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DOE OSTI2021

Deciphering the source of primary biological aerosol particles: a pollen case study

Primary biological aerosol particles (PBAPs) are microscopic solids suspended in the atmosphere emitted by biological systems and play critical roles in the atmosphere and at the atmosphere-biosphere interface, impacting human health, climate, and the ecosystem function. Understanding the sources of PBAPs is necessary to decipher the mechanistic interactions between aerosols, climate, and distinct ecosystem components. However, the detection of specific PBAPs in complex ambient aerosol samples is challenging. We performed metabolomics analyses of pollen from three pollinating tree species and ambient samples collected during the peak pollination period of each species. Random Forest and sPLS-DA machine learning methods were employed to evaluate whether metabolic signatures of ambient samples can reveal the source of the main pollen particles present in the atmosphere. Our results suggest that atmospheric eco-metabolomics techniques combined with sophisticated statistical methods can decipher the origin of abundant PBAPs from complex ambient samples. Developing complete libraries containing high-resolution metabolomic fingerprints of the major PBAPs present in the atmosphere would significantly advance future research to accurately understand the role of PBAPs in the atmosphere, ecosystems and human health.

Rivas-Ubach, Albert↗

DOE OSTI2026

The Maximal Entanglement Limit in Statistical and High-energy Physics

These lectures advocate the idea that quantum entanglement provides a unifying foundation for both statistical physics and high-energy interactions. I argue that, at sufficiently long times or high energies, most quantum systems approach a Maximal Entanglement Limit (MEL) in which phases of quantum states become unobservable, reduced density matrices acquire a thermal form, and probabilistic descriptions emerge without invoking ergodicity or classical randomness. Within this framework, the emergence of probabilistic parton model, thermalization in the break-up of confining strings and in high-energy collisions, and the universal small-x behavior of structure functions arise as direct consequences of entanglement and geometry of high-dimensional Hilbert space.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Estimates of Lake Nitrogen, Phosphorus, and Chlorophyll‐ a Concentrations to Characterize Harmful Algal Bloom Risk Across the United States

Abstract Excess nutrient pollution contributes to the formation of harmful algal blooms (HABs) that compromise fisheries and recreation and that can directly endanger human and animal health via cyanotoxins. Efforts to quantify the occurrence, drivers, and severity of HABs across large areas is difficult due to the resource intensive nature of field monitoring of lake nutrient and chlorophyll‐aconcentrations. To better characterize how nutrients interact with other environmental factors to produce algal blooms in freshwater systems, we used spatially explicit and temporally matched climate, landscape, in‐lake characteristic, and nutrient inventory data sets to predict nutrients and chlorophyll‐aacross the conterminous US (CONUS). Using a nested modeling approach, three random forest (RF) models were trained to explain the spatiotemporal variation in total nitrogen (TN), total phosphorus (TP), and chlorophyll‐aconcentrations across US EPA's National Lakes Assessment (n = 2,062). Concentrations of TN and TP were the most important predictors and, with other variables, the RF model accounted for 68% of variation in chlorophyll‐a. We then used these RF models to extrapolate lake TN and TP predictions to lakes without nutrient observations and predict chlorophyll‐afor ∼112,000 lakes across the CONUS. Risk for high chlorophyll‐aconcentrations is highest in the agriculturally dominated Midwest, but other areas of risk emerge in nutrient pollution hot spots across the country. These catchment and lake‐specific results can help managers identify potential nutrient pollution and chlorophyll‐ahot spots that may fuel blooms, prioritize at‐risk lakes for additional monitoring, and optimize management to protect human health and other environmental end goals.

