Results for “Next-generation sequencing” — Page 3

DOE OSTI2025

Comprehensive model for evaluating voltage losses and performance improvements in thin-film photovoltaic devices

Progress of state-of-the-art and next-generation thin-film photovoltaic devices is often stymied by open-circuit voltage (𝑉 oc ) that is significantly lower than theoretical and practical limits. Yet, effectively diagnosing the primary sources of voltage loss remains challenging. Herein, a sequence of device-level characterization techniques and simulations are employed to identify and rank loss mechanisms. For the research-based Cd⁡(Se,Te) device under study, most of the loss was at the front semiconductor heterointerface due to a clifflike conduction-band offset that lowered the recombination activation energy. Additional losses due to band tails were quantified by photoluminescence analysis. The latter provided the absorption coefficient and activation energy reduction associated with band tails as inputs to device models. Simulations showed that alleviating front-interface issues would improve 𝑉 oc , but it would then be limited by bulk recombination. Further improvement of the bulk would then lead to back-contact limitations. Reducing band tails is beneficial in any circumstance. In conclusion, this analysis provides guidance for reaching toward the radiative 𝑉 oc limit.

14 SOLAR ENERGY↗

DOE OSTI2026

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.

Draisma, Arjan [Wageningen University & Research (↗

DOE OSTI2023

Emergent layer stacking arrangements in c-axis confined MoTe 2

The layer stacking order in 2D materials strongly affects functional properties and holds promise for next-generation electronic devices. In bulk, octahedral MoTe 2 possesses two stacking arrangements, the ferroelectric Weyl semimetal T d phase and the higher-order topological insulator 1T' phase. However, in thin flakes of MoTe 2 , it is unclear if the layer stacking follows the T d , 1T', or an alternative stacking sequence. Here, we use atomic-resolution scanning transmission electron microscopy to directly visualize the MoTe 2 layer stacking. In thin flakes, we observe highly disordered stacking, with nanoscale 1T' and T d domains, as well as alternative stacking arrangements not found in the bulk. We attribute these findings to intrinsic confinement effects on the MoTe 2 stacking-dependent free energy. Our results are important for the understanding of exotic physics displayed in MoTe 2 flakes. More broadly, this work suggests c-axis confinement as a method to influence layer stacking in other 2D materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Automation of Laser Plasma Focused Ion Beam Microscopy for Next-Gen Energy Materials

Automation can revolutionize the use of ultrafast laser ablation and plasma-focused ion beam (PFIB) techniques for high-throughput, reproducible cross-sectioning and various sample preparation in materials characterization. As these methods become essential for analyzing complex energy materials and next-generation devices, efficient, standardized workflows are needed to minimize variability and enhance precision. This work highlights our advancements in developing automated processes for sample preparation that integrates machine learning, workflow optimization, and large-scale data acquisition to improve efficiency and scalability in applications such as electrolyzers, photovoltaic cells, and microelectronics. To streamline cross-sectioning and lamella fabrication, we have implemented fully automated workflows that standardize laser ablation and PFIB milling sequences. These workflows incorporate pre-programmed protocols for material removal, alignment, and thinning, reducing user intervention and ensuring consistency across different sample types. Machine learning algorithms further enhance automation by predicting optimal milling strategies and adapting parameters based on material properties and sectioning requirements. This approach significantly improves throughput while maintaining the structural integrity of prepared samples for high-resolution imaging and analysis, including transmission electron microscopy. Beyond sample preparation, our automation platform enables the acquisition of large, high-resolution datasets through serial sectioning, image alignment, and 3D reconstruction. These automated routines facilitate multi-scale characterization, capturing structural and compositional details from the nanoscale to the device level. By reducing variability and increasing efficiency, our automated approach enhances defect analysis, failure diagnostics, and process optimization, accelerating advancements in materials research and device engineering.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Variational quantum state preparation for quantum-enhanced metrology in noisy systems

Here, we investigate optimized quantum state preparation for quantum metrology applications in noisy environments. Using the QFI-OPT package, we simulate a low-depth variational quantum circuit (VQC) composed of a sequence of global rotations and entangling operations applied to a chain of qubits that are subject to dephasing noise. The parameters controlling the VQC are numerically optimized to maximize the quantum Fisher information, which characterizes the ultimate metrological sensitivity of a quantum state with respect to a global rotation. We find that, regardless of the details of the entangling operation implemented in the VQC, the optimal quantum states can be broadly classified into a trio of qualitative regimes, i.e., catlike, squeezed like, and product states, associated with different dephasing rates. Our findings are relevant for designing optimal state-preparation strategies for next-generation quantum sensors exploiting entanglement, such as time and frequency standards and magnetometers, aimed at achieving state-of-the-art performance in the presence of noise and decoherence.

