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At least 271 records · Page 15

Ta Based Damascene Resonators

Transmon qubits have become a leading technology in quantum information science (QIS), with fabrication techniques widely accessible. Historically, devices were predominantly made from aluminum (Al) and niobium (Nb), but state-of-the-art transmons now use tantalum (Ta) achieving coherence times up to and exceeding 0.5 milliseconds [1-3]. The differentiation in performance between Ta and Nb-based devices is attributed to the surface oxidation states affecting Two-Level-System (TLS) noise. One approach to quickly evaluating material and device performance consists of fabricating only the readout resonator of a qubit and evaluating the quality factor which is the strategy employed in this project. Our research focuses on Ta coplanar waveguide (CPW) resonators fabricated using a damascene technique producing pristine metal structures within silicon substrates. This approach increases the dielectric substrate's participation ratio while keeping device edges oxide-free due to entrenchment. This collaborative effort, involving Pacific Northwest National Laboratory (PNNL), NY CREATES/SUNY Poly, and Brookhaven National Laboratory (BNL), has resulted in resonators with Q factors as high as 104 at low power. Ongoing studies aim to further understand and improve device performance by systematic analysis of oxygen trapped between device layers during processing. This research showcases the potential for significant improvements in superconducting qubit performance via the damascene process, heralding new possibilities for the advancement of scalable QIS technology.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Fast superconducting qubit control with subharmonic drives

Increasing the fidelity of single-qubit gates requires a combination of faster pulses and increased qubit coherence. However, these requirements can be contradictory. Additionally, increasing the drive power can heat the qubit’s environment and degrade coherence. In this work, we circumvent this issue and achieve rapid gates by pumping a transmon’s native Kerr at approximately one third of the qubit’s resonant frequency. The subharmonic Rabi rate of the process is proportional to applied drive amplitude cubed, allowing for rapid gates. In addition, we demonstrate that filtering can be used to protect the qubit’s coherence while performing rapid gates. Single qubit gates as short as 37.4 ns are demonstrated with fidelity of 99.91%. We present theoretical calculations indicating that drive induced multi-photon decay will not limit qubit lifetime; calculated power absorption also indicates that this technique could reduce cryostat heating for fast gates, a vital requirement for large-scale quantum computers.

Xia, Mingkang [Univ. of Pittsburgh, PA (United Sta↗

Photochemistry of Pyrimidine in Astrophysical Ices: Formation of Nucleobases and Other Prebiotic Species

Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA. They are divided into two molecular groups: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites, and their extraterrestrial origin confirmed by isotopic measurements. Although no N-heterocycles have ever been observed in the ISM, the positions of the 6.2- m interstellar emission features suggest a population of such molecules is likely to be present. However, laboratory experiments have shown that the ultraviolet (UV) irradiation of pyrimidine in ices of astrophysical relevance such as H2O, NH3, CH3OH, CH4, CO, or combinations of these at low temperature (less than or equal to 20 K) leads to the formation of several pyrimidine derivatives including the nucleobases uracil and cytosine, as well as precursors such as 4(3H)-pyrimidone and 4-aminopyrimidine. Quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways.10 In those residues, other species of prebiotic interest such as urea as well as the amino acids glycine and alanine could also be identified. However, only very small amounts of pyrimidine derivatives containing CH3 groups could be detected, suggesting that the addition of methyl groups to pyrimidine is not an efficient process. For this reason, the nucleobase thymine was not observed in any of the samples. In this work, we study the formation of nucleobases and other photo-products of prebiotic interest from the UV irradiation of pyrimidine in ices containing H2O, NH3, CH3OH, and CO, mixed in astrophysical proportions.

