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Microscopy and Microanalysis

Comparative S/TEM Study of Superconducting Ta Quantum Resonators by Wet and Dry Etching Types

Junsik Mun, Chenyu Zhou, Nana Shumiya, Kim Kisslinger, Rebecca Cummings, Nathalie P. de Leon, Mingzhao Liu, Yimei Zhu

Published Jul 1, 2024• 0 citations
Publisher

Abstract

Superconducting resonator systems, including a superconducting qubit, require exceptional coherence and longevity lifetime performance. However, these systems have been impeded by dielectric loss and quasiparticle loss, many of which have been caused by the materials imperfection [1]. In this work, we report a comparative scanning transmission electron microscopy (S/TEM) investigation of the impacts of wet and dry etching on superconducting Tantalum (Ta) films. This work has been sparked by the critical importance of superconducting resonators in a wide range of quantum technological applications, which necessitates optimizing their fabrications to improve the performance of various quantum devices and communication systems [2]. The primary objective of this work is to understand the morphology, substrate crystallinity degradation, chemical segregation, and strain of etched Ta films, as well as the characteristics of the oxidized sidewalls that can influence the performance and homogeneity of the superconducting device. In the pursuit of deeper insights, advanced characterization techniques such as atomic-resolution STEM imaging, electron energy loss spectroscopy (EELS) chemical mapping, and 4-dimensional STEM (4D STEM) strain mapping were employed. The key findings of this work are the significant variations in sidewall morphology, chemical composition, and strain fields depending on the type of etching employed (wet or dry). The findings suggest that sidewall formation induces localized strain fields in proximity to amorphized oxidation layers of the superconducting resonator sidewalls, which potentially impacting the coherence and homogeneity of the superconducting quantum devices [3]. This study, therefore, emphasizes the need to optimize the morphology of the sidewall to minimize local strain field generation. Additionally, the research underscores the importance of precise and meticulous fabrication in the construction of quantum devices, emphasizing the need for a chemically robust and uniform coating process to protect the resonator film from oxidation and wet etchants without affecting the operation of the superconducting device. These insights are crucial for advancing the performance and coherence of superconducting qubits, ultimately contributing to the optimization of quantum devices and the progress of quantum technologies and high-frequency communication systems [4]. Top-view schematics of Ta superconducting resonators at (a) zoom-out view and (b) zoom-in view. Cross-sectional HAADF STEM images of (c) dry- and (d) wet-etched Ta film on sapphire substrate. These images show the overall dimensions and morphologies of the resonators. The BF STEM images, εxx, εzz, εxz, and ωxz mapping results were virtually reconstructed from 4D STEM for the (a) dry- and (b) wet-etched samples, respectively. The positive (negative) value is represented by the color red (blue) in the colorbar. Lattice elongation (shrinkage), is represented by positive (negative) values in εxx and εzz. Lattice shearing, which has a positive value in εxz, is defined as distortion from the top to the right and the bottom to the left of the lattice. The Ta lattice rotates counterclockwise (clockwise) represented by positive (negative) numbers in ωxz.

DOI
10.1093/mam/ozae044.554

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Comparative S/TEM study of superconducting Ta quantum resonators by wet and dry etching types

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Superconducting resonators play a pivotal role in various quantum technology applications, such as quantum computing and high-frequency communication systems. The performance of these resonators is closely tied to the properties of the superconducting films used in their fabrication. In this study, we investigated the impact of wet and dry etching on tantalum (Ta) films leveraging advanced scanning transmission electron microscopy-based characterization methods and examined the morphological, chemical, and strain changes caused by the etching processes. Consequently, we report the significant differences between the two etching methods, with dry etching resulting in straight slanted sidewalls and a thinner oxidized layer, while wet etching produced curved sidewalls and undercuts. Both methods led to the formation of a residual Ta wedge at the lower part of the sidewall, causing lattice deformation, which could adversely influence the homogeneous operations of superconducting devices. These insights enhance our understanding of how etching influences superconducting films, offering valuable guidance for optimizing resonators and related devices. Our findings mark a significant stride in advancing quantum technologies and high-frequency communication by enhancing our practical understanding of superconducting material fabrication.