Environmental Sciences & Ecology↗

DOE OSTI2021

Seamless High-Q Microwave Cavities for Multimode Circuit Quantum Electrodynamics

Multimode cavity quantum electrodynamics ---where a two-level system interacts simultaneously with many cavity modes---provides a versatile framework for quantum information processing and quantum optics. Due to the combination of long coherence times and large interaction strengths, one of the leading experimental platforms for cavity QED involves coupling a superconducting circuit to a 3D microwave cavity. In this work, we realize a 3D multimode circuit QED system with single photon lifetimes of $2$ ms and cooperativities of $0.5-1.5\times10^9$ across 9 modes of a novel seamless cavity. We demonstrate a variety of protocols for universal single-mode quantum control applicable across all cavity modes, using only a single drive line. We achieve this by developing a straightforward flute method for creating monolithic superconducting microwave cavities that reduces loss while simultaneously allowing control of the mode spectrum and mode-qubit interaction. We highlight the flexibility and ease of implementation of this technique by using it to fabricate a variety of 3D cavity geometries, providing a template for engineering multimode quantum systems with exceptionally low dissipation. This work is an important step towards realizing hardware efficient random access quantum memories and processors, and for exploring quantum many-body physics with photons.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Spectral anomalies and broken symmetries in maximally chaotic quantum maps

Spectral statistics such as the level spacing statistics and spectral form factor (SFF) are widely expected to accurately identify “ergodicity,” including the presence of underlying macroscopic symmetries, in generic quantum systems ranging from quantized chaotic maps to interacting many-body systems. By studying various quantizations of maximally chaotic maps that break a discrete classical symmetry upon quantization, we demonstrate that this approach can be misleading and fail to detect macroscopic symmetries. Notably, the same classical map can exhibit signatures of different random matrix symmetry classes in short-range spectral statistics depending on the quantization. While the long-range spectral statistics encoded in the early time ramp of the SFF are more robust and correctly identify macroscopic symmetries in several common quantizations, we also demonstrate analytically and numerically that the presence of Berry-like phases in the quantization leads to spectral anomalies, which break this correspondence. Finally, we provide numerical evidence that long-range spectral rigidity remains directly correlated with ergodicity in the quantum dynamical sense of visiting a complete orthonormal basis.

Shou, Laura [Univ. of Maryland, College Park, MD (↗

DOE OSTI2024

Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro

Abstract Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter “nicking” and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.

Science & Technology - Other Topics↗

DOE OSTI2020

Lagrangian and Eulerian drag models that are consistent between Euler-Lagrange and Euler-Euler (two-fluid) approaches for homogeneous systems

The undisturbed flow of a particle is of fundamental importance since it controls both the undisturbed flow force and the perturbation force (which includes quasisteady, added-mass, and history forces). Here we use the pairwise interaction extended point particle framework to evaluate the undisturbed flow of each particle through superposition of the perturbation flow induced by all its neighbors. This approach allows calculation of various statistics related to undisturbed fluid velocity under conditions of both stationary and nonstationary particles. In a random distribution of stationary particles, while the macroscale undisturbed flow is slowly varying, the microscale undisturbed flow that arises due to the perturbation flow of neighbors varies substantially from one particle to another and this in turn leads to large variation in the hydrodynamic force exerted on the particles. The effect of particle motion is generally to increase the particle-to-particle variation in the undisturbed fluid velocity of the particles. We observe that this increase is greater for the transverse component than for the streamwise component. As a result, with increasing random particle motion, the distribution of undisturbed fluid-velocity fluctuation becomes isotropic. Three different normalized forces are defined: $Φ^L$ is the Lagrangian normalized force on an individual particle suitable for application in a microscale-informed Euler-Lagrange simulation, $Φ^E$ is the Eulerian normalized average force suitable for application in an Euler-Euler simulation, and $Φ^{LE}$ is the Lagrangian normalized force on an individual particle suitable for application in the standard Euler-Lagrange simulation. In this work, we establish precise relations between these different definitions. The drag laws developed based on particle-resolved direct numerical simulation results and experiments are appropriate for application only as the Eulerian normalized average force. We introduce the force consistency relation and use it to obtain an expression for $Φ^L$, which when applied to each particle and averaged over all the particles equals $Φ^E$. The results are first obtained in the limit of stationary particles and then extended to the general case of nonstationary particles.

