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Capturing 3D atomic defects and phonon localization at the 2D heterostructure interface

September 15, 2021|

2D lateral and vertical heterostructures have been actively studied for fundamental interest and practical applications. Although aberration-corrected electron microscopy and scanning probe microscopy have been used to characterize a wide range of 2D heterostructures, the 3D local atomic structure and crystal defects at the heterostructure interface have thus far defied any direct experimental determination. Now, a collaborative team from UCLA, Harvard University, MIT and UC Irvine demonstrates a correlative experimental and first principles method to determine the 3D atomic positions and crystal defects in a MoS2-WSe2 heterojunction with picometer prevision and capture the localized vibrational properties at the epitaxial interface. They observe various crystal defects, including vacancies, substitutional defects, bond distortion and atomic-scale ripples, and quantitatively characterize the 3D atomic displacements and full strain tensor across the heterointerface. The experimentally measured 3D atomic coordinates, representing a metastable state of the  heterojunction, are used as direct input to first principles calculations to reveal new phonon modes localized at the heterointerface, which are corroborated by spatially resolved electron energy-loss spectroscopy. In contrast, the phonon dispersion derived from the minimum energy state of the  heterojunction is absent of the local interface phonon modes, indicating the importance of using experimental 3D atomic coordinates as direct input to better predict the properties of heterointerfaces. Looking forward, it is expected that the ability to couple the 3D atomic structures and crystal defects with the properties of heterostructure interfaces will transform materials design and engineering across different disciplines.

X. TianX. YanG. VarnavidesY. YuanD. S. KimC. J. CiccarinoP. AnikeevaM. LiL. LiP. NarangX. PanJ. Miao, "Capturing 3D atomic defects and phonon localization at the 2D heterostructure interface," Science Advances7eabi6699(2021). DOI: 10.1126/sciadv.abi6699

Revealing trimer cluster superstructures at ultrafast timescales in TaTe2

July 2, 2021|

Understanding and controlling the forces that drive the formation of symmetry-broken phases in quantum materials is a key challenge in condensed matter physics. The nature of the correlated interplay between charge, spin, and lattice degrees of freedom, however, often remains hidden in equilibrium studies where adiabatic tuning masks the causal ordering of rapid interactions. This motivates the use of ultrafast electron diffraction (UED) to capture structural dynamics on intrinsic time scales, for insight into the role of atomic-scale lattice distortions and vibrational excitations in driving, stabilizing and ultimately controlling emergent phases.

In a recent publication, a STROBE team carried out the first-ever ultrafast study of tantalum telluride (TaTe2), yielding direct insight into its structural dynamics. The material exhibits unique periodic charge and lattice trimer order, which transitions from stripe-like chains into a (3×3) superstructure of trimer clusters at low temperatures. After cooling to 10 K, the thin crystalline films were optically excited and the structural dynamics was probed with the high-brightness electron bunches. Satellite peaks as well as sign changes in the complex diffraction patterns yield a fingerprint of the periodic order and structural transition. Our experiments captured the photo-induced melting of the trimer clusters in TaTe2, evidencing an ultrafast phase transition into the stripe-like phase on a ~1.4 ps time scale. Subsequently, thermalization into a hot cluster superstructure occurred. Density-functional calculations indicate that the initial quench is triggered by intra-trimer Ta charge transfer, which destabilizes the clusters unlike CDW melting in other TaX2 compounds.

Critical to this project were new methods and algorithms, enhanced microscopes and samples, advanced sample preparation as well as a unique high repetition rate ultrafast electron diffraction beamline utilized by the STROBE team from UC Berkeley, LBNL and UCLA

K. M. SiddiquiD. B. DurhamF. CroppC. OphusS. RajpurohitY. ZhuJ. D. CarlströmC. StavrakasZ. MaoA. RajaP. MusumeciL. Z. TanA. M. MinorD. FilippettoR. A. Kaindl, "Ultrafast optical melting of trimer superstructure in layered 1T′-TaTe2," Communications Physics4(2021). DOI: 10.1038/s42005-021-00650-z

2D vibrational exciton nano-imaging of domain formation in self-assembled monolayer

