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DOE OSTI2023

Investigating permafrost carbon dynamics in Alaska with artificial intelligence

Abstract Positive feedbacks between permafrost degradation and the release of soil carbon into the atmosphere impact land–atmosphere interactions, disrupt the global carbon cycle, and accelerate climate change. The widespread distribution of thawing permafrost is causing a cascade of geophysical and biochemical disturbances with global impacts. Currently, few earth system models account for permafrost carbon feedback (PCF) mechanisms. This research study integrates artificial intelligence (AI) tools and information derived from field-scale surveys across the tundra and boreal landscapes in Alaska. We identify and interpret the permafrost carbon cycling links and feedback sensitivities with GeoCryoAI, a hybridized multimodal deep learning (DL) architecture of stacked convolutionally layered, memory-encoded recurrent neural networks (NN). This framework integratesin-situmeasurements and flux tower observations for teacher forcing and model training. Preliminary experiments to quantify, validate, and forecast permafrost degradation and carbon efflux across Alaska demonstrate the fidelity of this data-driven architecture. More specifically, GeoCryoAI logs the ecological memory and effectively learns covariate dynamics while demonstrating an aptitude to simulate and forecast PCF dynamics—active layer thickness (ALT), carbon dioxide flux (CO 2 ), and methane flux (CH 4 )—with high precision and minimal loss (i.e. ALT RMSE : 1.327 cm [1969–2022]; CO 2 RMSE : 0.697µmolCO 2 m −2 s −1 [2003–2021]; CH 4 RMSE : 0.715 nmolCH 4 m −2 s −1 [2011–2022]). ALT variability is a sensitive harbinger of change, a unique signal characterizing the PCF, and our model is the first characterization of these dynamics across space and time.

Environmental Sciences & Ecology↗

DOE OSTI2022

Suppressing simulation bias in multi-modal data using transfer learning

Abstract Many problems in science and engineering require making predictions based on few observations. To build a robust predictive model, these sparse data may need to be augmented with simulated data, especially when the design space is multi-dimensional. Simulations, however, often suffer from an inherent bias. Estimation of this bias may be poorly constrained not only because of data sparsity, but also because traditional predictive models fit only one type of observed outputs, such as scalars or images, instead of all available output data modalities, which might have been acquired and simulated at great cost. To break this limitation and open up the path for multi-modal calibration, we propose to combine a novel, transfer learning technique for suppressing the bias with recent developments in deep learning, which allow building predictive models with multi-modal outputs. First, we train an initial neural network model on simulated data to learn important correlations between different output modalities and between simulation inputs and outputs. Then, the model is partially retrained, or transfer learned, to fit the experiments; a method that has never been implemented in this type of architecture. Using fewer than 10 inertial confinement fusion experiments for training, transfer learning systematically improves the simulation predictions while a simple output calibration, which we design as a baseline, makes the predictions worse. We also offer extensive cross-validation with real and carefully designed synthetic data. The method described in this paper can be applied to a wide range of problems that require transferring knowledge from simulations to the domain of experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

From Optimization to Sampling Through Gradient Flows

Optimization and sampling algorithms play a central role in science and engineering as they enable finding optimal predictions, policies, and recommendations, as well as expected and equilibrium states of complex systems. The notion of “optimality” is formalized by the choice of an objective function, while the notion of an “expected” state is specified by a probabilistic model for the distribution of states. Optimizing rugged objective functions and sampling multimodal distributions is computationally challenging, especially in high-dimensional problems. Here, for this reason, many optimization and sampling methods have been developed by researchers working in disparate fields such as Bayesian statistics, molecular dynamics, genetics, quantum chemistry, machine learning, weather forecasting, econometrics, and medical imaging.

Trillos, N. García↗

DOE OSTI2024

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗

DOE OSTI2025

MTUQ: a framework for estimating moment tensors, point forces, and their uncertainties

SUMMARY We introduce MTUQ, an open-source Python package for seismic source estimation and uncertainty quantification, emphasizing flexibility and operational scalability. MTUQ provides MPI-parallelized grid search and global optimization capabilities, compatibility with 1-D and 3-D Green’s function database formats, customizable data processing, C-accelerated waveform and first-motion polarity misfit functions, and utilities for plotting seismic waveforms and visualizing misfit and likelihood surfaces. Applicability to a range of full- and constrained-moment tensor, point force, and centroid inversion problems is possible via a documented application programming interface, accompanied by example scripts and integration tests. We demonstrate the software using three different types of seismic events: (1) a 2009 intraslab earthquake near Anchorage, Alaska; (2) an episode of the 2021 Barry Arm landslide in Alaska; and (3) the 2017 Democratic People’s Republic of Korea underground nuclear test. With these events, we illustrate the well-known complementary character of body waves, surface waves, and polarities for constraining source parameters. We also convey the distinct misfit patterns that arise from each individual data type, the importance of uncertainty quantification for detecting multimodal or otherwise poorly constrained solutions, and the software’s flexible, modular design.

