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At least 325 records · Page 18

Applicability of the Delplot method for the determination of catalytic reaction sequences: Hydrodeoxygenation of $\gamma$-valerolactone on Ni 2 P/MCM-41

Contact-time measurements based on sites are used to investigate the reaction sequence of the hydrodeoxygenation of γ-valerolactone (GVL) on Ni 2 P/MCM-41. Here the study is carried out at 300 °C and 0.5 MPa with site times of 0.29–6.1 s. A reaction network is proposed in which pentanoic acid and 2-methyltetrahydrofuran (2-MTHF) are formed in parallel initially and pentanal, butane and pentane are formed subsequently. A first-rank Delplot analysis (selectivity) gives a good fit, but higher-rank Delplots do not. The lack of applicability is explained by the magnitude of the rate constants, in which the rate constant for one of the later steps (the consumption of pentanal) is substantially larger than those for the preceding steps. For this reason, pentanal demonstrated the characteristics of a primary product and consequently affected the discrimination of higher rank products. A simulation of a model sequence with assumed rate constants confirms the reason why the Delplot method does not work for this reaction. Since the rate constants cannot be determined a priori to be of close magnitude, the Delplot method cannot be generally used to ascertain reaction sequences.

42 ENGINEERING↗

Intercomparison of flood inundation models across land use types and hydrological flood stages

Flood Inundation Mapping (FIM) model selection is a key operational decision because accurate, rapid mapping underpins early warning and resource allocation. FIM performance is context-dependent and can vary with hydrograph phase, land-use/land-cover (LULC), and the evaluation benchmark. Intercomparison studies typically assess a single near-peak snapshot against one reference dataset. Here, we provide a context-stratified intercomparison across (i) multiple hydrograph phases, (ii) LULC classes, and (iii) benchmark types, for five FIM approaches spanning a wide range of physical complexity and operational cost (TRITON, LISFLOOD-FP, HEC-RAS 2D, ARC-Curve2Flood, and OWP HAND-FIM). We use the Hurricane Matthew flood (2016) in the Neuse River Basin, North Carolina, USA, as a case study. Using high-resolution remote sensing-derived flood inundation maps, hand-labeled points, and building footprints, we assess model skill across two rising and two falling hydrograph limbs and across major LULC types. Results show that model rankings shift systematically across contexts: LISFLOOD-FP ranks highest in three of four flood phases, while TRITON leads during one rising limb phase; LISFLOOD-FP performs best in vegetated areas, whereas HEC-RAS improves relative performance in agricultural and urban areas; and benchmark choice influences conclusions, with LISFLOOD-FP performing best for flooded-building detection in the late falling limb, while TRITON ranks highest against hand-labeled points. We also report representative wall-clock runtimes for each workflow to provide use-case context for operational feasibility. Together, these results offer transferable guidance for model selection and for designing large-scale, benchmark-aware FIM intercomparison studies.

Nikrou, Parvaneh [University of Alabama]↗

Structural Characteristics and Graphitizability of Tars from Thermal versus Microwave Plasma Pyrolysis of Coals

This work investigates the structural characteristics and graphitizability of tars obtained from thermal pyrolysis versus the reactive microwave (MW) plasma pyrolysis of coals. Powder River Basin (PRB) coal tars obtained by thermal pyrolysis have been compared with tars obtained from MW plasma pyrolysis containing H 2 . To study the effect of coal rank and MW plasma environment, the PRB tars have been compared with Middle Kittanning (MK) coal tars obtained from an argon–hydrogen MW plasma (hp) and an argon-CO 2 MW plasma (cdp) environment. Fourier transform infrared spectroscopy has been used for investigating the structural differences among the tar samples. The tars have been graphitized (GR-) at 2500 °C and the graphitic quality assessment has been performed using X-ray diffraction and transmission electron microscopy. MW plasma-derived tars have higher aromaticity, lower condensation, and lower oxygenated molecules compared to thermally derived tars. These advantageous features of MW plasma-derived tars lead to the formation of crystallites several times larger than thermally derived tars after graphitization. When considering coal of the same rank (bituminous), the choice of the MW plasma environment has a substantial impact on the graphitic quality of the tars. The utilization of MW plasma containing H 2 leads to a significant increase in both the crystallite diameter (by 60%) and stacking height (by 40%) compared to MW plasma containing CO 2 . Furthermore, within the same MW plasma environment, the coal rank plays a significant role in determining the crystallite diameter and stacking height of the GR-tars. In particular, GR-MK tar obtained from hp exhibits a 135% larger crystallite diameter and 85% larger stacking height compared with GR-PRB tar obtained from hp. These findings demonstrate the potential to tailor the composition of coal-derived tars and consequently influence their graphitizability by adjusting the reactive environment during MW plasma treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

What Technical Choices Matter to Characterize Heat Wave and Cold Snap Events in Support of Bulk Power Grid Reliability Studies?

