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At least 163 records · Page 9

Nonnegative canonical tensor decomposition with linear constraints: nnCANDELINC

Abstract There is an emerging interest for tensor factorization applications in big‐data analytics and machine learning. To speed up the factorization of extra‐large datasets, organized in multidimensional arrays (also known as tensors), easy to compute compression‐based tensor representations, such as, Tucker and tensor train formats, are used to approximate the initial large‐tensor. Further, tensor factorization is used to extract latent features that can facilitate discoveries of new mechanisms and signatures hidden in the data, where the explainability of the latent features is of principal importance. Nonnegative tensor factorization extracts latent features that are naturally sparse and parts of the data, which makes them easily interpretable. However, to take into account available domain knowledge and subject matter expertise, often additional constraints need to be imposed, which lead us to canonical decomposition with linear constraints (CANDELINC), a canonical polyadic decomposition with rank deficient factors. In CANDELINC, Tucker compression is used as a preprocessing step, which lead to a larger residual error but to more explainable latent features. Here, we propose a nonnegative CANDELINC (nnCANDELINC) accomplished via a specific nonnegative Tucker decomposition; we refer to as minimal or canonical nonnegative Tucker. We derive several results required to understand the specificity of nnCANDELINC, focusing on the difficulties of preserving the nonnegative rank of a tensor to its Tucker core and comparing the real valued to nonnegative case. Finally, we demonstrate nnCANDELINC performance on synthetic and real‐world examples.

97 MATHEMATICS AND COMPUTING↗

Comparative life cycle assessment of woody biomass processing: air classification, drying, and size reduction powered by bioelectricity versus grid electricity

Sulfur accumulation during biofuel production is pollutive and toxic to conversion catalysts and causes the premature breakdown of processing equipment. Air classification is an effective preprocessing technology for ash and sulfur reduction from biomass feedstocks. Here, a life cycle assessment (LCA) sought to understand the environmental impact of implementing air classification as a sulfur-mitigation technique to improve feedstock quality for pine residues using a grid electricity scenario (GES) versus a bioelectricity scenario (BES). Global warming potential (GWP) for preprocessing was simulated using inventory databases embedded in SimaPro and the Argonne National Laboratory’s GREET model, specifically focusing on comparing the GWP of a GES versus a BES. Overall, the GES had a GWP impact over seven times that of the BES (136 versus 18 kg CO 2 equivalent per tonne of usable feedstock), with steam generation during rotary drying accounting for 57% of the GES’s GWP. Air classification represents 0.4% and 1.6% of the total GWP impact for the GES and BES, respectively. Therefore, air classification can facilitate a 30% reduction in feedstock sulfur content to improve feedstock quality for biofuel conversion and lessen corrosion of equipment while contributing minimal GWP impact during preprocessing.

Air classification↗

Residual Insoluble Solids Expected from Saltcake Dissolution

A review of previous SRS saltcake dissolution and characterization studies was performed to inform the analysis of the amount of residual insoluble solids that may result from saltcake dissolution. A realistic value covering most cases for the maximum volume of a settled layer of residual insoluble solids that would result from dissolution of a volume of saltcake was calculated as 0.08 mL/mL (8 vol%). Applying factors to account for dissolution test uncertainty and differences between in-tank settling and laboratory testing, the recommended value for a settled layer of residual insoluble solids that would result from dissolution of a volume of saltcake is 0.16 mL/mL (16 vol%). This should apply to dissolution of saltcake with typical minimal amounts of entrained sludge but may not apply to saltcake with significant sludge. As it is composed of primarily non-radioactive isotopes, the precipitated aluminum hydroxide material does not contribute to the heat load.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding

Antigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptides into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental data set from the Immune Epitope Database, and theoretical data sets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of nine neutral residues from a six-residue subset with an average R 2 coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an receiver operating characteristic (ROC) AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2 value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting seven neutral residues from an eight-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enzymatic Laser-Induced Graphene Biosensor for Electrochemical Sensing of the Herbicide Glyphosate

