Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. Here we develop a workflow based on a machine learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow is universal and can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.
Low-temperature scanning tunneling microscopy is used here to study dynamic bonding of gold atoms on surfaces under low coordination conditions. In the experiments, using an atomically-sharp gold tip, a gold adatom is deposited onto a gold surface with atomic precision either on the first hollow site near a step edge, or far away from it. Classical molecular dynamics simulations at 4.2 K and density functional theory calculations serve to elucidate the difference in the bonding behavior between these two different placements, while also providing information on the crystalline classification o…
Atomically-resolved mappings of the indium composition in InGaN/GaN multi-quantum wellstructures have been obtained by quantifying the contrast in HAADF-STEM. The quantificationprocedure presented here does not rely on computation-intensive simulations, but rather uses EDXmeasurements to calibrate the HAADF-STEM contrast. The histogram of indium compositionsobtained from the mapping provides unique insights into the growth of InGaN: the transitionfrom GaN to InGaN and vice versa occurs in discreet increments of composition; each incrementcorresponds to one monolayer of the interface, indicatin…
Rock-salt lead selenide nanocrystals can be used as building blocks for large scale square superlattices via two-dimensional assembly of nanocrystals at a liquid-air interface followed by oriented attachment. Here we report measurements of the local density of states of an atomically coherent superlattice with square geometry made from PbSe nanocrystals. Controlled annealing of the sample permits the imaging of a clean structure and to reproducibly probe the band gap and the valence hole and conduction electron states. The measured band gap and peak positions are compared to the results of opt…
The physics of ferroelectric domain walls is explored using the Bayesian inference analysis of atomically resolved STEM data. We demonstrate that domain wall profile shapes are ultimately sensitive to the nature of the order parameter in the material, including the functional form of Ginzburg-Landau-Devonshire expansion, and numerical value of the corresponding parameters. The preexisting materials knowledge naturally folds in the Bayesian framework in the form of prior distributions, with the different order parameters forming competing (or hierarchical) models. Here, we explore the physics o…
Order and randomness in dopant distributions: exploring the thermodynamics of solid solutions from atomically resolved imaging
作为掺杂剂浓度的函数的结构-性质关系的探索通常基于固溶体的平均场论。然而，这些理论在半导体中很好地工作，在具有强相关性的材料中往往会失败，无论是在电子行为还是化学分离方面。在这些情况下，原子排列的细节通常不会被探索和分析。材料的生成物理和化学的知识可以解决这个问题，因为可以生成作为原子级结构的随机表示的缺陷配置库，或者可以导出介观热力学模型的参数。为了获得这些信息，以改进预测，我们使用原子分辨的显微图像，可视化系统内复杂的结构相关性，并将其转化为结构形成的统计力学模型的数据。鉴于材料加工历史的微观方面存在显著的不确定性，以及可用图像的数量有限，我们将模型优化技术与统计假设检验的原则相结合。我们证明了从一系列的原子分辨扫描透射电子显微镜图像的Mo $_x$ Re $_{1-x}$ S $_2$在不同比例的Mo/Re化学计量的数据上的方法，为此，我们提出了一个有效的相互作用模型，然后用于生成原子配置，并在一系列的浓度和形成温度进行可测试的预测。
The development of high-resolution imaging methods such as electron and scanning probe microscopy and atomic probe tomography have provided a wealth of information on structure and functionalities of solids. The availability of this data in turn necessitates development of approaches to derive quantitative physical information, much like the development of scattering methods in the early XX century which have given one of the most powerful tools in condensed matter physics arsenal. Here, we argue that this transition requires adapting classical macroscopic definitions, that can in turn enable …
Composition-Driven Phase Evolution in Sm-Doped BiFeO3 via Latent-Field Reconstruction of Atomically Resolved STEM Data
University of Tennessee（田纳西大学）；Oak Ridge National Laboratory（橡树岭国家实验室）；National Academy of Sciences of Ukraine（乌克兰国家科学院）；Frantsevich Institute for Problems of Materials Science（弗兰采维奇材料科学问题研究所）；University of Maryland（马里兰大学）
We demonstrate the existence of atomically-sized topological solitons in a quasi one-dimensional charge density wave system: indium atomic wires on Si(111). Performing joint scanning tunneling microscopy and density-functional calculations, we show that the Si(111)-(8x2)In surface features two conceptually different types of abrupt phase flip structures. One is caused by In adatoms and is, hence, non-solitonic in nature. The other one is an abrupt left-chiral soliton.