Applied Physics Letters•Oct 14, 2024•3 citations

Characterization of Tantalum and Tantalum-alloyed Films for Quantum Devices

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Superconducting qubits are among the most advanced platforms for quantum information, offering potential scalability and compatibility with standard device fabrication techniques [1-5]. Among the materials investigated for superconducting qubits, Tantalum (Ta) has emerged as a compelling candidate due to its self-terminating stoichiometric surface oxide and chemical resistance to harsh post-fabrication processes. Efforts to mitigate surface loss by treating the surface oxides and utilizing high-resistivity silicon substrates have led to Ta-based qubits with lifetime and coherence times exceeding 1 ms [3]. Guided by these successes in reducing dielectric loss in Ta-based devices, we are interested in exploring material engineering approaches that enhance the superconducting gap. Alloying Ta with another element to enhance the superconducting performance expands the range of viable material candidates available to tackle different loss channels in superconducting circuits [1]. Recently, we explore superconducting gap engineering in Ta-based devices as a powerful strategy for expanding the range of suitable host materials. By alloying 20 at.% hafnium (Hf) into Ta thin films, we achieve a superconducting transition temperature (Tc) of 6.09 K as observed in direct current (DC) transport measurements, reflecting an increase in the superconducting gap. Here we demonstrate an approach for controlling varying deposition conditions to control film orientation and transport properties of Ta and Ta-Hf alloy thin films. We investigate the microstructure and composition distribution of the thin films by using high-resolution scanning transmission electron microscopy (STEM) with super-X EDS system (no serious beam damage issue [6-8]). Our structural analysis using TEM diffraction and STEM verifies the BCC structure across all the films (Figure 1), and direct current (DC) transport measurements reveal a 40% enhancement in Tc relative to undoped Ta (Tc=4.3 K). We monitored oxide growth over an 18-day period following film deposition to better understand how Hf incorporation influences surface oxides. In both Ta and Hf spectra, the fraction of fully oxidized (Ta2O5 and HfO2) states gradually increased during the 18-day exposure, indicating progressive surface oxidation. To estimate the surface oxide thickness, we use cross-sectional TEM/EDS mapping (Figure 1c). The analysis reveals that the oxide thickness for the 1 ks Ta-Hf alloy film is approximately 3 nm in thickness, comparable to the 3 nm oxide observed on native Ta [2]. For the 2 ks Ta-Hf film, the oxide thickness increases slightly to about 4 nm (Figure 1). The measured surface loss tangent of the Ta-Hf alloy remains comparable to that of native Ta. This result suggests that the surface oxide of the Ta-Hf alloy, which contains a measurable fraction of HfOx, does not introduce additional dielectric loss. By engineering the alloy composition and film deposition, this study achieves both improved superconducting properties and compatibility with fabrication processes. These findings show that material doping and alloying can strategically expand the suite of viable materials for superconducting quantum devices. This approach provides a pathway for tailoring material properties to support the next generation of quantum technologies and offers broad relevance to researchers in materials science, quantum information, and device engineering [9]. STEM images on cross sections of 1 ks (a) and 2 ks (b) Ta-Hf thin films, both films were sputtered at 750 ◦C. (c) Cross-sectional EDS elemental mapping on Ta-Hf. Cross-sectional EDS mapping Ta (blue) and Hf (orange) confirmed a uniform Ta-Hf alloy with the Ta to Hf atomic ratios for the bulk to be (83% : 17%). The oxygen (red) map reveals a surface oxide layer with the estimated surface oxide thickness of around 4 nm. The 1 ks Ta-Hf film exhibits an oxide thickness of approximately 3 nm, similar to that of native Ta. The EDS resolution limit is 0.5 atomic percent.

