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1. Fresnel diffraction imaging of surface nanostructure using coherent resonant x-ray scattering

   https://doi.org/10.1063/5.0273192  

   Burgard, L.; Neupane, C.; Balodhi, A.; Bista, S.; Butun, S.; Jangid, R.; Barbour, A.; Basit, N.; Agterberg, D_F; Weinert, M.; et al (July 2025, Journal of Applied Physics)

   We investigated surface nanostructures on an antiferromagnet MnBi2Te4 using a novel imaging technique, direct (real)-space and real time coherent x-ray imaging (direct-CXI). This technique has provided new insights into antiferromagnetic textures, including the formation of anti-phase antiferromagnetic (AFM) domains and thermal dynamics of AFM domains and domain walls. While this method produces real-space images of AFM textures without requiring a complex imaging retrieval process, its underlying imaging mechanism has not been fully understood, limiting a deep understanding of AFM textures and the information they contain. By investigating the well-defined structural characteristics of the nanostructures fabricated on MnBi2Te4, we elucidate the imaging principle of this novel technique. We find that the observed images can be well explained by the Fresnel diffraction integral. Using a simple model from classical optics, our calculations successfully reproduce the experimentally observed images of the nanostructures. This demonstrates that direct-CXI not only provides straightforward real-space imaging but also contains phase information through its Fresnel diffraction integral. 

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2. Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects

   https://doi.org/10.1021/acsnano.1c01976  

   Green, Christopher M.; Hughes, William L.; Graugnard, Elton; Kuang, Wan (June 2021, ACS Nano)

   null (Ed.)

   To bring real-world applications of DNA nanostructures to fruition, advanced microscopy techniques are needed to shed light on factors limiting the availability of addressable sites. Correlative microscopy, where two or more microscopies are combined to characterize the same sample, is an approach to overcome the limitations of individual techniques, yet it has seen limited use for DNA nanotechnology. We have developed an accessible strategy for high resolution, correlative DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution and atomic force microscopy (AFM) of DNA nanostructures, enabled by a simple and robust method to selectively bind DNA origami to cover glass. Using this technique, we examined addressable “docking” sites on DNA origami to distinguish between two defect scenarios–structurally incorporated but inactive docking sites, and unincorporated docking sites. We found that over 75% of defective docking sites were incorporated but inactive, suggesting unincorporated strands played a minor role in limiting the availability of addressable sites. We further explored the effects of strand purification, UV irradiation, and photooxidation on availability, providing insight on potential sources of defects and pathways toward improving the fidelity of DNA nanostructures. 

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3. Atomic Force Microscopy Reveals Complexity Underlying General Secretory System Activity

   https://doi.org/10.3390/ijms24010055  

   Weaver, Dylan R.; King, Gavin M. (January 2023, International Journal of Molecular Sciences)

   The translocation of specific polypeptide chains across membranes is an essential activity for all life forms. The main components of the general secretory (Sec) system of E. coli include integral membrane translocon SecYEG, peripheral ATPase SecA, and SecDF, an ancillary complex that enhances polypeptide secretion by coupling translocation to proton motive force. Atomic force microscopy (AFM), a single-molecule imaging technique, is well suited to unmask complex, asynchronous molecular activities of membrane-associated proteins including those comprising the Sec apparatus. Using AFM, the dynamic structure of membrane-external protein topography of Sec system components can be directly visualized with high spatial-temporal precision. This mini-review is focused on AFM imaging of the Sec system in near-native fluid conditions where activity can be maintained and biochemically verified. Angstrom-scale conformational changes of SecYEG are reported on 100 ms timescales in fluid lipid bilayers. The association of SecA with SecYEG, forming membrane-bound SecYEG/SecA translocases, is directly visualized. Recent work showing topographical aspects of the translocation process that vary with precursor species is also discussed. The data suggests that the Sec system does not employ a single translocation mechanism. We posit that differences in the spatial frequency distribution of hydrophobic content within precursor sequences may be a determining factor in mechanism selection. Precise AFM investigations of active translocases are poised to advance our currently vague understanding of the complicated macromolecular movements underlying protein export across membranes. 