Atom probe tomography (APT) helps elucidate the link between the nanoscale chemical variations and physical properties, but it has limited structural resolution. Field ion microscopy (FIM), a predecessor technique to APT, is capable of attaining atomic resolution along certain sets of crystallographic planes albeit at the expense of elemental identification. We demonstrate how two commercially-available atom probe instruments, one with a straight flight path and one fitted with a reflectron-lens, can be used to acquire time-of-flight mass spectrometry data concomitant with a FIM experiment. We…
Atomically resolved intrinsic superconducting gap in (La,Pr)3Ni2O7 films
Southern University of Science and Technology（南方科技大学）；Quantum Science Center of Guangdong-Hong Kong-Macao Greater Bay Area（粤港澳大湾区量子科学中心）；Shanghai Jiao Tong University（上海交通大学）；Tsinghua University（清华大学）
Quasiparticle interference on the surface of 3D topological insulator Bi$_{2}$Se$_{3}$ induced by cobalt adatom in the absence of ferromagnetic ordering
用扫描隧道显微镜、角分辨光电子能谱和X射线磁圆二色性研究了钴原子在拓扑绝缘体Bi $_{2}$ Se $_{3}$表面引起的准粒子干涉.研究发现，Co原子被选择性地吸附在Se位的顶部，并在表面作为强散射体，产生各向异性的驻波。一个长程磁序被发现是缺席的，和表面状态狄拉克锥保持无隙。驻波的各向异性归因于未占据态的严重翘曲的等能轮廓，其中散射由于非零的面外自旋而被允许。
Atomically Resolved Acoustic Dynamics Coupled with Magnetic Order in a van der Waals Antiferromagnet
Materials Science Division, Argonne National Laboratory（阿贡国家实验室材料科学部）；Department of Physics, University of Washington（华盛顿大学物理系）；Center for Ultrafast Phase Transformation, Department of Physics, Sogang University（西江大学物理系超快相变中心）；Department of Materials Science and Engineering, University of Washington（华盛顿大学材料科学与工程系）；Pohang Accelerator Laboratory, POSTECH（韩国科学技术院浦项加速器实验室）；Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, The University of Edinburgh（爱丁堡大学物理与天文学学院凝聚态与复杂系统研究所）；Donostia International Physics Center（圣塞巴斯蒂安国际物理中心）；Department of Physics, Cambridge, Massachusetts Institute of Technology（麻省理工学院物理系）；Departments of Physics and Applied Physics, Stanford University（斯坦福大学物理与应用物理系）
Aurivillius ferroelectric $Bi_2WO_6$ (BWO) encompasses a broad range of functionalities, including robust fatigue-free ferroelectricity, high photocatalytic activity, and ionic conductivity. Despite these promising characteristics, an in-depth study on the growth of BWO thin films and ferroelectric characterization, especially at the atomic scale, is still lacking. Here, we report pulsed laser deposition (PLD) of BWO thin films on (001) $SrTiO_3$ substrates and characterization of ferroelectricity using the scanning transmission electron microscopy (STEM) and piezoresponse force microscopy (PF…
Analyzing atomically resolved images is a time-consuming process requiring solid experience and substantial human intervention. In addition, the acquired images contain a large amount of information such as crystal structure, presence and distribution of defects, and formation of domains, which need to be resolved to understand a material's surface structure. Therefore, machine learning techniques have been applied in scanning probe and electron microscopies during the last years, aiming for automatized and efficient image analysis. This work introduces a free and open source tool (AiSurf: Aut…
