Improvements in fundamental performance of in-liquid frequency modulation atomic force microscopy

Unraveling dynamics of nuclear pore and chromatin via HS-AFM

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

Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water

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.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality

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.