Glyphosate is a globally applied herbicide yet it has been relatively undetectable in-field samples outside of gold-standard techniques. Its presumed nontoxicity toward humans has been contested by the International Agency for Research on Cancer, while it has been detected in farmers’ urine, surface waters and crop residues. Rapid, on-site detection of glyphosate is hindered by lack of field-deployable and easy-to-use sensors that circumvent sample transportation to limited laboratories that possess the equipment needed for detection. Herein, the flavoenzyme, glycine oxidase, immobilized on platinum-decorated laser-induced graphene (LIG) is used for selective detection of glyphosate as it is a substrate for GlyOx. The LIG platform provides a scaffold for enzyme attachment while maintaining the electronic and surface properties of graphene. The sensor exhibits a linear range of 10–260 µm, detection limit of 3.03 µm, and sensitivity of 0.991 nA µm -1 . The sensor shows minimal interference from the commonly used herbicides and insecticides: atrazine, 2,4-dichlorophenoxyacetic acid, dicamba, parathion-methyl, paraoxon-methyl, malathion, chlorpyrifos, thiamethoxam, clothianidin, and imidacloprid. Sensor function is further tested in complex river water and crop residue fluids, which validate this platform as a scalable, direct-write, and selective method of glyphosate detection for herbicide mapping and food analysis.

47 OTHER INSTRUMENTATION↗

Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site

Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Grampositive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the D-Ala-D-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (V D ) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue V D to L-Lys-D-Ala-D-Ala and L-Lys-D-Ala-D-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of V D , which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the D-Ala-D-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycinresistant S. aureus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Island scanning pattern optimization for residual deformation mitigation in laser powder bed fusion via sequential inherent strain method and sensitivity analysis

Laser powder bed fusion (L-PBF) has emerged as one of the mainstream additive manufacturing approaches for fabricating metal parts with complex geometries and intricate internal structures. However, large deformation associated with rapid heating and cooling can lead to build failure and requires post-processing which may increase manufacturing cost and prolong the production period. Here in this work, an island scanning pattern design method is proposed to optimize the scanning direction of each island in order to reduce part deformation after cutting off the build platform. The objective of this optimization is to minimize the upward bending of the part after sectioning, which allows the part deformation to satisfy the tolerance requirement or reduce the post heat treatment time. Inherent strain method is employed in the sequential finite element analysis consisting of layer-by-layer activations and sectioning for fast residual distortion prediction. Full sequential sensitivity analysis for the formulated optimization is provided to update the island scanning directions. To show the feasibility and effectiveness of the proposed method, the scanning patterns of a block structure and a connecting rod were designed and parts were fabricated using an open architecture L-PBF machine. The fabrication experiments demonstrated that the residual deformation of both parts fabricated by optimized scanning pattern can be reduced by over 50% compared to the initial scanning patterns, which demonstrate the effectiveness of the proposed method.

36 MATERIALS SCIENCE↗

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of semivolatile organics in liquid radioactive residue using sorptive stir bar and solvent back-extraction

Current methods for semivolatiles analysis in radioactive samples can produce large volumes of radioactive solvent residue. A method utilizing stir-bar sorptive extraction has been explored in this work for its applicability to radioactive waste samples. This low solvent analytical method may accelerate remediation, minimize hazardous solvent waste, and reduce exposure risk to workers. Organic compounds (polyaromatic hydrocarbons, chlorinated aromatics, and phenolic compounds) were chosen as surrogates for common Liquid Waste System (LWS) contaminants at Savannah River Site (Aiken, SC). Stir-bar extraction parameters (extraction time, matrix modification, and effective pH range) and solvent back extraction parameters (solvent type, volume, and extraction time) were optimized experimentally for the chosen compounds. Affinity of the stir-bar extraction polymer to radionuclides Cs-137 and Am-241 was observed to determine radionuclide concentration effects. The stir-bar method achieved mean recovery of 100 ± 0.7% (1σ), relative to 114 ± 7% using solvent extraction, while reducing weekly method hands-on time by 93.4% and solvent volume consumption by 99.3%. Sensitivity was improved by 378% in simulated tank waste and 278% in real-world LWS matrix, relative to solvent extraction. This work has produced a safe and optimized method for the low solvent analysis of organics in legacy radioactive tank waste by stir-bar sorptive extraction.

