Liquid Structures Characterized by a Combination of the Persistent Homology Analysis and Molecular Dynamics Simulation

K Sasaki and R Okajima and T Yamashita, INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2018 (ICCMSE-2018), 2040, 020015 (2018).

DOI: 10.1063/1.5079057

We demonstrate that persistent homology (PH) analysis, a new technique of the computational topology, combined with molecular dynamics simulations, can successfully characterize the complex liquid structure. First, we applied PH analysis to an antigen-antibody complex solution, showing that the interfacial water can be automatically detected. Second, we used PH analysis to characterize the structure of a mixture consisting of epoxy resin and amine curing agent, finding that amine nitrogen rings become larger due to the presence of the large epoxy domain.

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