arXiv subjects

Peter Ercius

Publications and source records attributed to Peter Ercius.

At least 19 recordsLinked to original sources

arXiv2025

TEM Agent: enhancing transmission electron microscopy (TEM) with modern AI tools

Recent improvements in large language models (LLMs) have had a dramatic effect on capabilities and productivity across many disciplines involving critical thinking and writing. The development of the model context protocol (MCP) provides a way to extend the power of LLMs to a specific set of tasks or scientific equipment with help from curated tools and resources. Here, we describe a framework called TEM Agent designed for transmission electron microscopy (TEM) that leverages the benefits of LLMs through a MCP approach. We simultaneously access and control several subsystems of the TEM, a data management platform, and high performance computing resources through text-based instructions. We demonstrate the abilities of the TEM Agent to set up and complete intricate workflows using a simplified set of MCP tools and resources accompanying a commercial LLM without any additional training. The use of a framework such as the TEM Agent simplifies access to complex microscope ecosystems comprised of several vendor and custom systems enhancing the ability of users to accomplish microscopy experiments across a range of difficulty levels.

cond-mat.mtrl-sci↗

arXiv2025

Robust electron counting for direct electron detectors with the Back-Propagation Counting method

Electron microscopy (EM) is a foundational tool for directly assessing the structure of materials. Recent advances in direct electron detectors have improved signal-to noise ratios via single-electron counting. However, accurately counting electrons at high fluence remains challenging. We developed a new method of electron counting for direct electron detectors, Back-Propagation Counting (BPC). BPC uses machine learning techniques designed for mathematical operations on large tensors but does not require large training datasets. In synthetic data, we show BPC is able to count multiple electron strikes per pixel and is robust to increasing occupancy. In experimental data, frames counted with BPC are shown to reconstruct diffraction peaks corresponding to individual nanoparticles with relatively higher intensity and produce images with improved contrast when compared to a standard counting method. Together, these results show that BPC excels in experiments where pixels see a high flux of electron irradiation such as in situ TEM movies and diffraction.

physics.ins-det↗

arXiv2025

Crystal nucleation and growth in high-entropy alloys revealed by atomic electron tomography

High-entropy alloys (HEAs) balance mixing entropy and intermetallic phase formation enthalpy, creating a vast compositional space for structural and functional materials (1-6). They exhibit exceptional strength-ductility trade-offs in metallurgy (4-10) and near-continuum adsorbate binding energies in catalysis (11-16). A deep understanding of crystal nucleation and growth in HEAs is essential for controlling their formation and optimizing their structural and functional properties. However, atomic-scale nucleation in HEAs challenges traditional theories based on one or two principal elements (17-23). The intricate interplay of structural and chemical orders among multiple principal elements further obscures our understanding of nucleation pathways (5,24-27). Due to the lack of direct three-dimensional (3D) atomic-scale observations, previous studies have relied on simulations and indirect measurements (28-32), leaving HEA nucleation and growth fundamentally elusive. Here, we advance atomic electron tomography (33,34) to resolve the 3D atomic structure and chemical composition of 7,662 HEA and 498 medium-entropy alloy nuclei at different nucleation stages. We observe local structural order that decreases from core to boundary, correlating with local chemical order. As nuclei grow, structural order improves. At later stages, most nuclei coalesce without misorientation, while some form coherent twin boundaries. To explain these experimental observations, we propose the gradient nucleation pathways model, in which the nucleation energy barrier progressively increases through multiple evolving intermediate states. We expect these findings to not only provide fundamental insights into crystal nucleation and growth in HEAs, but also offer a general framework for understanding nucleation mechanisms in other materials.

cond-mat.mtrl-sci↗

arXiv2024

Atomic-scale 3D structural dynamics and functional degradation of Pt alloy nanocatalysts during the oxygen reduction reaction

Pt-based electrocatalysts are the primary choice for fuel cells due to their superior oxygen reduction reaction (ORR) activity. To enhance ORR performance and durability, extensive studies have investigated transition metal alloying, doping, and shape control to optimize the three key governing factors for ORR: geometry, local chemistry, and strain of their surface and subsurface. However, systematic optimization remains incomplete, as it requires an atomic-scale understanding of these factors and their dynamics over potential cycling, as well as their relationship to ORR activity. Here, we implement neural network-assisted atomic electron tomography to measure the 3D atomic structural dynamics and their effects on the functional degradation of PtNi alloy catalysts. Our results reveal that PtNi catalysts undergo shape changes, surface alloying, and strain relaxation during cycling, which can be effectively mitigated by Ga doping. By combining geometry, local chemistry, and strain analysis, we calculated the changes in ORR activity over thousands of cycles and observed that Ga doping leads to higher initial activity and greater stability. These findings offer a pathway to understanding 3D atomic structural dynamics and their relation to ORR activity during cycling, paving the way for the systematic design of durable, high-efficiency nanocatalysts.

