Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach
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arXiv
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| Format: | Preprint |
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2024
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| author | Okada, Kazushi Kikutsuji, Takuma Okazaki, Kei-ichi Mori, Toshifumi Kim, Kang Matubayasi, Nobuyuki |
| author_facet | Okada, Kazushi Kikutsuji, Takuma Okazaki, Kei-ichi Mori, Toshifumi Kim, Kang Matubayasi, Nobuyuki |
| contents | The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable states of alanine dipeptide in vacuum, i.e., C$7_{\mathrm{eq}}$ ($β$-sheet structure) and C$7_{\mathrm{ax}}$ (left handed $α$-helix structure), have been primarily characterized using the main chain dihedral angles, $φ$ (C-N-C$_α$-C) and $ψ$ (N-C$_α$-C-N). However, our recent deep learning combined with "Explainable AI" (XAI) framework has shown that the transition state can be adequately captured by a free energy landscape using $φ$ and $θ$ (O-C-N-C$_α$) [T. Kikutsuji, et al. J. Chem. Phys. 156, 154108 (2022)]. In perspective of extending these insights to other collective variables, a more detailed characterization of transition state is required. In this work, we employ the interatomic distances and bond angles as input variables for deep learning, rather than the conventional and more elaborate dihedral angles. Our approach utilizes deep learning to investigate whether changes in the main chain dihedral angle can be expressed in terms of interatomic distances and bond angles. Furthermore, by incorporating XAI into our predictive analysis, we quantified the importance of each input variable and succeeded in clarifying the specific interatomic distance that affects the transition state. The results indicate that constructing a free energy landscape based on using the identified interatomic distance can clearly distinguish between the two stable states and provide a comprehensive explanation for the energy barrier crossing. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2402_08448 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach Okada, Kazushi Kikutsuji, Takuma Okazaki, Kei-ichi Mori, Toshifumi Kim, Kang Matubayasi, Nobuyuki Chemical Physics Soft Condensed Matter The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable states of alanine dipeptide in vacuum, i.e., C$7_{\mathrm{eq}}$ ($β$-sheet structure) and C$7_{\mathrm{ax}}$ (left handed $α$-helix structure), have been primarily characterized using the main chain dihedral angles, $φ$ (C-N-C$_α$-C) and $ψ$ (N-C$_α$-C-N). However, our recent deep learning combined with "Explainable AI" (XAI) framework has shown that the transition state can be adequately captured by a free energy landscape using $φ$ and $θ$ (O-C-N-C$_α$) [T. Kikutsuji, et al. J. Chem. Phys. 156, 154108 (2022)]. In perspective of extending these insights to other collective variables, a more detailed characterization of transition state is required. In this work, we employ the interatomic distances and bond angles as input variables for deep learning, rather than the conventional and more elaborate dihedral angles. Our approach utilizes deep learning to investigate whether changes in the main chain dihedral angle can be expressed in terms of interatomic distances and bond angles. Furthermore, by incorporating XAI into our predictive analysis, we quantified the importance of each input variable and succeeded in clarifying the specific interatomic distance that affects the transition state. The results indicate that constructing a free energy landscape based on using the identified interatomic distance can clearly distinguish between the two stable states and provide a comprehensive explanation for the energy barrier crossing. |
| title | Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach |
| topic | Chemical Physics Soft Condensed Matter |
| url | https://arxiv.org/abs/2402.08448 |