42 ENGINEERING↗

DOE OSTI2021

Plasmons in two-dimensional topological insulators

Here, we analyze collective excitations in models of two-dimensional topological insulators using the random phase approximation. In a two-dimensional extension of the Su-Schrieffer-Heeger model, edge plasmonic excitations with induced charge-density distributions localized at the boundaries of the system are found in the topologically nontrivial phase, dispersing similarly as one-dimensional bulk plasmons in the conventional Su-Schrieffer-Heeger chain. For two-dimensional bulk collective modes, we reveal regimes of enhanced interband wave function correlations, leading to characteristic hardening and softening of inter- and intraband bulk plasmonic branches, respectively. In the two-dimensional Haldane Chern insulator model, chiral, unidirectional edge plasmons in nano-ribbon architectures are observed, which can be characterized by an effective Coulomb interaction cross section. Bulk collective excitations in the two-dimensional Haldane model are shown to be originated by single-particle band structure details in different topological phases.

2-dimensional systems↗

DOE OSTI2023

Toward more accurate adiabatic connection approach for multireference wavefunctions

A multiconfigurational adiabatic connection (AC) formalism is an attractive approach to compute the dynamic correlation within the complete active space self-consistent field and density matrix renormalization group (DMRG) models. Practical realizations of AC have been based on two approximations: (i) fixing one- and two-electron reduced density matrices (1- and 2-RDMs) at the zero-coupling constant limit and (ii) extended random phase approximation (ERPA). This work investigates the effect of removing the “fixed-RDM” approximation in AC. The analysis is carried out for two electronic Hamiltonian partitionings: the group product function- and the Dyall Hamiltonians. Exact reference AC integrands are generated from the DMRG full configuration interaction solver. Two AC models are investigated, employing either exact 1- and 2-RDMs or their second-order expansions in the coupling constant in the ERPA equations. Calculations for model molecules indicate that lifting the fixed-RDM approximation is a viable way toward improving the accuracy of existing AC approximations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A particle-in-cell code comparison for ion acceleration: EPOCH, LSP, and WarpX

There are now more Particle-in-Cell (PIC) codes than ever before that researchers use to simulate intense laser-plasma interactions. To date, there have been relatively few direct comparisons of these codes in the literature, especially for relativistic intensity lasers interacting with thin overdense targets. To address this we perform a code comparison of three PIC codes: EPOCH, LSP, and WarpX for the problem of laser-driven ion acceleration in a 2D(3v) geometry for a 10 20 W cm -2 intensity laser. We examine the plasma density, ion energy spectra, and laser-plasma coupling of the three codes and find strong agreement. We also run the same simulation 20 times with different random seeds to explore statistical fluctuations of the outputs. We then compare the execution times and memory usage of the codes (without “tuning” to improve performance) using between 1 and 48 processors on one node. We provide input files to encourage larger and more frequent code comparisons in this field.

36 MATERIALS SCIENCE↗

DOE OSTI2021

YPK9 and WHI2 Negatively Interact during Oxidative Stress

Yeast PARK9 (YPK9) shares homology with human ATP13A2, which encodes a polyamine transporter implicated in juvenile forms of Parkinson’s disease. We used YPK9 to gain insight into how ATP13A2 affects cell growth and sensitivity to oxidative stress. Surprisingly, the YPK9 deletion strain from the Saccharomyces cerevisiae deletion collection (YKO) in wildtype BY4741 (mating type a) grew faster and was more resistant to hydrogen peroxide than a commercial, putative parental BY4741 wildtype strain (BY4741 COM ). In contrast, deleting YPK9 from BY4741 COM rendered it very sensitive to hydrogen peroxide, suggesting its background is different from that of the deletion collection. Whole-genome sequencing revealed that BY4741 COM and BY4741 COM ypk9Δ contain a novel premature stop codon near the 3' end of WHI2 (WHI2 G1324T ), whereas the collection’s YPK9 deletion strain contains WHI2, which encodes a 486 amino acid protein, Whi2p. Replacing full-length WHI2 with the sequence coding for the predicted truncation (Whi2p E442* ) rendered strains more sensitive to hydrogen peroxide, whereas the converse replacement rendered them more resistant. The sequences of WHI2 in 20 randomly chosen strains from the collection encode the full-length protein, indicating that the putative parental BY4741 WHI2 G1324T strain’s genetic background differs from that of the deletion collection. Examination of WHI2 sequences in several commonly used wildtype S. cerevisiae strains and isolates revealed other Whi2p truncations that might yield altered phenotypes. Together, these results demonstrate a novel premature stop codon in WHI2 that renders yeast sensitive to hydrogen peroxide; they also reveal a negative genetic interaction between WHI2 and YPK9 in the presence of hydrogen peroxide in the BY4741 background.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Coupling between collective modes in the deformed 98 Zr nucleus: Insights from consistent HFB + QRPA calculations with the Gogny interaction