cond-mat.mtrl-sci↗

arXiv2024

BEACON -- Automated Aberration Correction for Scanning Transmission Electron Microscopy using Bayesian Optimization

Aberration correction is an important aspect of modern high-resolution scanning transmission electron microscopy. Most methods of aligning aberration correctors require specialized sample regions and are unsuitable for fine-tuning aberrations without interrupting on-going experiments. Here, we present an automated method of correcting first- and second-order aberrations called BEACON which uses Bayesian optimization of the normalized image variance to efficiently determine the optimal corrector settings. We demonstrate its use on gold nanoparticles and a hafnium dioxide thin film showing its versatility in nano- and atomic-scale experiments. BEACON can correct all first- and second-order aberrations simultaneously to achieve an initial alignment and first- and second-order aberrations independently for fine alignment. Ptychographic reconstructions are used to demonstrate an improvement in probe shape and a reduction in the target aberration.

cond-mat.mtrl-sci↗

arXiv2024

Operando probing of nanocracking in CuO-derived Cu during CO$_2$ electroreduction

Identifying and controlling active sites in electrocatalysis remains a grand challenge due to restructuring of catalysts in the complex chemical environments during operation. Inactive precatalysts can transform into active catalysts under reaction conditions, such as oxide-derived Cu (OD-Cu) for CO$_2$ electroreduction displaying improved production of multicarbon (C$_{2+}$) chemicals. Revealing the mechanism of active site origin in OD-Cu catalysts requires in situ/operando characterizations of structure, morphology, and valence state evolution with high spatial and temporal resolution. Applying newly developed electrochemical liquid cell transmission electron microscopy combined with X-ray absorption spectroscopy, our multimodal operando techniques unveil the formation pathways of OD-Cu active sites from CuO bicrystal nanowire precatalysts. Rapid reduction of CuO directly to Cu within 60 seconds generates a nanocrack network throughout the nanowire, via formation of "boundary nanocracks" along the twin boundary and "transverse nanocracks" propagating from the surface to the center of the nanowire. The nanocrack network further reconstructs, leading to a highly porous structure rich in Cu nanograins, with a boosted specific surface area and density of active sites for C$_{2+}$ products. These findings suggest a means to optimize active OD-Cu nanostructures through nanocracking by tailoring grain boundaries in CuO precatalysts. More generally, our advanced operando approach opens new opportunities for mechanistic insights to enable improved control of catalyst structure and performance.

cond-mat.mtrl-sci↗

arXiv2024

Streaming Large-Scale Electron Microscopy Data to a Supercomputing Facility

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy (NCEM) generates data at a nominal rate of 480 Gbit/s (87,000 frames/s) producing a 700 GB dataset in fifteen seconds. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera's data acquisition (DAQ) system to supercomputing nodes at the National Energy Research Scientific Computing Center (NERSC), bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a post-mortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.

physics.ins-det↗

arXiv2024

Mapping electron beam-induced radiolytic damage in molecular crystals

Every electron crystallography experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive molecular crystals. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space snapshots of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting zones (CDZs) continuously undergoes spatial reorientation as a function of accumulating electron exposure, causing the intensities of many Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the concentric propagation of delocalized radiolytic damage well beyond the initial point of impact. These results sharpen our understanding of molecular crystals as conglomerates of CDZs whose complex lattice structure deteriorates through a series of dynamic internal changes during exposure to ionizing radiation.

cond-mat.mtrl-sci↗

arXiv2024

Accelerating Time-to-Science by Streaming Detector Data Directly into Perlmutter Compute Nodes

Recent advancements in detector technology have significantly increased the size and complexity of experimental data, and high-performance computing (HPC) provides a path towards more efficient and timely data processing. However, movement of large data sets from acquisition systems to HPC centers introduces bottlenecks owing to storage I/O at both ends. This manuscript introduces a streaming workflow designed for an high data rate electron detector that streams data directly to compute node memory at the National Energy Research Scientific Computing Center (NERSC), thereby avoiding storage I/O. The new workflow deploys ZeroMQ-based services for data production, aggregation, and distribution for on-the-fly processing, all coordinated through a distributed key-value store. The system is integrated with the detector's science gateway and utilizes the NERSC Superfacility API to initiate streaming jobs through a web-based frontend. Our approach achieves up to a 14-fold increase in data throughput and enhances predictability and reliability compared to a I/O-heavy file-based transfer workflow. Our work highlights the transformative potential of streaming workflows to expedite data analysis for time-sensitive experiments.