58 GEOSCIENCES↗

DOE OSTI2023

Impact of Blast Overpressure on the Pharmacokinetics of Various Antibiotics in Sprague Dawley Rats

ABSTRACT Introduction Combat injuries are complex and multimodal. Most injuries to the extremities occur because of explosive devices such as improvised explosive devices. Blast exposure dramatically increases the risk of infection in combat wounds, and there is limited available information on the best antibiotic treatments for these injuries. We previously demonstrated that mice exposed to blast displayed a delayed clearance of cefazolin from the plasma and liver; further semi-mechanistic modeling determined that cefazolin concentrations in the skin of these mice were reduced. Our objective was to investigate the effects of blast on the pharmacokinetics of antibiotics of different types used for the treatment of combat wounds in the rat model. Materials and Methods Male Sprague Dawley rats were exposed to blast overpressure followed by injection of a bolus of animal equivalent doses of an antibiotic (cefazolin, cefepime, ertapenem, or clindamycin) into the tail vein at 1-hour post-blast exposure. Blood was collected at predetermined time points via repeated sampling from the tail vein. Animals were also euthanized at predetermined time points, at which time liver, kidney, skin, and blood via cardiac puncture were collected. Antibiotic concentrations were determined by ultra-performance liquid chromatography–tandem mass spectrometry. Results Blast-exposed rats exhibited a similar rate of clearance compared to non-blasted rats in the blood, liver, kidney, and skin, which is inconsistent with the data regarding cefazolin in blast-exposed mice. Conclusions Our results in rats do not recapitulate our previous observation of delayed cefazolin clearance in mice following the blast overpressure exposure. Although using rats permitted us to collect multiple blood samples from the same animals, rats may not be a suitable model for measuring the pharmacokinetics of antibiotics following blast. The interpretation of the results may be challenging because of variation in data among rat subjects in the same sample groups.

General & Internal Medicine↗

DOE OSTI2024

Nanoscale elemental and morphological imaging of nitrogen-fixing cyanobacteria

Nitrogen-fixing cyanobacteria bind atmospheric nitrogen and carbon dioxide using sunlight. This experimental study focused on a laboratory-based model system, Anabaena sp., in nitrogen-depleted culture. When combined nitrogen is scarce, the filamentous prokaryotes reconcile photosynthesis and nitrogen fixation by cellular differentiation into heterocysts. To better understand the influence of micronutrients on cellular function, 2D and 3D synchrotron X-ray fluorescence mappings were acquired from whole biological cells in their frozen-hydrated state at the Bionanoprobe, Advanced Photon Source. To study elemental homeostasis within these chain-like organisms, biologically relevant elements were mapped using X-ray fluorescence spectroscopy and energy-dispersive X-ray microanalysis. Higher levels of cytosolic K + , Ca 2+ , and Fe 2+ were measured in the heterocyst than in adjacent vegetative cells, supporting the notion of elevated micronutrient demand. P-rich clusters, identified as polyphosphate bodies involved in nutrient storage, metal detoxification, and osmotic regulation, were consistently co-localized with K + and occasionally sequestered Mg 2+ , Ca 2+ , Fe 2+ , and Mn 2+ ions. Machine-learning-based k-mean clustering revealed that P/K clusters were associated with either Fe or Ca, with Fe and Ca clusters also occurring individually. In accordance with XRF nanotomography, distinct P/K-containing clusters close to the cellular envelope were surrounded by larger Ca-rich clusters. The transition metal Fe, which is a part of nitrogenase enzyme, was detected as irregularly shaped clusters. The elemental composition and cellular morphology of diazotrophic Anabaena sp. was visualized by multimodal imaging using atomic force microscopy, scanning electron microscopy, and fluorescence microscopy. This paper discusses the first experimental results obtained with a combined in-line optical and X-ray fluorescence microscope at the Bionanoprobe.

Anabaena sp↗

DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Uncovering Hidden Entanglement in Twin Beams

Proper characterization of quantum correlations in multimode optical quantum states is critical for applications in quantum information science. However, standard entanglement measurements can lead to incomplete state reconstruction and characterization. Here, we implement a resonator-based detection system that reveals entanglement between sideband modes of twin beams, achieving full tomography and retrieving often ignored quantum correlations. Unlike standard spectral measurements such as homodyne detection, resonator detection can independently address the sidebands of each beam, thereby accessing these hidden correlations. Additionally, we show how phase shifts between the carrier and the sideband modes of the involved fields redistribute information and modify the observation of entanglement for different witnesses. The ability of the resonant detection to independently address sideband modes of entangled states can contribute to enhancing the capacity for secure communication and quantum networking protocols.