Nuevo, Michel↗

Review of SiC material development for nuclear fusion applications: Cross-cutting research and emerging opportunities

The SiC-based materials, particularly SiC-fiber-reinforced SiC matrix (SiC/SiC) composites, show strong potential for structural and functional applications in future fusion power plants because they can operate at high temperatures with a range of coolants and breeders, thereby enabling higher energy conversion efficiency. Here, this paper presents recent advancements in the development of SiC-based materials, focusing on processing techniques and material performance and resistance under fusion-relevant environments. The processing activities have emphasized near-net-shape fabrication and the joining of SiC subcomponents, with processing methods and material compositions informed by previous irradiation experiments on various grades of SiC. Research on irradiation effects has remained focused on degradation mechanisms and the microstructural optimization of SiC/SiC composites irradiated to high neutron damage levels. Analysis of irradiation defects in SiC has advanced via the application of cutting-edge characterization methods, among which Raman spectroscopy is becoming a common tool to assess atomic-scale chemical disorder. Fusion–fission crosscutting irradiation research has explored combined effects in SiC/SiC composites with application-relevant geometries, including bowing of SiC/SiC composite channels under neutron flux gradients, stress evolution in SiC/SiC composite tubes under through-thickness temperature gradients, and irradiation-enhanced corrosion in SiC. Finally, research opportunities for component testing and assessment under fusion-relevant conditions, in support of emerging concepts from the private fusion sector, are discussed.

Advanced manufacturing↗

Overlapping qubits from non-isometric maps and de Sitter tensor networks

The emergence of a local effective theory from a more fundamental theory of quantum gravity with seemingly fewer degrees of freedom is a major puzzle of theoretical physics. A recent approach to this problem is to consider general features of the Hilbert space maps relating these theories. In this work, we construct approximately local observables, or overlapping qubits, from such non-isometric maps. We show that local processes in effective theories can be spoofed with a quantum system with fewer degrees of freedom, with deviations from actual locality identifiable as features of quantum gravity. For a concrete example, we construct two tensor network models of de Sitter space-time, demonstrating how exponential expansion and local physics can be spoofed for a long period before breaking down. Our results highlight the connection between overlapping qubits, Hilbert space dimension verification, degree-of-freedom counting in black holes, holography, and approximate locality in quantum gravity.

Quantum information↗

Disruptive Technologies and Their Putative Impacts Upon Society and Aerospace- Entering The Virtual Age

Developments in technology over the recent decades have been extraordinary. They include the IT, bio, nano, and now quantum and energetics technology arenas and their many combinatorial interactions and impacts. In the main, these are at the frontiers of the small and in a combinational, synergistic feeding frenzy with each other. They fall under the broad category of Disruptive Technologies and have greatly altered society. The outlook for the runout of these and other technology developments augers mid-term to later alterations in components of the human existence theorem, including the requirement to work for our living and our physiological makeup and longevity (Ref 1). The IT revolution began in the 1950s with the development of solid-state electronics. The biologics revolution began later in the 1960s and 1970s with DNA and genomics, and the nano revolution in the 1990s with self-forming nano systems and carbon nanotubes. Quantum technology is now developing rapidly, aided by enabling nano systems, and the energetics revolution is providing ever more efficient and less expensive renewable energy sources. The IT revolution has produced improvements of an astounding eleven orders of magnitude in computing speed since the late 1950s. As we shift from silicon to biological, optical, nano, molecular, and atomic computing, improvements of some 4 orders of magnitude are evidently possible from either optical or DNA computing [Refs 2and 3], then there are combinatorials. Then there is quantum computing, under development worldwide for an increasing number of applications and proffering phenomenal capabilities. The current fastest computers are considerably beyond human brain speed. Machine intelligence is developing well after decades of inadequate machine capability, now no longer the case, and a detour into expert systems. Researchers in machine intelligence are now pursuing deep learning approaches using neural nets, which are proving to be extremely useful. Some believe the frontier of potential human-level machine intelligence may be found in biomimetics and brain-emulation approaches. There is even a possibility of “emergence”—i.e., when the machine intelligence is complex enough that it “wakes up,” as when human intelligence emerged via evolution during the million-plus years of the hunter-gatherer epoch [ Ref 4]. In fact, some posit that human intelligence can be improved upon and is only a cul-de-sac of what is conceivable. The IT revolution has produced massive changes in human society and economics—from the Internet, enabling the rapid expansion of knowledgeability (and even what is knowable), to an increasingly pervasive trend of “tele-everything.” The extraordinary compilation, storage, and availability of truly massive amounts of information could, when combined with AI and under the mantra of “big data,” greatly improve many of our technical and commercial processes and their content including elucidating new heuristic governing laws.

