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Homology and machine learning for materials informatics
KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. KTH, School of Engineering Sciences (SCI), Physics, Condensed Matter Theory.ORCID iD: 0000-0002-6688-270x
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Materials informatics is the field of study where materials science is combined with modern data science. This data-driven approach is powered by the growing availability of computational power and storage capability. The development and application of these methods accelerates materials science and represents an effective way to study and model material properties. This thesis is a compilation of theoretical and computational works that can be divided into three key areas: materials databases, machine learning for materials, and homology for materials.

Machine learning and data mining rely on the availability of materials databases to test methods and models. The Organic Materials Database (OMDB), for example, contains a large number of organic crystals and their corresponding electronic structures. The electronic properties of the organic crystals are computed using atomic scale materials modelling, which is computationally expensive because organic crystals typically contain many atoms in the unit cell. However, the resulting data can be used in a variety of materials informatics applications. We demonstrate data mining for dark matter sensors as an example application.

Accurate machine learning models can capture the structure-property relationship of materials and accelerate the discovery of new materials with desired properties. This is explored by investigating the properties of the organic crystals in the OMDB. For example, we employ supervised learning on the electronic band gap, an important material property for technological applications. Unsupervised learning is used to construct a dimensionality-reduced chemical space that reveals interesting clusters of materials.

Finally, persistent homology is a relatively new method from the field of algebraic topology that studies the shapes that are present in data at different length scales. In this thesis, the method is used to study magnetic materials and their phase transitions. More specifically, in the case of classical models, we use persistent homology to detect the phase transition directly from sampled spin configurations. For quantum spin models, the shapes in the entanglement structure are captured and a sudden change reveals a quantum phase transition.

In summary, these three topics provide an overview on how to study material properties with modern data science methods. The tools can be used in combination with the traditional methods in materials science and accelerate materials design.

Abstract [sv]

Materialinformatik är ett forskningsområde där materialvetenskap kombineras med modern datavetenskap. Detta datadrivna tillvägagångssätt drivs av den växande tillgängligheten av beräkningskraft och lagringskapacitet. Utvecklingen och tillämpningen av dessa metoder accelererar materialvetenskapen och utgör ett effektivt sätt att studera och modellera materialegenskaper. Denna avhandling är en sammanställning av teoretiska och beräkningstekniska arbeten som kan delas in i tre nyckelområden: materialdatabaser, maskininlärning för material och homologi för material.

Maskininlärning och datautvinning är beroende av tillgången på materialdatabaser för att testa metoder och modeller. Organic Materials Database (OMDB) innehåller data för kristallin struktur och elektroniska egenskaper för ett stort antal organiska kristaller. De elektroniska egenskaperna hos de organiska kristallerna beräknas med hjälp av materialmodellering i atomskala, vilket är beräkningsmässigt dyrt då organiska kristaller vanligtvis innehåller många atomer i enhetscellen. Emellertid kan den resulterande datan användas i en mängd olika materialinformatikapplikationer. Vi demonstrerar datautvinning för att söka material till sensor för mörk materia som ett exempel på applikation.

Maskininlärningsmetoder kan fånga förhållanden mellan struktur och egenskap hos material, och därmed påskynda upptäckten av nya material med önskade egenskaper. Detta utforskas genom att undersöka egenskaperna hos de organiska kristallerna i OMDB. Till exempel använder vi övervakat lärande på elektroniska bandgap, en viktig materiell egenskap för tekniska tillämpningar. Oövervakat lärande används för att konstruera en dimensionsreducerad kemisk rymd som avslöjar intressanta kluster av material.

Slutligen är ihållande homologi en relativt ny metod från området algebraisk topologi som studerar de former som finns i data i olika längdskalor. I denna avhandling används metoden för att studera magnetiska material och deras fasövergångar. Mer specifikt, när det gäller klassiska modeller, använder vi ihållande homologi för att detektera fasövergången direkt från samplade spin-konfigurationer. För kvantspinnmodeller fångas faserna i strukturen hos den kvantmekaniska sammanflätningen och en plötslig förändring avslöjar en kvantfasövergång.

Sammantaget utgör dessa tre ämnen ett bra exempel på hur materialegenskaper kan studeras med moderna datavetenskapliga metoder. Verktygen kan användas i kombination med traditionella metoder inom materialvetenskap och påskynda materialdesign.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2023. , p. 63
Series
TRITA-SCI-FOU ; 2022:08
National Category
Condensed Matter Physics
Research subject
Physics, Theoretical Physics
Identifiers
URN: urn:nbn:se:kth:diva-324302ISBN: 978-91-8040-505-8 (print)OAI: oai:DiVA.org:kth-324302DiVA, id: diva2:1739524
Public defence
2023-03-24, Hörsal 4, Hus 2 and Zoom, Albanovägen 18, Stockholm, 15:00 (English)
Opponent
Supervisors
Note

