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Updated: Dec 25, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Construction of a Pathway Map on a Complicated Energy Landscape
Jianyuan Yin1, Yiwei Wang2, Jeff Z Y Chen3
1School of Mathematical Sciences, Laboratory of Mathematics and Applied Mathematics, Peking University, Beijing 100871, China.
Abstract:
How do we search for the entire family tree of possible intermediate states, without unwanted random guesses, starting from a stationary state on the energy landscape all the way down to energy minima? Here we introduce a general numerical method that constructs the pathway map, which guides our understanding of how a physical system moves on the energy landscape. The method identifies the transition state between energy minima and the energy barrier associated with such a state. As an example, we solve the Landau-de Gennes energy incorporating the Dirichlet boundary conditions to model a liquid crystal confined in a square box; we illustrate the basic concepts by examining the multiple stationary solutions and the connected pathway maps of the model.
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