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Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices

preprint
revised on 05.06.2019 and posted on 05.06.2019 by Stephanie Hare, Lars Bratholm, David Glowacki, Barry Carpenter
Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space, as well as the physical meaning of the reduced dimensional axes, are discussed.

Funding

EPSRC grant EP/P021123/1

History

Email Address of Submitting Author

stephanie.hare@bristol.ac.uk

Institution

University of Bristol

Country

United Kingdom

ORCID For Submitting Author

0000-0003-3153-143X

Declaration of Conflict of Interest

No conflicts to declare.

Version Notes

Version 2.0 -- text has been edited to better reflect the impact of the applications to example systems analysed. Figures have also been improved.

Exports