GC-MS↗

Practical considerations for amino acid isotope analysis

Over the last few decades, isotopic analysis of amino acids at the compound- and position-specific levels has been rapidly advancing across diverse fields. As these techniques progress, evaluation of isotopic fractionation associated with sample workup is essential. This critical review of analytical methods through the lens of isotope geochemistry provides a benchmark for researchers across disciplines seeking to make compound- and position-specific amino acid isotope measurements. We focus on preparation, acid hydrolysis, clean-up, derivatization, separation, and C, H, N, and S isotope measurement. Despite substantial customizability across these steps, the following general recommendations should maximize recovery while minimizing isotopic fractionation. Samples should be freeze-dried and stored anoxically at ≤ –20 °C prior to conventional acid hydrolysis (6N HCl, 110 °C, 20–24 h, anoxic), which suffices for many residues. Both gas and liquid chromatographic (GC and LC, respectively) techniques are well-established and separate about 15 amino acids; LC bypasses the need for derivatization, while GC provides higher sensitivity. Furthermore, when derivatization is needed, n-acetyl and alkoxycarbonyl esters provide the most reproducible C isotope ratios. For compound-specific analyses, online GC–IRMS and LC–IRMS systems offer the easiest workflow, but EA–IRMS enables potential multi-element isotope analysis. Emerging techniques like high-resolution mass spectrometry are also promising for multi-element analysis and recover position-specific isotopic information. Looking forward to the next decade of innovation, isotope geochemists and ecologists can improve amino acid isotope analysis by focusing on streamlining multi-element analysis and standardizing calibration practices across laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Detailed modeling of hydrogen release and particle shrinkage during pyrolysis of inhomogeneous wood

Hydrogen release during pyrolysis of woody biomass is studied considering anisotropicity and inhomogeneity of wood structure. A new anisotropic shrinkage model is proposed based on the decomposition of main wood constituents, i.e., cellulose, hemicellulose, and lignin. The new shrinkage model can predict the temporal evolution of the wood structure, and the differences between axial and radial shrinkage during pyrolysis. The model agrees very well with several experimental data from the literature. Based on particle temperature during conversion, the pyrolysis is partitioned into four stages, and the hydrogen release and H 2 formation from each stage are investigated. Stage (IV) of pyrolysis, from 1000 to 1273 K, is found to be efficient for H 2 production owing to the production of considerable mass of H with a minimal amount of tar species. Furthermore, the char quality is found to be different at the end of stages (II), (III), and (IV), where around 67.7, 80.5, and 93.4% wt. of solid residue is made of carbon, respectively. The model is also used to explain how the heating rate affects the temperature distribution inside the particle and how it shifts the peak of hydrogen release. Finally, the pyrolysis of two inhomogeneous wood samples — a beech twig with bark and a beech dowel with growth rings — are investigated. The bark can affect the pyrolysis rate, products, and flow pattern inside the particle. The growth rings do not have a considerable effect on the pyrolysis rate and products, but they have a significant impact on the flow pattern. This has an important implication for char conversion studies where the internal surface area and porosity field distribution have a significant effect on the gasification and oxidation rates.