quantum Fisher information↗

DOE OSTI2024

Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge

Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Data for High Yield Production of 3-Hydroxypropionic Acid Using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Bioproducts↗

DOE OSTI2025

Scalable freeform optimization of wide-aperture 3D metalenses by zoned discrete axisymmetry

We introduce a novel framework for design and optimization of 3D freeform metalenses that attains nearly linear scaling of computational cost with diameter, by breaking the lens into a sequence of radial “zones” with 𝑛-fold discrete axisymmetry, where 𝑛 increases with radius. This allows vastly more design freedom than imposing continuous axisymmetry, while avoiding the compromises of the locally periodic approximation (LPA) or scalar diffraction theory. Using a GPU-accelerated finite-difference time-domain (FDTD) solver in cylindrical coordinates, we perform full-wave simulation and topology optimization within each supra-wavelength zone. We validate our approach by designing millimeter and centimeter-scale, poly-achromatic, 3D freeform metalenses which outperform the state of the art. By demonstrating the scalability and resulting optical performance enabled by our “zoned discrete axisymmetry” (ZDA) and supra-wavelength domain decomposition, we highlight the potential of our framework to advance large-scale meta-optics and next-generation photonic technologies.

Sun, Mengdi [Wesleyan University]↗

DOE OSTI2023

TRINIDI: Time-of-Flight Resonance Imaging With Neutrons for Isotopic Density Inference

Accurate reconstruction of 2D and 3D isotope densities is a desired capability with great potential impact in applications such as evaluation and development of next-generation nuclear fuels. Neutron time-of-flight (TOF) resonance imaging offers a potential approach by exploiting the characteristic neutron absorption spectra of each isotope. However, it is a major challenge to compute quantitatively accurate images due to a variety of confounding effects such as severe Poisson noise, background scatter, beam non-uniformity, absorption non-linearity, and extended source pulse duration. We present the TRINIDI algorithm which is based on a two-step process in which we first estimate the neutron flux and background counts, and then reconstruct the areal densities of each isotope and pixel. Both components are based on the inversion of a forward model that accounts for the highly non-linear absorption, energy-dependent emission profile, and Poisson noise, while also modeling the substantial spatio-temporal variation of the background and flux. Further, to do this, we formulate the non-linear inverse problem as two optimization problems that are solved in sequence. We demonstrate on both synthetic and measured data that TRINIDI can reconstruct quantitatively accurate 2D views of isotopic areal density that can then be reconstructed into quantitatively accurate 3D volumes of isotopic volumetric density.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Replace Human Intelligence with Fast and Smart Geometric Reasoning and Graph Neural Network to Accelerate Next Gen ModSim Workflows

We present an agent-guided approach to CAD geometry decomposition that automates hex/hybrid meshing with graph neural networks (GNNs) to accelerate next-generation ModSim workflows. Our end-to-end pipeline (i) reduces 3D boundary-representation (B-Rep) models to a 2D chordal axis skeleton (CAT) and then to a 1D bipartite graph of surface and curve nodes, (ii) assigns per node labels as Cubit® WebCut actions, (iii) trains a multi-action GNN under supervised learning, and (iv) predicts five surface-node and three curve-node actions on out-of-distribution test geometries. Each graph node carries geometric, topological, and meshing attributes drawn from the B-Rep “skin” and CAT “skeleton,” with two-way mappings across 3D↔2D↔1D representations to maintain traceability back to 3D CAD. The supervised learning model exhibits stable convergence of the binary cross-entropy loss and achieves 98.7% accuracy on unseen lattice models. To operationalize decision-making, we rank predicted commands by geometric significance and prototyped the agent-guided workflow through the Cubit® Meshing PowerTool GUI. As a stretch goal, we explore reinforcement learning (RL) to reduce or remove label requirements and to learn policies for action sequences that maximize total reward (e.g., size of hex-meshable regions and resulting hex mesh quality). When all-hex meshing is not feasible, the agent assists in producing hybrid meshes—prioritizing hex in critical regions and transitioning to tetrahedral elements (tets) elsewhere—maintaining fidelity while ensuring robustness. The overarching objective is to replace manual, heuristics-based decomposition with data-driven, reproducible automation, cutting meshing turnaround time by orders of magnitude. We anticipate direct impact on simulation workflows through intelligent, scalable decomposition of complex CAD models into hex-meshable subdomains.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Closing the Loop between In Situ Stress Complexity and EGS Fracture Complexity

