@article{ShinCherstvyMetzler2014,
  author    = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size},
  series = {Soft Matter},
  journal   = {Soft Matter},
  editor    = {Metzler, Ralf},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1744-683X},
  pages     = {472 -- 488},
  year      = {2014},
  abstract  = {The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.},
  language  = {en}
}
@misc{ShinCherstvyMetzler2014,
  author    = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76961},
  pages     = {472 -- 488},
  year      = {2014},
  abstract  = {The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.},
  language  = {en}
}
@article{ShinCherstvyMetzler2015,
  author    = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions},
  series = {New journal of physics : the open-access journal for physics},
  volume    = {17},
  journal   = {New journal of physics : the open-access journal for physics},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/17/11/113028},
  pages     = {12},
  year      = {2015},
  abstract  = {We examine by extensive computer simulations the self-diffusion of anisotropic star-like particles in crowded two-dimensional solutions. We investigate the implications of the area coverage fraction phi of the crowders and the crowder-crowder adhesion properties on the regime of transient anomalous diffusion. We systematically compute the mean squared displacement (MSD) of the particles, their time averaged MSD, and the effective diffusion coefficient. The diffusion is ergodic in the limit of long traces, such that the mean time averaged MSD converges towards the ensemble averaged MSD, and features a small residual amplitude spread of the time averaged MSD from individual trajectories. At intermediate time scales, we quantify the anomalous diffusion in the system. Also, we show that the translational-but not rotational-diffusivity of the particles Dis a nonmonotonic function of the attraction strength between them. Both diffusion coefficients decrease as the power law D(phi) similar to (1 - phi/phi*)(2 ... 2.4) with the area fraction phi occupied by the crowders and the critical value phi*. Our results might be applicable to rationalising the experimental observations of non-Brownian diffusion for a number of standard macromolecular crowders used in vitro to mimic the cytoplasmic conditions of living cells.},
  language  = {en}
}