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Attention to quantum complexity

The imminent era of error-corrected quantum computing demands robust methods to characterize quantum state complexity from limited, noisy measurements. We introduce the Quantum Attention Network (QuAN), a classical artificial intelligence (AI) framework leveraging attention mechanisms tailored for learning quantum complexity. Inspired by large language models, QuAN treats measurement snapshots as tokens while respecting permutation invariance. Combined with our parameter-efficient miniset self-attention block, this enables QuAN to access high-order moments of bit-string distributions and preferentially attend to less noisy snapshots. We test QuAN across three quantum simulation settings: driven hard-core Bose-Hubbard model, random quantum circuits, and toric code under coherent and incoherent noise. QuAN directly learns entanglement and state complexity growth from experimental computational basis measurements, including complexity growth in random circuits from noisy data. In regimes inaccessible to existing theory, QuAN unveils the complete phase diagram for noisy toric code data as a function of both noise types, highlighting AI’s transformative potential for assisting quantum hardware.

Kim, Hyejin [Cornell Univ., Ithaca, NY (United Sta↗

Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface

Kinetochores connect mitotic-spindle microtubules with chromosomes, allowing microtubule depolymerization to pull chromosomes apart during anaphase while resisting detachment as the microtubule shortens. The heterodecameric DASH/Dam1 complex (DASH/Dam1c), an essential component of yeast kinetochores, assembles into a microtubule-encircling ring. The ring associates with rodlike Ndc80 complexes to organize the kinetochore-microtubule interface. Here, we report the cryo–electron microscopy structure (at ~4.5-angstrom resolution) of a DASH/Dam1c ring and a molecular model of its ordered components, validated by evolutionary direct-coupling analysis. Integrating this structure with that of the Ndc80 complex and with published interaction data yields a molecular picture of kinetochore-microtubule attachment, including how flexible, C-terminal extensions of DASH/Dam1c subunits project and contact widely separated sites on the Ndc80 complex rod and how phosphorylation at previously identified sites might regulate kinetochore assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Oxygen isotopic investigation of silicic magmatism in the Stillwater caldera complex, Nevada: Generation of large-volume, low-δ 18 O rhyolitic tuffs and assessment of their regional context in the Great Basin of the western United States

Successive caldera-forming eruptions from ca. 30 to 25 Ma generated a large nested caldera complex in western Nevada that was subsequently dissected by Basin and Range extension, providing extraordinary cross-sectional views through diverse volcanic and plutonic rocks. A high-resolution oxygen isotopic study was conducted on units that represent all major parts of the Job Canyon, Louderback Mountains, Poco Canyon, and Elevenmile Canyon caldera cycles (29.2–25.1 Ma), and several Cretaceous plutons that flank the Stillwater caldera complex. We provide new oxygen and strontium isotope data for 12 additional caldera centers in the Great Basin, which are synthesized with >150 published oxygen and strontium isotope analyses for regional Mesozoic basement rocks. Stillwater zircons span a large isotopic range (δ 18 O zircon of 3.6‰–8.2‰), and all caldera cycles possess low-δ 18 O zircons. In some cases, they are a small proportion of the total populations, and in others, they dominate, such as in the low-δ 18 O rhyolitic tuffs of Job Canyon and Poco Canyon (δ 18 O zircon = 4.0‰–4.3‰; δ 18 O magma = 5.5‰–6‰). These are the first low-δ 18 O rhyolites documented in middle Cenozoic calderas of the Great Basin, adding to the global occurrence of these important magma types that fingerprint recycling of shallow crust altered by low-δ 18 O meteoric waters. The appearance of low-δ 18 O rhyolites in the Stillwater caldera complex is overprinted on a Great Basin–wide trend of miogeoclinal sediment contribution to silicic magmas that elevates δ 18 O compositions, making identification of 18 O depletions difficult. Though not a nominally low-δ 18 O rhyolite, the tuff of Elevenmile Canyon possesses both low-δ 18 O and high-δ 18 O zircon cores that are overgrown by homogenized zircon rims that approximate the bulk zircon average, pointing to batch assembly of isotopically diverse upper crustal melts to generate one of the most voluminous (2500–5000 km 3 ) tuff eruptions in the Great Basin. Despite overlapping in space and time, each caldera-forming cycle of the Stillwater complex has a unique oxygen isotope record as retained in single zircons. Most plutons that were spatially and temporally coincident with calderas have isotopic compositions that diverge from the caldera-forming tuffs and cannot be their cogenetic remnants.

