacement occurs quite ubiquitously in numerous complex systems. Often, this anomalous diffusion is characterised by crossovers between regimes with different anomalous diffusion exponents alpha(i). Here we consider the case when such a crossover occurs from a first regime with alpha(1) to a second regime with alpha(2) such that alpha(2) > alpha(1), i.e., accelerating anomalous diffusion. A widely used framework to describe such crossovers in a one-dimensional setting is the bi-fractional diffusion equation of the so-called modified type, involving two time-fractional derivatives defined in the Riemann-Liouville sense. We here generalise this bi-fractional diffusion equation to higher dimensions and derive its multidimensional propagator (Green's function) for the general case when also a space fractional derivative is present, taking into consideration long-ranged jumps (Levy flights). We derive the asymptotic behaviours for this propagator in both the short- and long-time as well the short- and long-distance regimes. Finally, we also calculate the mean squared displacement, skewness and kurtosis in all dimensions, demonstrating that in the general case the non-Gaussian shape of the probability density function changes.},
  language  = {en}
}
@article{AydinerCherstvyMetzler2018,
  author    = {Aydiner, Ekrem and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Wealth distribution, Pareto law, and stretched exponential decay of money},
  series = {Physica : europhysics journal ; A, Statistical mechanics and its applications},
  volume    = {490},
  journal   = {Physica : europhysics journal ; A, Statistical mechanics and its applications},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0378-4371},
  doi       = {10.1016/j.physa.2017.08.017},
  pages     = {278 -- 288},
  year      = {2018},
  abstract  = {We study by Monte Carlo simulations a kinetic exchange trading model for both fixed and distributed saving propensities of the agents and rationalize the person and wealth distributions. We show that the newly introduced wealth distribution - that may be more amenable in certain situations - features a different power-law exponent, particularly for distributed saving propensities of the agents. For open agent-based systems, we analyze the person and wealth distributions and find that the presence of trap agents alters their amplitude, leaving however the scaling exponents nearly unaffected. For an open system, we show that the total wealth - for different trap agent densities and saving propensities of the agents - decreases in time according to the classical Kohlrausch-Williams-Watts stretched exponential law. Interestingly, this decay does not depend on the trap agent density, but rather on saving propensities. The system relaxation for fixed and distributed saving schemes are found to be different.},
  language  = {en}
}
@article{AydinerCherstvyMetzler2019,
  author    = {Aydiner, Ekrem and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Money distribution in agent-based models with position-exchange dynamics},
  series = {The European physical journal : B, Condensed matter and complex systems},
  volume    = {92},
  journal   = {The European physical journal : B, Condensed matter and complex systems},
  number    = {5},
  publisher = {Springer},
  address   = {New York},
  issn      = {1434-6028},
  doi       = {10.1140/epjb/e2019-90674-0},
  pages     = {4},
  year      = {2019},
  abstract  = {Wealth and income distributions are known to feature country-specific Pareto exponents for their long power-law tails. To propose a rationale for this, we introduce an agent-based dynamic model and use Monte Carlo simulations to unveil the wealth distributions in closed and open economical systems. The standard money-exchange scenario is supplemented with the position-exchange agent dynamics that vitally affects the Pareto law. Specifically, in closed systems with position-exchange dynamics the power law changes to an exponential shape, while for open systems with traps the Pareto law remains valid.},
  language  = {en}
}
@misc{BarkaiGariniMetzler2013,
  author    = {Barkai, Eli and Garini, Yuval and Metzler, Ralf},
  title     = {Electrostatic effects in living cells Reply},
  series = {PHYSICS TODAY},
  volume    = {66},
  journal   = {PHYSICS TODAY},
  number    = {7},
  publisher = {AMER INST PHYSICS},
  address   = {MELVILLE},
  issn      = {0031-9228},
  pages     = {11 -- 11},
  year      = {2013},
  language  = {en}
}
@article{BarkaiGariniMetzler2012,
  author    = {Barkai, Eli and Garini, Yuval and Metzler, Ralf},
  title     = {Strange Kinetics of single molecules in living cells},
  series = {Physics today},
  volume    = {65},
  journal   = {Physics today},
  number    = {8},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0031-9228},
  pages     = {29 -- 35},
  year      = {2012},
  language  = {en}
}
@article{BauerGodecMetzler2014,
  author    = {Bauer, Maximilian and Godec, Aljaz and Metzler, Ralf},
  title     = {Diffusion of finite-size particles in two-dimensional channels with random wall configurations},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {16},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  number    = {13},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c3cp55160a},
  pages     = {6118 -- 6128},
  year      = {2014},
  abstract  = {Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick-Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda},
  language  = {en}
}