New methods for applying topological data analysis to materials science

Thesis

Abstract

Acknowledgements

About the Author

List of Collaborators and Publications

Table of Contents

List of Figures

List of Tables

List of Algorithms

1 Introduction

2 Mathematical Background

3 The Persistent Homology of Dual Digital Image Constructions

4 The Impact of Changes in Resolution on the Persistent Homology of Images

5 The Density Fingerprint of a Periodic Point Set

6 Merge Trees of Periodic Filtrations

7 Conclusion

Bibliography

Many chemical and physical properties of materials are determined by the material’s shape, for example the size of its pores and the width of its tunnels. This makes materials science a prime application area for geometrical and topological methods. Nevertheless many methods in topological data analysis have not been satisfyingly extended to the needs of materials science. This thesis provides new methods and new mathematical theorems targeted at those specific needs by answering four different research questions. While the motivation for each of the research questions arises from materials science, the methods are versatile and can be applied in different areas as well. The first research question is concerned with image data, for example a three-dimensional computed tomography (CT) scan of a material, like sand or stone. There are two commonly used topologies for digital images and depending on the application either of them might be required. However, software for computing the topological data analysis method persistence homology, usually supports only one of the two topologies. We answer the question how to compute persistent homology of an image with respect to one of the two topologies using software that is intended for the other topology. The second research question is concerned with image data as well, and asks how much of the topological information of an image is lost when the resolution is coarsened. As computer tomography scanners are more expensive the higher the resolution, it is an important question in materials science to know which resolution is enough to get satisfying persistent homology. We give theoretical bounds on the information loss based on different geometrical properties of the object to be scanned. In addition, we conduct experiments on sand and stone CT image data. The third research question is motivated by comparing crystalline materials efficiently. As the atoms within a crystal repeat periodically, crystalline materials are either modeled by unmanageable infinite periodic point sets, or by one of their fundamental domains, which is unstable under perturbation. Therefore a fingerprint of crystalline materials is needed, with appropriate properties such that comparing the crystals can be eased by comparing the fingerprints instead. We define the density fingerprint and prove the necessary properties. The fourth research question is motivated by studying the hole-structure or connectedness, i.e. persistent homology or merge trees, of crystalline materials. A common way to deal with periodicity is to take a fundamental domain and identify opposite boundaries to form a torus. However, computing persistent homology or merge trees on that torus loses some of the information materials scientists are interested in and is additionally not stable under certain noise. We therefore decorate the merge tree stemming from the torus with additional information describing the density and growth rate of the periodic copies of a component within a growing spherical window. We prove all desired properties, like stability and efficient computability.