June 22, 2021|

Understanding the chemical and physical properties of surfaces at the molecular level is highly relevant in the fields of medicine, semiconductors, batteries, etc. where precise atomic level control of determines materials and device performance. In particular, molecular order and domains affect many of the desired functional properties with carrier transport, wettability, and chemical reactivity often controlled by intermolecular coupling. However, both imaging of molecular surfaces and spectroscopy of molecular coupling has long been challenged by limited chemically specific contrast, spatial resolution, sensitivity, and precision. In this work, a team of  STROBE researchers demonstrate vibrational excitons as a molecular ruler of intermolecular coupling and quantum sensor for wave function delocalization to image nanodomain formation in self-assembled monolayers. In novel precision spatio-spectral infrared scattering scanning near-field optical microscopy combined with theoretical modelling few nanometer domain sizes and their distribution across micron scale fields of view could be resolved. This approach of vibrational exciton nanoimaging is generally applicable to study structural phases and domains in a wide range of molecular interfaces and the method can be used for engineering better molecular interfaces, with controlled properties for molecular electronic, photonic, or biomedical applications.

T. P. GrayJ. NishidaS. C. JohnsonM. B. Raschke, "2D Vibrational Exciton Nanoimaging of Domain Formation in Self-Assembled Monolayers," Nano Letters215754-5759(2021). DOI: 10.1021/acs.nanolett.1c01515

New phase retrieval methods enabled by the world’s fastest electron detector

May 19, 2021|

The need for rapid and accurate image analysis is increasing in electron microscopy studies of nanomaterials. With newly developed fast, high-efficiency electron detectors and automated imaging protocols, incorporating electron microscopy into high throughput materials design efforts is becoming possible. These new capabilities strongly motivate automated methods to extract relevant structural features, such as nanoparticle size, shape, and defect content, from high resolution transmission electron microscopy (HRTEM) data to link these features to bulk properties and study the influence of heterogeneity on bulk behavior. In general, protocols that surpass the accuracy of traditional image analysis and do not require time-consuming manual analysis are needed. Recent advances in image interpretation using deep learning using machine learning make it a promising route toward automatic interpretation of HRTEM micrographs.

In this STROBE collaboration, we demonstrate a pipeline to detect and classify regions of interest in HRTEM micrographs. Our pipeline uses a convolutional neural net (CNN) to identify crystalline regions (nanoparticles) from an amorphous background in the images, and then feeds individual regions of interest into a random forest classifier to detect whether or not they contain a crystallographic defect. Our CNN has a lightweight U-Net architecture and accurately segments a diverse population of nanoparticles with only a small number of training images. After segmentation, individual nanoparticle regions can be isolated and fed directly into existing python tools to extract size and shape statistics. To detect the presence of defects in nanoparticle regions, we implement a random forest classifier. We demonstrated the random forest classifier’s ability to detect stacking faults in the CdSe subset of identified nanoparticles. Both the CNN and classifier demonstrate state of the art performance at their respective tasks. While this work focuses on HRTEM images of nanoparticles supported on a carbon substrate, in principle the tool can be used to detect any regions of crystallinity in HRTEM data.

K. Groschner, C. Choi, M. C. Scott, “Machine Learning Pipeline for Segmentation and Defect Identification from High-Resolution Transmission Electron Microscopy Data,” Microscopy and Microanalysis, 1-8, (2021).

Compressive and adaptive nano imaging for enhanced speed and content

May 18, 2021|

Scattering scanning near-field optical microscopy (s-SNOM) provides for spectroscopic imaging from molecular to quantum materials with few nanometer deep sub-diffraction limited spatial resolution. However, conventional acquisition methods are often too slow to fully capture a large field of view spatio-spectral dataset. Through this collaboration, STROBE researchers, at CU Boulder and the ALS –Berkeley, demonstrated how the data acquisition time and sampling rate can be significantly reduced while maintaining or even enhancing the physical or chemical image information content. The novel data acquisition and mathematical concepts implemented are based on advanced data compressed sampling, matrix completion, and adaptive random sampling. This research is of particular interest in synchrotron based nano-imaging facilities. This work paves the way to true spatio-spectral chemical and materials nano-spectroscopy with a reduction of sampling rate by up to 30 times.