We present an agent-guided approach to CAD geometry decomposition that automates hex/hybrid meshing with graph neural networks (GNNs) to accelerate next-generation ModSim workflows. Our end-to-end pipeline (i) reduces 3D boundary-representation (B-Rep) models to a 2D chordal axis skeleton (CAT) and then to a 1D bipartite graph of surface and curve nodes, (ii) assigns per node labels as Cubit® WebCut actions, (iii) trains a multi-action GNN under supervised learning, and (iv) predicts five surface-node and three curve-node actions on out-of-distribution test geometries. Each graph node carries geometric, topological, and meshing attributes drawn from the B-Rep “skin” and CAT “skeleton,” with two-way mappings across 3D↔2D↔1D representations to maintain traceability back to 3D CAD. The supervised learning model exhibits stable convergence of the binary cross-entropy loss and achieves 98.7% accuracy on unseen lattice models. To operationalize decision-making, we rank predicted commands by geometric significance and prototyped the agent-guided workflow through the Cubit® Meshing PowerTool GUI. As a stretch goal, we explore reinforcement learning (RL) to reduce or remove label requirements and to learn policies for action sequences that maximize total reward (e.g., size of hex-meshable regions and resulting hex mesh quality). When all-hex meshing is not feasible, the agent assists in producing hybrid meshes—prioritizing hex in critical regions and transitioning to tetrahedral elements (tets) elsewhere—maintaining fidelity while ensuring robustness. The overarching objective is to replace manual, heuristics-based decomposition with data-driven, reproducible automation, cutting meshing turnaround time by orders of magnitude. We anticipate direct impact on simulation workflows through intelligent, scalable decomposition of complex CAD models into hex-meshable subdomains.

42 ENGINEERING↗

DOE OSTI2026

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗

DOE OSTI2023

Octofitter: Fast, Flexible, and Accurate Orbit Modeling to Detect Exoplanets

As next-generation imaging instruments and interferometers search for planets closer to their stars, they must contend with increasing orbital motion and longer integration times. These compounding effects make it difficult to detect faint planets but also present an opportunity. Increased orbital motion makes it possible to move the search for planets into the orbital domain, where direct images can be freely combined with the radial velocity and proper motion anomaly, even without a confirmed detection in any single epoch. In this paper, we present a fast and differentiable multimethod orbit-modeling and planet detection code called Octofitter. This code is designed to be highly modular and allows users to easily adjust priors, change parameterizations, and specify arbitrary function relations between the parameters of one or more planets. Octofitter further supplies tools for examining model outputs including prior and posterior predictive checks and simulation-based calibration. We demonstrate the capabilities of Octofitter on real and simulated data from different instruments and methods, including HD 91312, simulated JWST/NIRISS aperture masking interferometry observations, radial velocity curves, and grids of images from the Gemini Planet Imager. We show that Octofitter can reliably recover faint planets in long sequences of images with arbitrary orbital motion. This publicly available tool will enable the broad application of multiepoch and multimethod exoplanet detection, which could improve how future targeted ground- and space-based surveys are performed. Finally, its rapid convergence makes it a useful addition to the existing ecosystem of tools for modeling the orbits of directly imaged planets.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape

The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

First-principles study of the structures and redox mechanisms of Ni-rich lithium nickel manganese cobalt oxides

To reduce the cobalt (Co) content in lithium-ion batteries, Ni-rich (high-Ni) lithium nickel manganese cobalt oxides (NMC) are pursued as one of the next-generation cathode materials. However, there is still debate on the crystal and electronic structures of the baseline, LiNiO 2 . Density Functional Theory (DFT) calculations were performed to provide a theoretical understanding of Ni-rich NMC. First, it was found that the commonly used $R\bar{3}m$ structure for LiNiO 2 is metallic, contrary to the experimentally reported mix-conducting behavior. Among the four different space groups, $R\bar{3}m$, C2/m, P2 1 /c, and P2/c, P2/c with charge disproportionation of Ni 2+ and Ni 4+ is the most energetically stable and semiconducting structure of LiNiO 2 . Therefore, the atomic structures of representative Ni-rich NMC were built by partially replacing Ni with Co or Mn in the P2/c LiNiO 2 to form Li x Ni y Mn z Co 1-y-z O 2 . In the fully lithiated (x=1.0) high Ni content NMC (y>0.5), the oxidation state of all Mn ions becomes 4+, while Co ions still maintain 3+, and part of the Ni ions become 3+ to compensate for the charge. Upon delithiation, the local environment shows more variation of the charge states on the transition metal (TM) ions. The average oxidation on each TM follows a sequence of losing electrons that starts from Ni 2+ to Ni 3+ , then oxidizing Ni 3+ and Co 3+ , while Mn 4+ remains electrochemically inactive till x=0. Finally, a general relationship for the oxidation state change in each TM as a function of x is derived and shows agreement with both modeling and experimental data.