Rincon Celis, Raul [University of Sao Paulo, Brazi↗

DOE OSTI2025

A Flux-Tunable cavity for Dark matter detection

Developing a dark matter detector with wide mass tunability is an immensely desirable property, yet it is challenging due to maintaining strong sensitivity. Resonant cavities for dark matter detection have traditionally employed mechanical tuning, moving parts around to change electromagnetic boundary conditions. However, these cavities have proven challenging to operate in sub-Kelvin cryogenic environments due to differential thermal contraction, low heat capacities, and low thermal conductivities. Instead, we develop an electronically tunable cavity architecture by coupling a superconducting 3D microwave cavity with a DC flux tunable SQUID. With a flux delivery system engineered to maintain high coherence in the cavity, we perform a hidden-photon dark matter search below the quantum-limited threshold. A microwave photon counting technique is employed through repeated quantum non-demolition measurements using a transmon qubit. With this device, we perform a hidden-photon search and constrain the kinetic mixing angle to ${\varepsilon}< 8.2\times 10^{-15}$ in a tunable band from 5.672 GHz to 5.694 GHz. By coupling multimode tunable cavities to the transmon, wider hidden-photon searching ranges are possible.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Squeezing-Enhanced Sensing at an Exceptional Point

Pushing the boundaries of measurement precision is central for sensing and metrology, pursued by nonclassical resources such as squeezing, as well as non-Hermitian degeneracies with distinct spectral response. Their convergence, however, remains challenging. We find extraordinary enhancement of sensitivity by unifying both effects in a general framework for quantum sensing in open systems. At the parametric oscillation threshold and an exceptional point, the sensing precision exhibits a unique quartic scaling with the perturbation strength. The result generalizes to multimode squeezed-state sensors with higher-order exceptional points catered to various quantum sensing platforms.

Wang, Changqing [Fermilab] (ORCID:0000000198073045↗

DOE OSTI2022

Construction of bias-preserving operations for pair-cat codes

Fault-tolerant quantum computation with depolarization error often requires demanding error threshold and resource overhead. If the operations can maintain high noise bias—dominated by dephasing error with small bit-flip error—we can achieve hardware-efficient fault-tolerant quantum computation with a more favorable error threshold. Distinct from two-level physical systems, multilevel systems (such as harmonic oscillators) can achieve a desirable set of bias-preserving quantum operations while using continuous engineered dissipation or Hamiltonian protection to stabilize to the encoding subspace. For example, cat codes stabilized with driven-dissipation or Kerr nonlinearity can possess a set of bias-preserving gates while continuously correcting bosonic dephasing error. However, cat codes are not compatible with continuous quantum error correction against excitation loss error, because it is challenging to continuously monitor the parity to correct photon loss errors. In this work, we generalize the bias-preserving operations to pair-cat codes, which can be regarded as a multimode generalization of cat codes, to be compatible with continuous quantum error correction against both bosonic loss and dephasing errors. In conclusion, our results open the door towards hardware-efficient robust quantum information processing with both bias-preserving operations and continuous quantum error correction simultaneously correcting bosonic loss and dephasing errors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Experimental generation of polarization entanglement from spontaneous parametric down-conversion pumped by spatiotemporally highly incoherent light

Here, we investigate the cross influence of the pump coherence on the entanglement produced from spontaneous parametric down-conversion (SPDC) in different degrees of freedom (DOFs). We experimentally demonstrate the generation of polarization entanglement from SPDC pumped by a spatiotemporally highly incoherent (STHI) light-emitting diode. Our quantum state tomography measurements using multimode collection fibers to avoid postselection yield a two-qubit state with the concurrence of 0.531 ± 0.006 and purity of 0.647 ± 0.005, in excellent agreement with our theoretically predicted concurrence of 0.552 and purity of 0.652. We find that using an STHI pump reduces the entanglement and purity of the output polarization two-qubit state due to a coupling between the spatiotemporal and polarization DOFs introduced by the birefringence and dispersion of the nonlinear crystal. The viability of SPDC with STHI pumps is important for two reasons: (i) STHI sources are ubiquitous and available at a wider range of wavelengths than lasers, and (ii) the generated STHI polarization-entangled two-photon states could potentially be useful in long-distance quantum communication schemes due to their robustness to scattering.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Hybrid Magnonics for Short-Wavelength Spin Waves Facilitated by a Magnetic Heterostructure

