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Cobeña-Reyes J, Ye T, Martini A. Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:147-156. [PMID: 37235190 PMCID: PMC10208375 DOI: 10.1021/cbmi.3c00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 05/28/2023]
Abstract
Achieving high-resolution images using dynamic atomic force microscopy (AFM) requires understanding how chemical and structural features of the surface affect image contrast. This understanding is particularly challenging when imaging samples in water. An initial step is to determine how well-characterized surface features interact with the AFM tip in wet environments. Here, we use molecular dynamics simulations of a model AFM tip apex oscillating in water above self-assembled monolayers (SAMs) with different chain lengths and functional groups. The amplitude response of the tip is characterized across a range of vertical distances and amplitude set points. Then relative image contrast is quantified as the difference of the amplitude response of the tip when it is positioned directly above a SAM functional group vs positioned between two functional groups. Differences in contrast between SAMs with different lengths and functional groups are explained in terms of the vertical deflection of the SAMs due to interactions with the tip and water during dynamic imaging. The knowledge gained from simulations of these simple model systems may ultimately be used to guide selection of imaging parameters for more complex surfaces.
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Affiliation(s)
- José Cobeña-Reyes
- Department
of Mechanical Engineering, University of
California Merced, Merced, California 95343, United States
| | - Tao Ye
- Department
of Chemistry & Biochemistry, University
of California Merced, Merced, California 95343, United States
| | - Ashlie Martini
- Department
of Mechanical Engineering, University of
California Merced, Merced, California 95343, United States
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Sumikama T, Federici Canova F, Gao DZ, Penedo M, Miyazawa K, Foster AS, Fukuma T. Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality. J Phys Chem Lett 2022; 13:5365-5371. [PMID: 35678499 PMCID: PMC9208010 DOI: 10.1021/acs.jpclett.2c01093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
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.
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Affiliation(s)
- Takashi Sumikama
- PRESTO,
JST, Kawaguchi, Saitama 332-0012, Japan
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
| | - Filippo Federici Canova
- Nanolayers
Research Computing Ltd., 1 Granville Court, Granville Road, London N12 0HL, United Kingdom
- Department
of Applied Physics, Aalto University, Aalto 00076, Finland
| | - David Z. Gao
- Nanolayers
Research Computing Ltd., 1 Granville Court, Granville Road, London N12 0HL, United Kingdom
- Department
of Physics, Norwegian University of Science
and Technology (NTNU), 7491 Trondheim, Norway
| | - Marcos Penedo
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Laboratory
for Bio and Nanoinstrumentation, Institute for Bioengineering, École Polytechnique Fédérale
de Lausanne, Lausanne CH-1015, Switzerland
| | - Keisuke Miyazawa
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Division
of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
- Faculty of
Frontier Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Adam S. Foster
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Department
of Applied Physics, Aalto University, Aalto 00076, Finland
| | - Takeshi Fukuma
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Division
of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
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