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At least 505 records · Page 28

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Assessment of DFT methods for the prediction of detachment energies and electronic structures of complex and multiply charged anions

Here, in this work, we assess the ability of different density functional theory methods to reproduce the vertical/adiabatic detachment energies (VDEs/ADEs) of a series of 40 anions, including monoanion versus multiply charged anions (MCAs) and covalent versus noncovalent interaction. The statistical analysis of errors is firstly performed by comparing the theoretical values with the experimental benchmark data obtained from the negative ion photoelectron spectroscopy (NIPES). The proposed optimally tuned range-separated (OTRS) functionals are proved to not only well reproduce the experimental VDEs/ADEs, but also simulate experimental NIPES. The result implies a more serious issue of delocalization error for MCAs and a balanced description of electron-rich/- deficient region of anions is necessary. The radius of the spherically symmetric average electron localization function (ELF) region is demonstrated as a useful descriptor for the characterization of electronic structure of anionic systems and a quasilinear fitting model is proposed to efficiently obtain their OTRS parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accurate Prediction of HSE06 Band Structures for a Diverse Set of Materials Using Δ-Learning

Here we used machine learning (ML) to accurately predict eigenvalues of the hybrid HSE06 functional using eigenvalues computed by the less computationally expensive PBE functional and associated electronic features based on the k-point resolved atomic band character. The ML model was trained by using eigenvalues from only one k-point for each of the 168 compounds in the training set. The HSE06 eigenvalues across all k-points were then predicted for a separate set of 169 compounds with a mean absolute error (MAE) of 0.13 eV, representing a significant improvement over the error of PBE-computed eigenvalues relative to that of HSE06 (MAE = 0.96 eV). These accurately predicted eigenvalues result in remarkably accurate predictions for the band structures, projected density of states, and band gaps, even though the model was not explicitly trained on these other properties. Finally, we demonstrate that our ML model has a similar accuracy for both ternary and quaternary compounds well outside the initial training set and on systems with 112 and 160 atoms, demonstrating its potential to rapidly predict HSE06-quality electronic structures of complex materials that are practically unfeasible for HSE06.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicting Patient-specific Dosimetric Benefits of Proton Therapy for Skull-base Tumors Using a Geometric Knowledge-based Method

Purpose: To predict the organ at risk (OAR) dose levels achievable with proton beam therapy (PBT), solely based on the geometric arrangement of the target volume in relation to the OARs. A comparison with an alternative therapy yields a prediction of the patient-specific benefits offered by PBT. This could enable physicians at hospitals without proton capabilities to make a better-informed referral decision or aid patient selection in model-based clinical trials. Methods and Materials: Skull-base tumors were chosen to test the method, owing to their geometric complexity and multitude of nearby OARs. By exploiting the correlations between the dose and distance-to-target in existing PBT plans, the models were independently trained for 6 types of OARs: brainstem, cochlea, optic chiasm, optic nerve, parotid gland, and spinal cord. Once trained, the models could estimate the feasible dose–volume histogram and generalized equivalent uniform dose (gEUD) for OAR structures of new patients. The models were trained using 20 patients and validated using an additional 21 patients. Validation was achieved by comparing the predicted gEUD to that of the actual PBT plan. Results: The predicted and planned gEUD were in good agreement. Considering all OARs, the prediction error was +1.4 ± 5.1 Gy (mean ± standard deviation), and Pearson's correlation coefficient was 93%. By comparing with an intensity modulated photon treatment plan, the model could classify whether an OAR structure would experience a gain, with a sensitivity of 93% (95% confidence interval: 87%-97%) and specificity of 63% (95% confidence interval: 38%-84%). Conclusions: We trained and validated models that could quickly and accurately predict the patient-specific benefits of PBT for skull-base tumors. Similar models could be developed for other tumor sites. Such models will be useful when an estimation of the feasible benefits of PBT is desired but the experience and/or resources required for treatment planning are unavailable.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Monitoring solid metal structures with a nervous system embedded with ultrasonic 3D printing