Microscopy and Microanalysis•Jul 1, 2026•0 citations

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Microscopy and Microanalysis•Jul 1, 2024•0 citations

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Microscopy and Microanalysis•Jul 1, 2026•0 citations
Superconducting resonator systems, including a superconducting qubit, require exceptional coherence and longevity lifetime performance. However, these systems have been impeded by dielectric loss and quasiparticle loss, many of which have been caused by the materials imperfection [1]. In this work, we report a comparative scanning transmission electron microscopy (S/TEM) investigation of the impacts of wet and dry etching on superconducting Tantalum (Ta) films. This work has been sparked by the critical importance of superconducting resonators in a wide range of quantum technological applications, which necessitates optimizing their fabrications to improve the performance of various quantum devices and communication systems [2]. The primary objective of this work is to understand the morphology, substrate crystallinity degradation, chemical segregation, and strain of etched Ta films, as well as the characteristics of the oxidized sidewalls that can influence the performance and homogeneity of the superconducting device. In the pursuit of deeper insights, advanced characterization techniques such as atomic-resolution STEM imaging, electron energy loss spectroscopy (EELS) chemical mapping, and 4-dimensional STEM (4D STEM) strain mapping were employed. The key findings of this work are the significant variations in sidewall morphology, chemical composition, and strain fields depending on the type of etching employed (wet or dry). The findings suggest that sidewall formation induces localized strain fields in proximity to amorphized oxidation layers of the superconducting resonator sidewalls, which potentially impacting the coherence and homogeneity of the superconducting quantum devices [3]. This study, therefore, emphasizes the need to optimize the morphology of the sidewall to minimize local strain field generation. Additionally, the research underscores the importance of precise and meticulous fabrication in the construction of quantum devices, emphasizing the need for a chemically robust and uniform coating process to protect the resonator film from oxidation and wet etchants without affecting the operation of the superconducting device. These insights are crucial for advancing the performance and coherence of superconducting qubits, ultimately contributing to the optimization of quantum devices and the progress of quantum technologies and high-frequency communication systems [4]. Top-view schematics of Ta superconducting resonators at (a) zoom-out view and (b) zoom-in view. Cross-sectional HAADF STEM images of (c) dry- and (d) wet-etched Ta film on sapphire substrate. These images show the overall dimensions and morphologies of the resonators. The BF STEM images, εxx, εzz, εxz, and ωxz mapping results were virtually reconstructed from 4D STEM for the (a) dry- and (b) wet-etched samples, respectively. The positive (negative) value is represented by the color red (blue) in the colorbar. Lattice elongation (shrinkage), is represented by positive (negative) values in εxx and εzz. Lattice shearing, which has a positive value in εxz, is defined as distortion from the top to the right and the bottom to the left of the lattice. The Ta lattice rotates counterclockwise (clockwise) represented by positive (negative) numbers in ωxz.
Superconducting resonators play a pivotal role in various quantum technology applications, such as quantum computing and high-frequency communication systems. The performance of these resonators is closely tied to the properties of the superconducting films used in their fabrication. In this study, we investigated the impact of wet and dry etching on tantalum (Ta) films leveraging advanced scanning transmission electron microscopy-based characterization methods and examined the morphological, chemical, and strain changes caused by the etching processes. Consequently, we report the significant differences between the two etching methods, with dry etching resulting in straight slanted sidewalls and a thinner oxidized layer, while wet etching produced curved sidewalls and undercuts. Both methods led to the formation of a residual Ta wedge at the lower part of the sidewall, causing lattice deformation, which could adversely influence the homogeneous operations of superconducting devices. These insights enhance our understanding of how etching influences superconducting films, offering valuable guidance for optimizing resonators and related devices. Our findings mark a significant stride in advancing quantum technologies and high-frequency communication by enhancing our practical understanding of superconducting material fabrication.