Labouesse, S. C. Johnson, H. A. Bechtel, M. B. Raschke, R. Piestun, “Smart Scattering Scanning Near-Field Optical Microscopy,” ACS Photonics, 7, 3346-3352, (2020).

Atomic structures determined from digitally defined nanocrystalline regions

May 17, 2021|

Three-dimensional (3D) structures of molecules determined from nanoscale regions of crystalline arrays could potentially illuminate the subtle differences that engender crystal defects or the multiple states accessible to subpopulations of molecules within an ensemble. A step toward this goal involves the extraction of meaningful diffraction data from 3D regions on the nanoscale. This is achieved using a near-parallel electron beam designed to illuminate sub-10nm regions of a sample. Scanning such a beam across a sample allows for digital logic to be applied to the measured data, facilitating the expostfacto assortment of information and reduction from desired 3D subvolumes.

A STROBE team from UCLA, UC Berkeley and LBNL collaborated to determine the first molecular structures determined by 4DSTEM. The structures were determined from a digitally defined subregion of a nanocrystal. After collecting TB of data, the team obtained reconstructions that revealed the atomic structure of a peptide, and showed that radiation damage imparted on the sample during data collection was not prohibitive for structure determination. Compared to other approaches, the approach allows for a much greater degree of control and obviates the need for spatial separation of samples. New methods, algorithms, enhanced microscopes and advanced sample preparation techniques developed by the STROBE collaboration were key to enabling the success of this project.

Gallagher-Jones, K. C. Bustillo, C. Ophus, L. S. Richards, J. Ciston, S. Lee, A. M. Minor, J. A. Rodriguez, “Atomic structures determined from digitally defined nanocrystalline regions,” IUCrJ, 7, (2020).

STROBE solved a century-old scientific problem: Determining the 3D atomic structure of amorphous solids

April 13, 2021|

Amorphous solids such as glass, plastics and rubber are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells. However, due to the lack of any crystal-like long-range order, the traditional X-ray crystallographic methods for extracting the three-dimensional (3D) atomic arrangement of amorphous solids simply do not work. STROBE advanced atomic electron tomography to determine the 3D atomic positions and chemical species of an amorphous solid for the first time – with a stunning precision of 21 picometer. We found that instead of long-range order characteristic of crystals such as diamond, this amorphous metallic glass had regions of short- and medium-range order. Moreover, although the 3D atomic packing is disordered, some regions connect with each other to form crystal-like networks, which exhibit translational but no orientational order. Looking forward, we anticipate this approach will open the door to determining the 3D atomic coordinates of a wide range of amorphous solids, whose impact on non-crystalline solids may be comparable to the first 3D crystal structure solved by x-ray crystallography over a century ago.

Y. Yang, J. Zhou, F. Zhu, Y. Yuan, D. Chang, D. S. Kim, M. Pham, A. Rana, X. Tian, Y. Yao, S. Osher, A. K. Schmid, L. Hu, P. Ercius and J. Miao, “Determining the three-dimensional atomic structure of an amorphous solid”, Nature 592, 60–64 (2021).

Investigating the potential for entangled two-photon excited fluorescence imaging

April 6, 2021|

Setting bounds on the absorption cross-sections of molecular systems. There has been a long-running controversy regarding the “quantum advantage” for multiphoton excitation of molecules with entangled photons and if quantum multiphoton imaging can be realized. Although theoretical proposals have been advanced for decades, no experimental work (with the exception of a publication by Jeff Kimble’s group in the 1990s) appeared in the literature until 2006 when reports from a small number of groups began to emerge of a large quantum enhancement (e.g. up to 10 orders of magnitude) of the two photon excitation rate using entangled pairs compared to classical light. Last year, a paper describing a microscope based on the “entangled two-photon absorption” (E2PA) effect was published in Journal of the American Chemical Society. On the other hand, it has emerged from discussions at scientific meetings that many researchers have failed to replicate the results in these numerous publications, or to find any other evidence for this enhancement. As a result, there is considerable skepticism of the publications making these remarkable claims. Unfortunately, these negative results haven’t been published and therefore a rigorous basis for resolving the controversy hasn’t yet been established. Finally, new experiments at JILA have finally set upper-bounds for the E2PA cross-sections in molecular fluorophores, including those investigated in previous reports. We performed both classical and quantum light excitation in the same optical transmission and fluorescence-based systems with rigorously characterized states of light and measurement sensitivities. We find that E2PA cross-sections are at least four to five orders of magnitude smaller than previously reported. Our results imply that the signals and images reported in previous publications are artifacts. Although we don’t expect this contribution to be the last word on the subject, this work introduces a new level of experimental rigor that will lead towards new designs for quantum microscopes and sensors.