Active and regular monitoring of structural components is a critical safety precaution, particularly as it concerns infrastructure, aerospace, industry, and many other applications. Solutions for effective structural health monitoring need to be able to probe surface and bulk properties using durable and low-power engineering. Towards these ends it is possible to build smarter, highly networked, and secure materials in order to enable remote real-time material sensing with a lesser-known form of 3D printing, ultrasonic consolidation (UC). This approach harnesses sound waves to weld metal layers in a low temperature process that does not damage sensors and electronics as they are embedded into a solid metal structure. This makes UC perfectly suited for designing solid metal parts with active embedded sensing components. However, the process parameters, material influences and mechanical factors that result in high-quality UC metal components are difficult to control or are loosely understood. The use of trial-and-error optimization during fabrication represents the chief hurdle between its current state of use and its potential to transform rapid prototyping and manufacturing of high-impact technologies (e.g., metal smart structures, wearable sensors, lab-on-a-chip, etc.). In this paper we will describe how embedded sensors may be used for in situ process monitoring and optimization. We will also discuss efforts towards standardizing UC welding for similar and dissimilar metal bonding and for embedding active sensors that can be used to create smart structures that will enable long-term structural health monitoring and other high impact applications.

Suter, Jonathan D.↗

FAIR Data and Interpretable AI Framework for Architectured Metamaterials (Final Report)

This research program established a transformative framework for the discovery and design of mechanical metamaterials, which are architected structures engineered to control physical phenomena like sound and vibration in ways natural materials cannot. To overcome the traditional reliance on trial-and-error, the project developed an interpretable Artificial Intelligence (AI) framework that moves beyond "black box" models to reveal the specific geometric patterns—such as "unit-cell templates"—that govern a material’s performance. A major breakthrough was the development of a hierarchical design method, which allows a single material to block vibrations across multiple frequency ranges simultaneously by layering patterns at different scales without them interfering with one another. This was further expanded to include irregular, graph-based designs that use spanning tree algorithms to ensure structural connectivity while allowing for customized, direction-dependent properties like stiffness and acoustic impedance. Beyond design, the project addressed the practicalities of real-world production by developing uncertainty quantification techniques that account for manufacturing defects and material variability, reducing the need for expensive physical testing by orders of magnitude. To speed up the discovery process, the team implemented Gaussian Process Regression and other surrogate models that provide accurate performance predictions at a fraction of the traditional computational cost. The AI-generated designs were successfully validated through fabrication of physical samples and wave propagation experiments, confirming their ability to accurately guide or reflect waves as predicted. By contributing these tools and high-quality FAIR benchmark datasets to the wider scientific community, this work provides a scalable foundation for advancing technologies in aerospace vibration control, medical imaging, and noise reduction.

36 MATERIALS SCIENCE↗

Configurational-Bias Monte Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures into Atomistic Models

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. The error in the RDFs of backmapped relative to reference configuration for the CCBMC, MD, and MC were found to be 6.9, 8.7, and 12.9 respectively for the hexagonal system. For the cubic system the relative error of the RDFs for the CCBMC, MD, and MC were found to be 18.2, 34.6, and 39.0 respectively. Finally, our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

74 ATOMIC AND MOLECULAR PHYSICS↗

Reduced‐Order Modeling for Linearized Representations of Microphysical Process Rates

Abstract Representing cloud microphysical processes in large scale atmospheric models is challenging because many processes depend on the details of the droplet size distribution (DSD, the spectrum of droplets with different sizes in a cloud). While full or partial statistical moments of droplet size distributions are the typical variables used in bulk models, prognostic moments are limited in their ability to represent microphysical processes across the range of conditions experienced in the atmosphere. Microphysical parameterizations employing prognostic moments are known to suffer from structural uncertainty in their representations of inherently higher dimensional cloud processes, which limit model fidelity and lead to forecasting errors. Here we investigate how data‐driven reduced‐order modeling can be used to learn predictors for microphysical process rates in bulk microphysics schemes in an unsupervised manner from higher dimensional bin distributions. Using simulations characteristic of marine stratiform clouds, we simultaneously learn lower dimensional representations of droplet size distributions and predict the evolution of the microphysical state of the system. Droplet collision‐coalescence, the main process for generating warm rain, is estimated to have an intrinsic dimension of three. This intrinsic dimension provides a lower limit on the number of degrees of freedom needed to accurately represent collision‐coalescence in models. We demonstrate how deep learning based reduced‐order modeling can be used to discover intrinsic coordinates describing the microphysical state of the system, where process rates such as collision‐coalescence are globally linearized. These implicitly learned representations of the DSD retain more information about the DSD than typical moment‐based representations.

