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Mar 4

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use

Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution electron microscopy offers a potential source of structural data, converting these images into simulation-ready formats remains labor-intensive and error-prone, creating a bottleneck for model training and validation. We introduce AutoMat, an end-to-end, agent-assisted pipeline that automatically transforms scanning transmission electron microscopy (STEM) images into atomic crystal structures and predicts their physical properties. AutoMat combines pattern-adaptive denoising, physics-guided template retrieval, symmetry-aware atomic reconstruction, fast relaxation and property prediction via MatterSim, and coordinated orchestration across all stages. We propose the first dedicated STEM2Mat-Bench for this task and evaluate performance using lattice RMSD, formation energy MAE, and structure-matching success rate. By orchestrating external tool calls, AutoMat enables a text-only LLM to outperform vision-language models in this domain, achieving closed-loop reasoning throughout the pipeline. In large-scale experiments over 450 structure samples, AutoMat substantially outperforms existing multimodal large language models and tools. These results validate both AutoMat and STEM2Mat-Bench, marking a key step toward bridging microscopy and atomistic simulation in materials science.The code and dataset are publicly available at https://github.com/yyt-2378/AutoMat and https://huggingface.co/datasets/yaotianvector/STEM2Mat.

  • 17 authors
·
May 18, 2025 2

STEM: Scaling Transformers with Embedding Modules

Fine-grained sparsity promises higher parametric capacity without proportional per-token compute, but often suffers from training instability, load balancing, and communication overhead. We introduce STEM (Scaling Transformers with Embedding Modules), a static, token-indexed approach that replaces the FFN up-projection with a layer-local embedding lookup while keeping the gate and down-projection dense. This removes runtime routing, enables CPU offload with asynchronous prefetch, and decouples capacity from both per-token FLOPs and cross-device communication. Empirically, STEM trains stably despite extreme sparsity. It improves downstream performance over dense baselines while reducing per-token FLOPs and parameter accesses (eliminating roughly one-third of FFN parameters). STEM learns embedding spaces with large angular spread which enhances its knowledge storage capacity. More interestingly, this enhanced knowledge capacity comes with better interpretability. The token-indexed nature of STEM embeddings allows simple ways to perform knowledge editing and knowledge injection in an interpretable manner without any intervention in the input text or additional computation. In addition, STEM strengthens long-context performance: as sequence length grows, more distinct parameters are activated, yielding practical test-time capacity scaling. Across 350M and 1B model scales, STEM delivers up to ~3--4% accuracy improvements overall, with notable gains on knowledge and reasoning-heavy benchmarks (ARC-Challenge, OpenBookQA, GSM8K, MMLU). Overall, STEM is an effective way of scaling parametric memory while providing better interpretability, better training stability and improved efficiency.

  • 8 authors
·
Jan 15 1

Imaging and controlling electron motion and chemical structural dynamics of biological system in real time and space

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

  • 7 authors
·
Oct 2, 2025

Toward quantitative fractography using convolutional neural networks

The science of fractography revolves around the correlation between topographic characteristics of the fracture surface and the mechanisms and external conditions leading to their creation. While being a topic of investigation for centuries, it has remained mostly qualitative to date. A quantitative analysis of fracture surfaces is of prime interest for both the scientific community and the industrial sector, bearing the potential for improved understanding on the mechanisms controlling the fracture process and at the same time assessing the reliability of computational models currently being used for material design. With new advances in the field of image analysis, and specifically with machine learning tools becoming more accessible and reliable, it is now feasible to automate the process of extracting meaningful information from fracture surface images. Here, we propose a method of identifying and quantifying the relative appearance of intergranular and transgranular fracture events from scanning electron microscope images. The newly proposed method is based on a convolutional neural network algorithm for semantic segmentation. The proposed method is extensively tested and evaluated against two ceramic material systems (Al_2O_3,MgAl_2O_4) and shows high prediction accuracy, despite being trained on only one material system (MgAl_2O_4). While here attention is focused on brittle fracture characteristics, the method can be easily extended to account for other fracture morphologies, such as dimples, fatigue striations, etc.

  • 3 authors
·
Aug 1, 2019

Creation of single vacancies in hBN with electron irradiation

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of two-dimensional materials. The displacement cross sections of monolayer hBN are measured using aberration-corrected scanning transmission electron microscopy in near ultra-high vacuum at primary beam energies between 50 and 90 keV. Damage rates below 80 keV are up to three orders of magnitude lower than previously measured at edges under poorer residual vacuum conditions where chemical etching appears to have been dominant. Notably, is possible to create single vacancies in hBN using electron irradiation, with boron almost twice as likely as nitrogen to be ejected below 80 keV. Moreover, any damage at such low energies cannot be explained by elastic knock-on, even when accounting for vibrations of the atoms. A theoretical description is developed to account for lowering of the displacement threshold due to valence ionization resulting from inelastic scattering of probe electrons, modelled using charge-constrained density functional theory molecular dynamics. Although significant reductions are found depending on the constrained charge, quantitative predictions for realistic ionization states are currently not possible. Nonetheless, there is potential for defect-engineering of hBN at the level of single vacancies using electron irradiation.

