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A measurement technique is described which has the potential to map the atomic site occupancies of ultracold atoms in a short-period three-dimensional optical lattice. The method uses accordion and pinning lattices, together with…

Quantum Gases · Physics 2013-05-29 Martin Shotter

Atomic force microscopy (AFM) is a key tool for characterising nanoscale structures, with functionalised tips now offering detailed images of the atomic structure. In parallel, AFM simulations using the particle probe model provide a…

Materials Science · Physics 2025-09-03 Jie Huang , Niko Oinonen , Fabio Priante , Filippo Federici Canova , Lauri Kurki , Chen Xu , Adam S. Foster

Three-dimensional volumetric imaging of cells allows for in situ visualization, thus preserving contextual insights into cellular processes. Despite recent advances in machine learning methods, morphological analysis of sub-nuclear…

Quantitative Methods · Quantitative Biology 2022-07-21 Niraj Gupta , Eric J. Roberts , Song Pang , C. Shan Xu , Harald F. Hess , Fan Wu , Abby Dernburg , Danielle Jorgens , Petrus H. Zwart , Vignesh Kasinath

Due to the rapid temporal and fine-grained nature of complex human assembly atomic actions, traditional action segmentation approaches requiring the spatial (and often temporal) down sampling of video frames often loose vital fine-grained…

Computer Vision and Pattern Recognition · Computer Science 2022-11-28 Matthew Kent Myers , Nick Wright , Stephen McGough , Nicholas Martin

Programmable electron-beam scanning offers new opportunities to improve dose efficiency and suppress scan-induced artifacts in scanning transmission electron microscopy. Here, we systematically benchmark the impact of non-raster…

Cryo-electron microscopy (cryo-EM) is a powerful imaging technique for reconstructing three-dimensional molecular structures from noisy tomographic projection images of randomly oriented particles. We introduce a new data fusion framework,…

Computer Vision and Pattern Recognition · Computer Science 2025-12-15 Joe Kileel , Oscar Mickelin , Amit Singer , Sheng Xu

Discrete Element Methods (DEM), i.e.~the simulation of many rigid particles, suffer from very stiff differential equations plus multiscale challenges in space and time. The particles move smoothly through space until they interact almost…

Mathematical Software · Computer Science 2023-09-28 Peter Noble , Tobias Weinzierl

The ongoing development of single electron, nano and atomic scale semiconductor devices would benefit greatly from a characterization tool capable of detecting single electron charging events with high spatial resolution, at low…

Mesoscale and Nanoscale Physics · Physics 2024-03-22 José Bustamante , Yoichi Miyahara , Logan Fairgrieve-Park , Kieran Spruce , Patrick See , Neil Curson , Taylor Stock , Peter Grutter

Three-dimension real-time tracking of single emitters is an emerging tool for assessment of biological behavior as intraneuronal transport, for which spatiotemporal resolution is crucial to understand the microscopic interactions between…

Scanning Transmission Electron Microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In…

Instrumentation and Detectors · Physics 2019-01-15 Xin Li , Ondrej Dyck , Sergei V. Kalinin , Stephen Jesse

Resolving the locations and discriminating the spin states of individual trapped ions with high fidelity is critical for a large class of applications in quantum computing, simulation, and sensing. We report on a method for high-fidelity…

(Scanning) transmission electron microscopy ((S)TEM) has significantly advanced materials science but faces challenges in correlating precise atomic structure information with the functional properties of devices due to its time-intensive…

Optical absorption imaging has become a common technique for detecting the density distribution of ultracold atoms. The defocus effect generally produces artificial spatial structures in the obtained images, which confuses our understanding…

Atomic Physics · Physics 2019-03-27 Tianyou Gao , Dongfang Zhang , Lingran Kong , Ruizong Li , Kaijun Jiang

Recent advances in scanning transmission electron microscopy (STEM) allow to observe solid-state transformations and reactions in materials induced by thermal stimulus or electron beam on the atomic level. However, despite the rate at which…

Materials Science · Physics 2019-11-26 Maxim Ziatdinov , Ondrej Dyck , Stephen Jesse , Sergei V. Kalinin

Transmission electron microscopy (TEM) has reached ~ 50 picometer resolution in a high vacuum, enabling single-atom sensitive imaging of nanomaterials. Extending this capability to gaseous environments would allow for similar visualizations…

We present a method using Zernike moments for quantifying rotational and reflectional symmetries in scanning transmission electron microscopy (STEM) images, aimed at improving structural analysis of materials at the atomic scale. This…

Materials Science · Physics 2024-05-29 Jiadong Dan , Cheng Zhang , Xiaoxu Zhao , N. Duane Loh

Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural…

Machine Learning · Computer Science 2019-02-13 Kui Xu , Zhe Wang , Jiangping Shi , Hongsheng Li , Qiangfeng Cliff Zhang

Determining the three-dimensional structure of proteins and protein complexes at atomic resolution is a fundamental task in structural biology. Over the last decade, remarkable progress has been made using "single particle" cryo-electron…

Numerical Analysis · Mathematics 2017-06-05 Alex Barnett , Leslie Greengard , Andras Pataki , Marina Spivak

We present an advanced scanning probe microscopy system enhanced with artificial intelligence (AI-SPM) designed for self-driving atomic-scale measurements. This system expertly identifies and manipulates atomic positions with high…

Computational Physics · Physics 2024-04-18 Zhuo Diao , Keiichi Ueda , Linfeng Hou , Fengxuan Li , Hayato Yamashita , Masayuki Abe

In this paper, we propose a new generic method for detecting the number and locations of structural breaks or change points in piecewise linear models under stationary Gaussian noise. Our method transforms the change point detection problem…

Methodology · Statistics 2026-01-14 Zhibing He , Dan Cheng , Yunpeng Zhao