cs.NI↗

arXiv2024

Intrinsic Optical Bistability of Photon Avalanching Nanocrystals

Optically bistable materials respond to a single input with two possible optical outputs, contingent upon excitation history. Such materials would be ideal for optical switching and memory, yet limited understanding of intrinsic optical bistability (IOB) prevents development of nanoscale IOB materials suitable for devices. Here, we demonstrate IOB in Nd3+-doped KPb2Cl5 avalanching nanoparticles (ANPs), which switch with high contrast between luminescent and non-luminescent states, with hysteresis characteristic of bistability. We elucidate a nonthermal mechanism in which IOB originates from suppressed nonradiative relaxation in Nd3+ ions and from the positive feedback of photon avalanching, resulting in extreme, >200th-order optical nonlinearities. Modulation of laser pulsing tunes hysteresis widths, and dual-laser excitation enables transistor-like optical switching. This control over nanoscale IOB establishes ANPs for photonic devices in which light is used to manipulate light.

physics.optics↗

arXiv2024

Uncovering the Three-Dimensional Structure of Upconverting Core-Shell Nanoparticles with Multislice Electron Ptychography

In photon upconverting core-shell nanoparticles, structure strongly dictates performance. Conventional imaging in scanning transmission electron microscopy has sufficient resolution to probe the atomic structure of these nanoparticles, but contrast, dose, and projection limitations make conventional imaging modes insufficient for fully characterizing these structures. Phase retrieval methods provide a promising alternative imaging mode, and in particular, multislice electron ptychography can recover depth-dependent information. Here, we study beam-sensitive photon upconverting core-shell nanoparticles with a multislice ptychography approach using a low electron dose to avoid damage. Large strain fields arise in these heterostructures due to the mismatch in lattice parameter between the core and the shell. We reconstruct both a nanoparticle that appears defect-free and one that has a large break in the side and map the distribution of strain in 3D by computing distortion fields from high-resolution potential images of each slice. In the defect-free nanoparticle, we observe twisting of the shell, while in the broken nanoparticle we measure the 3D position of the crack, the core, and dislocations. These results highlight the advantage of multislice electron ptychography to recover 3D information from a single scan, even under strict electron dose requirements from beam-sensitive samples.

cond-mat.mtrl-sci↗

arXiv2023

Imaging the electron charge density in monolayer MoS2 at the Ångstrom scale

Four-dimensional scanning transmission electron microscopy (4D-STEM) has recently gained widespread attention for its ability to image atomic electric fields with sub-Ångstrom spatial resolution. These electric field maps represent the integrated effect of the nucleus, core electrons and valence electrons, and separating their contributions is non-trivial. In this paper, we utilized simultaneously acquired 4D-STEM center of mass (CoM) images and annular dark field (ADF) images to determine the electron charge density in monolayer MoS2. We find that both the core electrons and the valence electrons contribute to the derived electron charge density. However, due to blurring by the probe shape, the valence electron contribution forms a nearly featureless background while most of the spatial modulation comes from the core electrons. Our findings highlight the importance of probe shape in interpreting charge densities derived from 4D STEM.

cond-mat.mtrl-sci↗

arXiv2023

Three-dimensional atomic positions and local chemical order of medium- and high-entropy alloys

Medium- and high-entropy alloys (M/HEAs) mix multiple principal elements with near-equiatomic composition and represent a paradigm-shift strategy for designing new materials for metallurgy, catalysis, and other fields. One of the core hypotheses of M/HEAs is lattice distortion. However, experimentally determining the 3D local lattice distortion in M/HEAs remains a challenge. Additionally, the presumed random elemental mixing in M/HEAs has been questioned by atomistic simulations, energy dispersive x-ray spectroscopy (EDS), and electron diffraction, which suggest the existence of local chemical order in M/HEAs. However, the 3D local chemical order has eluded direct experimental observation since the EDS elemental maps integrate the composition of atomic columns along the zone axes, and the diffuse reflections/streaks in electron diffraction of M/HEAs may originate from planar defects. Here, we determine the 3D atomic positions of M/HEA nanocrystals using atomic electron tomography, and quantitatively characterize the local lattice distortion, strain tensor, twin boundaries, dislocation cores, and chemical short-range order (CSRO) with unprecedented 3D detail. We find that the local lattice distortion and strain tensor in the HEAs are larger and more heterogeneous than in the MEAs. We observe CSRO-mediated twinning in the MEAs. that is, twinning occurs in energetically unfavoured CSRO regions but not in energetically favoured CSRO ones. This observation confirms the atomistic simulation results of the bulk CrCoNi MEA and represents the first experimental evidence of correlating local chemical order with structural defects in any material system. We expect that this work will not only expand our fundamental understanding of this important class of materials, but also could provide the foundation for tailoring M/HEA properties through lattice distortion and local chemical order.

