@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}
}
@article{ShinCherstvyMetzler2014,
  author    = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects},
  series = {New journal of physics : the open-access journal for physics},
  volume    = {16},
  journal   = {New journal of physics : the open-access journal for physics},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/16/5/053047},
  pages     = {19},
  year      = {2014},
  abstract  = {During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behavior of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions phi of crowders. We also examine the entropic demixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analyzed. In particular, on systematic variation of the fraction of crowding molecules, a (1 - phi)-scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number with a maximum at phi approximate to 0.2 is obtained. Our results demonstrate that polymer rings are demixed and separated by particular entropy-favourable partitioning of crowders along the axis of the cylindrical simulation box. These findings help to rationalize the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localized cellular compartments inside eukaryotic cells.},
  language  = {en}
}
@article{ShinCherstvyMetzler2014,
  author    = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Sensing viruses by mechanical tension of DNA in responsive hydrogels},
  series = {Physical review : X, Expanding access},
  volume    = {4},
  journal   = {Physical review : X, Expanding access},
  number    = {2},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {2160-3308},
  doi       = {10.1103/PhysRevX.4.021002},
  pages     = {13},
  year      = {2014},
  abstract  = {The rapid worldwide spread of severe viral infections, often involving novel mutations of viruses, poses major challenges to our health-care systems. This means that tools that can efficiently and specifically diagnose viruses are much needed. To be relevant for broad applications in local health-care centers, such tools should be relatively cheap and easy to use. In this paper, we discuss the biophysical potential for the macroscopic detection of viruses based on the induction of a mechanical stress in a bundle of prestretched DNA molecules upon binding of viruses to the DNA. We show that the affinity of the DNA to the charged virus surface induces a local melting of the double helix into two single-stranded DNA. This process effects a mechanical stress along the DNA chains leading to an overall contraction of the DNA. Our results suggest that when such DNA bundles are incorporated in a supporting matrix such as a responsive hydrogel, the presence of viruses may indeed lead to a significant, macroscopic mechanical deformation of the matrix. We discuss the biophysical basis for this effect and characterize the physical properties of the associated DNA melting transition. In particular, we reveal several scaling relations between the relevant physical parameters of the system. We promote this DNA-based assay as a possible tool for efficient and specific virus screening.},
  language  = {en}
}