54 ENVIRONMENTAL SCIENCES↗

Propagating sample variance uncertainties in redshift calibration: simulations, theory, and application to the COSMOS2015 data

ABSTRACT Cosmological analyses of galaxy surveys rely on knowledge of the redshift distribution of their galaxy sample. This is usually derived from a spectroscopic and/or many-band photometric calibrator survey of a small patch of sky. The uncertainties in the redshift distribution of the calibrator sample include a contribution from shot noise, or Poisson sampling errors, but, given the small volume they probe, they are dominated by sample variance introduced by large-scale structures. Redshift uncertainties have been shown to constitute one of the leading contributions to systematic uncertainties in cosmological inferences from weak lensing and galaxy clustering, and hence they must be propagated through the analyses. In this work, we study the effects of sample variance on small-area redshift surveys, from theory to simulations to the COSMOS2015 data set. We present a three-step Dirichlet method of resampling a given survey-based redshift calibration distribution to enable the propagation of both shot noise and sample variance uncertainties. The method can accommodate different levels of prior confidence on different redshift sources. This method can be applied to any calibration sample with known redshifts and phenotypes (i.e. cells in a self-organizing map, or some other way of discretizing photometric space), and provides a simple way of propagating prior redshift uncertainties into cosmological analyses. As a worked example, we apply the full scheme to the COSMOS2015 data set, for which we also present a new, principled SOM algorithm designed to handle noisy photometric data. We make available a catalogue of the resulting resamplings of the COSMOS2015 galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

C 60 -induced Devil's Staircase transformation on a Pb/Si(111) wetting layer

Density functional theory is used to study structural energetics of Pb vacancy cluster formation on C 60 /Pb/Si(111) to explain the unusually fast and error-free transformations between the “Devil's Staircase” (DS) phases on the Pb/Si(111) wetting layer at low temperature (~110K). The formation energies of vacancy clusters are calculated in C 60 /Pb/Si(111) as Pb atoms are progressively ejected from the initial dense Pb wetting layer. Vacancy clusters larger than five Pb atoms are found to be stable with seven being the most stable, while vacancy clusters smaller than five are highly unstable, which agrees well with the observed ejection rate of ~5 Pb atoms per C 60 . Furthermore, the high energy cost (~0.8 eV) for the small vacancy clusters to form indicates convincingly that the unusually fast transformation observed experimentally between the DS phases, upon C 60 adsorption at low temperature, cannot be the result of single-atom random walk diffusion but of correlated multi-atom processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Modelling Charged Defects in Non-Cubic Semiconductors for Radiation Effects Studies in Next Generation Materials

This final report summarizes the results of the Laboratory Directed Research and Development (LDRD) Project Number 212587 entitled "Modeling Charged Defects in Non-Cubic Semiconductors for Radiation Effects Studies in Next Generation Electronic Materials" . The goal of this project was to extend a predictive capability for modeling defect level energies using first principle density functional theory methods (e.g., for radiation effects assessments) to semiconductors with non-cubic crystal structures. Computational methods that proved accurate for predicting defect levels in standard cubic semiconductors, were found to have shortcomings when applied to the lowered symmetry structures prevalent in next generation electronic materials such as SiC, GaN, and Ga 2 0 3 , stemming from an error in the treatment of the electrostatic boundary conditions. I describe methods to generalized the local moment countercharge (LMCC) scheme to position a charge in bulk supercell calculations of charged defects, circumventing the problem of measuring a dipole in a periodically replicated bulk calculation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cosmological Probes of Fundamental Physics

The Lyman-alpha forest is a key probe of the expansion history and of structure formation in the Universe at intermediate redshifts (2<z<5). This report describes two investigations into astrophysical systematic errors in the Lyman-alpha forest: reionization imprints (which affect the broadband power spectrum) and streaming velocities (which affect the baryon-acoustic oscillation feature).