09 BIOMASS FUELS↗

The effect of relative humidity and temperature on the response of stomatal conductance to vapor pressure deficit in tropical trees

Understanding how leaf gas exchange responds to changes in vapor pressure deficit (VPD) is key to predicting tropical forest resilience to climate change. Stomata regulate leaf water and CO2 diffusion, and respond to changes in temperature and relative humidity (RH), two drivers of VPD. At high temperatures, the cuticular pathway may also become significant and participate in the overall leaf conductance. Here, we measured gas exchange under light and dark conditions to investigate the stomatal and cuticular responses to temperature and RH on detached branches in five tropical tree species. Leaf conductance in the dark, when stomata are essentially closed, was not markedly impacted by temperature and RH, suggesting a minimal response of the cuticular pathway to these conditions. We compared six steady-state conductance models incorporating different effects of photosynthesis and evaporative demand on stomatal control. All models performed well (residual standard deviation, σ, < 0.025 mol m-2 s-1), but the best-fitting model (σ = 0.017 mol m-2 s-1) used a nonlinear relationship between photosynthesis and stomatal conductance and incorporated RH rather than vapor pressure difference. All models overestimated the steady-state conductance at high RH. Furthermore, leaf conductance immediately increased after a decrease in RH (wrong-way response), but not after an increase in leaf temperature. This suggests that the mechanisms underlying stomatal response to VPD need further investigation. The non-linear coupling between photosynthetic rate and stomatal conductance indicates a sharper physiological response than previously acknowledged.

Lamour, Julien↗

Fast tensor disentangling algorithm

Many recent tensor network algorithms apply unitary operators to parts of a tensor network in order to reduce entanglement. However, many of the previously used iterative algorithms to minimize entanglement can be slow. We introduce an approximate, fast, and simple algorithm to optimize disentangling unitary tensors. Our algorithm is asymptotically faster than previous iterative algorithms and often results in a residual entanglement entropy that is within 10 to 40% of the minimum. For certain input tensors, our algorithm returns an optimal solution. When disentangling order-4 tensors with equal bond dimensions, our algorithm achieves an entanglement spectrum where nearly half of the singular values are zero. We further validate our algorithm by showing that it can efficiently disentangle random 1D states of qubits.

Slagle, Kevin↗

Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of μNS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448–605 of μNS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP-μNS (448–605) crystallization in Sf9 cells was monitored and verified by several imaging techniques. Cells infected with the EGFP-μNS (448–605) baculovirus formed rod-shaped microcrystals (5–15 µm in length) which were reconstituted in high-viscosity media (LCP and agarose) and investigated by serial femtosecond X-ray diffraction using viscous jets at an X-ray free-electron laser (XFEL). The crystals diffracted to 4.5 Å resolution. A total of 4227 diffraction snapshots were successfully indexed into a hexagonal lattice with unit-cell parameters a = 109.29, b = 110.29, c = 324.97 Å. The final data set was merged and refined to 7.0 Å resolution. Preliminary electron-density maps were obtained. While more diffraction data are required to solve the structure of μNS (448–605) , the current experimental strategy, which couples high-viscosity crystal delivery at an XFEL with in cellulo crystallization, paves the way towards structure determination of the μNS protein.

59 BASIC BIOLOGICAL SCIENCES↗

Residual Strains in an Additively Processed Ni-based Superalloy Transpiration-Cooled Aerodynamic Leading Edge Structure using Neutron Diffraction

Selective Laser Melting (SLM) is a well-known additive manufacturing method based on a layer-by-layer building process that is capable of fabricating gas turbine Ni-based superalloy parts with complex and integrated cooling geometries that are typically not achievable using conventional casting methods. However, the impact of residual stress concentration on SLM component life is a concern. In this work, residual strains present at room temperature in an SLM Inconel 718 generic aerodynamic leading edge segment with transpiration cooling were investigated using neutron diffraction at Oak Ridge National Laboratory. This study reveals that areas of the part where complex cooling holes were printed exhibit residual tensile strains that can be detrimental to its integrity. The study paves the way for future studies of the design of cooling hole geometries and manufacturing parameters that achieve improved cooling while minimizing stress concentration effects.