Recent research on hybrid magnonics has been restricted by the long magnon wavelengths of the ferromagnetic resonance modes. Here, we present an experiment on the hybridization of 250-nm-wavelength magnons with microwave photons in a multimode magnonic system consisting of a planar cavity and a magnetic bilayer. The coupling between magnon modes in the two magnetic layers, i.e., the uniform mode in Permalloy and the perpendicular standing spin waves (PSSWs) in yttrium iron garnet, serves as an effective means for exciting short-wavelength PSSWs, which is further hybridized with the photon mode of the microwave resonator. The demonstrated magnon-photon coupling approaches the superstrong coupling regime, and can even be achieved near zero bias field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Lifetime renormalization of weakly anharmonic superconducting qubits. I. Role of number nonconserving terms

The dynamics of a weakly anharmonic superconducting qubit in a complex electromagnetic environment is generally well described by an effective multimode Kerr Hamiltonian at sufficiently weak excitation. This Hamiltonian can be embedded in a master equation with losses determined by the details of the electromagnetic environment. Recent experiments indicate, however, that when a superconducting circuit is driven with microwave signals populating the system with sufficiently high excitations, the observed relaxation rates appear to be substantially different from expectations based on the electromagnetic environment of the qubit alone. This issue is a limiting factor in the optimization of superconducting qubit readout schemes. We claim here that an effective master equation with drive-power-dependent parameters is an efficient approach to model such quantum dynamics. In this sequence of papers, we derive effective master equations, whose parameters exhibit nonlinear dependence on the excitation level of the circuit as well as the electromagnetic environment of the qubit. Further, we show that the number nonconserving terms in the qubit nonlinearity generally lead to a renormalization of dissipative parameters of the effective master equation, while the number conserving terms give rise to a renormalization of the system frequencies. Here, in Paper I, we consider the excitation-relaxation dynamics of a transmon qubit that is prepared in a certain initial state, but is not driven otherwise. A unitary transformation technique is introduced to study the renormalization of (i) qubit relaxation due to coupling to a generic bath and (ii) Purcell decay. Analytic expressions are provided for the dependence of the nonlinear dissipative terms on the details of the electromagnetic environment of the qubit. The perturbation technique based on unitary transformations developed here is generalized to the continuously driven case in Paper II.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Compositional patterning in irradiated alloys: Effective potentials and effective interfacial energy

Compositional patterning (CP) in binary alloys during energetic particle irradiation is studied using a kinetic model that considers two competing kinetic processes, a thermally activated one promoting macroscopic phase separation (MPS) of the concentration field c(r,t) and a forced one resulting in finite-range random atomic mixing. The forced mixing is modeled by a Gaussian relocation distribution with a characteristic distance R. A series of approximate kinetic models are introduced by expanding the mixing function into a series of n terms, thus replacing the non-local evaluations of the concentration field c(r'-r,t) by local derivatives of c(r,t). This approach makes it possible to obtain exact effective potentials and build steady-state diagrams for each order-n model. Phase field (PF) simulations using these order-n models reveal that near the onset of patterning, phase evolution is accurately described using an order-3 model, which changes smoothly from an extended Cahn-Hilliard free energy in the MPS regime to a one-mode Swift-Hohenberg functional in the CP regime. Deeper into the patterning regime, higher-order models are required to achieve convergence, yielding square-like concentration profiles characteristic of a strong segregation regime. These higher-order effective free energies are analogous to multimodal Swift-Hohenberg functionals. Here, a new definition for the effective interfacial energy is proposed in the CP regime, since the interfacial area is no longer an excess quantity in that regime, precluding the use of the standard thermodynamic definition of interfacial energy.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Deciphering the archaeological record: Cosmological imprints of nonminimal dark sectors

Many proposals for physics beyond the Standard Model give rise to a dark sector containing many degrees of freedom. In this work, we explore the cosmological implications of the nontrivial dynamics which may arise within such dark sectors, focusing on decay processes which take place entirely among the dark constituents. First, we demonstrate that such decays can leave dramatic imprints on the resulting dark-matter phase-space distribution. In particular, this distribution need not be thermal—it can even be multimodal, exhibiting a nontrivial pattern of peaks and troughs as a function of momentum. We then proceed to show how these features can induce modifications to the matter power spectrum. Finally, we assess the extent to which one can approach the archaeological “inverse” problem of deciphering the properties of an underlying dark sector from the matter power spectrum. Indeed, one of the main results of this paper is a remarkably simple conjectured analytic expression which permits the reconstruction of many of the important features of the dark-matter phase-space distribution directly from the matter power spectrum. Here, our results provide an interesting toolbox of methods for learning about, and potentially constraining, the features of nonminimal dark sectors and their dynamics in the early universe.

79 ASTRONOMY AND ASTROPHYSICS↗