@article{PalyulinAlaNissilaMetzler2014,
  author    = {Palyulin, Vladimir V. and Ala-Nissila, Tapio and Metzler, Ralf},
  title     = {Polymer translocation: the first two decades and the recent diversification},
  series = {Soft matter},
  volume    = {45},
  journal   = {Soft matter},
  number    = {10},
  editor    = {Metzler, Ralf},
  publisher = {the Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1744-683X},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76266},
  pages     = {9016 -- 9037},
  year      = {2014},
  abstract  = {Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous-infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.},
  language  = {en}
}
@misc{PalyulinAlaNissilaMetzler2014,
  author    = {Palyulin, Vladimir V. and Ala-Nissila, Tapio and Metzler, Ralf},
  title     = {Polymer translocation: the first two decades and the recent diversification},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76287},
  pages     = {9016 -- 9037},
  year      = {2014},
  abstract  = {Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous-infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.},
  language  = {en}
}
@article{JeonChechkinMetzler2014,
  author    = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion},
  series = {Physical chemistry, chemical physics : PCCP},
  volume    = {30},
  journal   = {Physical chemistry, chemical physics : PCCP},
  number    = {16},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  doi       = {10.1039/C4CP02019G},
  pages     = {15811 -- 15817},
  year      = {2014},
  abstract  = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.},
  language  = {en}
}
@misc{JeonChechkinMetzler2014,
  author    = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76302},
  pages     = {15811 -- 15817},
  year      = {2014},
  abstract  = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.},
  language  = {en}
}
@article{GoychukKharchenkoMetzler2014,
  author    = {Goychuk, Igor A. and Kharchenko, Vasyl O. and Metzler, Ralf},
  title     = {Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion},
  series = {Physical Chemistry Chemical Physics},
  journal   = {Physical Chemistry Chemical Physics},
  number    = {16},
  publisher = {the Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  pages     = {16524 -- 16535},
  year      = {2014},
  abstract  = {The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient.},
  language  = {en}
}
@misc{GoychukKharchenkoMetzler2014,
  author    = {Goychuk, Igor A. and Kharchenko, Vasyl O. and Metzler, Ralf},
  title     = {Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion},
  series = {Physical Chemistry Chemical Physics},
  journal   = {Physical Chemistry Chemical Physics},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76478},
  pages     = {16524 -- 16535},
  year      = {2014},
  abstract  = {The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient.},
  language  = {en}
}
@article{BauerGodecMetzler2014,
  author    = {Bauer, Maximilian and Godec, Aljaž and Metzler, Ralf},
  title     = {Diffusion of finite-size particles in two-dimensional channels with random wall configurations},
  series = {Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies},
  volume    = {16},
  journal   = {Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies},
  number    = {13},
  publisher = {RSC Publications},
  address   = {Cambridge},
  issn      = {1463-9084},
  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 [J. Chem. Phys., 2012, 137, 024107].},
  language  = {en}
}
@misc{BauerGodecMetzler2014,
  author    = {Bauer, Maximilian and Godec, Aljaž and Metzler, Ralf},
  title     = {Diffusion of finite-size particles in two-dimensional channels with random wall configurations},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76199},
  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 [J. Chem. Phys., 2012, 137, 024107].},
  language  = {en}
}
@article{MetzlerBauerRasmussenetal.2015,
  author    = {Metzler, Ralf and Bauer, Maximilian and Rasmussen, Emil S. and Lomholt, Michael A.},
  title     = {Real sequence effects on the search dynamics of transcription factors on DNA},
  series = {Scientific Reports},
  volume    = {5},
  journal   = {Scientific Reports},
  number    = {10072},
  publisher = {Nature Publishing Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/srep10072},
  year      = {2015},
  abstract  = {Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs.},
  language  = {en}
}
@misc{MetzlerBauerRasmussenetal.2015,
  author    = {Metzler, Ralf and Bauer, Maximilian and Rasmussen, Emil S. and Lomholt, Michael A.},
  title     = {Real sequence effects on the search dynamics of transcription factors on DNA},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-79411},
  year      = {2015},
  abstract  = {Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs.},
  language  = {en}
}