58 GEOSCIENCES↗

The Complexity Classes of Angular Diagrams of the Metal Conductivity in Strong Magnetic Fields

We consider angular diagrams describing the dependence of the magnetic conductivity of metals on the direction of the magnetic field in rather strong fields. As it can be shown, all angular conductivity diagrams can be divided into a finite number of classes with different complexities. The greatest interest among such diagrams is represented by diagrams with the maximal complexity, which can occur for metals with rather complicated Fermi surfaces. In describing the structure of complex diagrams, in addition to the description of the conductivity itself, the description of the Hall conductivity for different directions of the magnetic field plays very important role. For the evaluation of the complexity of angular diagrams of the conductivity of metals, it is also convenient to compare such diagrams with the full mathematical diagrams that are defined (formally) for the entire dispersion relation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Metal Organic Complexation in Seawater: Historical Background and Future Directions

The speciation of most biologically active trace metals in seawater is dominated by complexation by organic ligands. This review traces the history of work in this area, from the early observations that showed surprisingly poor recoveries using metal preconcentration protocols to the present day, where advances in mass spectroscopy and stable isotope geochemistry are providing new insights into the structure, origin, fate, and biogeochemical impact of organic ligands. Many long-standing hypotheses about the specific biological origin of ligands such as siderophores in seawater are finally being validated. This work has revealed the complexity of organic complexation, with multiple ligands and, in some cases, timescales of ligand exchange that are much slower than originally thought. The influence of organic complexation on scavenging is now a key parameter in biogeochemical models of biologically essential metals, especially iron. New insights about the sources and sinks of ligands are required to enhance the usefulness of these models.

Geochemistry & Geophysics↗

Two-Layer Dynamic Recycling Model (2L-DRM): Learning from Moisture Tracking Models of Different Complexity

Atmospheric moisture tracking models are used to identify and quantify sources and sinks of water in the atmospheric branch of the hydrologic cycle. These models are primarily used to investigate the origin of moisture resulting in precipitation for particular regions around the globe. Moisture tracking models vary widely in their level of complexity, depending on the number of physical processes represented. Complex models are comprehensive in their physical representation, but computationally much more expensive than simple models, which only focus on specific physical processes and use simplifying assumptions. We present the mathematical derivation of the new two-layer dynamical recycling model (2L-DRM), a simple analytical moisture tracking model that relaxes the vertically-integrated formulation of the original one-layer DRM (Dominguez et al., 2006). By comparing the simple DRM to a very complex moisture tracking model that uses water vapor tracers embedded within the Weather Research and Forecast regional climate model (WRF-WVT) for the North American Monsoon region, we pinpoint the absence of vertical wind shear as the main deficiency in the simple DRM. When comparing both simple models (DRM and 2L-DRM) to the WRF-WVT (which we treat as ‘truth’), the 2L-DRM better captures the spatial extent, the net amount and the temporal variability of precipitation that originates from oceanic and local terrestrial sources. The 2L-DRM is well suited to study the large-scale climatological sources of moisture, and for these applications, performs on-par with the much more complex and computationally demanding WRF-WVT model.

Dominguez, Francina↗

X-Band Radar and Surface-Based Observations of Cold-Season Precipitation in Western Colorado’s Complex Terrain

Abstract Hydrologic processes associated with intermountain cold-season precipitation in the Upper Colorado River basin have important impacts on avalanche forecasting and water resource management. However, traditional weather radar networks struggle with observations in this complex terrain. Data collected during the Study of Precipitation, the Lower Atmosphere, and the Surface for Hydrometeorology (SPLASH) and its sister campaign, Surface Atmosphere Integrated Field Laboratory (SAIL) in the East River watershed of western Colorado, are used to examine a multistorm period from 23 December 2021 to 1 January 2022 that contributed 35% of the total winter precipitation in this watershed. Dual-polarization X-band radar and disdrometer measurements show ∼30-mm differences in precipitation amount at two sites in proximity over four distinct storm events within the period. Wind patterns, synoptic forcings, microphysical characteristics of precipitation, and surface meteorology are analyzed to explain the observed spatial variability of cold-season precipitation in complex mountainous terrain. Analysis shows that differences over time within this event are mainly accounted for by synoptic forcings, such as frontal passages; differences between sites are accounted for by the impact of variations in local wind patterns on precipitation microphysics. Patterns of surface precipitation intensity are compared and found to be correlated with X-band radar signatures; a relationship between a strong dendritic growth stage and intense low-density surface precipitation is reinforced by this study. This relationship demonstrates the importance of particle growth mechanisms on surface snowfall patterns in high-altitude complex terrain, underscoring the importance of realistic microphysical parameterizations. Significance Statement The amount and density of snowpack from western Colorado winter storms have significant impacts on water resources in the Upper Colorado River basin. Snowpack characteristics are affected by small-scale differences in how snow forms in the atmosphere. These differences are hard to study in the complex terrain of the Rockies, but data from the SPLASH and SAIL field campaigns allows us to investigate how snow crystal formation and mountain-driven wind patterns affect snow near the surface. Our study finds that snow crystal growth varies over small space and time scales and is likely controlled by the terrain beneath a given location and resultant local wind patterns. These results imply that predicting snowpack in the Rockies requires properly representing local wind patterns and crystal growth processes in models.

