English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Zendy Plus

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Zendy Tools

Zendy Open

To gain insight into reaction mechanism of activated processes, we introducean exact approach for quantifying the topology of high-dimensional probabilitysurfaces of the underlying dynamic processes. Instead of Morse indexes, westudy the homology groups of a sequence of superlevel sets of the probabilitysurface over high-dimensional configuration spaces using persistent homology.For alanine-dipeptide isomerization, a prototype of activated processes, weidentify locations of probability peaks and connecting-ridges, along withmeasures of their global prominence. Instead of a saddle-point, the transitionstate ensemble (TSE) of conformations are at the most prominent probabilitypeak after reactants/products, when proper reaction coordinates are included.Intuition-based models, even those exhibiting a double-well, fail to capturethe dynamics of the activated process. Peak occurrence, prominence, andlocations can be distorted upon subspace projection. While principal componentanalysis account for conformational variance, it inflates the complexity of thesurface topology and destroy dynamic properties of the topological features. Incontrast, TSE emerges naturally as the most prominent peak beyond thereactant/product basins, when projected to a subspace of minimum dimensioncontaining the reaction coordinates. Our approach is general and can be appliedto investigate the topology of high-dimensional probability surfaces of otheractivated process.

Exact Topology of Dynamic Probability Surface of an Activated Process by Persistent Homology