419 citations · 703 across the 13 of their papers we have counts for
13 papers
Reproducing Reaction Route Map on the Shape Space from its Quotient by Complete Nuclear Permutation-Inversion group
Hiroshi Teramoto, Takuya Saito, Masamitsu Aoki +4
This study develops an algorithm to reproduce reaction route maps (RRMs) in shape space from the outputs of potential search algorithms. To demonstrate this, GRRM is utilized as a…
Characterizing Reaction Route Map of Realistic Molecular Reactions based on Weight Rank Clique Filtration of Persistent Homology
Burai Murayama, Masato Kobayashi, Masamitsu Aoki +5
A reaction route map (RRM) constructed using the GRRM program is a collection of elementary reaction pathways, each of which comprises two equilibrium (EQ) geometries and one trans…
Persistent Homology Analysis for Materials Research and Persistent Homology Software: HomCloud
Ippei Obayashi, Takenobu Nakamura, Yasuaki Hiraoka
This paper introduces persistent homology, which is a powerful tool to characterize the shape of data using the mathematical concept of topology. We explain the fundamental idea of…
Persistence Homology Of Entangled Rings
Fabio Landuzzi, Takenobu Nakamura, Davide Michieletto +1
Topological constraints (TCs) between polymers determine the behaviour of complex fluids such as creams, oils and plastics. Most of the polymer solutions used every day life employ…
Derivation of the Invariant Free-Energy Landscape Based on Langevin Dynamics
Takenobu Nakamura
Conventionally defined free-energy landscape (FEL) exhibits unphysical dependence on the choice of reaction coordinates and hence lacks universal predictive ability. We here show t…
Microscopic Description of Yielding in Glass Based on Persistent Homology
Tatsuhiko Shirai, Takenobu Nakamura
Persistent homology (PH) was applied to probe the structural changes of glasses under shear. PH associates each local atomistic structure in an atomistic configuration to a geometr…