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A Coupled Experiment-finite Element Modeling Methodology for Assessing High Strain Rate Mechanical Response of Soft Biomaterials
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Force probe simulations using a hybrid scheme with virtual sites.

Ken Schäfer1, Marco Oestereich1, Jürgen Gauss1

  • 1Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.

The Journal of Chemical Physics
|October 9, 2017
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Summary

Hybrid simulations combine atomistic and coarse-grained methods for faster molecular studies. This approach accurately captures mechanical unfolding and refolding, even under demanding simulation conditions.

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Hybrid simulations offer a balance between computational efficiency and accuracy.
  • Studying molecular complex dynamics requires robust simulation methodologies.

Purpose of the Study:

  • To investigate the mechanical unfolding and refolding of a molecular complex using a hybrid simulation scheme.
  • To evaluate the accuracy and efficiency of hybrid simulations compared to all-atom simulations.

Main Methods:

  • Application of a hybrid simulation scheme combining atomistic and coarse-grained models.
  • Utilizing force probe molecular dynamics (FPMD) for mechanical unfolding studies.
  • Employing virtual sites for coupling coarse-grained solvent and atomistic solute.

Main Results:

  • Both iterative Boltzmann inversion and force matching coarse-graining procedures yielded similar results.
  • Hybrid simulations showed comparable accuracy to all-atom simulations, with differences within the range of atomistic force field variations.
  • The hybrid scheme provided qualitatively correct results for systems under strong non-equilibrium conditions.

Conclusions:

  • Hybrid simulations are a viable and accurate method for studying complex molecular systems, especially under non-equilibrium conditions.
  • The tested coarse-graining methodologies are suitable for hybrid simulations.
  • This approach enables faster sampling without significant loss of accuracy in molecular dynamics.