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DOE OSTI2022

The QICK (Quantum Instrumentation Control Kit): Readout and control for qubits and detectors

We introduce a Xilinx RF System-on-Chip (RFSoC)-based qubit controller (called the Quantum Instrumentation Control Kit, or QICK for short), which supports the direct synthesis of control pulses with carrier frequencies of up to 6 GHz. The QICK can control multiple qubits or other quantum devices. The QICK consists of a digital board hosting an RFSoC field-programmable gate array, custom firmware, and software and an optional companion custom-designed analog front-end board. We characterize the analog performance of the system as well as its digital latency, important for quantum error correction and feedback protocols. We benchmark the controller by performing standard characterizations of a transmon qubit. We achieve an average gate fidelity of ℱ avg =99.93%. All of the schematics, firmware, and software are open-source.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Superconducting microwave cavities and qubits for quantum information systems

Superconducting microwave cavities featuring ultrahigh Q-factors, which measure the efficiency of energy storage in relation to energy loss in a system, are revolutionizing quantum computing by providing long coherence times exceeding 1 ms, crucial for the development of scalable multi-qubit quantum systems with low error rates. Here, in this work, we provide an in-depth analysis of recent advances in ultrahigh Q-factor cavities, integration of Josephson junction-based qubits, and bosonic-encoded qubits in 3D cavities. We examine the sources of quantum state dephasing caused by damping and noise mechanisms in cavities and qubits, highlighting the critical challenges that need to be addressed to achieve even higher coherence times. We critically survey the latest progress made in implementing single 3D qubits using superconducting materials, normal metals, and multi-qubit and multi-state quantum systems. Our work sheds light on the promising future of this research area, including novel materials for cavities and qubits, modes with nontrivial topological properties, error correction techniques for bosonic qubits, and new light–matter interaction effects.

3D printing↗

DOE OSTI2024

Accurate numerical simulations of open quantum systems using spectral tensor trains

Decoherence between qubits is a major bottleneck in quantum computations. Decoherence results from intrinsic quantum and thermal fluctuations as well as noise in the external fields that perform the measurement and preparation processes. With prescribed colored noise spectra for intrinsic and extrinsic noise, we present a numerical method, Quantum Accelerated Stochastic Propagator Evaluation (Q-ASPEN), to solve the time-dependent noise-averaged reduced density matrix in the presence of intrinsic and extrinsic noise. Q-ASPEN is arbitrarily accurate and can be applied to provide estimates for the resources needed to error-correct quantum computations. We employ spectral tensor trains, which combine the advantages of tensor networks and pseudospectral methods, as a variational ansatz to the quantum relaxation problem and optimize the ansatz using methods typically used to train neural networks. Here, the spectral tensor trains in Q-ASPEN make accurate calculations with tens of quantum levels feasible. We present benchmarks for Q-ASPEN on the spin-boson model in the presence of intrinsic noise and on a quantum chain of up to 32 sites in the presence of extrinsic noise. In our benchmark, the memory cost of Q-ASPEN scales as a low-order polynomial in the size of the system once the number of system states surpasses the number of basis functions used in the spectral expansion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Scalable quantum computational science: A perspective from block-encodings and polynomial transformations

Significant developments made in quantum hardware and error correction recently have been driving quantum computing toward practical utility. However, gaps remain between abstract quantum algorithmic development and practical applications in computational sciences. In this perspective article, we propose several properties that scalable quantum computational science methods should possess. We further discuss how block-encodings and polynomial transformations can potentially serve as a unified framework with the desired properties. Recent advancements on these topics are presented, including the construction and assembly of block-encodings, and various generalizations of quantum signal processing (QSP) algorithms to perform polynomial transformations. The scalability of QSP methods on parallel and distributed quantum architectures is also highlighted. Promising applications in simulation and observable estimation in chemistry, physics, and optimization problems are presented. We hope this perspective serves as a gentle introduction to state-of-the-art quantum algorithms for the computational science community and inspires future development of scalable quantum computational science methodologies that bridge theory and practice.

