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arXiv:2603.14113

Analysis of Hydrogen Contamination in Al/AlOx/Al Josephson Junctions

Yu Zhu, Aldilene Saraiva-Souza, Félix Beaudoin, Hong Guo

quant-phSubmitted Mar 14, 2026• Announced Mar 17, 2026• 0 citations• Revised May 22, 2026 (v2)
v1 · Mar 14, 2026v2 · May 22, 2026v3 · Oct 16, 2026
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Abstract

Hydrogen contamination in Josephson junctions is a potential source of device-to-device variability and two-level-system loss in superconducting qubits. In this work, we investigate hydrogen incorporation in oxidized aluminum barriers by combining molecular dynamics simulations with atomistic quantum transport calculations. The oxide growth simulations are performed using CHGNet for Al surfaces exposed to dense O$_{\text{2}}$ and H$_{\text{2}% }$O environments, yielding amorphous AlO$_{\text{x}}$ layers with hydrogen content comparable to experimentally relevant levels. From $400$ statistically independent samples, we find that the number of H atoms in the oxide is well described by a beta-binomial distribution, reflecting correlations induced by the self-limiting oxidation process. Structural analysis shows that most hydrogen atoms reside near the AlO$_{\text{x}}$ surface and predominantly form Al-OH and Al-OH-Al motifs. To assess the impact of hydrogen on transport, we construct Al/Al$_{\text{2}}$O$_{\text{3}} $/Al junction models and perform NEGF-DFT calculations with NanoDCAL, using a GGA+U scheme to calibrate the band gap and band alignment. H atoms are found to increase the transmission coefficient near the Fermi level and shift the electronic structure in a manner consistent with effective p-type doping. By combining the H atom number statistics from molecular dynamics with the transmission coefficients from quantum transport calculations, we obtain a probability distribution for the Josephson energy. For a Josephson junction with an average hydrogen content of $2.56$ at.\%, the resulting Josephson energy is predicted to be $% E_{J}/h=10.92\pm 0.26$ GHz. These results provide an atomistic picture of hydrogen contamination and an estimate of device variability in Josephson junctions.

