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DOE OSTI2025

SymbolFit: Automatic Parametric Modeling with Symbolic Regression

We introduce SymbolFit (API: https://github.com/hftsoi/symbolfit), a framework that automates parametric modeling by using symbolic regression to perform a machine-search for functions that fit the data while simultaneously providing uncertainty estimates in a single run. Traditionally, constructing a parametric model to accurately describe binned data has been a manual and iterative process, requiring an adequate functional form to be determined before the fit can be performed. The main challenge arises when the appropriate functional forms cannot be derived from first principles, especially when there is no underlying true closed-form function for the distribution. In this work, we develop a framework that automates and streamlines the process by utilizing symbolic regression, a machine learning technique that explores a vast space of candidate functions without requiring a predefined functional form because the functional form itself is treated as a trainable parameter, making the process far more efficient and effortless than traditional regression methods. We demonstrate the framework in high-energy physics experiments at the CERN Large Hadron Collider (LHC) using five real proton-proton collision datasets from new physics searches, including background modeling in resonance searches for high-mass dijet, trijet, paired-dijet, diphoton, and dimuon events. We show that our framework can flexibly and efficiently generate a wide range of candidate functions that fit a nontrivial distribution well using a simple fit configuration that varies only by random seed, and that the same fit configuration, which defines a vast function space, can also be applied to distributions of different shapes, whereas achieving a comparable result with traditional methods would have required extensive manual effort.

Tsoi, Ho Fung [Univ. of Pennsylvania, Philadelphia↗

DOE OSTI2024

Active interlocking metasurfaces enabled by shape memory alloys

Interlocking metasurfaces (ILMs) are a newly developed joining technology that relies on arrays of interlocking features that transmit force and constrain motion between adjoining bodies in one or more directions. This study explores harnessing the shape memory effect (SME) in Nickel-Titanium shape memory alloys (NiTi SMAs) in structures fabricated using additive manufacturing (AM) to advance the development of active ILMs by creating unit cells that open or close at specific temperatures. The study encompasses designing and fabricating two distinct interlocking array configurations using near-equiatomic NiTi powder and the laser powder bed fusion (L-PBF) AM technique, following a previously developed AM process optimization framework to manufacture defect-free parts. To guide the design process, finite element analysis (FEA) was employed to predict strain values during engage-disengage cycles. The martensitic transformation characteristics of the ILMs were characterized. Thermomechanical testing revealed that the ILMs demonstrate high locking force once engaged, coupled with complete shape recovery and good cyclic stability. Digital image correlation (DIC) was also employed to validate the FEA predictions during the engage-disengage cycles. The results indicate that NiTi SMA-based ILMs can be designed and fabricated into complex shapes using L-PBF. By leveraging the SME, the functionality of an ILM can be improved upon. The combination of computational modeling, additive manufacturing, and thermomechanical and physical property characterization provides a framework for designing future ILMs out of active materials.

Additive manufacturing↗

DOE OSTI2020

Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures

Molecular assemblies inside cells often undergo structural reconfiguration in response to stimuli to alter their function. Adaptive reconfiguration of cytoskeletal networks, for example, enables cellular shape change, movement, and cargo transport and plays a key role in driving complex processes such as division and differentiation. The cellular cytoskeleton is a self-assembling polymer network composed of simple filaments, so reconfiguration often occurs through the rearrangement of its component filaments’ connectivities. DNA nanotubes have emerged as promising building blocks for constructing programmable synthetic analogs of cytoskeletal networks. Nucleating seeds can control when and where nanotubes grow and capping structures can bind nanotube ends to stop growth. Such seeding and capping structure, collectively called termini, can organize nanotubes into larger architectures. However, these structures cannot be selectively activated or inactivated in response to specific stimuli to rearrange nanotube architectures, a key property of cytoskeletal networks. Here we demonstrate how selective regulation of the binding affinity of DNA nanotube termini for DNA nanotube monomers or nanotube ends can direct the reconfiguration of nanotube architectures. Using DNA hybridization and strand displacement reactions that specifically activate or inactivate four orthogonal nanotube termini, we demonstrate that nanotube architectures can be reconfigured by selective addition or removal of unique termini. Lastly, we show how terminus activation could be a sensitive detector and amplifier of a DNA sequence signal. These results could enable the development of adaptive and multifunctional materials or diagnostic tools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Surface-mediated spontaneous emulsification of the acylated peptide, semaglutide