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4. Automated Registration and Clustering for Enhanced Localization Atomic Force Microscopy of Flexible Membrane Proteins

   https://doi.org/10.1101/2025.06.30.662259  

   Lisowski, Creighton M; King, Gavin M; Kosztin, Ioan (July 2025, bioRxiv)

   Atomic Force Microscopy (AFM) can create images of biomolecules under near-native conditions but suffers from limited lateral resolution due to the finite AFM tip size and recording frequency. The recently developed Localization Atomic Force Microscopy or LAFM (Heath et al., Nature 594, 385 (2021)) enhances lateral resolution by reconstructing peak positions in AFM image stacks, but it is less effective for flexible proteins with multiple conformations. Here we introduce an unsupervised deep learning algorithm that simultaneously registers and clusters images by protein conformation, thus making LAFM applicable to more flexible proteins. Using simulated AFM images from molecular dynamics simulations of the SecYEG translocon as a model membrane protein system, we demonstrate improved resolution for individual protein conformations. This work represents a step towards a more general LAFM algorithm that can handle biological macromolecules with multiple distinct conformational states such as SecYEG. Author summaryAtomic Force Microscopy (AFM) enables high-resolution imaging of biomolecules under near-native conditions but faces lateral resolution limits due to the finite AFM tip size and recording frequency. The recently developed Localization Atomic Force Microscopy (LAFM) method addresses this by reconstructing peak positions from AFM image stacks, achieving almost atomic resolution for rigid proteins like bacteriorhodopsin (Heath et al., Nature 594, 385 (2021)). However, flexible membrane proteins with dynamic conformations, such as the SecYEG translocon, which exhibits large and highly mobile cytoplasmic loops, lead to non-physical smearing in standard LAFM reconstructions. Here, we present a computational framework combining unsupervised deep clustering and LAFM to enhance the lateral resolution of AFM images of flexible membrane proteins. Our neural network algorithm (i) groups AFM images into conformationally homogeneous clusters and (ii) registers images within each cluster. Applying LAFM separately to these clusters minimizes smearing artifacts, yielding high-resolution reconstructions for distinct conformations. We validate this approach using synthetic AFM images generated from all-atom molecular dynamics simulations of SecYEG in a solvated POPE lipid bilayer. This advancement extends LAFM’s utility to encompass conformationally diverse membrane proteins. 

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5. Holey Substrate-Directed Strain Patterning in Bilayer MoS₂

   https://doi.org/10.1021/acsnano.1c08348  

   Zhang, Yichao; Choi, Moon-Ki; Haugstad, Greg; Tadmor, Ellad B.; Flannigan, David J. (November 2021, ACS Nano)

   null (Ed.)

   Key properties of two-dimensional (2D) layered materials are highly strain tunable, arising from bond modulation and associated reconfiguration of the energy bands around the Fermi level. Approaches to locally controlling and patterning strain have included both active and passive elastic deformation via sustained loading and templating with nanostructures. Here, by float-capturing ultrathin flakes of single-crystal 2H-MoS₂ on amorphous holey silicon nitride substrates, we find that highly symmetric, high-fidelity strain patterns are formed. The hexagonally arranged holes and surface topography combine to generate highly conformal flake-substrate coverage creating patterns that match optimal centroidal Voronoi tessellation in 2D Euclidean space. Using TEM imaging and diffraction, as well as AFM topographic mapping, we determine that the substrate-driven 3D geometry of the flakes over the holes consists of symmetric, out-of-plane bowl-like deformation of up to 35 nm, with in-plane, isotropic tensile strains of up to 1.8% (measured with both selected-area diffraction and AFM). Atomistic and image simulations accurately predict spontaneous formation of the strain patterns, with van der Waals forces and substrate topography as the input parameters. These results show that predictable patterns and 3D topography can be spontaneously induced in 2D materials captured on bare, holey substrates. The method also enables electron scattering studies of precisely aligned, substrate-free strained regions in transmission mode. 

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