The unique structural aspects of tetrapods can be utilized to model a variety of systems ranging from generic ZnO structures to DNA hydrogels. In this study, we introduce two distinctly different coarse-grained models representing the basic building blocks. One is the 3D inert model representing a central core each connected to three arms via a harmonic bond mimicking the ZnO tetrapod structure. Second is 3D non-inert model of tetrapod whose features mimics three double-stranded DNA arms with single-stranded sticky ends, represented by bead chains and patchy particles, to accurately capture both the geometry and interactions of the complementary units. We did a comparative study of the dynamics and self-assembly of these two models. We study the dynamical properties of tetrapods using extensive Langevin dynamics simulation. The finite size effect and defined structure of tetrapods highlight an optimum surface deposition density. We quantify the dynamics by observing the mean squared displacement at distinct time scales compared to the relaxation time and diffusion constant of the centre of mass of each model of the tetrapods.

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Coarse Grain Modeling of ZnO Tetrapods and Generic DNA Hydrogels

  • Vrinda Garg,
  • Mehul Mishra,
  • Yuvashree Jayavelu,
  • K. Satish Kumar,
  • D. Paul Joseph,
  • Surya K. Ghosh

摘要

The unique structural aspects of tetrapods can be utilized to model a variety of systems ranging from generic ZnO structures to DNA hydrogels. In this study, we introduce two distinctly different coarse-grained models representing the basic building blocks. One is the 3D inert model representing a central core each connected to three arms via a harmonic bond mimicking the ZnO tetrapod structure. Second is 3D non-inert model of tetrapod whose features mimics three double-stranded DNA arms with single-stranded sticky ends, represented by bead chains and patchy particles, to accurately capture both the geometry and interactions of the complementary units. We did a comparative study of the dynamics and self-assembly of these two models. We study the dynamical properties of tetrapods using extensive Langevin dynamics simulation. The finite size effect and defined structure of tetrapods highlight an optimum surface deposition density. We quantify the dynamics by observing the mean squared displacement at distinct time scales compared to the relaxation time and diffusion constant of the centre of mass of each model of the tetrapods.