The zirconium isotopes exhibit structural properties that present multiple challenges to nuclear theory. Investigations of the coupling present within isoscalar modes and within isovector modes are scarce but important for advancing our understanding of the microscopic picture of nuclei. To explore some of these underlying coupling features, and to test the predictive power of a state-of-the-art nuclear structure approach, we provide a detailed analysis of the properties of 90,96,98 Zr . This region includes a benchmarking case and offers insights into nuclear deformation phenomena. Here, to investigate the coupling between collective modes in deformed nuclei, we focused our analysis on the ground and excited-state properties of these isotopes, employing a consistent approach with the axially symmetric deformed Hartree-Fock-Bogoliubov (HFB) and the quasiparticle random phase approximation (QRPA) framework, both using the Gogny D1M force. This approach effectively describes both low-lying and giant-resonance states. We devoted special attention to the deformed 98 Zr nucleus, where we confirm the existence of coupling between monopole and quadrupole excitations through the 𝐾 𝜋 = 0 + QRPA components and demonstrate an analogous dipole-octupole coupling through the 𝐾 𝜋 = 0 − and 𝐾 𝜋 = 1 − components. Intrinsic transition densities and associated radial projections illustrate the coupling. Our work complements and extends earlier studies carried out using density-functional-based methods and notably, we included the complete Coulomb interaction also in the pairing fields, i.e., we treat terms exactly that are approximated in typical calculations that use the Gogny D1 and D2 interaction families.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Coupling between collective modes in the deformed 98 Zr nucleus: Insights from consistent HFB+QRPA calculations with the Gogny interaction

The Zirconium isotopes exhibit structural properties that present multiple challenges to nuclear theory. Investigations of the coupling present within isoscalar modes and within isovector modes are scarce but important for advancing our understanding of the microscopic picture of nuclei. To explore some of these underlying coupling features, and to test the predictive power of a state-of the-art nuclear structure approach, we provide a detailed analysis of the properties of 90,96,98Zr. This region includes a benchmarking case and offers insights into nuclear deformation phenomena. To investigate the coupling between collective modes in deformed nuclei, we focused our analysis on the ground and excited-state properties of these isotopes, employing a consistent approach with the axially-symmetric deformed Hartree-Fock-Bogoliubov (HFB) and the Quasiparticle Random Phase Approximation (QRPA) framework, both using the Gogny D1M force. This approach effectively describes both low-lying and giant-resonance states. We devoted special attention to the deformed 98Zr nucleus, where we confirm the existence of coupling between monopole and quadrupole excitations through the K π = 0 + QRPA components and demonstrate an analogous dipole-octupole coupling through the K π = 0 − and K π = 1 − components. Intrinsic transition densities and associ ated radial projections illustrate the coupling. Our work complements and extends earlier studies carried out using density-functional-based methods and notably, we included the complete Coulomb interaction also in the pairing fields, i.e. we treat terms exactly that are approximated in typical calculations that use the Gogny D1 and D2 interaction families.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Tunable Stochasticity in an Artificial Spin Network

Metamaterials present the possibility of artificially generating advanced functionalities through engineering of their internal structure. Artificial spin networks, in which a large number of nanoscale magnetic elements are coupled together, are promising metamaterial candidates that enable the control of collective magnetic behavior through tuning of the local interaction between elements. In this work, the motion of magnetic domain-walls in an artificial spin network leads to a tunable stochastic response of the metamaterial, which can be tailored through an external magnetic field and local lattice modifications. This type of tunable stochastic network produces a controllable random response exploiting intrinsic stochasticity within magnetic domain-wall motion at the nanoscale. An iconic demonstration used to illustrate the control of randomness is the Galton board. In this system, multiple balls fall into an array of pegs to generate a bell-shaped curve that can be modified via the array spacing or the tilt of the board. A nanoscale recreation of this experiment using an artificial spin network is employed to demonstrate tunable stochasticity. Furthermore, this type of tunable stochastic network opens new paths toward post-Von Neumann computing architectures such as Bayesian sensing or random neural networks, in which stochasticity is harnessed to efficiently perform complex computational tasks.

