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Characterization of medium-range order in amorphous materials and its relation to short-range order is discussed. A new topological approach is presented here to extract a hierarchical structure of amorphous materials, which is robust…

Soft Condensed Matter · Physics 2015-02-27 Takenobu Nakamura , Yasuaki Hiraoka , Akihiko Hirata , Emerson G. Escolar , Yasumasa Nishiura

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 geometric object, namely, a hole, and evaluates the robustness of…

Statistical Mechanics · Physics 2019-06-20 Tatsuhiko Shirai , Takenobu Nakamura

This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the…

Ring polymers are characterized by topology-specific entanglements called threadings. In the limit of large rings, it is conjectured that a "topological glass" should emerge due to the proliferation of threadings. In this study, we used…

Soft Condensed Matter · Physics 2024-11-19 Shota Goto , Takenobu Nakamura , Davide Michieletto , Kang Kim , Nobuyuki Matubayasi

Topological data analysis (TDA) is a new emerging and powerful tool to understand the medium range structure ordering of multi-scale data. This study investigates the density anomalies observed during cooling of liquid silica from…

Materials Science · Physics 2023-10-05 Andrea Tirelli , Kousuke Nakano

The structure of the low redshift Universe is dominated by a multi-scale void distribution delineated by filaments and walls of galaxies. The characteristics of voids; such as morphology, average density profile, and correlation function,…

Cosmology and Nongalactic Astrophysics · Physics 2024-09-04 Manu Aggarwal , Motonari Tonegawa , Stephen Appleby , Changbom Park , Vipul Periwal

Silica is the paradigmatic network glass-former and understanding its response to pressure is essential for comprehending the mechanical properties of silica-based materials and the behavior of silicate melts in the Earth's interior. While…

Disordered Systems and Neural Networks · Physics 2025-10-16 Zhen Zhang , Zhencheng Xie , Walter Kob

Persistent Homology is a widely used topological data analysis tool that creates a concise description of the topological properties of a point cloud based on a specified filtration. Most filtrations used for persistent homology depend…

Algebraic Topology · Mathematics 2024-06-05 Vincent P. Grande , Michael T. Schaub

Analyzing the atomic structure of glassy materials is a tremendous challenge both experimentally and computationally, and the lack of direct, detailed insights into glass structure hinders our ability to navigate structure-property…

Materials Science · Physics 2022-08-25 Aik Rui Tan , Shingo Urata , Masatsugu Yamada , Rafael Gómez-Bombarelli

Persistent homology is a popular computational tool for analyzing the topology of point clouds, such as the presence of loops or voids. However, many real-world datasets with low intrinsic dimensionality reside in an ambient space of much…

Machine Learning · Computer Science 2024-11-01 Sebastian Damrich , Philipp Berens , Dmitry Kobak

Persistent homology (PH) studies the topology of data across multiple scales by building nested collections of topological spaces called filtrations, computing homology and returning an algebraic object that can be vizualised as a…

Algebraic Topology · Mathematics 2024-11-14 David Beers , Heather A Harrington , Jacob Leygonie , Uzu Lim , Louis Theran

Persistent Homology (PH) is a fundamental tool in computational topology, designed to uncover the intrinsic geometric and topological features of data across multiple scales. Originating within the broader framework of Topological Data…

Algebraic Topology · Mathematics 2025-05-13 Aurelie Jodelle Kemme , Collins Amburo Agyingi

Persistent homology (PH) is a popular tool for topological data analysis that has found applications across diverse areas of research. It provides a rigorous method to compute robust topological features in discrete experimental…

Machine Learning · Computer Science 2023-07-19 Manu Aggarwal , Vipul Periwal

The liquid crystalline compound, forming the glass of the smectic C$_A$* phase, is investigated by the X-ray diffraction in the 18-298 K range. The characteristic distances within the smectic C$_A$* phase are determined. The electron…

Persistent homology analysis, a recently developed computational method in algebraic topology, is applied to the study of the phase transitions undergone by the so-called XY-mean field model and by the phi^4 lattice model, respectively. For…

The problems of the intermediate-range atomic structure of glasses and of the mechanism for the glass transition are approached from the low-temperature end in terms of a scenario for the atomic organization that justifies the use of an…

Mesoscale and Nanoscale Physics · Physics 2017-05-30 Giancarlo Jug

We develop an analysis pipeline for characterizing the topology of large scale structure and extracting cosmological constraints based on persistent homology. Persistent homology is a technique from topological data analysis that quantifies…

Cosmology and Nongalactic Astrophysics · Physics 2021-06-14 Matteo Biagetti , Alex Cole , Gary Shiu

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 persistent homology from scratch using some examples. We…

Algebraic Topology · Mathematics 2022-05-25 Ippei Obayashi , Takenobu Nakamura , Yasuaki Hiraoka

The medium range order (MRO) in amorphous systems has been linked to complex features such as the dynamic heterogeneity of supercooled liquids or the plastic deformation of glasses. However, the nature of the MRO in these materials has…

Disordered Systems and Neural Networks · Physics 2024-06-14 Zhen Zhang , Walter Kob

We introduce several geometric notions, including the width of a homology class, to the theory of persistent homology. These ideas provide geometric interpretations of persistence diagrams. Indeed, we give quantitative and geometric…

Algebraic Topology · Mathematics 2022-12-27 Henry Adams , Baris Coskunuzer
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