Bayesian inference↗

DOE OSTI2019

Recording of pulsed currents by a fibre-optic Faraday effect-based sensor with limited frequency band

We have studied, experimentally and theoretically, the dependence of the amplitude and noise response parameters of a fibre-optic Faraday effect-based current sensor on the photodetector frequency band in recording rectangular current pulses, the duration of which does not exceed the time of light propagation through the sensing fibre. The presence of an optimal band at which the signal-to-noise ratio has a pronounced maximum is demonstrated. It is shown that the optimal bandwidth is close in magnitude to the inverse time of light passage through the fibre. The revealed feature is explained by the difference in dependences of the response amplitude and the white noise level of optical radiation on the frequency band of the photodetector. A technique for amplitude error correction at the optimal band is proposed. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Optimization on fixed low latency implementation of the GBT core in FPGA

We present that in the upgrade of ATLAS experiment, the front-end electronics components are subjected to a large radiation background. Meanwhile high speed optical links are required for the data transmission between the on-detector and off-detector electronics. The GBT architecture and the Versatile Link (VL) project are designed by CERN to support the 4.8 Gbps line rate bidirectional high-speed data transmission which is called GBT link. In the ATLAS upgrade, besides the link with on-detector, the GBT link is also used between different off-detector systems. The GBTX ASIC is designed for the on-detector front-end, correspondingly for the off-detector electronics, the GBT architecture is implemented in Field Programmable Gate Arrays (FPGA). CERN launches the GBT-FPGA project to provide examples in different types of FPGA. In the ATLAS upgrade framework, the Front-End LInk eXchange (FELIX) system is used to interface the front end electronics of several ATLAS subsystems. The GBT link is used between them, to transfer the detector data and the timing, trigger, control and monitoring information. The trigger signal distributed in the down-link from FELIX to the front-end requires a fixed and low latency. In this paper, several optimizations on the GBT-FPGA IP core are introduced, to achieve a lower fixed latency. For FELIX, a common firmware will be used to interface different front-ends with support of both GBT modes: the forward error correction mode and the wide mode. The modified GBT-FPGA core has the ability to switch between the GBT modes without FPGA reprogramming. Finally, the system clock distribution of the multi-channel FELIX firmware is also discussed in this paper.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

The hybrid topological longitudinal transmon qubit

We introduce a new hybrid qubit consisting of a Majorana qubit interacting with a transmon longitudinally coupled to a resonator. To do so, we equip the longitudinal transmon qubit with topological quasiparticles, supported by an array of heterostructure nanowires, and derive charge- and phase-based interactions between the Majorana qubit and the resonator and transmon degrees of freedom. Inspecting the charge coupling, we demonstrate that the Majorana self-charging can be eliminated by a judicious choice of charge offset, thereby maintaining the Majorana degeneracy regardless of the quasiparticles spatial arrangement and parity configuration. We perform analytic and numerical calculations to derive the effective qubit-qubit interaction elements and discuss their potential utility for state readout and quantum error correction. Further, we find that select interactions depend strongly on the overall superconducting parity, which may provide a direct mechanism to characterize deleterious quasiparticle poisoning processes.

36 MATERIALS SCIENCE↗

DOE OSTI2022

RF-Net 2: fast inference of virus reassortment and hybridization networks

Abstract Motivation A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. Results Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. Availability and implementation RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. Supplementary information Supplementary data are available at Bioinformatics online.

Markin, Alexey (ORCID:0000000332809050)↗

DOE OSTI2022

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Red Dragon: a redshift-evolving Gaussian mixture model for galaxies

ABSTRACT Precision-era optical cluster cosmology calls for a precise definition of the red sequence (RS), consistent across redshift. To this end, we present the Red Dragon algorithm: an error-corrected multivariate Gaussian mixture model (GMM). Simultaneous use of multiple colours and smooth evolution of GMM parameters result in a continuous RS and blue cloud (BC) characterization across redshift, avoiding the discontinuities of red fraction inherent in swapping RS selection colours. Based on a mid-redshift spectroscopic sample of SDSS galaxies, an RS defined by Red Dragon selects quiescent galaxies (low specific star formation rate) with a balanced accuracy of over $90{{\ \rm per\ cent}}$. This approach to galaxy population assignment gives more natural separations between RS and BC galaxies than hard cuts in colour–magnitude or colour–colour spaces. The Red Dragon algorithm is publicly available at bitbucket.org/wkblack/red-dragon-gamma/.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions

Abstract Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene libraries by compartmentalizing and assembling microarray-derived oligonucleotides in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia

Abstract The ability to deduce carcinogenic potential from subchronic, repeat dose rodent studies would constitute a major advance in chemical safety assessment and drug development. This study investigated an error-corrected NGS method (CarcSeq) for quantifying cancer driver mutations (CDMs) and deriving a metric of clonal expansion predictive of future neoplastic potential. CarcSeq was designed to interrogate subsets of amplicons encompassing hotspot CDMs applicable to a variety of cancers. Previously, normal human breast DNA was analyzed by CarcSeq and metrics based on mammary-specific CDMs were correlated with tissue donor age, a surrogate of breast cancer risk. Here we report development of parallel methodologies for rat. The utility of the rat CarcSeq method for predicting neoplastic potential was investigated by analyzing mammary tissue of 16-week-old untreated rats with known differences in spontaneous mammary neoplasia (Fischer 344, Wistar Han, and Sprague Dawley). Hundreds of mutants with mutant fractions ≥ 10−4 were quantified in each strain, most were recurrent mutations, and 42.5% of the nonsynonymous mutations have human homologs. Mutants in the mammary-specific target of the most tumor-sensitive strain (Sprague Dawley) showed the greatest nonsynonymous/synonymous mutation ratio, indicative of positive selection consistent with clonal expansion. For the mammary-specific target (Hras, Pik3ca, and Tp53 amplicons), median absolute deviation correlated with percentages of rats that develop spontaneous mammary neoplasia at 104 weeks (Pearson r = 1.0000, 1-tailed p = .0010). Therefore, this study produced evidence CarcSeq analysis of spontaneously occurring CDMs can be used to derive an early metric of clonal expansion relatable to long-term neoplastic outcome.

McKim, Karen L.↗

DOE OSTI2023

Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 ‘loop’ structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 ‘loop’ is a stiff, α-helical ‘switchback’ structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore–microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Constant Overhead Entanglement Distillation via Scrambling

High-fidelity quantum entanglement enables key quantum networking capabilities such as secure communication and distributed quantum computing, but long-distance entanglement distribution is limited by noise and loss. Entanglement distillation protocols address this problem by extracting high-fidelity Bell pairs from multiple noisy ones. The primary objective is minimizing the resource overhead: the number of noisy input pairs needed to distill each high-fidelity output pair. While protocols achieving optimal overhead are known in theory, they often require complex decoding operations that make practical implementation challenging. We circumvent this challenge by introducing protocols that use quantum scrambling—the spreading of quantum information under chaotic dynamics—through random Clifford operations. Based on this scrambling mechanism, our protocol maintains asymptotically constant overhead, independent of the desired output error rate $\bar{𝜖}$ , and can be implemented with shallow quantum circuits of depth 𝑂⁡(poly log log⁡ $\bar{𝜖}$ −1 ) and memory 𝑂⁡(poly log⁡ $\bar{𝜖}$ −1 ). Our protocol remains effective even with noisy quantum gates. By incorporating error correction, our protocol achieves state-of-the-art performance: starting with pairs of 10% initial infidelity, we require only seven noisy inputs per output pair to distill a single Bell pair with infidelity $\bar{𝜖}$ =10 −12 , substantially outperforming existing schemes. We demonstrate the utility of our protocols for quantum repeater networks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Hybrid Oscillator-Qubit Quantum Processors: Instruction Set Architectures, Abstract Machine Models, and Applications