QC 230227

Available from: 2023-02-27 Created: 2023-02-26 Last updated: 2023-03-13Bibliographically approved
List of papers
1. Persistent homology of quantum entanglement
Open this publication in new window or tab >>Persistent homology of quantum entanglement
(English)Manuscript (preprint) (Other academic)
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-324301 (URN)
Available from: 2023-02-26 Created: 2023-02-26 Last updated: 2023-02-27Bibliographically approved
2. Shifting computational boundaries for complex organic materials
Open this publication in new window or tab >>Shifting computational boundaries for complex organic materials
2021 (English)In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 17, no 2, p. 152-154Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Springer Nature, 2021
National Category
Ecology Environmental Sciences Business Administration
Identifiers
urn:nbn:se:kth:diva-304644 (URN)10.1038/s41567-020-01135-6 (DOI)000607333000001 ()2-s2.0-85100150984 (Scopus ID)
Note

QC 20211115

Available from: 2021-11-15 Created: 2021-11-15 Last updated: 2023-02-26Bibliographically approved
3. Finding hidden order in spin models with persistent homology
Open this publication in new window or tab >>Finding hidden order in spin models with persistent homology
2020 (English)In: Physical Review Research, E-ISSN 2643-1564, Vol. 2, no 4, article id 043308Article in journal (Refereed) Published
Abstract [en]

Persistent homology (PH) is a relatively new field in applied mathematics that studies the components and shapes of discrete data. In this paper, we demonstrate that PH can be used as a universal framework to identify phases of classical spins on a lattice. This demonstration includes hidden order such as spin-nematic ordering and spin liquids. By converting a small number of spin configurations to barcodes we obtain a descriptive picture of configuration space. Using dimensionality reduction to reduce the barcode space to color space leads to a visualization of the phase diagram.

Place, publisher, year, edition, pages
American Physical Society (APS), 2020
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-289550 (URN)10.1103/PhysRevResearch.2.043308 (DOI)000605417800005 ()2-s2.0-85099286295 (Scopus ID)
Note

QC 20210204

Available from: 2021-02-04 Created: 2021-02-04 Last updated: 2024-03-18Bibliographically approved
4. Identification of strongly interacting organic semimetals
Open this publication in new window or tab >>Identification of strongly interacting organic semimetals
2020 (English)In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 102, no 20, article id 205134Article in journal (Refereed) Published
Abstract [en]

Dirac and Weyl point- and line-node semimetals are characterized by a zero band gap with simultaneously vanishing density of states. Given a sufficient interaction strength, such materials can undergo an interaction instability, e.g., into an excitonic insulator phase. Due to generically flatbands, organic crystals represent a promising materials class in this regard. We combine machine learning, density functional theory, and effective models to identify specific example materials. Without taking into account the effect of many-body interactions, we found the organic charge transfer salts [bis(3,4-diiodo-3',4'-ethyleneditio-tetrathiafulvalene), 2,3-dichloro-5,6-dicyanobenzoquinone, acetenitrile] [(EDT-TTF-I-2)(2)](DDQ)center dot(CH3CN) and 2, 2', 5, 5'-tetraselenafulvalene-7, 7, 8, 8-tetracyano-p-quinodimethane (TSeF-TCNQ) and a bis-1,2,3-dithiazolyl radical conductor to exhibit a semimetallic phase in our ab initio calculations. Adding the effect of strong particle-hole interactions for (EDT-TTF-I-2)(2)(DDQ)center dot(CH3CN) and TSeF-TCNQ opens an excitonic gap on the order of 60 and 100 meV, which is in good agreement with previous experiments on these materials.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2020
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-287797 (URN)10.1103/PhysRevB.102.205134 (DOI)000594089300005 ()2-s2.0-85097196714 (Scopus ID)
Note

QC 20210126

Available from: 2021-01-26 Created: 2021-01-26 Last updated: 2023-02-26Bibliographically approved
5. Mass fluctuations and absorption rates in dark-matter sensors based on Dirac materials
Open this publication in new window or tab >>Mass fluctuations and absorption rates in dark-matter sensors based on Dirac materials
2020 (English)In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 101, no 4, article id 045120Article in journal (Refereed) Published
Abstract [en]

We study the mass fluctuations in gapped Dirac materials by treating the mass term as both a continuous and discrete random variable. Gapped Dirac materials were proposed to be used as materials for dark-matter sensors. One thus would need to estimate the role of disorder and fluctuations on the interband absorption of dark matter. We find that both continuous and discrete fluctuations across the sample introduce tails (e.g., Dirac-Lifshitz tails) in the density of states and the interband absorption rate. We estimate the strength of the gap filling and discuss implications of these fluctuations on the performance as sensors for dark matter detection. The approach used in this work provides a basic framework to model the disorder by any arbitrary mechanism on the interband absorption of Dirac material sensors.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2020
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-267156 (URN)10.1103/PhysRevB.101.045120 (DOI)000507511400006 ()2-s2.0-85078402113 (Scopus ID)
Note

QC 20200217

Available from: 2020-02-17 Created: 2020-02-17 Last updated: 2023-02-26Bibliographically approved
6. Band gap prediction for large organic crystal structures with machine learning
Open this publication in new window or tab >>Band gap prediction for large organic crystal structures with machine learning
2019 (English)In: Advanced Quantum Technologies, ISSN 2511-9044, Vol. 2, no 7-8, article id UNSP 1900023Article in journal (Refereed) Published
Abstract [en]