79 ASTRONOMY AND ASTROPHYSICS↗

A Block-Structured Adaptive Mesh Framework to Solve Radiation Transfer Equation in Irregular Embedded Geometries

Radiation transport arises in various scientific, industrial, and medical fields, and understanding its effect in applications is needed to make accurate predictions, safety assessments and performance optimizations. Solving the Radiation Transport Equation (RTE) is challenging due to its integro-differential nature, which involves both differential and integral terms. The differential term describes the change in radiation intensity due to absorption and emission, while the integral term accounts for scattering. The accurate modeling of radiation is further complicated in many applications due to the complex, irregular geometries. Various methods exist for solving the RTE, including the zonal, Monte Carlo, spherical harmonics, discrete ordinates, and finite volume methods. Traditional mesh-based approaches, which rely on structured or unstructured meshes, struggle with irregular geometries due to: a) the difficulty of conforming structured grids to irregular domains, b) challenges in enforcing boundary conditions correctly, and c) the additional computational cost of unstructured mesh methods. This work presents a second-order accurate method for solving the RTE in irregular geometries. The radiation intensity is discretized using the finite-volume method in both spatial and angular directions on regular Cartesian grid blocks. Leveraging the block-structured adaptive mesh refinement (AMR) framework provided by AMReX, our method refines the grid locally to reduce spatial discretization error, ensuring a converged numerical solution while minimizing computational costs elsewhere. A two-stage deferred correction approach is employed: First, a first-order discretization on grid blocks is solved using an algebraic multigrid method in HYPRE. Second, a correction term is applied explicitly to achieve second-order accuracy. The correction term is calculated by approximating the radiation flux on cell faces using a Total Variation Diminishing (TVD) scheme. This approach ensures quick convergence of the multigrid method while preserving higher-order accuracy of the numerical solution. Irregular geometries are resolved as embedded boundaries (EB), resulting in both cut cells and regular cells. In cut cells, we modify the fluxes using face fractions and incorporate additional contributions from EB boundary conditions. To ensure higher-order convergence near the EB interface, the correction term is modified by interpolating the radiation intensity to fictitious ghost points. The implementation takes advantage of modern supercomputers by leveraging AMReX’sMPI/X parallelization strategy where X can be MPI or a GPU accelerator including CUDA, HIP and DPC++. We validate our solver using classical test cases, both with and without EB, demonstrating accuracy and efficiency. Additionally, we analyze the impact of adaptive mesh refinement on solution accuracy and computational cost, highlighting the advantages of our approach for high-resolution radiation transport simulations.

computational fluid dynamics (CFD)↗

Baryon fraction from the BAO amplitude: a consistent approach to parameterizing perturbation growth

Galaxy clustering constrains the baryon fraction Omega_b/Omega_m through the amplitude of baryon acoustic oscillations and the suppression of perturbations entering the horizon before recombination. This produces a different pre-recombination distribution of baryons and dark matter. After recombination, the gravitational potential responds to both components in proportion to their mass, allowing robust measurement of the baryon fraction. This is independent of new-physics scenarios altering the recombination background (e.g. Early Dark Energy). The accuracy of such measurements does, however, depend on how baryons and CDM are modeled in the power spectrum. Previous template-based splitting relied on approximate transfer functions that neglected part of information. We present a new method that embeds an extra parameter controlling the balance between baryons and dark matter in the growth terms of the perturbation equations in the CAMB Boltzmann solver. This approach captures the baryonic suppression of CDM prior to recombination, avoids inconsistencies, and yields a clean parametrization of the baryon fraction in the linear power spectrum, separating out the simple physics of growth due to the combined matter potential. We implement this framework in an analysis pipeline using Effective Field Theory of Large-Scale Structure with HOD-informed priors and validate it against noiseless LCDM and EDE cosmologies with DESI-like errors. The new scheme achieves comparable precision to previous splitting while reducing systematic biases, providing a more robust way to baryon-fraction measurements. In combination with BBN constraints on the baryon density and Alcock-Paczynski estimates of the matter density, these results strengthen the use of baryon fraction measurements to derive a Hubble constant from energy densities, with future DESI and Euclid data expected to deliver competitive constraints.