The emergence of transition metal dichalcogenides (TMD) as crystalline atomically thin semiconductors has created a tremendous amount of scientific and technological interest. Many novel device concepts have been proposed and realized (1-3). Nonetheless, progress in k-space investigations of ground/excited state electronic structures has been slow due to the challenge to create large scale, laterally homogeneous samples. Taking advantage of recent advancements in chemical vapor deposition, here we create a wafer-size MoS2 monolayer with well-aligned lateral orientation for advanced electron sp…
Spin- and angle-resolved photoemission studies of the electronic structure of Si(110)"16x2" surfaces
用自旋和角分辨光电子能谱研究了Si（110）“16 × 2”双畴、单畴和1 × 1表面的电子结构。使用水平和垂直偏振的60 eV和80 eV光子进行角分辨光电发射。带色散图显示了四个表面状态（$S_1$到$S_4$），这些状态被分配给硅悬挂键的基础上测得的结合能和水平和垂直光偏振之间的光发射强度变化。在Si（110）“16 × 2”重构中观察到的三种表面态（$S_1$、$S_2$和$S_4$）被分配给存在于波纹状平台结构边缘的Si吸附原子和Si原子。在Si（110）“16 x 2”和1 x 1能带图中仅观察到四种表面态之一，$S_3$，因此归因于作为Si（110）“16 x 2”和1 x 1表面的组分的普遍Si之字形链。体带区域中的状态归因于面内键。所有数据与Si（110）“16 × 2”表面的原子屈曲模型一致。虽然$P_y$和$P_z$的室温测量值在统计学上与零相容，但对映体A型和B型Si（110）“16 x 2”表面的$P_x$测量值给出了约1.5%的小平均偏振，其符号相反。在77 K下对A型Si（110）“16 x 2”表面的进一步测量给出了+0.3\%的较小值。因此，对于纵向极化，可以采用$\sim1\%$的上限。
Atomically precise triple-step staircase on a vicinal silicon surface: Is it Si(5 5 7), Si(7 7 10) or Si(8 8 11)?
Osipyan Institute of Solid State Physics Russian Academy of Sciences（俄罗斯科学院奥西皮扬固体物理研究所）；Institute for Physics of Microstructures Russian Academy of Sciences（俄罗斯科学院微结构物理研究所）；Center for Advanced Mesoscience and Nanotechnology, Moscow Institute of Physics and Technology（莫斯科物理技术学院先进介观与纳米技术中心）；Lobachevsky State University of Nizhny Novgorod（下诺夫哥罗德罗巴切夫斯基国立大学）；National Research University Higher School of Economics (HSE University)（国立研究高等经济学院）
Excitonic emission from atomically precise graphene nanoribbons (GNRs) synthesised on a metal surface is probed with atomic-scale spatial resolution using a scanning tunneling microscopy (STM) approach. A STM-based strategy to transfer the GNRs to a partially insulating surface is used to prevent light emission quenching of the ribbons by the metal substrate. Sub-nanometer resolved STM-induced fluorescence spectra reveal emission from localized dark excitons build upon the topological end states of the GNRs. A low frequency vibronic emission comb whose characteristics change with the GNR lengt…
AtomAI is an open-source software package bridging instrument-specific Python libraries, deep learning, and simulation tools into a single ecosystem. AtomAI allows direct applications of the deep convolutional neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically-resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of …
We suggest and implement an approach for the bottom-up description of systems undergoing large-scale structural changes and chemical transformations from dynamic atomically resolved imaging data, where only partial or uncertain data on atomic positions are available. This approach is predicated on the synergy of two concepts, the parsimony of physical descriptors and general rotational invariance of non-crystalline solids, and is implemented using a rotationally-invariant extension of the variational autoencoder applied to semantically segmented atom-resolved data seeking the most effective re…