Acylated peptides composed of glucagon-like peptide-1 receptor agonists modified with a fatty acid side chain are an important class of therapeutics for type 2 diabetes and obesity but are susceptible to an unusual physical instability in the presence of hydrophobic surfaces, i.e., spontaneous emulsification, also known as ouzo formation in practice. In this work, light scattering, small-angle X-ray scattering, and circular dichroism measurements are used to characterize the physical properties of the semaglutide colloidal phase, including size distribution, shape, secondary structure, internal structure, and internal composition, as a function of solution physico-chemical conditions. The existence and size of the colloids formed are successfully predicted by a classical Rayleigh model, which identifies the parameters controlling their size and formation. Colloid formation is found to be catalyzed by hydrophobic surfaces, and formation rates are modeled as an autocatalytic reaction, enabling the formation of a master curve for various surfaces that elucidates the mechanism. Surfaces differ due to differences in surface wettability, which can be correlated with Hansen solubility parameters. This work provides insights into this unusual colloidal phenomenon and guides the peptide synthesis process and drug product formulation in the pharmaceutical industry.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Defect Equilibria from First Principles: From Widegap Oxides to Topological Semimetals

Materials functionality and performance is rarely determined by the ideal crystal alone but is usually affected by formation of imperfections and the solution of impurities. In some applications, such as solar thermochemical hydrogen generation, defect formation is the fundamentally enabling mechanism of the desired functionality. In other cases, such as Cd3As2 topological semimetals, unintentional self-doping presents an obstacle to the access to the unique electronic properties. In either case, a quantitative understanding of the relevant defect mechanism is essential for developing design strategies. This presentation will touch upon numerous aspects in the computational simulation of defect equilibria, including non-equilibrium design strategies, the coupling of solid state and gas-phase reactions, dopant-defect and defect-defect interactions, both attractive and repulsive, the accuracy of total energy functionals and electronic structure methods, and the role of the shape of the density of states for the charge balance condition and Fermi level position, as well as machine-learning prediction of defect energies (1). Specific materials systems include Ga2O3 (2), Cd3As2 (3), and (Sr,Ce)MnO3 (4). (1) M.D. Witman, A. Goyal, T. Ogitsu, A.H. McDaniel, S. Lany, Nat. Comput. Sci. 3, 675 (2023). (2) A. Goyal, A. Zakutayev, V. Stevanovic, S. Lany, J. Appl. Phys. 129, 245704 (2021). (3) C. Brooks, M. van Schilfgaarde, D. Pashov, J.N. Nelson, K. Alberi, D.S. Dessau, S. Lany, Phys. Rev. B 107, 224110 (2023). (4) A. Goyal, M.D. Sanders, R.P. O'Hayre, S. Lany, PRX Energy 3, 013008 (2024).

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗

DOE OSTI2022

Extracting dark-matter velocities from halo masses: A reconstruction conjecture

Increasing attention has recently focused on nontraditional dark-matter production mechanisms which result in primordial dark-matter velocity distributions with highly nonthermal shapes. Here, in this paper, we undertake an assessment of how the detailed shape of a general dark-matter velocity distribution impacts structure formation in the nonlinear regime. In particular, we investigate the impact on the halo-mass and subhalo-mass functions, as well as on astrophysical observables such as satellite and cluster-number counts. We find that many of the standard expectations no longer hold in situations in which this velocity distribution takes a highly nontrivial, even multimodal shape. For example, we find that the nominal free-streaming scale alone becomes insufficient to characterize the effect of free-streaming on structure formation. In addition, we propose a simple one-line conjecture which can be used to “reconstruct” the primordial dark-matter velocity distribution directly from the shape of the halo-mass function. Although our conjecture is completely heuristic, we show that it successfully reproduces the salient features of the underlying dark-matter velocity distribution even for nontrivial distributions which are highly nonthermal and/or multimodal, such as might occur for nonminimal dark sectors. Moreover, since our approach relies only on the halo-mass function, our conjecture provides a method of probing dark-matter properties even for scenarios in which the dark and visible sectors interact only gravitationally.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Surrogate approximation of the Grad–Shafranov free boundary problem via stochastic collocation on sparse grids