Superconducting qubits are among the most advanced platforms for quantum information, offering potential scalability and compatibility with standard device fabrication techniques [1-5]. Among the materials investigated for superconducting qubits, Tantalum (Ta) has emerged as a compelling candidate due to its self-terminating stoichiometric surface oxide and chemical resistance to harsh post-fabrication processes. Efforts to mitigate surface loss by treating the surface oxides and utilizing high-resistivity silicon substrates have led to Ta-based qubits with lifetime and coherence times exceeding 1 ms [3]. Guided by these successes in reducing dielectric loss in Ta-based devices, we are interested in exploring material engineering approaches that enhance the superconducting gap. Alloying Ta with another element to enhance the superconducting performance expands the range of viable material candidates available to tackle different loss channels in superconducting circuits [1]. Recently, we explore superconducting gap engineering in Ta-based devices as a powerful strategy for expanding the range of suitable host materials. By alloying 20 at.% hafnium (Hf) into Ta thin films, we achieve a superconducting transition temperature (Tc) of 6.09 K as observed in direct current (DC) transport measurements, reflecting an increase in the superconducting gap. Here we demonstrate an approach for controlling varying deposition conditions to control film orientation and transport properties of Ta and Ta-Hf alloy thin films. We investigate the microstructure and composition distribution of the thin films by using high-resolution scanning transmission electron microscopy (STEM) with super-X EDS system (no serious beam damage issue [6-8]). Our structural analysis using TEM diffraction and STEM verifies the BCC structure across all the films (Figure 1), and direct current (DC) transport measurements reveal a 40% enhancement in Tc relative to undoped Ta (Tc=4.3 K). We monitored oxide growth over an 18-day period following film deposition to better understand how Hf incorporation influences surface oxides. In both Ta and Hf spectra, the fraction of fully oxidized (Ta2O5 and HfO2) states gradually increased during the 18-day exposure, indicating progressive surface oxidation. To estimate the surface oxide thickness, we use cross-sectional TEM/EDS mapping (Figure 1c). The analysis reveals that the oxide thickness for the 1 ks Ta-Hf alloy film is approximately 3 nm in thickness, comparable to the 3 nm oxide observed on native Ta [2]. For the 2 ks Ta-Hf film, the oxide thickness increases slightly to about 4 nm (Figure 1). The measured surface loss tangent of the Ta-Hf alloy remains comparable to that of native Ta. This result suggests that the surface oxide of the Ta-Hf alloy, which contains a measurable fraction of HfOx, does not introduce additional dielectric loss. By engineering the alloy composition and film deposition, this study achieves both improved superconducting properties and compatibility with fabrication processes. These findings show that material doping and alloying can strategically expand the suite of viable materials for superconducting quantum devices. This approach provides a pathway for tailoring material properties to support the next generation of quantum technologies and offers broad relevance to researchers in materials science, quantum information, and device engineering [9]. STEM images on cross sections of 1 ks (a) and 2 ks (b) Ta-Hf thin films, both films were sputtered at 750 ◦C. (c) Cross-sectional EDS elemental mapping on Ta-Hf. Cross-sectional EDS mapping Ta (blue) and Hf (orange) confirmed a uniform Ta-Hf alloy with the Ta to Hf atomic ratios for the bulk to be (83% : 17%). The oxygen (red) map reveals a surface oxide layer with the estimated surface oxide thickness of around 4 nm. The 1 ks Ta-Hf film exhibits an oxide thickness of approximately 3 nm, similar to that of native Ta. The EDS resolution limit is 0.5 atomic percent.