This tutorial offers a pedagogical guide to hybrid quantum processors that integrate discrete-variable (DV) qubits and continuous-variable (CV) oscillators. Aimed at computer scientists, engineers, and physicists, it provides an overview of the experimental, algorithmic, and architectural aspects of this novel and rapidly developing hardware model. Experimental realizations of this model include superconducting, trapped-ion, and neutral-atom platforms. By combining DV and CV components, hybrid oscillator-qubit processors enable a powerful new paradigm that offers complementary strengths for quantum control, error correction, computation, and simulation. Working toward the goal of a full-stack system connecting applications to CV-DV hardware, we define and formulate abstract machine models and instruction set architectures. These essential abstractions enable codesign of hardware and software, and resource estimation for exploring the potential of current and future hardware for computational and simulation tasks. Using these abstractions, we present both new and existing examples that illustrate the benefits of hybrid CV-DV processors relative to traditional DV-only hardware in computation as well as quantum simulation of physical models. Examples include algorithms for transferring states between DV and CV systems, performing the quantum Fourier transform, and simulation of lattice gauge theories. Relative to qubit-only hardware, the bosonic degrees of freedom natively available in hybrid architectures can substantially reduce the circuit complexity of simulations for physical models containing bosons. A key technique is the extension of quantum signal processing ideas to CV-DV systems. This work is intended to serve as a timely and comprehensive guide to this relatively unexplored yet promising approach to quantum computation and to provide a road map to guide future development.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Profusion of symmetry-protected qubits from stable ergodicity breaking

We show how combining a discrete symmetry with topological Hilbert space fragmentation can give rise to exponentially many topologically stable qubits protected by a single discrete symmetry. We illustrate this explicitly with the example of the CZ𝑝 model, where the encoded qubits are prethermally stable to arbitrary symmetry-respecting perturbations for parametrically long times, substantially enhancing the robustness of a recently proposed construction based on nontopological fragmentation. In this model, the encoded qubits naturally come in pairs for which a universal set of transversal logical gates can be performed, ruling out (by the Eastin-Knill theorem) the possibility of using them for quantum error correction. We also comment on the combination of symmetry enrichment and topological fragmentation more generally, and the implications for use of systems exhibiting Hilbert space fragmentation as quantum memories.

kinetically constrained models↗

DOE OSTI2025

Braiding for the win: Harnessing braiding statistics in topological states to play quantum games

Nonlocal quantum games provide proof of principle that quantum resources can confer an advantage at certain tasks. They also provide a compelling way to explore the computational utility of phases of matter on quantum hardware. In a recent paper [O. Hart et al., Phys. Rev. Lett. 134, 130602 (2025)], we demonstrated that a toric code resource state conferred advantage at a certain nonlocal game, which remained robust to small deformations of the resource state. In this paper we demonstrate that this robust advantage is a generic property of resource states drawn from topological or fracton ordered phases of quantum matter. To this end, we illustrate how several other states from paradigmatic topological and fracton ordered phases can function as resources for suitably defined nonlocal games, notably the three-dimensional toric-code phase, the X-cube fracton phase, and the double-semion phase. The key in every case is to design a nonlocal game that harnesses the characteristic braiding processes of a quantum phase as a source of contextuality. We unify the strategies that take advantage of mutual statistics by relating the operators to be measured to order and disorder parameters of an underlying generalized symmetry-breaking phase transition. Additionally, by connecting the win probability to twist products, we show that success at the game serves as a many-body entanglement witness. Namely, if the players implement a perfect quantum strategy on large length scales, the quantum state they share cannot be connected to a trivial product state via a constant-depth local unitary circuit. Lastly, we massively generalize the family of games that admit perfect strategies when codewords of homological quantum error-correcting codes are used as resources.

Fractons↗

DOE OSTI2026

Noninvasive mid-circuit measurement and reset on atomic qubits

Mid-circuit measurement and reset of subsets of qubits are crucial ingredients of quantum error correction and many quantum information applications. Measurement of atomic qubits is accomplished through resonant fluorescence, which typically disturbs neighboring atoms due to photon scattering. We propose and prototype a scheme for measurement and reset that provides both spatial and spectral isolation by using tightly focused laser beams and narrow atomic transitions. The unique advantage of this scheme is that all operations are applied exclusively to the read-out qubit, with little overhead and negligible disturbance to the other qubits of the same species. In this paper, we pave the way for noninvasive and high-fidelity mid-circuit measurement and demonstrate all key building blocks on a single trapped barium ion.

atomic systems↗