Heflin, Stella↗

Why Travel for Complex Cancer Surgery? Americans React to ‘Brand-Sharing’ Between Specialty Cancer Hospitals and Their Affiliates

Introduction: Leading cancer hospitals have increasingly shared their ‘brand’ with smaller hospitals through affiliations. Because each brand evokes a distinct reputation for the care provided, ‘brand-sharing’ has the potential to impact the public’s ability to differentiate the safety and quality within hospital networks. The general public was surveyed to determine the perceived similarities and differences in the safety and quality of complex cancer surgery performed at top cancer hospitals and their smaller affiliate hospitals. Methods: A national, web-based KnowledgePanel (GfK) survey of American adults was conducted. Respondents were asked about their beliefs regarding the quality and safety of complex cancer surgery at a large, top-ranked cancer hospital and a smaller, local hospital, both in the presence and absence of an affiliation between the hospitals. Results: A total of 1010 surveys were completed (58.1% response rate). Overall, 85% of respondents felt ‘motivated’ to travel an hour for complex surgery at a larger hospital specializing in cancer, over a smaller local hospital. However, if the smaller hospital was affiliated with a top-ranked cancer hospital, 31% of the motivated respondents changed their preference to the smaller hospital. When asked to compare leading cancer hospitals and their smaller affiliates, 47% of respondents felt that surgical safety, 66% felt guideline compliance, and 53% felt cure rates would be the same at both hospitals. Conclusions: Approximately half of surveyed Americans did not distinguish the quality and safety of surgical care at top-ranked cancer hospitals from their smaller affiliates, potentially decreasing their motivation to travel to top centers for complex surgical care.

60 APPLIED LIFE SCIENCES↗

Structure of the 30S ribosomal decoding complex at ambient temperature

The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New light sources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation to structural studies of RNA and RNA–protein complexes at near-physiological temperatures.

59 BASIC BIOLOGICAL SCIENCES↗

Assembly of ordered DNA-curli fibril complexes during Salmonella biofilm formation correlates with strengths of the type I interferon and autoimmune responses

Deposition of human amyloids is associated with complex human diseases such as Alzheimer’s and Parkinson’s. Amyloid proteins are also produced by bacteria. The bacterial amyloid curli, found in the extracellular matrix of both commensal and pathogenic enteric bacterial biofilms, forms complexes with extracellular DNA, and recognition of these complexes by the host immune system may initiate an autoimmune response. Here, we isolated early intermediate, intermediate, and mature curli fibrils that form throughout the biofilm development and investigated the structural and pathogenic properties of each. Early intermediate aggregates were smaller than intermediate and mature curli fibrils, and circular dichroism, tryptophan, and thioflavin T analyses confirmed the establishment of a beta-sheet secondary structure as the curli conformations matured. Intermediate and mature curli fibrils were more immune stimulatory than early intermediate fibrils in vitro . The intermediate curli was cytotoxic to macrophages independent of Toll-like receptor 2. Mature curli fibrils had the highest DNA content and induced the highest levels of Isg15 expression and TNFα production in macrophages. In mice, mature curli fibrils induced the highest levels of anti-double-stranded DNA autoantibodies. The levels of autoantibodies were higher in autoimmune-prone NZBWxF/1 mice than wild-type C57BL/6 mice. Chronic exposure to all curli forms led to significant histopathological changes and synovial proliferation in the joints of autoimmune-prone mice; mature curli was the most detrimental. In conclusion, curli fibrils, generated during biofilm formation, cause pathogenic autoimmune responses that are stronger when curli complexes contain higher levels of DNA and in mice predisposed to autoimmunity.