25 ENERGY STORAGE↗

DOE OSTI2026

Small Molecule Inhibitor-Modulated Al 2 O 3 Atomic Layer Deposition on Monolayer MoS 2 for Controlled Nucleation

The integration of ultrathin dielectrics on two-dimensional (2D) semiconductors is essential for advancing beyond-Si electronics. However, the intrinsic inertness of van der Waals 2D basal planes remains a primary bottleneck to achieving uniform dielectric nucleation and growth. Here, in this study, we introduce a small molecule inhibitor (SMI)-modulated thermal atomic layer deposition (ALD) strategy, exemplified by aluminum oxide (Al 2 O 3 ) ALD on monolayer molybdenum disulfide (1L MoS 2 ) with acetic acid (HAc) SMI. The ABC-type sequence comprises HAc inhibitor (A), trimethylaluminum (TMA) precursor (B), and deionized H 2 O coreactant (C). In situ quartz crystal microbalance (QCM) studies reveal robust HAc adsorption on Al 2 O 3 and suppression of subsequent oxide growth on HAc-passivated surfaces. When applied to 1L MoS 2 , this inhibitory pathway enables HAc to selectively passivate nascent Al 2 O 3 nuclei formed on the MoS 2 surface, limiting their three-dimensional (3D) island coarsening and redirecting precursor adsorption toward the uncovered basal plane. Consequently, nearly continuous ultrathin (∼1.5 nm) Al 2 O 3 films are achieved on 1L MoS 2 with markedly improved uniformity compared to standard Al 2 O 3 ALD using TMA and H 2 O, as validated by atomic force microscopy (AFM), cross-sectional scanning transmission electron microscopy (STEM), and energy-dispersive X-ray spectroscopy (EDS). Density functional theory (DFT) calculations further provide atomistic insight into HAc-modulated Al 2 O 3 nucleation, corroborating the energetic preference of HAc for Al 2 O 3 over MoS 2 and attenuated TMA adsorption on HAc-passivated surfaces. Spatially resolved Raman spectroscopy also confirms that the HAc-modulated process preserves the structural integrity of 1L MoS 2 , with only minimal strain and doping perturbations observed after dielectric deposition. This SMI-modulated approach offers a broadly applicable framework for controlling ALD nucleation across various inhibitors, ALD chemistries, and 2D materials, opening opportunities for reliable dielectric integration in next-generation nanoelectronics.

36 MATERIALS SCIENCE↗

DOE OSTI2026

High yield production of 3-hydroxypropionic acid using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Biotechnology↗

DOE OSTI2024

Quasiparticle Poisoning of Superconducting Qubits from Resonant Absorption of Pair-Breaking Photons

The ideal superconductor provides a pristine environment for the delicate states of a quantum computer: because there is an energy gap to excitations, there are no spurious modes with which the qubits can interact, causing irreversible decay of the quantum state. As a practical matter, however, there exists a high density of excitations out of the superconducting ground state even at ultralow temperature; these are known as quasiparticles. Observed quasiparticle densities are of order 1 μ m - 3 , tens of orders of magnitude greater than the equilibrium density expected from theory. Nonequilibrium quasiparticles extract energy from the qubit mode and can induce dephasing. Here we show that a dominant mechanism for quasiparticle poisoning is direct absorption of high-energy photons at the qubit junction. We use a Josephson junction-based photon source to controllably dose qubit circuits with millimeter-wave radiation, and we use an interferometric quantum gate sequence to reconstruct the charge parity of the qubit. We find that the structure of the qubit itself acts as a resonant antenna for millimeter-wave radiation, providing an efficient path for photons to generate quasiparticles. A deep understanding of this physics will pave the way to realization of next-generation superconducting qubits that are robust against quasiparticle poisoning.

Liu, Chuan-Hong↗