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Understanding the role of atomic-level structures in determining amorphous material properties has been a long-standing challenge in solid-state physics. Upon mechanical loading, amorphous materials undergo both simple affine displacement and spatially inhomogeneous non-affine displacement. These two types of displacement contribute differently to the elastic modulus, i.e., the Born (or affine) and non-affine terms. Whether "soft" local structures characterized by either small Born terms or large non-affine displacements differ has remained an unanswered question despite the importance in fundamental and applied physics. To address this question, we combined molecular dynamics simulations and persistent homology analyses for amorphous Si. We found that the characteristics of local structures with large non-affine displacements differed significantly from those with small Born terms. The local structures surrounding atoms with small Born terms are characterized at the scale of short-range order (SRO), whereas those surrounding atoms with large non-affine displacements have hierarchical structures ranging from SRO to medium-range order. Furthermore, we found that these hierarchical structures are related to low-energy localized vibrational excitations. The correlation between the non-affine displacement and hierarchical geometric features elucidated by persistent homology provides a new viewpoint for understanding and designing the mechanical properties of amorphous materials based on their static structures., Comment: 23 pages, 8 figures

Contrast variation small-angle neutron scattering (CV-SANS) is a powerful tool to evaluate the structure of multi-component systems by decomposing scattering intensities $I$ measured with different scattering contrasts into partial scattering functions $S$ of self- and cross-correlations between components. The measured $I$ contains a measurement error, $\Delta I$, and $\Delta I$ results in an uncertainty of partial scattering functions, $\Delta S$. However, the error propagation from $\Delta I$ to $\Delta S$ has not been quantitatively clarified. In this work, we have established deterministic and statistical approaches to determine $\Delta S$ from $\Delta I$. We have applied the two methods to experimental SANS data of polyrotaxane solutions with different contrasts, and have successfully estimated the errors of $S$. The quantitative error estimation of $S$ offers us a strategy to optimize the combination of scattering contrasts to minimize error propagation.

A fundamental challenge in multiparameter persistent homology is the absence of a complete and discrete invariant. To address this issue, we propose an enhanced framework that realizes a holistic understanding of a fully commutative quiver's representation via synthesizing interpretations obtained from intervals. Additionally, it provides a mechanism to tune the balance between approximation resolution and computational complexity. This framework is evaluated on commutative ladders of both finite-type and infinite-type. For the former, we discover an efficient method for the indecomposable decomposition leveraging solely one-parameter persistent homology. For the latter, we introduce a new invariant that reveals persistence in the second parameter by connecting two standard persistence diagrams using interval approximations. We subsequently present several models for constructing commutative ladder filtrations, offering fresh insights into random filtrations and demonstrating our toolkit's effectiveness in analyzing the topology of materials.

This paper proposes a data analysis method using persistent homology and nonnegative matrix factorization. A concatenated persistence image technique is used to extract coexisting structures from the persistence diagrams of different dimensions hidden behind the data. To demonstrate the potential of our method, we apply the method to 3D voxel data of iron ore sinters obtained by X-ray computed tomography. The analysis successfully captures the coexistence structures in these iron ore sinters.

High-accuracy prediction of the physical properties of amorphous materials is challenging in condensed-matter physics. A promising method to achieve this is machine-learning potentials, which is an alternative to computationally demanding ab initio calculations. When applying machine-learning potentials, the construction of descriptors to represent atomic configurations is crucial. These descriptors should be invariant to symmetry operations. Handcrafted representations using a smooth overlap of atomic positions and graph neural networks (GNN) are examples of methods used for constructing symmetry-invariant descriptors. In this study, we propose a novel descriptor based on a persistence diagram (PD), a two-dimensional representation of persistent homology (PH). First, we demonstrated that the normalized two-dimensional histogram obtained from PD could predict the average energy per atom of amorphous carbon (aC) at various densities, even when using a simple model. Second, an analysis of the dimensional reduction results of the descriptor spaces revealed that PH can be used to construct descriptors with characteristics similar to those of a latent space in a GNN. These results indicate that PH is a promising method for constructing descriptors suitable for machine-learning potentials without hyperparameter tuning and deep-learning techniques., Comment: 24 pages, 6 figures

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 also review some applications of persistent homology to materials researches and software for persistent homology data analysis. HomCloud, one of persistent homology software, is especially featured in this paper.

This paper proposes a stable volume and a stable volume variant, referred to as a stable sub-volume, for more reliable data analysis using persistent homology. In prior research, an optimal cycle and similar ideas have been proposed to identify the homological structure corresponding to each birth-death pair in a persistence diagram. While this is helpful for data analysis using persistent homology, the results are sensitive to noise. In this paper, stable volumes and stable sub-volumes are proposed to solve this problem. For a special case, we prove that a stable volume is the robust part of an optimal volume against noise. We implemented stable volumes and sub-volumes on HomCloud, a data analysis software package based on persistent homology, and show examples of stable volumes and sub-volumes.