59 BASIC BIOLOGICAL SCIENCES↗

Thermodynamic parameters for the complexation of Tc(IV) with bromide under aqueous conditions

Technetium-99 is a long-lived fission product present in nuclear wastes, found mainly as Tc(VII) and Tc(IV) in the environment. The quantification of the equilibrium constants for the formation of Tc(IV) aqueous complexes has been limited to carboxylate ligands and interactions with the halides is mostly unknown. This work reports equilibrium constants of the formation of the TcO(OH) + complexes with Br - , in a 3 M NaClO 4 solution of pcH 2 and varied temperature, using a liquid-liquid extraction system. Neutron activation confirmed the suitability of the extraction technique for this work. Under the working conditions, Br - forms a weak exothermic TcO(OH)Br complex, with a Gibbs free energy (ΔG r ) of 3 ± 3 kJ · mol -1 at a temperature of 273.15 K. The values for ΔH r (-32 ± 3 kJ · mol -1 ) and ΔS r (106 ± 9 J · mol -1 · K -1 ) of the complexation reaction were quantified using a van’t Hoff analysis. This work also showed that bromide addition does not displace the hydroxide from TcO(OH) + , as the equilibrium constant of bromide addition is much weaker than the first hydrolysis constant of the metal.

Chemistry↗

Uranyl oxalate species in high ionic strength environments: stability constants for aqueous and solid uranyl oxalate complexes

Uranyl ion, UO 2 2+ , and its aqueous complexes with organic and inorganic ligands can be the dominant species for uranium transport on the Earth surface or in a nuclear waste disposal system if an oxidizing condition is present. As an important biodegradation product, oxalate, C 2 O 4 2– , is ubiquitous in natural environments and is known for its ability to complex with the uranyl ion. Oxalate can also form solid phases with uranyl ion in certain environments thus limiting uranium migration. Therefore, the determination of stability constants for aqueous and solid uranyl oxalate complexes is important not only to the understanding of uranium mobility in natural environments, but also to the performance assessment of nuclear waste disposal. In this work, we developed a thermodynamic model for the UO 2 2+ –Na + –H + –Cl – –ClO 4 – –C 2 O 4 2– –NO 3 – –H 2 O system to ionic strength up to ~11 mol•kg –1 . We constrained the stability constants for UO 2 C 2 O 4 (aq) and UO 2 (C 2 O 4 ) 2 2– at infinite dilution based on our evaluation of the literature data over a wide range of ionic strengths up to ~11 mol•kg –1 . We also obtained the solubility constants at infinite dilution for solid uranyl oxalates, UO 2 C 2 O 4 •3H 2 O, based on the solubility data over a wide range of ionic strengths. The developed model will enable for the accurate stability assessment of oxalate complexes affecting uranium mobility under a wide range of conditions including those in deep geological repositories.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.

59 BASIC BIOLOGICAL SCIENCES↗

Computational Data Associated with the publication: Formation of a Decanuclear Organometallic Dysprosium Complex via a Radical–Radical Cross–Coupling Reaction

Over the years, polynuclear cyclic or torus complexes have attracted increasing interest due to their unique metal topologies and properties. However, the isolation of polynuclear cyclic organometallic complexes is extremely challenging due to their inherent reactivity, which stems from the labile and reactive metal‐carbon bonds. In this study, the pyrazine ligand undergoes a radical‐radical cross‐coupling reaction leading to the formation of a decanuclear [(Cp*)20Dy10(L1)10] ⋅ 12(C7H8) (1; where L1 = anion of 2‐prop‐2‐enyl‐2H‐pyrazine; Cp* = pentamethylcyclopentadienyl) complex, where all DyIII metal centres are bridged by the anionic L1 ligand. Amongst the family of polynuclear Ln organometallic complexes bearing CpR2Lnx units (CpR = substituted cyclopentadienyl), 1 features the highest nuclearity obtained to date. In‐depth computational studies were conducted to elucidate the proposed reaction mechanism and formation of L1, while probing of the magnetic properties of 1, revealed slow magnetic relaxation upon application of a static dc field.