In magnetic confinement fusion devices, the equilibrium configuration of a plasma is determined by the balance between the hydrostatic pressure in the fluid and the magnetic forces generated by an array of external coils and the plasma itself. The location of the plasma is not known a priori and must be obtained as the solution to a free boundary problem. The partial differential equation that determines the behavior of the combined magnetic field depends on a set of physical parameters (location of the coils, intensity of the electric currents going through them, magnetic permeability, etc.) that are subject to uncertainty and variability. The confinement region is in turn a function of these stochastic parameters as well. In this work, we consider variations on the current intensities running through the external coils as the dominant source of uncertainty. This leads to a parameter space of dimension equal to the number of coils in the reactor. With the aid of a surrogate function built on a sparse grid in parameter space, a Monte Carlo strategy is used to explore the effect that stochasticity in the parameters has on important features of the plasma boundary such as the location of the x-point, the strike points, and shaping attributes such as triangularity and elongation. Furthermore, the use of the surrogate function reduces the time required for the Monte Carlo simulations by factors that range between 7 and over 30.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

The Cross-sectional and Longitudinal Association Between Thyroid Function and Depression: A Population-Based Study

Abstract Context An association of thyroid function with mood disorders has been widely suggested, but very few studies have examined this association longitudinally. Objective We assessed the cross-sectional and longitudinal association between thyroid function and depression in a population-based cohort. Methods A total of 9471 individuals were included in cross-sectional analyses, of whom 8366 had longitudinal data. At baseline, we assessed thyroid function using serum samples (thyrotropin [TSH], free thyroxine (FT4), and thyroid peroxidase antibodies) and depressive symptoms using the Centre for Epidemiologic Studies Depression (CES-D) scale. Incident depressive events (n = 1366) were continuously followed up with the CES-D and clinical interviews. We analyzed the cross-sectional association of thyroid function and thyroid disease with depressive symptoms using linear and logistic regression, and the longitudinal association with Cox proportional hazard models for depressive events. Results Lower TSH levels and lower and higher FT4 levels were cross-sectionally associated with more depressive symptoms with a B value of −0.07 per 1 unit increase of natural log-transformed TSH (95% CI −0.11; −0.04). Furthermore, hypothyroidism was cross-sectionally associated with less depressive symptoms and hyperthyroidism with more depressive symptoms. Longitudinally, there was a U-shaped association between FT4 and incident depressive events but only in euthyroid participants. Conclusion We show a cross-sectional association between thyroid (dys)function with depressive symptoms, and a U-shaped association between FT4 and incident depressive events in euthyroid individuals. Our findings suggest an association of thyroid function with the risk of developing depression, albeit small. Reverse causation and additional underlying factors may also contribute to the association.

Roa Dueñas, Oscar Hernando (ORCID:0000000207522261↗

DOE OSTI2023

High-Order Mesh Morphing for Boundary and Interface Fitting to Implicit Geometries

Here, we propose a method that morphs high-order meshes such that their boundaries and interfaces coincide/align with implicitly defined geometries. Our focus is particularly on the case when the target surface is prescribed as the zero isocontour of a smooth discrete function. Common examples of this scenario include using level set functions to represent material interfaces in multimaterial configurations, and evolving geometries in shape and topology optimization. The proposed method formulates the mesh optimization problem as a variational minimization of the sum of a chosen mesh-quality metric using the Target-Matrix Optimization Paradigm (TMOP) and a penalty term that weakly forces the selected faces of the mesh to align with the target surface. The distinct features of the method are use of a source mesh to represent the level set function with sufficient accuracy, and adaptive strategies for setting the penalization weight and selecting the faces of the mesh to be fit to the target isocontour of the level set field. We demonstrate that the proposed method is robust for generating boundary- and interface-fitted meshes for curvilinear domains using different element types in 2D and 3D.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Joint cosmological fits to DESI-DR1 full-shape clustering and weak gravitational lensing in configuration space

