Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models

Ryo Kawada, Katsuhiro Endo, Kenji Yasuoka, Hidekazu Kojima, Nobuyuki Matubayasi

Research output: Contribution to journalArticlepeer-review

Abstract

Permeation through polymer membranes is an important technology in the chemical industry, and in its design, the self-diffusion coefficient is one of the physical quantities that determine permeability. Since the self-diffusion coefficient sensitively reflects intra- and intermolecular interactions, analysis using an all-atom model is required. However, all-atom simulations are computationally expensive and require long simulation times for the diffusion of small molecules dissolved in polymers. MD-GAN, a machine learning model, is effective in accelerating simulations and reducing computational costs. The target systems for MD-GAN prediction were limited to polyethylene melts in previous studies; therefore, this study extended MD-GAN to systems containing copolymers with branches and successfully predicted water diffusion in various polymers. The correlation coefficient between the predicted self-diffusion coefficient and that of the long-time simulation was 1.00. Additionally, we found that incorporating statistical domain knowledge into MD-GAN improved accuracy, reducing the mean-square displacement prediction outliers from 14.6% to 5.3%. Lastly, the distribution of latent variables with embedded dynamics information within the model was found to be strongly related to accuracy. We believe that these findings can be useful for the practical applications of MD-GAN.

Original languageEnglish
Pages (from-to)76-86
Number of pages11
JournalJournal of Chemical Information and Modeling
Volume63
Issue number1
DOIs
Publication statusPublished - 2023 Jan 9

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

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