A new method in electron microscopy enables sub-20-picometer targeting of individual atoms without prior exposure, opening the door to atom-specific analysis and control.
(Nanowerk Spotlight) Controlling individual atoms is one of the most ambitious goals in modern materials science. It promises new ways to design quantum devices, customize electronic properties, and build structures from the bottom up. But achieving this level of control is technically demanding. One key tool, scanning transmission electron microscopy (STEM), can image atoms with sub-ångström resolution.
Yet despite its power, STEM still struggles to reliably target a single atom without damaging it or shifting the beam slightly off course. High-energy electrons can knock atoms out of place before any useful data is gathered, and slow, distortion-prone scan methods make it difficult to hold the beam steady at the atomic scale. Without a reliable way to aim at and stay locked onto a specific atom, many potential experiments in atomic manipulation and spectroscopy have remained out of reach.
Called atomic lock-on (ALO), the technique achieves sub-20-picometer accuracy in beam placement—precise enough to land on a single atom within a crystal lattice without irradiating the target area beforehand. This approach enables more accurate spectroscopic measurements, tracks atom-scale movements in real time, and may help realize deterministic control over individual atomic events in sensitive materials.
In situ positioning inaccuracy due to linear and nonlinear imaging distortions in STEM. a) Conventional raster scan showing the “fast” and “slow” scan axes and a non-uniform electron beam velocity (v(t) ≠ const.), illustrated with CrSBr. The real atomic lattice L′(x, y) (light gray) or target atom position (green) deviates from the measured lattice L(x, y) (dark gray) or target atom position (red). b) Annular scan with a near-constant electron beam velocity (v(t) ≈ const.). The minimization of scan distortions in the annular scan allows the real atomic lattice to be inferred from sparse atom column information using atomic lock-on because L′(x, y) ∼ L(x, y). (Image: reprinted from DOI:10.1002/advs.202502551, CC BY) (click on image to enlarge)
The central innovation of ALO is the use of a sparse annular scan instead of a conventional raster scan. Traditional STEM methods move the beam over a grid of points to build up an image, but this process involves significant electron exposure to the entire field, including the region of interest. This makes it unsuitable for targeting a specific atom that must remain undisturbed.
The annular scan, by contrast, collects data from a ring-shaped region surrounding the target. The area containing the chosen atom is left untouched. Using the signals from surrounding atoms and known crystal structure parameters, the method reconstructs the lattice in real time and calculates the exact position of the target site. The beam can then be moved to that location with high precision.
The entire process—from the scan to lattice reconstruction to beam placement—takes approximately 200 milliseconds and uses a low electron dose. The scan itself typically lasts 100 milliseconds at a beam current of 20 picoamperes. During this time, the dose delivered is around 9.2 × 10⁴ electrons per square ångström. The beam is then blanked to prevent further exposure until the positioning is complete. Because the target region is never directly imaged, this method avoids damaging or modifying the site before data collection begins.
To validate ALO’s performance, the team tested it on different types of samples, including a 16-layer crystal of chromium sulfur bromide (CrSBr) and a single-layer of molybdenum disulfide (MoS₂). These materials were chosen for their structural contrast and relevance to quantum optoelectronic applications. ALO achieved a targeting precision of 18 ± 10 picometers in the CrSBr crystal and 29 ± 15 picometers in monolayer MoS₂.
In comparison, attempts to target atoms using a deep convolutional neural network (DCNN) applied to conventional images produced errors of more than 100 picometers, often misplacing the beam onto neighboring atomic columns.
The high precision achieved with ALO enabled a series of measurements that would not be possible with previous methods. In one experiment, the researchers tracked a single vanadium dopant atom in MoS₂ and measured its electron energy loss spectrum (EELS), a technique used to probe local electronic structure. Because the EELS signal from a single atom is extremely weak, the beam had to remain focused on the atom for extended periods to collect enough signal.
Over the course of 10 seconds, the beam was repositioned twelve times using ALO to compensate for drift. Each cycle included a brief scan, reconstruction, lock-on, and EELS measurement. The resulting spectra showed consistent energy peaks corresponding to the vanadium atom’s characteristic signals, even as the sample drifted at rates exceeding one ångström per second.
The method was also used to observe atomic dynamics in real time. In a set of experiments on single-layer tungsten disulfide (WS₂), the beam was directed to either tungsten (W) or sulfur (S) atom columns and held in place while recording the scattered signal at intervals of 10 microseconds. Changes in the high-angle annular dark field (HAADF) signal, which scales with atomic number, were used to infer structural changes at the target site.
At tungsten sites, which are relatively stable due to higher displacement energies, most experiments showed no change. However, in a few cases, the beam caused the W atom to move, evidenced by a sudden drop in signal intensity. Post-experiment images confirmed the atom had shifted to a neighboring site. At sulfur sites, more complex behavior was observed. Because sulfur atoms are more weakly bound, they were more likely to be ejected.
About 28 percent of experiments showed a clear step-down in signal intensity, indicating the removal of a single sulfur atom to form a mono-vacancy. Some of these events were followed by the displacement of a second sulfur atom, resulting in a di-vacancy.
Unexpectedly, in many cases where sulfur was ejected, the signal later increased again, implying that the atom had returned or moved nearby. The researchers interpreted these fluctuations as bistable atomic behavior, where the displaced sulfur atom remained partially bonded to the lattice and moved between two positions. In other instances, the signal switched rapidly between two levels, a phenomenon known as random telegraph noise. This indicated that the atom was hopping back and forth between the original site and a nearby position. These transitions occurred on timescales shorter than one millisecond, demonstrating that ALO-enabled measurements can resolve atomic-scale events in real time.
The advantages of ALO extend beyond dynamics. Because it allows the beam to be placed on a chosen atom without exposing the rest of the sample, it reduces unnecessary damage. In contrast to grid-based spectrum imaging, where a full field is scanned and only data from the region of interest is later extracted, ALO enables direct, site-specific measurement.
This is particularly important for beam-sensitive materials such as monolayer crystals or organic systems. ALO’s targeting can also be automated, allowing for repeated measurements on different atomic sites without manual intervention. In the experiments described, 50 measurements were carried out sequentially on different W and S sites in under two minutes.
The technique can be integrated into standard STEM workflows and is compatible with existing scan controllers and detectors. The authors suggest that small modifications to the algorithm could extend its applicability to materials with more complex structures, including those with phase boundaries or lattice defects. Although the current implementation targets atoms in the two-dimensional plane of the sample, future developments could include corrections for drift in the vertical direction, expanding the method’s three-dimensional precision.
ALO also creates opportunities for more precise experimental design in quantum materials research. By enabling atom-specific spectroscopic and structural measurements, it supports efforts to understand and engineer point defects, dopants, and other atomic-scale features that influence electronic and optical properties. The method could also support studies of beam-driven phase transitions, atomic-scale chemical reactions, or defect migration, all of which require precise, repeated interaction with the same site over time.
By making it possible to locate, measure, and manipulate individual atoms with unprecedented accuracy and minimal disturbance, ALO advances the capabilities of electron microscopy from passive imaging toward active, site-selective control. It opens the door to targeted experiments at the limit of spatial and temporal resolution, where the behavior of a single atom can be measured directly—and even influenced—by design.
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