Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

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2017
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Mukherjee, Biswaroop
Kremer, Kurt
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The Journal of Chemical Physics ; 147 (2017), 11. - 114501. - ISSN 0021-9606. - eISSN 1089-7690
Abstract
Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.
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540 Chemistry, 540 Chemistry
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ISO 690MUKHERJEE, Biswaroop, Christine PETER, Kurt KREMER, 2017. Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales. In: The Journal of Chemical Physics. 147(11), 114501. ISSN 0021-9606. eISSN 1089-7690. Available under: doi: 10.1063/1.5001482
BibTex
@article{Mukherjee2017-09-21Singl-40306,
  year={2017},
  doi={10.1063/1.5001482},
  title={Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales},
  number={11},
  volume={147},
  issn={0021-9606},
  journal={The Journal of Chemical Physics},
  author={Mukherjee, Biswaroop and Peter, Christine and Kremer, Kurt},
  note={Article Number: 114501}
}
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