Machine-learning models are capable of capturing the structure-property relationship from a dataset of computationally demanding ab initio calculations. Over the past two years, the Organic Materials Database (OMDB) has hosted a growing number of calculated electronic properties of previously synthesized organic crystal structures. The complexity of the organic crystals contained within the OMDB, which have on average 82 atoms per unit cell, makes this database a challenging platform for machine learning applications. In this paper, the focus is on predicting the band gap which represents one of the basic properties of a crystalline material. With this aim, a consistent dataset of 12 500 crystal structures and their corresponding DFT band gap are released, freely available for download at https://omdb.mathub.io/dataset. An ensemble of two state-of-the-art models reach a mean absolute error (MAE) of 0.388 eV, which corresponds to a percentage error of 13% for an average band gap of 3.05 eV. Finally, the trained models are employed to predict the band gap for 260 092 materials contained within the Crystallography Open Database (COD) and made available online so that the predictions can be obtained for any arbitrary crystal structure uploaded by a user.

Place, publisher, year, edition, pages
Wiley, 2019
Keywords
band gaps, organic crystals, Organic Materials Database, kernel regression, machine learning
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-279251 (URN)10.1002/qute.201900023 (DOI)000548079200009 ()2-s2.0-85106545447 (Scopus ID)
Note

QC 20200918

Available from: 2020-09-18 Created: 2020-09-18 Last updated: 2023-12-18Bibliographically approved
7. Materials Informatics for Dark Matter Detection
Open this publication in new window or tab >>Materials Informatics for Dark Matter Detection
Show others...
2018 (English)In: Physica Status Solidi. Rapid Research Letters, ISSN 1862-6254, E-ISSN 1862-6270, Vol. 12, no 11, article id 1800293Article in journal (Refereed) Published
Abstract [en]

Dark Matter particles are commonly assumed to be weakly interacting massive particles (WIMPs) with a mass in the GeV to TeV range. However, recent interest has shifted toward lighter WIMPs, which are more difficult to probe experimentally. A detection of sub-GeV WIMPs will require the use of small gap materials in sensors. Using recent estimates of the WIMP mass, we identify the relevant target space toward small gap materials (100 to 10 meV). Dirac Materials, a class of small- or zero-gap materials, emerge as natural candidates for sensors for Dark Matter detection. We propose the use of informatics tools to rapidly assay materials band structures to search for small gap semiconductors and semimetals, rather than focusing on a few preselected compounds. As a specific example of the proposed strategy, we use the organic materials database () to identify organic candidates for sensors: the narrow band gap semiconductors BNQ-TTF and DEBTTT with gaps of 40 and 38 meV, and the Dirac-line semimetal (BEDT-TTF)center dot Br which exhibits a tiny gap of approximate to 50 meV when spin-orbit coupling is included. We outline a novel and powerful approach to search for dark matter detection sensor materials by means of a rapid assay of materials using informatics tools.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2018
Keywords
BEDT-TTF, dark matter detection, Dirac materials, materials informatics, organic materials database
National Category
Materials Engineering
Identifiers
urn:nbn:se:kth:diva-239810 (URN)10.1002/pssr.201800293 (DOI)000450130300008 ()2-s2.0-85053502622 (Scopus ID)
Note

QC 20190107

Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2023-02-26Bibliographically approved
8. Online search tool for graphical patterns in electronic band structures
Open this publication in new window or tab >>Online search tool for graphical patterns in electronic band structures
Show others...
2018 (English)In: npj Computational Materials, E-ISSN 2057-3960, Vol. 4, article id UNSP 46Article in journal (Refereed) Published
Abstract [en]

Many functional materials can be characterized by a specific pattern in their electronic band structure, for example, Dirac materials, characterized by a linear crossing of bands; topological insulators, characterized by a "Mexican hat" pattern or an effectively free electron gas, characterized by a parabolic dispersion. To find material realizations of these features, manual inspection of electronic band structures represents a relatively easy task for a small number of materials. However, the growing amount of data contained within modern electronic band structure databases makes this approach impracticable. To address this problem, we present an automatic graphical pattern search tool implemented for the electronic band structures contained within the Organic Materials Database. The tool is capable of finding user-specified graphical patterns in the collection of thousands of band structures from high-throughput calculations in the online regime. Using this tool, it only takes a few seconds to find an arbitrary graphical pattern within the ten electronic bands near the Fermi level for 26,739 organic crystals. The source code of the developed tool is freely available and can be adapted to any other electronic band structure database.

Place, publisher, year, edition, pages
SPRINGERNATURE, 2018
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-239503 (URN)10.1038/s41524-018-0104-9 (DOI)000449676200002 ()2-s2.0-85052209206 (Scopus ID)
Note

QC 20181128

Available from: 2018-11-28 Created: 2018-11-28 Last updated: 2024-03-18Bibliographically approved

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