Browsing by Author "Miyazawa, Keisuke"

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Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality
(2022-06-16) Sumikama, Takashi; Canova, Filippo Federici; Gao, David Z.; Penedo, Marcos; Miyazawa, Keisuke; Foster, Adam S.; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.
Dissolution Processes at Step Edges of Calcite in Water Investigated by High-Speed Frequency Modulation Atomic Force Microscopy and Simulation
(2017-07-12) Miyata, Kazuki; Tracey, John; Miyazawa, Keisuke; Haapasilta, Ville; Spijker, Peter; Kawagoe, Yuta; Foster, Adam S.; Tsukamoto, Katsuo; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
The microscopic understanding of the crystal growth and dissolution processes have been greatly advanced by the direct imaging of nanoscale step flows by atomic force microscopy (AFM), optical interferometry, and X-ray microscopy. However, one of the most fundamental events that govern their kinetics, namely, atomistic events at the step edges, have not been well understood. In this study, we have developed high-speed frequency modulation AFM (FM-AFM) and enabled true atomic-resolution imaging in liquid at ∼1 s/frame, which is ∼50 times faster than the conventional FM-AFM. With the developed AFM, we have directly imaged subnanometer-scale surface structures around the moving step edges of calcite during its dissolution in water. The obtained images reveal that the transition region with typical width of a few nanometers is formed along the step edges. Building upon insight in previous studies, our simulations suggest that the transition region is most likely to be a Ca(OH)2 monolayer formed as an intermediate state in the dissolution process. On the basis of this finding, we improve our understanding of the atomistic dissolution model of calcite in water. These results open up a wide range of future applications of the high-speed FM-AFM to the studies on various dynamic processes at solid-liquid interfaces with true atomic resolution.
Inhibition of Silica Nanoparticle Adhesion to Poly(vinyl alcohol) Surfaces by Ammonia-Mediated Hydration: Implications for Effective Post-Chemical-Mechanical Planarization Cleaning
(2021-01-22) Ikarashi, Takahiko; Yoshino, Takumi; Nakajima, Naoki; Miyata, Kazuki; Miyazawa, Keisuke; Morais Jaques, Ygor; Foster, Adam S.; Uno, Megumi; Takatoh, Chikako; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Adhesion of silica abrasive nanoparticles to a poly(vinyl alcohol) (PVA) brush surface in post-CMP (chemical-mechanical planarization) cleaning leads to serious problems in yield enhancement of semiconductor fabrication. However, the nanoscale adhesion mechanism and its correlation with process conditions have hardly been understood. In this study, we investigated the influence of ammonia in the cleaning solution on silica nanoparticle adhesion to a PVA surface. By atomic force microscopy (AFM), we directly measured adhesion forces between a nanoscale silica probe and a PVA brush surface in various solutions and found that ammonia has a significant inhibitory effect against silica nanoparticle adhesion to a PVA surface. Importantly, we found that this effect cannot be explained by the electrostatic interactions alone but also involves steric repulsion between silica and hydrated PVA. We also performed molecular-scale three-dimensional scanning force microscopy (3D-SFM) imaging and contact angle measurements and found that ammonia promotes hydration and swelling of PVA. Furthermore, we performed molecular dynamics simulations and found that ammonia promotes dynamic rearrangements of hydrogen-bonding networks (HBNs) at a PVA-water interface, giving extra flexibility to the PVA chains. Such flexibility promotes local swelling of PVA and inhibits silica nanoparticle adhesion to a PVA surface. This provides important guidelines for optimizing nanoscale structures and interactions of brush surfaces and abrasive nanoparticles in post-CMP cleaning.
Mechanism of atomic force microscopy imaging of three-dimensional hydration structures at a solid-liquid interface
(2015) Fukuma, Takeshi; Reischl, Bernhard; Kobayashi, Naritaka; Spijker, Peter; Federici Canova, Filippo; Miyazawa, Keisuke; Foster, Adam S.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Here we present both subnanometer imaging of three-dimensional (3D) hydration structures using atomic force microscopy (AFM) and molecular dynamics simulations of the calcite-water interface. In AFM, by scanning the 3D interfacial space in pure water and recording the force on the tip, a 3D force image can be produced, which can then be directly compared to the simulated 3D water density and forces on a model tip. Analyzing in depth the resemblance between experiment and simulation as a function of the tip-sample distance allowed us to clarify the contrast mechanism in the force images and the reason for their agreement with water density distributions. This work aims to form the theoretical basis for AFM imaging of hydration structures and enables its application to future studies on important interfacial processes at the molecular scale.
Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy
(2022-10-14) Yurtsever, Ayhan; Wang, Pei Xi; Priante, Fabio; Morais Jaques, Ygor; Miyazawa, Keisuke; MacLachlan, Mark J.; Foster, Adam S.; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Cellulose, a renewable structural biopolymer, is ubiquitous in nature and is the basic reinforcement component of the natural hierarchical structures of living plants, bacteria, and tunicates. However, a detailed picture of the crystalline cellulose surface at the molecular level is still unavailable. Here, using atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we revealed the molecular details of the cellulose chain arrangements on the surfaces of individual cellulose nanocrystals (CNCs) in water. Furthermore, we visualized the three-dimensional (3D) local arrangement of water molecules near the CNC surface using 3D AFM. AFM experiments and MD simulations showed anisotropic water structuring, as determined by the surface topologies and exposed chemical moieties. These findings provide important insights into our understanding of the interfacial interactions between CNCs and water at the molecular level. This may allow the establishment of the structure-property relationship of CNCs extracted from various biomass sources.
Tip dependence of three-dimensional scanning force microscopy images of calcite-water interfaces investigated by simulation and experiments
(2020-06-28) Miyazawa, Keisuke; Tracey, John; Reischl, Bernhard; Spijker, Peter; Foster, Adam S.; Rohl, Andrew L.; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO3 and OH tip models. For all the 3D images, the z profiles at the surface Ca and CO3 sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing the xy slices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO3 tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.
Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy
(2016-09-09) Tracey, John; Miyazawa, Keisuke; Spijker, Peter; Miyata, Kazuki; Reischl, Bernhard; Canova, Filippo Federici; Rohl, Andrew L.; Fukuma, Takeshi; Foster, Adam S.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (1014) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.