Spectral Map: Embedding Slow Kinetics in Collective Variables
Fuente:
arXiv
Saved in:
| Main Author: | |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866916189343580160 |
|---|---|
| author | Rydzewski, Jakub |
| author_facet | Rydzewski, Jakub |
| contents | The dynamics of physical systems that require high-dimensional representation can often be captured in a few meaningful degrees of freedom called collective variables (CVs). However, identifying CVs is challenging and constitutes a fundamental problem in physical chemistry. This problem is even more pronounced when CVs information about slow kinetics related to rare transitions between long-lived metastable states. To address this issue, we propose an unsupervised deep-learning method called spectral map. Our method constructs slow CVs by maximizing the spectral gap between slow and fast eigenvalues of a transition matrix estimated by an anisotropic diffusion kernel. We demonstrate our method in several high-dimensional reversible folding processes. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2404_01809 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Spectral Map: Embedding Slow Kinetics in Collective Variables Rydzewski, Jakub Chemical Physics The dynamics of physical systems that require high-dimensional representation can often be captured in a few meaningful degrees of freedom called collective variables (CVs). However, identifying CVs is challenging and constitutes a fundamental problem in physical chemistry. This problem is even more pronounced when CVs information about slow kinetics related to rare transitions between long-lived metastable states. To address this issue, we propose an unsupervised deep-learning method called spectral map. Our method constructs slow CVs by maximizing the spectral gap between slow and fast eigenvalues of a transition matrix estimated by an anisotropic diffusion kernel. We demonstrate our method in several high-dimensional reversible folding processes. |
| title | Spectral Map: Embedding Slow Kinetics in Collective Variables |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2404.01809 |