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| Auteurs principaux: | , , |
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| Format: | Preprint |
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2024
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| Accès en ligne: | https://arxiv.org/abs/2501.06197 |
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| _version_ | 1866915098580221952 |
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| author | Hu, Chuan-Shen Liu, Xiang Xia, Kelin |
| author_facet | Hu, Chuan-Shen Liu, Xiang Xia, Kelin |
| contents | Normal mode analysis (NMA) provides a mathematical framework for exploring the intrinsic global dynamics of molecules through the definition of an energy function, where normal modes correspond to the eigenvectors of the Hessian matrix derived from the second derivatives of this function. The energy required to 'trigger' each normal mode is proportional to the square of its eigenvalue, with six zero-eigenvalue modes representing universal translation and rotation, common to all molecular systems. In contrast, modes associated with small non-zero eigenvalues are more easily excited by external forces and are thus closely related to molecular functions. Inspired by the anisotropic network model (ANM), this work establishes a novel connection between normal mode analysis and sheaf theory by introducing a cellular sheaf structure, termed the anisotropic sheaf, defined on undirected, simple graphs, and identifying the conventional Hessian matrix as the sheaf Laplacian. By interpreting the global section space of the anisotropic sheaf as the kernel of the Laplacian matrix, we demonstrate a one-to-one correspondence between the zero-eigenvalue-related normal modes and a basis for the global section space. We further analyze the dimension of this global section space, representing the space of harmonic signals, under conditions typically considered in normal mode analysis. Additionally, we propose a systematic method to streamline the Delaunay triangulation-based construction for more efficient graph generation while preserving the ideal number of normal modes with zero eigenvalues in ANM analysis. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2501_06197 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | A Physics-informed Sheaf Model Hu, Chuan-Shen Liu, Xiang Xia, Kelin Chemical Physics Algebraic Topology Normal mode analysis (NMA) provides a mathematical framework for exploring the intrinsic global dynamics of molecules through the definition of an energy function, where normal modes correspond to the eigenvectors of the Hessian matrix derived from the second derivatives of this function. The energy required to 'trigger' each normal mode is proportional to the square of its eigenvalue, with six zero-eigenvalue modes representing universal translation and rotation, common to all molecular systems. In contrast, modes associated with small non-zero eigenvalues are more easily excited by external forces and are thus closely related to molecular functions. Inspired by the anisotropic network model (ANM), this work establishes a novel connection between normal mode analysis and sheaf theory by introducing a cellular sheaf structure, termed the anisotropic sheaf, defined on undirected, simple graphs, and identifying the conventional Hessian matrix as the sheaf Laplacian. By interpreting the global section space of the anisotropic sheaf as the kernel of the Laplacian matrix, we demonstrate a one-to-one correspondence between the zero-eigenvalue-related normal modes and a basis for the global section space. We further analyze the dimension of this global section space, representing the space of harmonic signals, under conditions typically considered in normal mode analysis. Additionally, we propose a systematic method to streamline the Delaunay triangulation-based construction for more efficient graph generation while preserving the ideal number of normal modes with zero eigenvalues in ANM analysis. |
| title | A Physics-informed Sheaf Model |
| topic | Chemical Physics Algebraic Topology |
| url | https://arxiv.org/abs/2501.06197 |