Comments
6 pages, 5 figures

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Hydrogen contamination in Josephson junctions is a potential source of device-to-device variability and two-level-system loss in superconducting qubits. In this work, we investigate hydrogen incorporation in oxidized aluminum barriers by combining molecular dynamics simulations with atomistic quantum transport calculations. The oxide growth simulations are performed using CHGNet for Al surfaces exposed to dense O2_{\text{2}}2​ and H_{\text{2}% }O environments, yielding amorphous AlOx_{\text{x}}x​ layers with hydrogen content comparable to experimentally relevant levels. From 400400400 statistically independent samples, we find that the number of H atoms in the oxide is well described by a beta-binomial distribution, reflecting correlations induced by the self-limiting oxidation process. Structural analysis shows that most hydrogen atoms reside near the AlOx_{\text{x}}x​ surface and predominantly form Al-OH and Al-OH-Al motifs. To assess the impact of hydrogen on transport, we construct Al/Al2_{\text{2}}2​O3_{\text{3}} 3​/Al junction models and perform NEGF-DFT calculations with NanoDCAL, using a GGA+U scheme to calibrate the band gap and band alignment. H atoms are found to increase the transmission coefficient near the Fermi level and shift the electronic structure in a manner consistent with effective p-type doping. By combining the H atom number statistics from molecular dynamics with the transmission coefficients from quantum transport calculations, we obtain a probability distribution for the Josephson energy. For a Josephson junction with an average hydrogen content of 2.562.562.56 at.%, the resulting Josephson energy is predicted to be % E_{J}/h=10.92\pm 0.26 GHz. These results provide an atomistic picture of hydrogen contamination and an estimate of device variability in Josephson junctions.
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Josephson junctions are the key components used in superconducting qubits for quantum computing. The advancement of quantum computing is limited by a lack of stability and reproducibility of qubits, which ultimately originates in the amorphous tunnel barrier of the Josephson junctions and other material imperfections. Pinholes in the junction have been suggested as one of the possible contributors to these instabilities, but evidence of their existence and the effect they might have on transport is unclear. We use molecular dynamics to create three-dimensional atomistic models to describe $\mathrm{Al}\text{\ensuremath{-}}{\mathrm{AlO}}_{x}\text{\ensuremath{-}}\mathrm{Al}$ tunnel junctions, showing that pinholes form when oxidation of the barrier is incomplete. Following this, we use the atomistic model and simulate the electronic transport properties for tunnel junctions with different barrier thicknesses using the nonequilibrium Green's function formalism. We observe that pinholes may contribute to excess quasiparticle current flow in $\mathrm{Al}\text{\ensuremath{-}}{\mathrm{AlO}}_{x}\text{\ensuremath{-}}\mathrm{Al}$ tunnel junctions with thinner barriers, and in thicker barriers we observe weak-points that facilitate leakage currents even when the oxide is continuous. We find that the disordered nature of the amorphous barrier results in significant variations in the transport properties. Additionally, we determine the current-phase relationship for our atomistic structures, confirming that devices with pinholes and weak-points cause a deviation from the ideal sinusoidal Josephson relationship.
The aluminum oxide tunnel junction is a key component of the majority of superconducting quantum devices. For high-quality, reproducible, and scalably manufacturable qubits, the ability to fabricate Josephson junctions (JJs) with a targeted critical current and high uniformity is essential. We use first-principles modeling to assess fundamental aspects of the atomic structure of both amorphous and crystalline aluminum oxide tunnel junctions and relate the structure to predicted performance metrics. We use modified ab initio molecular dynamics to develop realistic models of the tunnel junction, from which interface roughness and local thickness fluctuations are analyzed in an unbiased manner by training a neural network to identify the boundary between metal and oxide. We show that the effective thickness of the insulating part of the junction can be different from the apparent physical thickness. We calculate the rate of Cooper pair tunneling for the atomically resolved electrostatic potential using direct numerical solution in 3D, which shows a channeling effect that impacts the junction critical current. The predicted critical current is a useful JJ design parameter that can be accessed from the ab initio calculations without fitting parameters. To assess the limits of uniformity and fabrication choices (e.g., oxidation vs epitaxy), we compare the amorphous junctions to crystalline models, which show order of magnitude more efficient tunneling compared to the amorphous case, underlining the connection between atomistic structure and Cooper pair tunneling efficiency. Further, this work provides a foundation for ab initio materials design and evaluation to help accelerate future development of improved tunnel junctions.
As quantum processors scale to large qubit numbers, device-to-device variability emerges as a critical challenge. Superconducting qubits are commonly realized using Al/AlOx_{\text{x}}x​/Al Josephson junctions operating in the tunneling regime, where even minor variations in device geometry can lead to substantial performance fluctuations. In this work, we develop a quantitative model for the variability of the Josephson energy EJE_{J}EJ​ induced by interface roughness at the Al/AlOx_{\text{x}}x​ interfaces. The roughness is modeled as a Gaussian random field characterized by two parameters: the root-mean-square roughness amplitude σσσ and the transverse correlation length ξξξ. These parameters are extracted from the literature and molecular dynamics simulations. Quantum transport is treated using the Ambegaokar--Baratoff relation combined with a local thickness approximation. Numerical simulations over 5,0005,0005,000 Josephson junctions show that EJE_{J}EJ​ follows a log-normal distribution. The mean value of EJE_{J}EJ​ increases with σσσ and decreases slightly with ξξξ, while the variance of EJE_{J}EJ​ increases with both σσσ and ξξξ. These results paint a quantitative and intuitive picture of Josephson energy variability induced by surface roughness, with direct relevance for junction design.
As quantum processors scale to large qubit numbers, device-to-device variability emerges as a critical challenge. Superconducting qubits are commonly realized using Al/AlOx/Al Josephson junctions operating in the tunneling regime, where even minor variations in device geometry can lead to substantial performance fluctuations. In this work, we develop a quantitative model for the variability of the Josephson energy EJ induced by interface roughness at the Al/AlOx interfaces. The roughness is modeled as a Gaussian random field characterized by two parameters: the root mean square roughness amplitude σ and the transverse correlation length ξ. These parameters are extracted from the literature and molecular dynamics simulations. Quantum transport is treated using the Ambegaokar–Baratoff relation combined with a local thickness approximation. Numerical simulations over 5000 Josephson junctions show that EJ follows a lognormal distribution. The mean value of EJ increases with σ and decreases slightly with ξ, while the variance of EJ increases with both σ and ξ. These results paint a quantitative and intuitive picture of Josephson energy variability induced by surface roughness, with direct relevance for junction design.
Al/AlOx/Al Josephson junctions are the building blocks of a wide range of superconducting quantum devices that are key elements for quantum computers, extremely sensitive magnetometers and radiation detectors. The properties of the junctions and the superconducting quantum devices are determined by the atomic structure of the tunnel barrier. The nanoscale dimension and disordered nature of the barrier oxide have been challenges for the direct experimental investigation of the atomic structure of the tunnel barrier. Here we show that the miniaturized dimension of the barrier and the interfacial interaction between crystalline Al and amorphous AlOx give rise to oxygen deficiency at the metal/oxide interfaces. In the interior of the barrier, the oxide resembles the atomic structure of bulk aluminium oxide. Atomic defects such as oxygen vacancies at the interfaces can be the origin of the two-level systems and contribute to decoherence and noise in superconducting quantum circuits.