cond-mat.mtrl-sci↗

arXiv2023

The 4D Camera: an 87 kHz direct electron detector for scanning/transmission electron microscopy

We describe the development, operation, and application of the 4D Camera -- a 576 by 576 pixel active pixel sensor for scanning/transmission electron microscopy which operates at 87,000 Hz. The detector generates data at approximately 480 Gbit/s which is captured by dedicated receiver computers with a parallelized software infrastructure that has been implemented to process the resulting 10 - 700 Gigabyte-sized raw datasets. The back illuminated detector provides the ability to detect single electron events at accelerating voltages from 30 - 300 keV. Through electron counting, the resulting sparse data sets are reduced in size by 10 - 300x compared to the raw data, and open-source sparsity-based processing algorithms offer rapid data analysis. The high frame rate allows for large and complex 4D-STEM experiments to be accomplished with typical STEM scanning parameters.

physics.ins-det↗

arXiv2023

Imaging 3D Chemistry at 1 nm Resolution with Fused Multi-Modal Electron Tomography

Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment completes. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one nanometer resolution in a Au-Fe$_3$O$_4$ metamaterial, Co$_3$O$_4$ - Mn$_3$O$_4$ core-shell nanocrystals, and ZnS-Cu$_{0.64}$S$_{0.36}$ nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99\% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX / EELS) signals. Now sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.

physics.comp-ph↗

arXiv2023

Advanced Techniques in Automated High Resolution Scanning Transmission Electron Microscopy

Scanning transmission electron microscopy is a common tool used to study the atomic structure of materials. It is an inherently multimodal tool allowing for the simultaneous acquisition of multiple information channels. Despite its versatility, however, experimental workflows currently rely heavily on experienced human operators and can only acquire data from small regions of a sample at a time. Here, we demonstrate a flexible pipeline-based system for high-throughput acquisition of atomic-resolution structural data using a custom built sample stage and automation program. The program is capable of operating over many hours without human intervention improving the statistics of high-resolution experiments.

physics.ins-det↗

arXiv2022

Indefinite and Bidirectional Near Infrared Nanocrystal Photoswitching

Materials whose luminescence can be switched by optical stimulation drive technologies ranging from superresolution imaging1-4, nanophotonics5, and optical data storage6-8, to targeted pharmacology, optogenetics, and chemical reactivity9. These photoswitchable probes, including organic fluorophores and proteins, are prone to photodegradation, and often require phototoxic doses of ultraviolet (UV) or visible light. Colloidal inorganic nanoparticles have significant stability advantages over existing photoswitchable materials, but the ability to switch emission bidirectionally, particularly with NIR light, has not been reported with nanoparticles. Here, we present 2-way, near-infrared (NIR) photoswitching of avalanching nanoparticles (ANPs), showing full optical control of upconverted emission using phototriggers in the NIR-I and NIR-II spectral regions useful for subsurface imaging. Employing single-step photodarkening10-13 and photobrightening12,14-18, we demonstrate indefinite photoswitching of individual nanoparticles (>1000 cycles over 7 h) in ambient or aqueous conditions without measurable photodegradation. Critical steps of the photoswitching mechanism are elucidated by modeling and by measuring the photon avalanche properties of single ANPs in both bright and dark states. Unlimited, reversible photoswitching of ANPs enables indefinitely rewritable 2D and 3D multi-level optical patterning of ANPs, as well as optical nanoscopy with sub-Å localization superresolution that allows us to distinguish individual ANPs within tightly packed clusters.

physics.optics↗

arXiv2022

Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high quality tomogram is available within 30 minutes. Real time tomography is integrated into tomviz, an open source and cross platform 3D analysis tool that contains intuitive graphical user interfaces (GUI) to enable any scientist to characterize biological and material structure in 3D.

cond-mat.mtrl-sci↗