Artificial spin network↗

DOE OSTI2021

Structure, Magnetism, and First-Principles Modeling of the Na 0.5 La 0.5 RuO 3 Perovskite

High-purity polycrystalline Na 0.5 La 0.5 RuO 3 was synthesized by a solid-state method, and its properties were studied by magnetic susceptibility, heat capacity, and resistivity measurements. In this study, we find it to be an orthorhombic perovskite, in contrast to an earlier report, with random La/Na mixing. With a Curie–Weiss temperature of –231 K and an effective moment of 2.74 μB/mol Ru, there is no magnetic ordering down to 1.8 K. A broad hump at 1.4 K in the heat capacity, however, indicates the presence of a glassy magnetic transition, which we attribute to the influence of the random distribution of Na and La on the perovskite A-sites. Comparison to CaRuO 3 , a structurally ordered ruthenate perovskite with a similar A-site ionic radius and magnetic properties, is presented. First-principles calculations indicate that the Na–La distribution determines the local magnetic exchange interactions between Ru ions, favoring either antiferromagnetic or ferromagnetic coupling when the local environment is Na- or La-rich. Thus, our data and analysis suggest that mixing cations with different charges and sizes on the A-site in this perovskite results in magnetic frustration through a balance of local magnetic exchange interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

In‐operando crystallization study of zinc nitrate hexahydrate using zinc oxide nucleators

Abstract Supercooling (∆T Sup ) is one of the crucial problems in utilizing a phase change material (PCM), which has been attempted to overcome using nucleators possessing small lattice disregistry without comprehensive understanding of the nucleation phenomenon. Here, this work studies the interactions between nucleators and PCM via in‐operando direct visualization for the first time, to the best of our knowledge, to better understand the crystallization process during freezing of a PCM using zinc nitrate hexahydrate (ZNH) and a zinc oxide (ZnO) nucleator. According to our in‐operando study, freezing was randomly initiated by only a fraction of the nucleator particles during each thermal cycling. However, previously unresponsive nucleators also suddenly crystalized PCM when the propagating crystal encountered them, improving the crystal initiation and thereby ∆T Sup . Consequently, for equal wt% of ZnO, better nucleation behavior was obtained using uniformly distributed small nucleator particles throughout the PCM, as compared to either large or poorly distributed aggregated nucleators. DSC results using ZnO‐needle as nucleator confirmed a 38% and 33.3% lower ∆T Sup upon employing 5 wt% small (individual) particles (~4 μm on average), as compared to using equal wt% of small (aggregated) particle clusters (~200 μm) and large particles (~46 μm), respectively. Crystallization of ZNH caused additional hair‐like ZnO growth preferentially decorated along lateral faces of the original nucleator particles. The in‐operando studies are valuable tools to correlate inherent crystallization phenomena to the practical thermal energy storage properties of the system.

Chakraborty, Anirban↗

DOE OSTI2021

The influence of preexisting host rock damage on fault network localization

The transition from stable to unstable fracture propagation occurs when fractures begin to interact and link. Thus, fracture network coalescence controls how rocks and engineered structures fail. Here, to constrain the factors that influence localization in shear zones under brittle conditions, we build discrete element method models with a rough fault embedded in a shear zone. We add varying numbers of diffuse, randomly-placed weaknesses to examine the influence of diffuse damage on fracture network localization. The number of weaknesses controls the localization behavior of the fault network and the final fault geometry. We quantify localization using the Gini coefficient of the fracture volume, which measures the nonuniformity in a population. Each model generally increases in localization toward failure. However, models with more diffuse damage experience delocalization phases that are superimposed on the overall trend of increasing localization. The observed link between delocalization and host rock damage may help explain the varying localization of low magnitude seismicity in southern California. Models with more diffuse damage produce more complex fault geometries comprised of several parallel strands of wing cracks. The propagation of these wing cracks reduces the shear stress acting on the model boundaries, indicating that this fracture development increases the mechanical efficiency of the system.

58 GEOSCIENCES↗