We present a joint $3\times2$-pt cosmological analysis of auto- and cross-correlations between the Dark Energy Spectroscopic Instrument Data Release 1 (DESI-DR1) Bright Galaxy Survey (BGS) and Luminous Red Galaxy (LRG) samples and overlapping shear measurements from the KiDS-1000, DES-Y3 and HSC-Y3 weak lensing surveys. We perform our analysis in configuration space and, in addition to the cosmic shear correlation functions for each weak lensing dataset, we fit the tangential shear of the weak lensing source galaxies around DESI lens galaxies. Finally, we make use of the anisotropic BGS and LRG clustering information by fitting the full shape of the two-point correlation function multipoles measured over the full DESI-DR1 footprint, presenting the first full-shape analysis of DESI measurements in configuration space. We find that the addition of weak lensing information serves to improve, with respect to the clustering-only case, the measurements of the power spectrum amplitude parameters $\ln(10^{10}A_{\rm{s}})$ and $σ_{12}$ by $15\%$ and $36\%$, respectively. It also improves measurements of the linear bias of the lens galaxies by $15-20\%$, depending on the tracer. Our results show excellent consistency, regardless of the weak lensing survey considered, and are furthermore consistent with a companion analysis that fits $3\times2$-pt correlations including DESI projected clustering measurements, as well as the results published by the weak lensing collaborations themselves. Our measured values for weak lensing amplitude are $S_{8}^{\mathrm{DESI\times HSC}}=0.787\pm0.020$, $S_{8}^{\mathrm{DESI\times DES}}=0.791\pm0.016$, $S_{8}^{\mathrm{DESI\times KiDS}}=0.771\pm0.017$, which are $1.9σ-2.9σ$ below the $S_8$ value preferred by Planck. Finally, our clustering-only results are in good agreement with the Fourier space full-shape analysis of all DESI tracers.

Semenaite, A. [Swinburne U., Ctr. Astrophys. Super↗

DOE OSTI2020

Shape-constrained Input Estimation for Efficient Multi-shaker Vibration Testing

Multi-shaker vibration testing is gaining interest from structural dynamics test engineers as it can provide a much more accurate match to complicated field vibration responses than traditional single-axis shaker tests. However, the force capabilities of the small modal shakers typically used in multi-shaker vibration tests has limited the achievable response levels. To date, most multi-shaker vibration tests have been performed using a variety of standard, commercially-available control systems. While these control systems are adequate for a wide range of multiple-input/multiple-output tests, their control algorithms have not been tailored for the specific problem of multi-shaker vibration tests: efficiently coordinating the various shakers to work together to achieve a desired response. Here, a new input estimation algorithm is developed and demonstrated using simulations and actual test data. This algorithm, dubbed shape-constrained input estimation, is shown to effectively coordinate multiple shakers using a set of constraint vectors based on the deflection shapes of the test structure. This is accomplished by using the singular vector shapes of the system frequency response matrix, which allows the constraint vectors to automatically change as a function of frequency. Simulation and test results indicate a significant reduction in the input forces required to achieve a desired response. Finally, the results indicate that shape-constrained input estimation is an effective method to achieve higher response levels from limited shaker forces which will enable higher level multi-shaker vibration tests to be performed.