Dennis M. Bushnell↗

Carbon-Based Quantum Information Science with Symmetry Protected Topological States (Final Report, DOE-BES award DE-SC0023105)

This research program established the scientific foundation for the rational, bottom-up design, synthesis, isolation, and investigation of symmetry-protected topological (SPT) electron spin qubits embedded in graphene nanoribbons (GNRs). The work focused on integrating atomically precise low-dimensional carbon nanostructures with emerging quantum logic architectures, providing a pathway toward scalable quantum materials for next-generation computing and sensing technologies. A central component of the program was the elucidation of fundamental relationships between real-space molecular architecture, local spin density distributions, electronic band dispersion, and energy level alignment in atomically precise GNR systems. These correlations define key operational parameters of SPT qubits and were systematically investigated to establish quantitative benchmarks against established molecular and solid-state spin qubit platforms. Attention was given to properties critical for quantum device performance, e.g. decoherence times, spectral sharpness of energy transitions, and tunable exchange interactions between spin states. The research demonstrated that these parameters can be engineered with atomic precision through scalable bottom-up synthetic strategies. Theory-guided design played a central role in identifying candidate structures hosting topologically protected spin states. Experimental validation was performed using both ensemble measurements and single-molecule characterization. In addition to advances in quantum materials synthesis, the program developed and applied spin-sensitive scanning probe microscopy techniques capable of directly probing quantum states and dynamic processes with atomic-scale spatial resolution. These capabilities enabled direct observation and characterization of quantum structures at the single-atom level. While the research activities were primarily hypothesis-driven fundamental investigations, the program adopted a comprehensive materials-by-design framework aimed at translating scientific discoveries into technological concepts compatible with scalable and intelligent manufacturing approaches.

36 MATERIALS SCIENCE↗

Studying phonon coherence with a quantum sensor

Nanomechanical oscillators offer numerous advantages for quantum technologies. Their integration with superconducting qubits shows promise for hardware-efficient quantum error-correction protocols involving superpositions of mechanical coherent states. Limitations of this approach include mechanical decoherence processes, particularly two-level system (TLS) defects, which have been widely studied using classical fields and detectors. In this manuscript, we use a superconducting qubit as a quantum sensor to perform phonon number-resolved measurements on a piezoelectrically coupled phononic crystal cavity. This enables a high-resolution study of mechanical dissipation and dephasing in coherent states of variable size ($\overline{n}$ ≃ 1 – 10 phonons). We observe nonexponential relaxation and state size-dependent reduction of the dephasing rate, which we attribute to TLS. Using a numerical model, we reproduce the dissipation signatures (and to a lesser extent, the dephasing signatures) via emission into a small ensemble (N = 5) of rapidly dephasing TLS. Our findings comprise a detailed examination of TLS-induced phonon decoherence in the quantum regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Enabling ambient stability and quantum integration of organometallic magnonic ferrimagnets via atomic layer encapsulation

Magnons, the quanta of spin waves in magnetic materials, are promising for hybrid quantum systems by bridging electromagnetic and spin degrees of freedom. The organometallic ferrimagnet vanadium tetracyanoethylene (V[TCNE] x , x ≈ 2) is especially well-suited for quantum magnonics due to its low Gilbert damping and substrate versatility. However, its rapid chemical degradation in ambient conditions hinders practical applications. Incumbent encapsulation methods provide some protection, but are bulky, obscure intrinsic properties of V[TCNE] x , introduce thermal stress at cryogenic temperatures, and complicate microwave device integration. Here, we demonstrate that ultrathin alumina films deposited via low-temperature atomic layer deposition effectively protect V[TCNE] x by preserving its magnetic and magnonic properties following ambient exposure. The sub-100 nm transparent films also enable advanced spectroscopy, magnetometry, and cavity magnonic measurements that reveal the intrinsic properties of V[TCNE] x . This encapsulation strategy advances molecule-based quantum information science by providing a robust route toward scalable, monolithic integration in hybrid quantum technologies.

magnetic materials↗

Towards universal unfolding of detector effects in high-energy physics using denoising diffusion probabilistic models