Bajaj, Neha↗

Stochastic Simulation of Complex Fluid Flows (Progress Report for period 07/01/2016 - 06/30/2018)

At a microscopic scale, fluids are composed of molecules whose positions and velocities are random. This gives rise to thermal fluctuations that span the whole range of scales from the microscopic through the mesoscopic, and even the macroscopic. The inclusion of thermal fluctuations is crucial in multi-scale models, which are an important theme in the research program of the DOE Office of Science, and in particular the ASCR Applied Mathematics program's priority focus area on modeling of complex systems involving processes that span vastly different time and/or length scales. In this five-year Early Career project, the PI Aleksandar Donev and collaborators developed computational algorithms for modeling complex fluid mixtures at small scales using a formulation based on fluctuating hydrodynamics. Novel computational methods were developed to model complex fluids with increasing physical complexity, starting from binary miscible and immiscible mixtures, going through multispecies non-reactive and reactive mixtures, and culminating with reactive electrolytes mixtures of neutral molecules and ions. In close collaboration with the group of John Bell at Lawrence Berkeley National Laboratory, the methods were implemented in a scalable computational framework suitable for modern parallel supercomputers, and made publicly available on github. A number of physical examples in which giant nonequilibrium fluctuations are improtant were studied, with a special focus on instabilities at a liquid-liquid interface driven by gravity, diffusion, reactions, and/or electric fields. The methods and codes developed in this project are expected to enable other novel applications in the DOE Basic Energy Sciences program, and engineering sciences more broadly.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Tomographic imaging of atmospheric pressure plasma on complex surfaces

Many plasma types and behaviors such as streamer, arcs, cathode spots, anode spots, ionization waves, and magnetic field interactions create non-symmetric, fully 3D plasma structures. The plasma distribution in 3D space is heavily influenced by complex surfaces and the coupling interactions between plasma properties and the interfacing material properties. For example, ionization waves propagate in directions where ionization rates are highest, leading to complex configurations that are not fully understood or well characterized. Recent advances in laser diagnostics and models have been able to investigate well-controlled idealized plasmas in 2D fashion, but the complex structure in actual plasmas requires a technique than can provide a more complete 3D picture. However, 3D plasma diagnostics do not currently exist. To address this limitation, this activity will leverage available equipment to build a new tomographic optical imaging capability and advance the state-of-the-art in plasma diagnostics to investigate 3D phenomena on complex surfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Project 18-15263 X-ray Studies of Interfacial Molecular Complexes in ALSEP Back-Extraction (Research Performance Final Report)

The objective of the project was to use synchrotron X-rays to measure the molecular-scale organization of extractants, complexants, buffers, and metal ions at the organic-aqueous (liquid-liquid) interface during solvent back-extraction under conditions relevant to ALSEP (Actinide-Lanthanide Separation Process). The capability of X-ray fluorescence near total reflection (XFNTR) was extended to explore the distribution of Eu(III) between the liquid-liquid interface and bulk organic and aqueous phases which contained extractants HDEHP (bis(2-ethylhexyl) phosphoric acid) and HEHEHP (2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester), the complexant DTPA (diethylene triamine pentaacetic acid), and citric and nitric acids. Although an Am-compatible sample cell was developed, extending x-ray measurements of flat liquid-liquid interfaces to the actinide Am(III) did not prove to be possible within constraints imposed by the Advanced Photon Source. However, preliminary measurements with a drop cell may eventually provide a path forward to investigate Am(III) at a liquid interface. It was also demonstrated that competitive binding that occurs during back-extraction of lanthanide ions to either a phosphoric acid extractant (DHDP, di-hexadecyl phosphate) at the liquid interface or to complexant DTPA in the bulk aqueous phase could be reversibly tuned by X-ray exposure. Separately, X-ray measurements from the liquid-vapor interface explored the role of the aqueous solubility of HDEHP and HEHEHP and their interactions with a range of lanthanides and transition metal ions. Finally, the capability of X-ray absorption spectroscopy (EXAFS) was extended to probe metal ion coordination in lanthanide ion-extractant complexes at the liquid-vapor interface. Complementary to the specific interfacial systems studied during this project, the development of x-ray techniques expands our ability to understand ion ordering at liquid interfaces.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Structure-Function and Nearest Neighbor Interactions of the Cytochrome b 6 f Complex

Test prediction from our (i) high resolution (2.5 Å) structure of cyanobacterial cytochrome b 6 f complex (Structure, 22, 1008-1015, 2014), and (ii) analysis of quinone/quinol traffic within the b 6 f complex (Biophys. J., 107, 1620-1628, 2014) concerning the rate-limiting step in the linear (non-cyclic) electron transport chain. It was concluded that it arises from access of plastoquinol, the electron/proton donor, to the high potential electron carriers, i. e., the Fe 2 S 2 and cytochrome f proteins. The directed motion of the quinol proceeds via a narrow channel on the lumen or electrochemically positive, p- (lumen) side of the b 6 f complex which was defined by crystal structures of the b 6 f complex with quinol analogue inhibitors (J. Mol. Biol., 370, 39-52, 2007).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