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Related Experiment Video

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Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer.

Hiroshi Fujisaki1, Motoyuki Shiga, Kei Moritsugu

  • 1Department of Physics, Nippon Medical School, Nakahara, Kawasaki 211-0063, Japan. fujisaki@nms.ac.jp

The Journal of Chemical Physics
|August 10, 2013
PubMed
Summary

We developed a new path sampling method using a coupled coarse-grained system to efficiently explore molecular configurations. This approach, based on the Onsager-Machlup action, corrects sampling bias for accurate results.

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Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

Published on: September 26, 2016

Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Molecular dynamics

Background:

  • Efficiently sampling complex molecular configurations is crucial for understanding chemical processes.
  • Existing methods like transition path sampling can be computationally intensive.
  • Multiscale enhanced sampling offers a promising avenue for improving efficiency.

Purpose of the Study:

  • To introduce a novel path sampling method based on the Onsager-Machlup action.
  • To generalize existing multiscale enhanced sampling techniques.
  • To enhance the efficiency of sampling configuration and path space in molecular systems.

Main Methods:

  • Coupling a target molecular system with a faster, coarse-grained (CG) system.
  • Simulating the combined system using Langevin dynamics with distinct heat baths.
  • Employing Hamiltonian replica exchange to correct sampling bias.
  • Utilizing the Onsager-Machlup action for path weighting.

Main Results:

  • The proposed method efficiently samples configuration and path space by guiding the original system with the CG system.
  • Hamiltonian replica exchange successfully corrects for coupling-induced bias.
  • An unbiased path ensemble for the original system is obtained from the weakest coupling ensemble.
  • The method is demonstrated on a model polymer with Asakura-Oosawa interaction.

Conclusions:

  • The novel Onsager-Machlup based path sampling method offers an efficient and unbiased approach for molecular simulations.
  • The strategy is readily implementable due to the formal equivalence of path weights to Boltzmann weights.
  • This technique provides a valuable tool for studying complex molecular dynamics and transitions.