@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}
}
@article{TalukderSenChakrabortietal.2014,
  author    = {Talukder, Srijeeta and Sen, Shrabani and Chakraborti, Prantik and Metzler, Ralf and Banik, Suman K. and Chaudhury, Pinaki},
  title     = {Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA},
  series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  volume    = {140},
  journal   = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  number    = {12},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0021-9606},
  doi       = {10.1063/1.4869112},
  pages     = {10},
  year      = {2014},
  abstract  = {We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction epsilon(hb)(AT) for an AT base pair and the ring factor. turn out to be the most sensitive parameters. In addition, the stacking interaction epsilon(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization. (c) 2014 AIP Publishing LLC.},
  language  = {en}
}
@misc{TalukderSenChakrabortietal.2014,
  author    = {Talukder, Srijeeta and Sen, Shrabani and Chakraborti, Prantik and Metzler, Ralf and Banik, Suman K. and Chaudhury, Pinaki},
  title     = {Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA},
  series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  volume    = {140},
  journal   = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  number    = {14},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0021-9606},
  doi       = {10.1063/1.4871297},
  pages     = {1},
  year      = {2014},
  abstract  = {We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction epsilon(hb)(AT) for an AT base pair and the ring factor. turn out to be the most sensitive parameters. In addition, the stacking interaction epsilon(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.},
  language  = {en}
}