Correcting for detector effects in experimental data, particularly through unfolding, is critical for enabling precision measurements in high-energy physics. However, traditional unfolding methods face challenges in scalability, flexibility, and dependence on simulations. We introduce a novel approach to multidimensional object-wise unfolding using conditional Denoising Diffusion Probabilistic Models (cDDPM). Our method utilizes the cDDPM for a non-iterative, flexible posterior sampling approach, incorporating distribution moments as conditioning information, which exhibits a strong inductive bias that allows it to generalize to unseen physics processes without explicitly assuming the underlying distribution. Our results highlight the potential of this method as a step towards a "universal" unfolding tool that reduces dependence on truth-level assumptions, while enabling the unfolding of a wide range of measured distributions with improved adaptability and accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Current-based metrology with two-terminal mesoscopic conductors

The traditional approach to quantum parameter estimation focuses on the quantum state, deriving fundamental bounds on precision through the quantum Fisher information. In most experimental settings, however, performing arbitrary quantum measurements is highly unfeasible. In open quantum systems, an alternative approach to metrology involves the measurement of stochastic currents flowing from the system to its environment. However, the present understanding of current-based metrology is mostly limited to Markovian master equations. Considering a parameter estimation problem in a two-terminal mesoscopic conductor, we identify the key elements that determine estimation precision within the Landauer-Büttiker formalism. Crucially, this approach allows us to address arbitrary coupling and temperature regimes. Furthermore, we obtain analytical results for the precision in linear-response and zero-temperature regimes. For the specific parameter estimation task that we consider, we demonstrate that the boxcar transmission function is optimal for current-based metrology in all parameter regimes.

Landauer formula↗

An Atom-Precise Approach to Damp First-Order Phase Transitions and Its Implications for Neuromorphic Signal Processing

Neuromorphic computing inspired by mammalian intelligence aims to emulate the nonlinear dynamics of biological neurons and synapses to achieve fast, low-energy, and highly efficient information processing. Brain-inspired computing relies on the design and discovery of materials exhibiting nonlinear current–voltage profiles, frequently underpinned by electronic state transitions, to achieve spiking neurons and dynamically tunable synapses. A signature challenge in the design of artificial neurons is controlling the steepness of first-order transitions in active elements, as abrupt transitions are at risk of driving unstable voltage and temperature oscillations, which result in catastrophic device failure. A critical knowledge gap is the lack of structure–function correlations mapping the composition and atomistic structure of crystalline solids to nonlinear dynamical response characteristics. Here, we address the key question of how modification of atomistic structure correlates with alteration of neuron-like functionality. Constructing oscillator circuits from millimeter-scale single crystals enables high-resolution atomic structure solutions, which we use to demonstrate that the selective positioning of Pb cations modifies charge ordering along a one-dimensional CuxV2O5 framework even at low insertion stoichiometries, thereby providing an atom-precise design parameter for damping first-order transitions. We use temperature-variant X-ray diffraction and X-ray spectroscopy to elucidate the suppression of Cu-ion shuttling based on the precise positioning of Pb ions in seven-coordinated tunnel interstitial sites as the mechanistic basis for transition broadening, thus bridging a critical gap between statistical mechanics and quantum chemical descriptions of phase transitions. Such mechanistic understanding thus paves the way to site-selective modification strategies for modulating the sharpness of first-order transitions, with an exemplary demonstration here in tuning neuronal signal processing.

Crystal structure↗

Designing open quantum systems with known steady states: Davies generators and beyond

We provide a systematic framework for constructing generic models of nonequilibrium quantum dynamics with a target stationary (mixed) state. Our framework identifies (almost) all combinations of Hamiltonian and dissipative dynamics that relax to a steady state of interest, generalizing the Davies’ generator for dissipative relaxation at finite temperature to nonequilibrium dynamics targeting arbitrary stationary states. We focus on Gibbs states of stabilizer Hamiltonians, identifying local Lindbladians compatible therewith by constraining the rates of dissipative and unitary processes. Moreover, given terms in the Lindbladian not compatible with the target state, our formalism identifies the operations – including syndrome measurements and local feedback – one must apply to correct these errors. Our methods also reveal new models of quantum dynamics: for example, we provide a “measurement-induced phase transition” in which measurable two-point functions exhibit critical (power-law) scaling with distance at a critical ratio of the transverse field and rate of measurement and feedback. Time-reversal symmetry – defined naturally within our formalism – can be broken both in effectively classical and intrinsically quantum ways. Our framework provides a systematic starting point for exploring the landscape of dynamical universality classes in open quantum systems, as well as identifying new protocols for quantum error correction.