Quantifying the correlation between the complex structures of amorphous materials and their physical properties has been a long-standing problem in materials science. In amorphous Si, a representative covalent amorphous solid, the presence of a medium-range order (MRO) has been intensively discussed. However, the specific atomic arrangement corresponding to the MRO and its relationship with physical properties, such as thermal conductivity, remain elusive. Here, we solve this problem by combining topological data analysis, machine learning, and molecular dynamics simulations. By using persistent homology, we constructed a topological descriptor that can predict the thermal conductivity. Moreover, from the inverse analysis of the descriptor, we determined the typical ring features that correlated with both the thermal conductivity and MRO. The results provide an avenue for controlling the material characteristics through the topology of nanostructures., Comment: 27 pages, 10 figures

This paper tackles the problem of coefficient field choice in persistent homology. When we compute a persistence diagram, we need to select a coefficient field before computation. We should understand the dependency of the diagram on the coefficient field to facilitate computation and interpretation of the diagram. We clarify that the dependency is strongly related to the torsion of $\mathbb{Z}$ relative homology in the filtration. We show the sufficient and necessary conditions of the independence of coefficient field choice. An efficient algorithm is proposed to verify the independence. In a numerical experiment with the algorithm, a persistence diagram rarely changes even when the coefficient field changes if we consider a filtration in $\mathbb{R}^3$. The experiment suggests that, in practical terms, changes in the field coefficient will not change persistence diagrams when the data are in $\mathbb{R}^3$.

Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the understanding of this process. In this study, we applied persistent homology, an emerging methods to analyze topological features in a dataset, to reveal protein folding dynamics. We developed a new method to characterize protein structure based on persistent homology and applied this method to molecular dynamics simulations of chignolin. Using principle component analysis or non-negative matrix factorization, our analysis method revealed two stable states and one saddle state, corresponding to the native, misfolded, and transition states, respectively. We also identified an unfolded state with slow dynamics in the reduced space. Our method serves as a promising tool to understand the protein folding process., Comment: To be published in Biophysical Journal

This paper shows a mathematical formalization, algorithms and computation software of volume optimal cycles, which are useful to understand geometric features shown in a persistence diagram. Volume optimal cycles give us concrete and optimal homologous structures, such as rings or cavities, on a given data. The key idea is the optimality on $(q + 1)$-chain complex for a $q$th homology generator. This optimality formalization is suitable for persistent homology. We can solve the optimization problem using linear programming. For an alpha filtration on $\mathbb{R}^n$, volume optimal cycles on an $(n-1)$-th persistence diagram is more efficiently computable using merge-tree algorithm. The merge-tree algorithm also gives us a tree structure on the diagram and the structure has richer information. The key mathematical idea is Alexander duality.

Persistence diagrams have been widely recognized as a compact descriptor for characterizing multiscale topological features in data. When many datasets are available, statistical features embedded in those persistence diagrams can be extracted by applying machine learnings. In particular, the ability for explicitly analyzing the inverse in the original data space from those statistical features of persistence diagrams is significantly important for practical applications. In this paper, we propose a unified method for the inverse analysis by combining linear machine learning models with persistence images. The method is applied to point clouds and cubical sets, showing the ability of the statistical inverse analysis and its advantages.

In this paper, we present a mathematical and algorithmic framework for the continuation of point clouds by persistence diagrams. A key property used in the method is that the persistence map, which assigns a persistence diagram to a point cloud, is differentiable. This allows us to apply the Newton-Raphson continuation method in this setting. Given an original point cloud $P$, its persistence diagram $D$, and a target persistence diagram $D'$, we gradually move from $D$ to $D'$, by successively computing intermediate point clouds until we finally find a point cloud $P'$ having $D'$ as its persistence diagram. Our method can be applied to a wide variety of situations in topological data analysis where it is necessary to solve an inverse problem, from persistence diagrams to point cloud data.

Passive dynamic walking is a useful model for investigating the mechanical functions of the body that produce energy-efficient walking. The basin of attraction is very small and thin, and it has a fractal-like shape; this explains the difficulty in producing stable passive dynamic walking. The underlying mechanism that produces these geometric characteristics was not known. In this paper, we consider this from the viewpoint of dynamical systems theory, and we use the simplest walking model to clarify the mechanism that forms the basin of attraction for passive dynamic walking. We show that the intrinsic saddle-type hyperbolicity of the upright equilibrium point in the governing dynamics plays an important role in the geometrical characteristics of the basin of attraction; this contributes to our understanding of the stability mechanism of bipedal walking.