42 ENGINEERING↗

DOE OSTI2025

Impacts of benchmarking choices on inferred model skill of the Arctic–Boreal terrestrial carbon cycle

Abstract Land surface models require continuous validation against observations to improve and reduce simulation uncertainty. However, inferred model performance can be heavily influenced by subjective choices made in the selection and application of observational data products. A key area often misrepresented by models is the Arctic–Boreal region, which is a potential tipping point region in Earth’s climate system due to large permafrost carbon stocks that are vulnerable to release with climate warming. We use the International Land Model Benchmarking (ILAMB) framework to evaluate how the model skill of TRENDY-v9 models varies based on the choice of observational-based benchmark and how benchmarks are applied in model evaluation. This analysis uses global datasets integrated into ILAMB and new, regionally-specific observational products from the Arctic–Boreal Vulnerability Experiment. Our results cover the overall time period of 1979–2019 and show that model scores can vary substantially depending on the data product applied, with higher model scores indicating better model performance against observations. The lowest model scores occur when benchmarked against regional, compared to global, datasets. We also evaluate observed and modeled functional relationships between ecosystem respiration and air temperature and between gross primary production and precipitation. Here, we find that the magnitude and shape of the responses are strongly impacted by the choice of observational dataset and the approach used to construct the functional relationship benchmark. These results suggest that model evaluation studies could conclude a false sense of model skill if only using a single benchmark data product or if not applying regional data products when performing a regional model analysis. Collectively, our findings highlight the influence of benchmarking choices on model evaluation and point to the need for benchmarking guidelines when assessing model skill.

Poe, Jeralyn (ORCID:0000000318495278)↗

DOE OSTI2024

Loss cone effects and monotonic sheath conditions of a partially magnetized plasma sheath

In this Letter, we propose the conditions for monotonic plasma sheaths adjacent to a floating wall in the presence of an applied, oblique magnetic field. The electron velocity distribution function (VDF) at the sheath edge obtained from a kinetic model exhibits a loss cone shaped truncation. Using an approximation of the truncated VDF, we derive an analytical framework of the sheath edge condition (i.e., Bohm condition), namely, the relation of ion injection velocity and sheath potential drop as a function of the magnetic field angle. The results show that the sheath edge velocity and total potential drop decrease for a steady-state sheath, which eventually collapses when the magnetic field lines become parallel to the wall.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland

Abstract Peatland ecosystems cover only 3% of the world’s land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.

Environmental Sciences & Ecology↗

DOE OSTI2022

Reduction of microbial diversity in grassland soil is driven by long-term climate warming

Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential for maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. Here, we examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture play a predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%) and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes, such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Influence of shape resonances on the angular dependence of molecular photoionization delays

Characterizing time delays in molecular photoionization as a function of the ejected electron emission direction relative to the orientation of the molecule and the light polarization axis provides unprecedented insights into the attosecond dynamics induced by extreme ultraviolet or X-ray one-photon absorption, including the role of electronic correlation and continuum resonant states. Here, we report completely resolved experimental and computational angular dependence of single-photon ionization delays in NO molecules across a shape resonance, relying on synchrotron radiation and time-independent ab initio calculations. The angle-dependent time delay variations of few hundreds of attoseconds, resulting from the interference of the resonant and non-resonant contributions to the dynamics of the ejected electron, are well described using a multichannel Fano model where the time delay of the resonant component is angle-independent. Comparing these results with the same resonance computed in e-NO + scattering highlights the connection of photoionization delays with Wigner scattering time delays.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Reconciling Chord Length Distributions and Area Distributions for Fields of Fractal Cumulus Clouds

While the total cover of broken cloud fields can in principle be obtained from one-dimensional measurements, the cloud size distribution normally differs between two-dimensional (area) and one-dimensional retrieval (chord length) methods. In this study, we use output from high-resolution Large Eddy Simulations to generate a transfer function between the two. We retrieve chord lengths and areas for many clouds, and plot the one as a function of the other, and vice versa. We find that the cloud area distribution conditional on the chord length behaves like a gamma distribution with well-behaved parameters, with a mean μ=1.1L and a shape parameter β=L−0.645. Using this information, we are able to generate a transfer function that can adjust the chord length distribution so that it comes much closer to the cloud area distribution. Our transfer function improves the error in predicting the mean cloud size, and is performs without strong biases for smaller sample sizes. However, we find that the method is still has difficulties in accurately predicting the frequency of occurrence of the largest cloud sizes.

54 ENVIRONMENTAL SCIENCES↗