Guo, Jinkang [Department of Physics and Center for↗

Time-dependent phenomena in correlated materials

Understanding time-dependent processes and light-matter interaction in strongly correlated materials, and the interplay between electronic, orbital, vibrational, and spin degrees of freedom, is a cornerstone of condensed matter. These mechanisms can be proven by measuring the response of the systems to time-dependent perturbations. The corresponding time scales are dictated by the way light couples to the different excitations, and how these excitations exchange energy and momentum. Our research advances our understanding of these processes, and the interpretation of different equilibrium and time-resolved spectroscopies. Our project encompasses two main themes: (i) developing and refining computational techniques to study non-equilibrium spectroscopies including non-perturbative effects and (ii) applications to non-equilibrium phenomena. We have developed a new computational approach that works directly in the time domain: by including all the degrees of freedom involved in the scattering process (e.g. electrons, photons, neutrons), we solve the time dependent problem: a faithful numerical simulation of the experiment. By measuring the energy and momentum of the outgoing particles, we can extract information about the energy and momentum absorbed by the system. Prior to our work, people attempting to model and calculate non-equilibrium spectral functions relied on a description of the scattering cross section based on a formulation in the frequency domain, a treatment that is extremely cumbersome and complex. Our technique works in and out of equilibrium and can reproduce spectra by several spectroscopic techniques, such as time-resolved photoemission, neutron scattering, Raman, X-ray spectroscopies (RIXS, Auger, XAS, XMCD), and, by not relying on analytical approximations, yields results that reveal novel overlooked transient mechanisms. These tools provide sorely needed intuition for understanding the phenomenology of strongly correlated materials and will help experimentalists in identifying signatures of relevant excitations in pump-probe experiments, such as those conducted in DOE supported facilities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Tomography of entangling two-qubit logic operations in exchange-coupled donor electron spin qubits

Scalable quantum processors require high-fidelity universal quantum logic operations in a manufacturable physical platform. Donors in silicon provide atomic size, excellent quantum coherence and compatibility with standard semiconductor processing, but no entanglement between donor-bound electron spins has been demonstrated to date. Here we present the experimental demonstration and tomography of universal one- and two-qubit gates in a system of two weakly exchange-coupled electrons, bound to single phosphorus donors introduced in silicon by ion implantation. We observe that the exchange interaction has no effect on the qubit coherence. We quantify the fidelity of the quantum operations using gate set tomography (GST), and we use the universal gate set to create entangled Bell states of the electrons spins, with fidelity 91.3 ± 3.0%, and concurrence 0.87 ± 0.05. These results form the necessary basis for scaling up donor-based quantum computers.

42 ENGINEERING↗

Meteorological and Soil Data from Ecohydrology Sensor Towers at Pump House and Snodgrass Mountain in East River Watershed, Colorado, 2019-2025

