Atom filtering algorithm and GPU-accelerated calculation of simulation atomic force microscopy images DOI Creative Commons
Romain Amyot, Noriyuki Kodera, Holger Flechsig

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 17, 2023

Abstract Simulation atomic force microscopy computationally emulates experimental scanning of a biomolecular structure to produce topographic images that can be correlated with measured images. Its application the enormous amount available high-resolution structures, as well molecular dynamics modelling data, facilitates quantitative interpretation observations by inferring atomistic information from resolution-limited topographies. The computation required generate simulated AFM image generally includes calculation contacts between tip and all atoms structure. However, since only surface are relevant, filtering method shall highly improve efficiency simulation computations. In this report we address issue present an elegant solution based on graphics processing unit (GPU) computations significantly accelerates not allows for visualization structures combined ultra-fast synchronized graphical representation corresponding (live AFM), but, demonstrate, also reduce computational effort during automatized fitting into topographies orders magnitude. Hence, developed will play important role in post-experimental analysis involving AFM. Implementation is realized our BioAFMviewer software package dynamics.

Language: Английский

Emerging Trends in Bioinspired Superhydrophobic and Superoleophobic Sustainable Surfaces DOI Creative Commons

Cerys M. Cormican,

Sinem Bektaş,

Francisco J. Martín‐Martínez

et al.

Advanced Materials, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 18, 2025

Abstract Inspired by nature's ability to master materials for performance and sustainability, biomimicry has enabled the creation of bioinspired structural color, superadhesion, hydrophobicity hydrophilicity, among many others. This review summarizes emerging trends in novel sustainable fluorocarbon‐free designs creating superhydrophobic superoleophobic surfaces. It discusses methods, challenges, future directions, alongside impact computational modeling artificial intelligence accelerating experimental development more surface materials. While significant progress is made materials, surfaces remain a challenge. However, bioinspiration techniques supported platforms are paving way new renewable biodegradable repellent that meet environmental standards without sacrificing performance. Nevertheless, despite concerns, policies, several still continue apply fluorination other environmentally harmful achieve required standard repellency. As discussed this critical review, paradigm integrates advanced characterization, nanotechnology, additive manufacturing, modeling, coming, generate with tailored superhydrophobicity superoleophobicity while adhering standards.

Language: Английский

Citations

2
Employing Atomic Force Microscopy (AFM) for Microscale Investigation of Interfaces and Interactions in Membrane Fouling Processes: New Perspectives and Prospects DOI Creative Commons
Mohan Wei, Yaozhong Zhang, Yifan Wang

et al.

Membranes, Journal Year: 2024, Volume and Issue: 14(2), P. 35 - 35

Published: Jan. 27, 2024

Membrane fouling presents a significant challenge in the treatment of wastewater. Several detection methods have been used to interpret membrane processes. Compared with other analysis and methods, atomic force microscopy (AFM) is widely because its advantages liquid-phase situ 3D imaging, ability measure interactive forces, mild testing conditions. Although AFM has study fouling, current literature not fully explored potential. This review aims uncover provide new perspective on application technology future studies fouling. Initially, rigorous was conducted morphology, roughness, interaction forces characterization membranes foulants. Then, process changing factors reviewed based measurement capability, it found that changes ionic conditions, pH, voltage, even time can cause morphology forces. Existing models are then discussed, role predicting these presented. Finally, potential improved techniques be applied field underestimated. In this paper, we elucidated potentials presented challenges directions for development an attempt insights into field.

Language: Английский

Citations

13
High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action DOI
Toshio Ando, Shingo Fukuda, Kien Xuan Ngo

et al.

Annual Review of Biophysics, Journal Year: 2023, Volume and Issue: 53(1), P. 19 - 39

Published: Dec. 7, 2023

Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the structure of proteins during their functional activity to better elucidate how they function. Among various approaches in high-speed atomic force microscopy (HS-AFM) unique ability film individual molecules action, although only topographical information acquirable. This review provides guide use HS-AFM for biomolecular imaging and showcases several examples, as well providing on up-to-date progress technology. Finally, we discuss future prospects context upcoming era.

Language: Английский

Citations

18
Nano-Scale Video Imaging of Motility Machinery by High-Speed Atomic Force Microscopy DOI Creative Commons

Steven John McArthur,

Kenichi Umeda, Noriyuki Kodera

et al.

Biomolecules, Journal Year: 2025, Volume and Issue: 15(2), P. 257 - 257

Published: Feb. 10, 2025

Motility is a vital aspect of many forms life, with wide range highly conserved as well unique systems adapted to the needs various organisms and environments. While motility are studied using structural techniques like X-ray crystallography electron microscopy, fluorescence microscopy methodologies, it difficult directly determine relationship between shape movement system due notable gap in spatiotemporal resolution. Bridging this understanding dynamic molecular movements that underpin mechanisms has been challenging. The advent high-speed atomic force (HS-AFM) provided new window into these nano-scale machines processes underlying motility. In review, we highlight some advances field, ranging from reconstituted purified higher-order supramolecular complexes live cells, both prokaryotic eukaryotic contexts.

Language: Английский

Citations

0
Biomembrane structure at the molecular level and its application in precision medicine DOI

Z.Q. Wang,

Zhiyuan Tian, Jing Gao

et al.

