Discovering Ice and Water Structures with High-Resolution AFM, Atomistic Modeling, and Machine Learning

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School of Science | Doctoral thesis (article-based) | Defence date: 2024-08-23
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Author
Date
2024
Department
Teknillisen fysiikan laitos
Department of Applied Physics
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Mcode
Degree programme
Language
en
Pages
88 + app. 44
Series
Aalto University publication series DOCTORAL THESES, 152/2024
Abstract
Since its invention several decades ago, Atomic Force Microscopy (AFM) has become an irreplaceable technique for the investigation of matter at the nanoscale. Specifically, the development of three-dimensional AFM (3D-AFM) enabled the observation of hydration structures in solid-liquid interfaces, while the use of tip functionalization in ultra-high vacuum has been crucial for reaching atomically resolved imaging of individual molecules. However, in both scenarios, only completely flat structures can be fully characterized by AFM. In more threedimensional samples, interpreting the measurements can be challenging, as only partial structural information is available. In this thesis, atomistic simulation and machine learning techniques are combined to tackle this problem in various systems, in all of which water molecules have central importance. First, a structure discovery workflow is developed for the case of ice nanoclusters on Au(111) and Cu(111) surfaces, centered about the use of neural network potentials. Then, molecular dynamics simulations are carried out to uncover the atomistic structure of cellulose-Iα and α-chitin nanocrystals surfaces in water. Finally, a high-throughput workflow is developed to identify the arrangement of solid-binding peptides assemblies on a graphite surface.
Description
Supervising professor
Foster, Adam Stuart, Prof., Aalto University, Department of Applied Physics, Finland
Thesis advisor
Foster, Adam Stuart, Prof., Aalto University, Department of Applied Physics, Finland
Keywords
atomic force microscopy, molecular dynamics, machine learning
Other note
Parts
  • [Publication 1]: Fabio Priante, Niko Oinonen, Ye Tian, Dong Guan, Chen Xu, Shuning Cai, Peter Liljeroth, Ying Jiang, and Adam S. Foster. Structure Discovery in Atomic Force Microscopy Imaging of Ice. ACS Nano, 18(7), 5546–5555, Feb 2024.
    Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202403062520
    DOI: 10.1021/acsnano.3c10958 View at publisher
  • [Publication 2]: Ayhan Yurtsever, Pei-Xi Wang, Fabio Priante, Ygor Morais Jaques, Keisuke Miyazawa, Mark J. MacLachlan, Adam S. Foster, Takeshi Fukuma. Molecular insights on the crystalline cellulose-water interfaces via threedimensional atomic force microscopy. Science Advances, 8(41), Oct 2022.
    Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202211096453
    DOI: 10.1126/sciadv.abq0160 View at publisher
  • [Publication 3]: Ayhan Yurtsever, Pei-Xi Wang, Fabio Priante, Ygor Morais Jaques, Kazuki Miyata, Mark J. MacLachlan, Adam S. Foster, and Takeshi Fukuma. Probing the Structural Details of Chitin Nanocrystal–Water Interfaces by Three-Dimensional Atomic Force Microscopy. Small Methods, 6(9), 2200320, Sep 2022.
    Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202210195963
    DOI: 10.1002/smtd.202200320 View at publisher
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https://urn.fi/URN:ISBN:978-952-64-1939-8
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[diss] Perustieteiden korkeakoulu / SCI