This data package includes hourly meteorological and soil sensor data at eight ecohydrology monitoring sites in East River Watershed, Colorado as part of the Watershed Function Scientific Focus Area (WFSFA) research led by Lawrence Berkeley National Lab (LBNL). Four field sites were located on the hillslope of East River (ER) near Pump House (PH) at Mount Crested Butte (ER-PHS1 to 4), and the other four are in the Snodgrass Mountain (SG) area (SG-EHS5 to 8). In terms of vegetation cover, three sites are in montane grasslands (ER-PHS1, ER-PHS2, and SG-EHS5), three are below evergreen conifer canopy (ER-PHS3, SG-EHS6, and SG-EHS7), and two are below deciduous aspen canopy (ER-PHS4 and SG-EHS8). The monitoring period began in October 2019 at the East River sites, in October 2020 at SG-EHS5 and SG-EHS6, and in October 2021 at SG-EHS7 and SG-EHS8. In September 2024, all four East River sites were fully retired. The four Snodgrass Mountain sites remain active. Each site is equipped with a comprehensive suite of meteorological sensors on a tripod and soil sensors that measure weather, energy fluxes, and soil variables. This data package includes measurements from ten different types of sensors and up to thirteen individual sensors per site, including (1) a weather station (measurement height ranges from 2.8~3.8 meters (m) above ground), (2) a quantum sensor for photosynthetic active radiation (PAR) (2.4~3.3m), (3) a net radiometer (1.7~2.1m), (4) an infrared radiometer (1.6~2.2m), (5) a sonic distance sensor (1.5~1.9m), (6) a soil carbon dioxide (CO2) flux chamber (0m), (7) a soil heat flux plate (-0.05m below ground), (8) a soil oxygen sensor (-0.3m), (9) a soil water potential sensor (-0.3m), and (10) soil water content sensors at 3~4 depths (-1.15 ~ -0.1m). A total of twenty-three variables is reported in this data package, including (1) atmospheric variables: air temperature (TA), atmospheric pressure (PA), vapor pressure (VP), and vapor pressure deficit (VPD), (2) precipitation variables: rain precipitation (P) and snow depth (D_SNOW), (3) energy fluxes variables: four-component net radiation (NETRAD) (shortwave/longwave incoming/outgoing radiation, SW_IN, SW_OUT, LW_IN, LW_OUT), photosynthetic photon flux density (PPFD), and soil heat flux (G), (4) soil variables: soil water content (SWC), soil water potential (SWP), soil temperature (TS), soil bulk electrical conductivity (COND_SOIL), and soil gaseous oxygen concentration (O2_SOIL), (5) wind variables: two-dimensional wind speed (WS), gust speed (WS_MAX), and wind direction (WD), and (6) surface variables: surface infrared temperature (T_CANOPY) and soil CO2 flux (CO2_SOIL). Please see the Methods section for data processing and QA/QC steps taken to generate the hourly datasets. The following files are included in this data package (notes on version: v{x}-{y}, where x is the metadata version, and y is the data version, when applicable): (1) “metadata_site_v{x}-{y}.csv” - a site metadata file that summarizes location information of all sites, including site ID, description, coordinates, timeframe, elevation, and vegetation cover, (2) “metadata_instrument_v{x}-{y}.csv” - an instrument metadata file that summarizes sensor information of all sites, including sensor manufacturer and model, measurement height, and sampling and averaging interval of all variables, (3) "data_{SITE_ID}_v{x}-{y}.csv" - eight data files that contain hourly data of each site indicated by {SITE_ID} in the filename, (4) “/figure/data_{SITE_ID}_v{x}-{y}.png" - eight figures that help visualize data of each site indicated by {SITE_ID} in the filename, (5) “/photo/*” - photos of each site indicated by {SITE_ID} in the filename, and (6) four file level metadata (flmd.csv) and data dictionary (*_dd.csv) files that summarize file, header, column, and variable information of all files. Notes: (1) Measurement height: Each variable name is followed by conventional positional qualifiers “H_V_R”, where H indicates the relative horizontal positions of that specific variable, V the vertical positions, and R the replicates. In this data package, only the vertical qualifier V varies, and V increases from the highest vertical position (V=1) to the lowest. Variables with the same qualifier are not necessarily measured by the same sensor, and the same variable with the same qualifier across different sites are not necessarily measured at the same height. Please refer to “metadata_instrument.csv” for the sensor information and measurement heights, and whether a variable is measured below the canopy. (2) Variable availability: Snow depth is not available at ER-PHS3 and SG-EHS7. SWC, soil temperature, and soil bulk EC at the deepest depth (<-1m) are not available at SG-EHS6 and SG-EHS7. The missing value code for numeric variables is -9999, except for SWP. For SWP, the missing value code is +9999, because SWP values are negative. (3) Sampling frequency: Please refer to “metadata_instrument.csv” for the increase of sampling frequency of some variables from 30-min to 1-min at ER-PHS1 to 4 in July 2020. (4) Sensors: While the methods of each sensor are not detailed, all sensors are commercially available, and their methods can be found in their manuals. Please refer to “metadata_instrument.csv” for the sensor manufacturer and model information. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a field grown transgenic poplar engineered with a monolignol 4-O-methyltransferase (MOMT4). The poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR experiments. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (hsqcetgpsisp2.2) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. The NMR spectra provides structural characteristics information about lignin in field grown transgenic MOMT4 poplar. Additional meta data is embedded in the raw spectra figures.

Lignin structure, HSQC, poplar, field trial, MOMT4↗

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING↗