Crespi, Andrea [U. Waterloo (main); Waterloo U., I↗

DFT Accurate Interatomic Potential for Molten NaCl from Machine Learning

Molten alkali chloride salts are a critical component in concentrated solar power and nuclear applications. Despite their ubiquity, the extreme chemical reactivity of molten alkali chlorides at high temperatures has presented a significant challenge in characterizing atomic structures and dynamic properties experimentally. In this work, we we investigate molten NaCl by performing high temperature molecular dynamics simulations using a Gaussian Approximation Potential (GAP) trained on Density Functional Theory (DFT) datasets. Our GAP model, trained with a meager 1000 atomic configurations, arrives at near ab initio accuracy with a mean absolute error of 1.5 meV/atom thus enabling fast analysis of high temperature salt properties on large length (5000 ion pairs) and time (> 1ns) scales currently inaccessible to ab initio simulations. Calculated structure factors and diffusion constants from our GAP model simulations show excellent agreement with experiments. Our results indicate that GAP models are able to capture the many-body interactions required to accurately model ionic-systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Process-Defect-Structure-Property Correlations During Laser Powder Bed Fusion of Alloy 718: Role of In Situ and Ex Situ Characterizations

Components made by laser powder bed fusion (L-PBF) additive processes require extensive trial and error optimization to minimize defects and arrive at targeted microstructure and properties. In this paper, in situ infrared thermography and ex situ surface roughness measurements were explored as methodologies to ensure Inconel ® 718-part quality. For a given laser energy of 200 Watts, prismatic samples were produced with different exposure times (80 to 110 µs) and point spacings (80 to 110 µm). The infrared intensities from laser–material interaction zones were measured spatially and temporally. The conditions leading to higher IR intensity and lowest surface roughness values correlated well with less porosity and coarse solidification grain structure. The transition from highly columnar to misoriented growth is attributed to changes in thermal gradients and liquid–solid interface velocities. Hardness measurements and electron microscopy of the as-processed and post-processed heat-treated samples show complex transitions in microstructural states including the heavily dislocated FCC matrix, reduction of dislocation density, and copious precipitation, respectively. These results show that the geometry-process-structure-property correlations are dynamic, and they cascade depending on the transitions of phase states from powder to liquid to solid, as well as phase decompositions and deformations within the solid FCC phase. Finally, validity of using analytical weld process models to describe the above phenomena is also highlighted.

36 MATERIALS SCIENCE↗

10-th order of accuracy for numerical solution of 3-D elasticity equations for heterogeneous materials on unfitted Cartesian meshes

We have developed the Optimal Local Truncation Error Method (OLTEM) with 10-th order of accuracy on unfitted Cartesian meshes for a system of 3-D elasticity equations with smooth irregular interfaces. 5 x 5 x 5 = 125-point stencils (similar to those for quadratic finite elements) for elastic heterogeneous materials are used for OLTEM. There are no unknowns at the interface points between different materials; the structure of the global discrete equations is the same for homogeneous and heterogeneous materials. The calculation of unknown stencil coefficients is based on the minimization of the local truncation error of the stencil equations and yields the optimal 10-th order of accuracy for OLTEM on unfitted Cartesian meshes, i.e., the increase by 7 orders in accuracy compared to quadratic finite elements on conformal meshes. A new post-processing procedure provides the 9-th order of accuracy for stresses in the 3-D case. Similar to basic computations it uses OLTEM with the 125-point stencils, the interface conditions and the elasticity equations. It was shown that the use of the elasticity equations for post-processing improves the accuracy of 0.1% stresses by 6 orders compared to post-processing without the use of PDEs. At an accuracy of for stresses, OLTEM with the new post-processing procedure reduces the number of degrees of freedom by 360 - 8000 times compared to quadratic finite elements with similar stencils. OLTEM with the 125-point stencils yields even more accurate results than high-order finite elements with much wider stencils. OLTEM provides accurate numerical results for compressible and nearly incompressible materials.

elasticity equations↗