M. Parzuchowski, A. Mikhaylov, M. D. Mazurek, R. N. Wilson, D. J. Lum, T. Gerrits, C. H. Camp, M. J. Stevens, R. Jimenez, “Setting Bounds on Entangled Two-Photon Absorption Cross Sections in Common Fluorophores,” Physical Review Applied, 15, 044012 , (2021).

Pycro-Manager: open-source software for customized and reproducible microscope control

March 5, 2021|

Innovative microscopy techniques are often impeded by a lack of control software that is capable of meeting demands for speed and performance, integrating new and diverse types of hardware, providing the flexibility to adapt in real time to the data being captured, and providing user-friendly programming interfaces. As a result, researchers often end up developing custom software that works only with specific instruments, using closed-source and/or proprietary programming languages. Pycro-Manager is a package that meets these challenges by enabling python control of Micro-Manager (an open-source microscopy control software) as well as the simple development of customized experiments that involve microscope hardware control integrated with real-time image processing. It is compatible with hundreds of microscope components and full microscopes and provides open source APIs for the integration of new hardware. More information can be found at:

H. PinkardN. StuurmanI. E. IvanovN. M. AnthonyW. OuyangB. LiB. YangM. A. TsuchidaB. ChhunG. ZhangR. MeiM. AndersonD. P. ShepherdI. Hunt-IsaakR. L. DunnW. JahrS. KatoL. A. RoyerJ. R. ThiagarajahK. W. EliceiriE. LundbergS. B. MehtaL. Waller, "Pycro-Manager: open-source software for customized and reproducible microscope control," Nature Methods18226-228(2021). DOI: 10.1038/s41592-021-01087-6

Nondestructive, high-resolution, chemically specific 3D nanostructure characterization using phase-sensitive EUV imaging reflectometry

January 27, 2021|

Next-generation nano and quantum devices have increasingly complex 3D structure. As the dimensions of these devices shrink to the nanoscale, their performance is often governed by interface quality or precise chemical or dopant composition. A STROBE team from CU Boulder, UCLA, UC Berkeley, as well as laser and nanoelectronics industry partners, worked together for 4 years to design, construct and commission the first phase-sensitive extreme ultraviolet imaging reflectometer. It combines the excellent phase stability of tabletop coherent extreme UV (EUV) light sources, the unique chemical- and phase-sensitivity of coherent EUV imaging, and state-of-the-art algorithms. This tabletop microscope can non-destructively probe surface topography, layer thicknesses, and interface quality, as well as dopant concentrations and profiles. High-fidelity imaging was achieved by implementing phase sensitive imaging at different angles, by using advanced methods to mitigate noise and artifacts in the reconstructed image, and by using a high-brightness, EUV source with excellent intensity and wavefront stability. These measurements were validated through multiscale electron and atomic force microscopy imaging to show that this approach has unique advantages compared with others. Critical to this project were new photon and electron-based imaging methods, advanced algorithms, unique samples, as well STROBE advances in tabletop coherent imaging in transmission and reflection mode. Several STROBE trainees received awards for this effort.

Tanksalvala, C. L. Porter, Y. Esashi, B. Wang, N. W. Jenkins, Z. Zhang, G. P. Miley, J. L. Knobloch, B. McBennett, N. Horiguchi, S. Yazdi, J. Zhou, M. N. Jacobs, C. S. Bevis, R. M. Karl, P. Johnsen, D. Ren, L. Waller, D. E. Adams, S. L. Cousin, C. Liao, J. Miao, M. Gerrity, H. C. Kapteyn, M. M. Murnane, “Nondestructive, high-resolution, chemically specific 3D nanostructure characterization using phase-sensitive EUV imaging reflectometry,” Science Advances, 7, eabd9667, (2021).
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