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Determination of reaction coordinates via locally scaled diffusion map
Abstract
We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the time scales of the molecular motion. To illustrate the approach, we present results for two model systems: all-atom alanine dipeptide and coarse-grained src homology 3 protein domain. We provide clear physical interpretation for the emerging coordinates and use them to calculate transition rates. The technique is general enough to be applied to any system for which a Boltzmann-sampled set of molecular configurations is available.
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“the construction of diffusion maps—which aim to approximate these eigenfunctions for overdamped Langevin dynamics—have been extended to model biomolecular dynamics, despite being originally introduced as a general data analysis tool [10].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [10]
In the citing paper
“methods such as diffusion maps 9,77-79 try to link geometric data to the characteristic time scale of the system's motion.”
From Unsupervised machine learning in atomistic simulations, between predictions and understanding (2019) · cites this paper as [79]
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Metadata
- Authors
- Rohrdanz, M. A., Zheng, W., Maggioni, M., & Clementi, C.
- Affiliations
- Rice University (US)
- Duke University (US)
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2011-03-28
- Volume
- 134
- Issue
- 12
- Pages
- 124116-124116
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W1971725855
- Cited by
- 292
- References
- 40
- Citations by year
- 2026: 8 · 2025: 12 · 2024: 15 · 2023: 12 · 2022: 14 · 2021: 18 · 2020: 18 · 2019: 22 · 2018: 23 · 2017: 46 · 2016: 24 · 2015: 25 · 2014: 19 · 2013: 19 · 2012: 9
- FWCI
- 7.12
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The Journal of Chemical Physics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0835712, 0835824, CHE-0349303, CNS-0421109, CNS-0821727, DMS-0650413, EIA-0216467)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › Model Reduction and Neural Networks
- Keywords
- reaction coordinate, diffusion maps, collective variables, macromolecular dynamics, intrinsic dimension, multiscale methods, alanine dipeptide, SH3 domain, transition rates
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