Superconducting qubits have become one of the leading contenders in making quantum computing a reality because of their robustness and scalability [1]. Replacing the widely adopted Al and Nb, Ta has become the most promising candidate material for superconducting qubit fabrication due to its exceptionally enhanced thermal relaxation time (i.e., T1 time). This time can exceed 0.3 milliseconds which is three orders of magnitude higher than the previous methods [2]. However, during the fabrication process, exposure of tantalum to air leads to the formation of an amorphous surface oxide layer. The presence of this oxide layer can affect the superconducting properties of the tantalum film and, hence, the performance of the qubit. This native amorphous oxidized surface results in a dielectric loss through an energy reduction mechanism called a two-level system caused by structural and chemical defects [3]. Although Ta exhibits superior performance, particularly T1 time, compared to other superconducting materials, its value remains insufficient for quantum processor hardware. Therefore, understanding the structural and chemical profile of the native amorphous surface of the oxides for superconducting qubits is required to optimize their performance. In this study, we employed scanning transmission electron microscopy (STEM) with a combination of electron energy loss spectroscopy (EELS) and four-dimensional STEM (4D-STEM) to probe the electronic and crystallographic structure of the local surface areas. Furthermore, to circumvent the spectral and diffractometric profiles that overlap as a function of depth position caused by electron beam broadening, we applied Multivariate curve resolution (MCR) analysis that can separate complex mixtures into their basis components. In the subsequent experiments, we investigated the surface morphology of (110)-oriented α-Ta film grown on an A-plane sapphire substrate using scanning electron microscopy (SEM) (Figure 1a), and high-angle annular dark-field (HAADF) STEM imaging (Figure 1b and 1c). We found that the surface of the Ta film is bumpy, and made of an amorphous material with a thickness of about 3 nm. The film exhibits a columnar structure along the [001] growth direction. EELS fine structure analysis reveals that most of the amorphous regions are in the Ta2O5 phase (Figure 2a and 2b). By extracting valuable basis components of O-K fine structures, we were able to quantify the concentration of the chemical species with Å-scale at the interface using MCR analysis. Specifically, a depth dependent composition variation, especially that of oxygen concentration, was observed. We further investigated amorphous oxide films and interfaces with 4D-STEM based fluctuation electron microscopy. (Figure 2c and 2d) We obtained results that were consistent with the chemical profiles obtained from the O-K edge EELS mapping. We also revealed the crystalline ordering information of each chemical species. The detailed descriptions of the results will be presented at the conference. These STEM analysis findings were supported by first-principles calculations of oxygen concentration changes and phase formation energies. Overall, our research provides important insights into the formation and properties of the native amorphous surface oxides of a superconducting qubit tantalum film, which is critical for the development of next-generation quantum computing technologies [4]. Surface morphology of α-Ta film on A-plane sapphire. (a) Top-view SEM image. Cross-sectional HAADF STEM images at (b) low and (c) high magnification. To protect the film surface during the FIB process, the coating layer is on top of the bumpy surface of the Ta film with a thin native oxidized layer of gray contrast. Crystal orientation is indicated on the left-bottom corner in (a) and (c) for the top-view and cross-sectional view images, respectively. STEM-EELS and 4D-STEM analysis across the interfaces between the native oxidized amorphous and the crystalline Ta film. (a) HAADF STEM image of the region-of-interest, simultaneously acquired with EELS mapping. (b) Representative EELS spectra of O-K edge fine structures and (c, d) electron diffraction patterns from the native oxidized amorphous region (green) and the crystalline Ta film region (blue).
Superconducting resonators and qubits have become a promising platform for quantum computation in the past decades; however, fault-tolerant operation of these devices remains out of reach. In addition to sources within the bulk, interfaces in the device induce dielectric losses and host two-level systems (TLS), diminishing single-photon excitation levels and signal coherence [1]. The metal-substrate (MS) interface has been observed to have disproportionately high electric-field participation in microwave circuits, but with no clear mechanism of how it becomes a dominant source of TLS losses [2]. Establishing a correlation between structural features and performance will be key in realizing fault-tolerant quantum information systems, but atomic-scale characterization of the structural and chemical identity of the MS interface remains limited, and for Ta-based devices, is almost entirely absent. This study presents the use of scanning transmission electron microscopy with electron energy loss spectroscopy (STEM-EELS) of sputtered Ta-on-Si films to investigate roughness and chemical changes of the MS interface when varying substrate deposition temperature and