Fouliard, Quentin↗

Driving mode analysis—How uncertain functional inputs propagate to an output

Abstract Driving mode analysis elucidates how correlated features of uncertain functional inputs jointly propagate to produce uncertainty in the output of a computation. Uncertain input functions are decomposed into three terms: the mean functions, a zero‐mean driving mode, and zero‐mean residual. The random driving mode varies along a single direction, having fixed functional shape and random scale. It is uncorrelated with the residual, and under linear error propagation, it produces an output variance equal to that of the full input uncertainty. Finally, the driving mode best represents how input uncertainties propagate to the output because it minimizes expected squared Mahalanobis distance amongst competitors. These characteristics recommend interpretation of the driving mode as the single‐degree‐of‐freedom component of input uncertainty that drives output uncertainty. We derive the functional driving mode, show its superiority to other seemingly sensible definitions, and demonstrate the utility of driving mode analysis in an application. The application is the simulation of neutron transport in criticality experiments. The uncertain input functions are nuclear data that describe how Pu reacts to bombardment by neutrons. Visualization of the driving mode helps scientists understand what aspects of correlated functional uncertainty have effects that either reinforce or cancel one another in propagating to the output of the simulation.

97 MATHEMATICS AND COMPUTING↗

Atomic-Scale Characterization and Electronic Properties of Gold-Capped Niobium Films for Superconducting Qubits

Niobium thin films are central to superconducting qubits, but their complex native oxides contribute significantly to microwave losses. A promising mitigation strategy is to suppress oxide formation using engineered thin-film encapsulation layers. Recent experiments have shown that ∼10 nm metallic overlayers on Nb capacitor films can improve the energy relaxation time T1 of transmon qubits. Here, we present a comparative study of Au-capped Nb films fabricated in situ by molecular beam epitaxy and ex situ by sequential deposition benchmarked against bare Nb films. Using complementary structural, chemical, and spectroscopic techniques, we correlate the interface quality with superconducting electronic properties of the Au surface. Low-temperature scanning tunneling spectroscopy (STS) provides spatially resolved quasiparticle density-of-states maps. While both Au-capped Nb samples exhibit large areas with uniform, fully gapped density of states, clear differences emerge between the two interfaces. Compared to in situ Nb-Au, ex situ Nb-Au exhibits a reduced induced superconducting gap, broadened coherence peak, and localized in-gap states, consistent with a residual NbxOy layer at the interface. Supported by complementary structural and chemical analyses, these findings demonstrate that STS directly links nanoscale superconducting properties to interface preparation, highlighting the importance of controlled in situ encapsulation for minimizing dissipation and improving quantum coherence.

Makita, Junki [MIT; Temple U.] (ORCID:000000026889↗

Search for a bound di-neutron by comparing 3 He(e,e'p)d and 3 H(e,e'p)X measurements

We report on a search for a bound di-neutron by comparing electron-induced proton-knockout $(e,e'p)$ measurements from Helium-3 ($^3$He) and Tritium ($^3$H). The measurements were performed at Jefferson Lab Hall A with a 4.326 GeV electron beam, and kinematics of large momentum transfer $Q^2 \approx 1.9$ (GeV/$c$)$^2$ and $x_B>1$, to minimize contributions from non quasi-elastic (QE) reaction mechanisms. Analyzing the measured $^3$He missing mass ($M_{miss}$) and missing energy ($E_{miss}$) distributions, we can distinguish the two-body break-up reaction, in which the residual proton-neutron system remains bound as a deuteron. In the $^3$H mirror case, under the exact same kinematic conditions, we do not identify a signature for a bound di-neutron with similar binding energy to that of the deuteron. We calculate exclusion limits as a function of the di-neutron binding energy and find that, for binding equivalent to the deuteron, the two-body break-up cross section on $^3$H is less than 0.9% of that on $^3$He in the measured kinematics at the 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