  • 9 authors
·
Mar 1, 2023

Microscale stress-geometry interactions in an additively manufactured NiTi cardiovascular stent: A synchrotron dual imaging tomography and diffraction study

This study explores cardiovascular stents fabricated using laser powder bed fusion (LPBF); an emerging method to offer patient-specific customisable parts. Here, the shape memory alloy NiTi, in a near equiatomic composition, was investigated to deconvolve the material response from macroscopic component effects. Specifically, stress-geometry interactions were revealed, in-situ, for a minaturised cardiovascular stent subjected to an externally applied cylindrical stress whilst acquiring synchrotron X-ray imaging and diffraction data. The approach enabled the collection of spatially resolved micromechanical deformation data; the formation of stress-induced martensite and R-phase was evident, occurring in locations near junctions between stent ligaments where stress concentrations exist. In the as-fabricated condition, hardness maps were obtained through nanoindentation, demonstrating that the localised deformation and deformation patterning is further controlled by porosity and microstructural heterogeneity. Electron backscatter diffraction (EBSD) supported these observations, showing a finer grain structure near stent junctions with higher associated lattice curvature. These features, combined with stress concentrations when loaded will initiate localised phase transformations. If the stent was subjected to repeated loading, representing in-vivo conditions, these regions would be susceptible to cyclic damage through transformation memory loss, leading to premature component failure. This study highlights the challenges that must be addressed for the post-processing treatment of LABF-processed stents for healthcare-related applications.

  • 11 authors
·
Dec 12, 2023

Foundation Models for Zero-Shot Segmentation of Scientific Images without AI-Ready Data

Zero-shot and prompt-based technologies capitalized on using frequently occurring images to transform visual reasoning tasks, which explains why such technologies struggle with valuable yet scarce scientific image sets. In this work, we propose Zenesis, a comprehensive no-code interactive platform designed to minimize barriers posed by data readiness for scientific images. We develop lightweight multi-modal adaptation techniques that enable zero-shot operation on raw scientific data, along with human-in-the-loop refinement and heuristic-based temporal enhancement options. We demonstrate the performance of our approach through comprehensive comparison and validation on challenging Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) data of catalyst-loaded membranes. Zenesis significantly outperforms baseline methods, achieving an average accuracy of 0.947, an Intersection over Union (IOU) of 0.858, and a Dice score of 0.923 for amorphous catalyst samples and accuracy of 0.987, an IOU of 0.857, and a Dice score of 0.923 for crystalline samples. These results mark a substantial improvement over traditional methods like Otsu thresholding and even advanced models like Segment Anything Model (SAM) when used in isolation. Our results demonstrate that Zenesis is a powerful tool for scientific applications, particularly in fields where high-quality annotated datasets are unavailable, accelerating accurate analysis of experimental imaging.

  • 7 authors
·
Jun 30, 2025

Analytical simulations of the resonant transmission of electrons in a closed nanocircuit for terahertz applications where a tunneling junction is shunted by a metallic nanowire

Earlier, in the CINT program at Los Alamos National Laboratory, we focused ultrafast mode-locked lasers on the tip-sample junction of a scanning tunneling microscope to generate currents at hundreds of harmonics of the laser pulse repetition frequency. Each harmonic has a signal-to-noise ratio of 20 dB with a 10-dB linewidth of only 3 Hz. Now we model closed quantum nanocircuits with rectangular, triangular, or delta-function barrier, shunted by a beryllium filament for quasi-coherent electron transport over mean-free paths as great as 68 nm. The time-independent Schrödinger equation is solved with the boundary conditions that the wavefunction and its derivative are continuous at both connections. These four boundary conditions are used to form a four-by-four complex matrix equation with only zeros in the right-hand column vector which is required to have a non-trivial solution with each of the closed nanocircuits. Each model has four parameters: (1) the barrier length, (2) the height and shape of the barrier, (3) the length of the pre-barrier, and (4) the electron energy. Any three of these may be specified and then the fourth is varied to bring the determinant to zero to find the solutions on lines or surfaces in the space defined by the four parameters. First, we use a simplistic model having a rectangular barrier. The second model has a triangular barrier as a first approximation to field emission, and we are considering applying this approach for a self-contained nanoscale extension of our earlier effort to generate the harmonics at Los Alamos. The third model has a delta-function barrier, and the fourth model is an extension of the first one where the width of the rectangular barrier is varied inversely with its height.