sputtering gas. Deposition conditions ranged between room temperature (RT) and 600 °C using either Kr or Ar gas. In all cases, an amorphous MS interlayer was found. This interlayer grows in thickness progressively with substrate temperature, and at 600 °C, becomes notably thicker in the Ar-sputtered films. The EELS low loss region is difficult to analyze due to overlapping effects from specimen thickness, electron density, and band structure, and discerning subtle changes to core-loss peaks between the metal and substrate is complicated by intermixing from the sputtering process. By using diffusion mapping (DM), individual spectra can be separated by subtle changes in the core-loss [3]. This enables clear distinction between changes in the spectra due to chemical gradients versus silicide formation. Figure 1 shows isolated component regions and spectra for the Si, Ta, and MS interlayer. The change in the Si L2,3 peak shape identifies the formation of a silicide compound at the interface. To corroborate these results, the depth profiles (Figure 2) of Ta and Si for films grown at or above 450° C have a clear shoulder present, also indicating a second interface that may induce its own associated interfacial losses in the device. Superconducting Ta-based resonators and qubits emerged as a promising platform in the quantum information community due to their long coherence times and sub-millisecond relaxation times; however, there is much more progress to be made on identifying and correcting sources of dielectric and TLS loss [1, 4]. In Ta-based films in particular, imaging of interfacial chemical structure has seen little research between the film and substrate, with more attention having instead been devoted to the oxide species at the metal-air interface [5]. This work expands the community’s understanding of where dielectric losses and two-level system behavior may arise in Ta films and highlights how EELS and DM can be leveraged in quantum information research [6]. EELS spectrum images, Si L2, 3 and Ta M5 edge maps, and spectra from Si (blue), interlayer (orange), and Ta (green) regions in the plasmon and Si L2,3, L1 energy ranges for a) RT, b) 450 °C, and c) 600 °C Ar-sputtered films. Scale bar = 5 nm. EELS line profiles across the metal-substrate interface for various 100 nm Ta films.
The development of quantum computers, capable of surpassing classical computing in solving specific complex problems, hinges on breakthroughs in materials science, precision device fabrication, and the optimization of quantum architectures [1]. Among the leading candidates for quantum computation, superconducting qubits, particularly those based on transmon designs, have shown promising advances with coherence times reaching hundreds of microseconds [2]. However, to fully unlock the potential of scalable quantum computing, further enhancements in coherence are necessary. The intricate structure-coherence relationship within these devices, especially at critical interfaces such as metal-air, metal-dielectric, and metal-substrate in Josephson junctions (JJs), poses a significant challenge due to the potential for two-level-system loss channels. Here, we detail our pioneering efforts to understand these structure-coherence relationships utilizing advanced electron microscopy techniques. Focusing on the Al-AlOx and Al-Si substrate interfaces in Josephson Junctions, we employ a combination of low-loss and core-loss electron energy loss spectroscopy (EELS) and four-dimensional scanning transmission electron microscopy (4D-STEM) conducted at room and ultra-low temperatures (sub-6 K). This approach allows for an unprecedented examination of the chemical composition, bonding environments, and nanoscale structures of key surfaces and interfaces critical to the quantum coherence. Figure 1 presents a typical superconducting architecture at the chip level; each superconducting qubit consists of a Josephson Junction in parallel with an ultra-low-loss capacitor to create a resonant structure in the 3-6GHz range. JJs are highlighted in the area boxed in Fig. 1A and can be observed in detail in Fig. 1B. Lamella cross-sections (as shown in Fig. 1C) were prepared using a dual-beam focused ion beam (FIB) FEI-SEM Helios Nanolab. The lift-off was performed using 30 kV Ga+ ions, and the final cleaning step was carried out at 2 kV to remove surface damage on the area of interest, resulting in a final sample thickness of 50-100 nm. Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) data were collected on a probe-corrected JEOL ARM200 S/TEM operating at 200 kV. The convergent angle for ADF-STEM imaging was 25 mrad. Electron energy loss spectra (EELS) were acquired at 200 kV using a Gatan GIF Quantum on a K2 pixelated detector. Data processing (background subtraction, plural scattering removal, and signal mapping) was conducted using Gatan GMS software. Four-dimensional STEM (4D-STEM) data were collected by a K3 and STELA cameras. The convergent angles were 0.5-1.5 mrad, and the camera length was 6-10 cm. The step size was 5-10 Å. Merging microscopic insights with electrical data and theoretical frameworks, we aim to reveal how atomic-scale irregularities affect coherence times. Our results highlight key decoherence mechanisms in superconducting qubits and suggest specific improvements for qubit design and manufacturing. By linking electron microscopy findings to device performance, we outline strategies to reduce decoherence, essential for achieving reliable quantum computing. This work bridges materials science and quantum engineering, driving efforts in making scalable quantum computers forward [3]. A) Microscopic view of a superconducting transmon qubit, highlighting its symmetric design with central island and capacitor pads. B) SEM image of a JJ displaying their Al top and bottom contacts. C) STEM image of a JJ showing its key components and interfaces: Al top and bottom contact, AlOx tunnel barrier, Si substrate and Al-Si interface. A) EELS chemical maps of two interfaces, Al/Al and Al/Si using K-edges of oxygen, aluminum and silicon of a Josephson junction. It is possible to detect a formation of oxides at both interfaces. Plots showing Al and Si K-edge at 1560 eV and 1839 eV, respectively, and the ELNES are shown on the right side (Scale bar in A – 20 nm). B) Analysis of the disordered Al phases at the interfaces utilizing ePDF.
In superconducting transmon qubits, macroscopic characterization is the primary method for probing performance metrics, such as relaxation T1 and dephasing T2 times, resonance frequency, and quality factor. While these measurements can aid our understanding of the dielectric loss of a transmon, they do not allow us to characterize the structural and chemical inhomogeneity of the interfaces which directly impacts this energy loss. These fundamental materials problems must be studied using transmission electron microscopy (TEM) to provide insight into these defects across different qubit interfaces at an atomic scale. In this contribution, we will examine qubits, such as those shown in Figure 1, fabricated at Fermi National Accelerator Laboratory (SQMS Center) [1]. The qubit devices consist of superconducting metal base layers, typically sputter deposited Nb or Ta, and Al/AlOx/Al junctions, where the AlOx barrier is roughly 3nm in thickness and prepared through in-situ oxidation [2]. Characterizing this system prior to its integration within a superconducting radio frequency cavity establishes a baseline for the system, allowing us to isolate fabrication-induced defects before they manifest in performance degradation during quantum measurements. With the samples and fabrication process well known on a macroscopic scale, we study the atomic structure and chemistry of different heterointerfaces within the Josephson junction (JJ) of the transmon qubit and between the sapphire substrate and Nb resonator pads to identify potential defects contributing to the decoherence for qubits constructed with particular geometries. To resolve these defects, atomic-resolution imaging, energy-dispersive X-ray spectroscopy (EDS), and electron-energy loss spectroscopy (EELS) are performed using the JEOL-ARM200CF, an aberration-corrected scanning transmission electron microscope (STEM). Figure 2 provides a clear image of the stacked layers formed as the JJ, but with the addition of a platinum and carbon protective coating added during the focus ion beam (FIB) milling process to preserve pristine Al/AlOx/Al interfaces. 4D-STEM approaches, such as ptychography, orientation mapping and nanoscale diffraction will be employed to further study the layered interfaces and defects in real space and reciprocal space. These techniques can also provide insight into any damage that incurs during lamella preparation using the FIB [3]. Magnetic field-free atomic resolution imaging, differential phase contrast mapping, and monochromated EELS can be achieved using the new MARS-MONO STEM (JEM-Z200MF) without inducing current fluctuations or magnetic field related distortions [4]. By integrating this work across the functional interfaces of the transmon qubits and their different geometries, we will identify possible structural and chemical defects which limit device performance using our multi-modal approach [5]. SQMS fabricated transmon qubits fabricated on HEMEX sapphire substrate imaged via a) ZEISS optical microscope, b) SEM and c) EDS. TEM image of Josephson Junction layered interface at on JEOL-ARM200CF on the ClearView camera with a 200kV accelerating voltage.