Biophysics Reviews, Journal Year: 2025, Volume and Issue: 6(1)

Published: Feb. 18, 2025

Biomembranes are fundamental to our understanding of the cell, basic building block all life. They form important barriers between cytoplasm and microenvironment cell separate organelles within cells. Despite substantial advances in study membrane structure models, they still stage model hypothesis due high complexity components, structures, functions membranes. In this review, we summarized progresses on structure, properties, at molecular level using newly developed technologies discussed some challenges future directions biomembrane research from perspective. Moreover, demonstrated dynamic proteins their role achieving early detection, precise diagnosis, development personalized treatment strategies level. Overall, review aims engage researchers related fields multidisciplinary readers understand explore biomembranes for accurate effective membrane-targeting therapeutic agents.

Language: Английский

Citations

0
A systematic review on the applications of atomic force microscopy for coal and rock characterization DOI
Xianghui Tian, Dazhao Song, Xueqiu He

et al.

Measurement, Journal Year: 2024, Volume and Issue: 232, P. 114722 - 114722

Published: April 15, 2024

Language: Английский

Citations

3
Flexible fitting to infer atomistic-precision models of large-amplitude conformational dynamics in biomolecules from high-speed atomic force microscopy imaging DOI Creative Commons
Romain Amyot, Osamu Miyashita,

Xuan Wu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: May 15, 2025

Abstract High-speed atomic force microscopy (HS-AFM) experiments allow direct observation of biomolecular dynamics at the single-molecule level, acquiring a large amount topographic imaging data that visualizes changes molecular surface during functional activity over an extended period time. Since images have no atomistic resolution, major challenge has been to develop post-experimental computational methods infer information from measurements. The recently developed NMFF-AFM flexible fitting method provides computationally efficient approach promising atomistic-precision models conformational resolution-limited AFM data. We report software integration this into well-established BioAFMviewer platform and demonstrate first applications experimental HS-AFM To facilitate applications, we workflow raw visualization analysis results. presented single protein domain, complex, megadalton size filament versatility modelling reproduce large-amplitude motions imaging. As step towards automated large-scale data, furthermore reconstruction movie dynamics, involving transitions, measured sequence. Implementation within standalone user-friendly interactive opens opportunity for broad range understanding

Language: Английский

Citations

0
Unraveling dynamics of nuclear pore and chromatin via HS-AFM DOI Creative Commons
Goro Nishide, Richard W. Wong

Anatomical Science International, Journal Year: 2025, Volume and Issue: unknown

Published: May 19, 2025

Abstract High-speed atomic force microscopy (HS-AFM) enables real-time visualization of biological processes with nanometer-level resolution. This review highlights how HS-AFM has been instrumental in uncovering the dynamic interplay between nuclear pore complexes (NPCs)—which regulate nucleocytoplasmic transport—and genome guardians, including DNA repair proteins and chromatin regulators. Structurally, NPCs resemble a multi-layered spider cobweb, serving as crucial molecular gatekeepers for maintaining cellular homeostasis, while guardians safeguard genomic integrity through organization. Through HS-AFM, researchers have gained unprecedented insights into NPC dynamics, revealing their adaptability during transport, reorganization, viral infection. It also elucidated interact NPCs, influencing organization at periphery regulating trafficking. These discoveries underscore critical role NPC-genome interactions stability, gene expression, broad implications diseases such cancer, infections, neurodegenerative disorders. In conclusion, transformed our ability to study landscape nanoscale, bridging gap structural biology functional genomics. By capturing dynamics chromatin, provides an essential tool unraveling mechanisms that govern transport regulation. Future advancements technology, higher temporal resolution, correlative imaging, AI-driven analysis, will further expand its potential biomedical research, paving way novel diagnostic therapeutic strategies.

Language: Английский

Citations

0
Technical advances in high-speed atomic force microscopy DOI
Shingo Fukuda, Toshio Ando

Biophysical Reviews, Journal Year: 2023, Volume and Issue: 15(6), P. 2045 - 2058

Published: Dec. 1, 2023

Language: Английский

Citations

8
Atomic force microscopy 3D structural reconstruction of individual particles in the study of amyloid protein assemblies DOI Creative Commons

Claudia Chitty,

Kinga Kuliga,

Wei‐Feng Xue

et al.

Biochemical Society Transactions, Journal Year: 2024, Volume and Issue: 52(2), P. 761 - 771

Published: April 11, 2024

Recent developments in atomic force microscopy (AFM) image analysis have made three-dimensional (3D) structural reconstruction of individual particles observed on 2D AFM height images a reality. Here, we review the emerging contact point (CPR-AFM) methodology and its application 3D helical amyloid filaments context challenges presented by highly polymorphous heterogeneous protein structures. How particle-level can contribute to resolving polymorph structure-function relationships, environmental triggers leading misfolding aggregation into species, influences conditions or minor fluctuations initial monomeric structure speed fibril formation, extent different types species that be formed, are discussed. Future perspectives capabilities AFM-based exploiting synergies with other recent technology advances also discussed highlight potential as an emergent general, accessible multimodal biology tool for biomolecules.

Language: Английский

Citations

2