  • 1 authors
·
Oct 24, 2023

UniEM-3M: A Universal Electron Micrograph Dataset for Microstructural Segmentation and Generation

Quantitative microstructural characterization is fundamental to materials science, where electron micrograph (EM) provides indispensable high-resolution insights. However, progress in deep learning-based EM characterization has been hampered by the scarcity of large-scale, diverse, and expert-annotated datasets, due to acquisition costs, privacy concerns, and annotation complexity. To address this issue, we introduce UniEM-3M, the first large-scale and multimodal EM dataset for instance-level understanding. It comprises 5,091 high-resolution EMs, about 3 million instance segmentation labels, and image-level attribute-disentangled textual descriptions, a subset of which will be made publicly available. Furthermore, we are also releasing a text-to-image diffusion model trained on the entire collection to serve as both a powerful data augmentation tool and a proxy for the complete data distribution. To establish a rigorous benchmark, we evaluate various representative instance segmentation methods on the complete UniEM-3M and present UniEM-Net as a strong baseline model. Quantitative experiments demonstrate that this flow-based model outperforms other advanced methods on this challenging benchmark. Our multifaceted release of a partial dataset, a generative model, and a comprehensive benchmark -- available at huggingface -- will significantly accelerate progress in automated materials analysis.

  • 11 authors
·
Aug 22, 2025

Measuring Casimir Force Across a Superconducting Transition

The Casimir effect and superconductivity are foundational quantum phenomena whose interaction remains an open question in physics. How Casimir forces behave across a superconducting transition remains unresolved, owing to the experimental difficulty of achieving alignment, cryogenic environments, and isolating small changes from competing effects. This question carries implications for electron physics, quantum gravity, and high-temperature superconductivity. Here we demonstrate an on-chip superconducting platform that overcomes these challenges, achieving one of the most parallel Casimir configurations to date. Our microchip-based cavities achieve unprecedented area-to-separation ratio between plates, exceeding previous Casimir experiments by orders of magnitude and generating the strongest Casimir forces yet between compliant surfaces. Scanning tunneling microscopy (STM) is used for the first time to directly detect the resonant motion of a suspended membrane, with subatomic precision in both lateral positioning and displacement. Such precision measurements across a superconducting transition allow for the suppression of all van der Waals, electrostatic, and thermal effects. Preliminary measurements suggest superconductivity-dependent shifts in the Casimir force, motivating further investigation and comparison with theories. By uniting extreme parallelism, nanomechanics, and STM readout, our platform opens a new experimental frontier at the intersection of Casimir physics and superconductivity.

  • 7 authors
·
Apr 14, 2025

Towards Efficient and Intelligent Laser Weeding: Method and Dataset for Weed Stem Detection

Weed control is a critical challenge in modern agriculture, as weeds compete with crops for essential nutrient resources, significantly reducing crop yield and quality. Traditional weed control methods, including chemical and mechanical approaches, have real-life limitations such as associated environmental impact and efficiency. An emerging yet effective approach is laser weeding, which uses a laser beam as the stem cutter. Although there have been studies that use deep learning in weed recognition, its application in intelligent laser weeding still requires a comprehensive understanding. Thus, this study represents the first empirical investigation of weed recognition for laser weeding. To increase the efficiency of laser beam cut and avoid damaging the crops of interest, the laser beam shall be directly aimed at the weed root. Yet, weed stem detection remains an under-explored problem. We integrate the detection of crop and weed with the localization of weed stem into one end-to-end system. To train and validate the proposed system in a real-life scenario, we curate and construct a high-quality weed stem detection dataset with human annotations. The dataset consists of 7,161 high-resolution pictures collected in the field with annotations of 11,151 instances of weed. Experimental results show that the proposed system improves weeding accuracy by 6.7% and reduces energy cost by 32.3% compared to existing weed recognition systems.

  • 8 authors
·
Feb 10, 2025

Logics-STEM: Empowering LLM Reasoning via Failure-Driven Post-Training and Document Knowledge Enhancement

We present Logics-STEM, a state-of-the-art reasoning model fine-tuned on Logics-STEM-SFT-Dataset, a high-quality and diverse dataset at 10M scale that represents one of the largest-scale open-source long chain-of-thought corpora. Logics-STEM targets reasoning tasks in the domains of Science, Technology, Engineering, and Mathematics (STEM), and exhibits exceptional performance on STEM-related benchmarks with an average improvement of 4.68% over the next-best model at 8B scale. We attribute the gains to our data-algorithm co-design engine, where they are jointly optimized to fit a gold-standard distribution behind reasoning. Data-wise, the Logics-STEM-SFT-Dataset is constructed from a meticulously designed data curation engine with 5 stages to ensure the quality, diversity, and scalability, including annotation, deduplication, decontamination, distillation, and stratified sampling. Algorithm-wise, our failure-driven post-training framework leverages targeted knowledge retrieval and data synthesis around model failure regions in the Supervised Fine-tuning (SFT) stage to effectively guide the second-stage SFT or the reinforcement learning (RL) for better fitting the target distribution. The superior empirical performance of Logics-STEM reveals the vast potential of combining large-scale open-source data with carefully designed synthetic data, underscoring the critical role of data-algorithm co-design in enhancing reasoning capabilities through post-training. We make both the Logics-STEM models (8B and 32B) and the Logics-STEM-SFT-Dataset (10M and downsampled 2.2M versions) publicly available to support future research in the open-source community.

  • 19 authors
·
Jan 4