Extreme weather events, such as Heat Waves (HW) and Cold Snaps (CS), pose significant risks to the power grid. The United States (U.S.) Federal Energy Regulatory Commission Order No. 896 mandates regional coordination standards that account for extreme thermal events. However, the lack of a universal definition for extreme thermal events may lead to inconsistent compliance efforts among neighboring entities, undermining the reliability of the transmission system. This study directly addresses this challenge by systematically evaluating how varying technical choices in defining HW and CS fundamentally impact the characterization and ranking of extreme events for power grid reliability studies. We used 12 event definitions and multiple temperature spatial aggregation approaches to construct historical (1980–2024) regional extreme thermal event libraries across North American Electric Reliability Corporation (NERC) subregions in the conterminous U.S. We examined the sensitivity of event characteristics (e.g., duration, frequency, intensity, and spatial coverage) to different definitions. While some definitions produced similar libraries and top event rankings, definitions based on moving-window-averaged temperatures yielded markedly different characteristics. Spatial aggregation methods had minimal impact on heat wave or cold snap intensity, frequency and duration but significantly influenced spatial coverage. The top events identified across different aggregation methods were consistent, but their ranking order varied. These findings offer critical insights for characterizing and selecting extreme thermal events and for supporting local and cross-regional coordination as required by reliability standards.

Wan, Heng [Pacific Northwest National Laboratory (↗

Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics

Abstract A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters. This provides a set of biomarkers that act as a proxy for the transcriptional state referred to as cell state. We construct low-dimensional models of gene expression dynamics and rank genes by their ability to capture the perturbation-specific cell state using a novel observability analysis. Using this ranking, we extract 15 analyte-responsive promoters for the organophosphate malathion in the underutilized host organism Pseudomonas fluorescens SBW25. We develop synthetic genetic reporters from each analyte-responsive promoter and characterize their response to malathion. Furthermore, we enhance malathion reporting through the aggregation of the response of individual reporters with a synthetic consortium approach, and we exemplify the library’s ability to be useful outside the lab by detecting malathion in the environment. The engineered host cell, a living malathion sensor, can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover perturbation-inducible gene expression systems in the compendium of host organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗

Systematic planning of moving target defence for maximising detection effectiveness against false data injection attacks in smart grid

Abstract Moving target defence (MTD) has been gaining traction to thwart false data injection attacks against state estimation (SE) in the power grid. MTD actively perturbs the reactance of transmission lines equipped with distributed flexible AC transmission system (D‐FACTS) devices to falsify the attacker's knowledge about the system configuration. However, the existing literature has not systematically studied what influences the detection effectiveness of MTD and how it can be improved based on the topology analysis. These problems are tackled here from the perspective of an MTD plan in which the D‐FACTS placement is determined. We first exploit the relation between the rank of the composite matrix and the detecting effectiveness. Then, we rigorously derive upper and lower bounds on the attack detecting probability of MTDs with a given rank of the composite matrix. Furthermore, we analyse existing planning methods and highlight the importance of bus coverage by D‐FACTS devices. To improve the detection effectiveness, we propose a novel graph theory–based planning algorithm to retain the maximum rank of the composite matrix while covering all necessary buses. Comparative results on multiple systems show the high detecting effectiveness of the proposed algorithm in both DC‐ and AC‐SE.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Extended Lagrangian Born–Oppenheimer molecular dynamics using a Krylov subspace approximation

It is shown how the electronic equations of motion in extended Lagrangian Born–Oppenheimer molecular dynamics simulations can be integrated using low-rank approximations of the inverse Jacobian kernel. This kernel determines the metric tensor in the harmonic oscillator extension of the Lagrangian that drives the evolution of the electronic degrees of freedom. The proposed kernel approximation is derived from a pseudoinverse of a low-rank estimate of the Jacobian, which is expressed in terms of a generalized set of directional derivatives with directions that are given from a Krylov subspace approximation. The approach allows a tunable and adaptive approximation that can take advantage of efficient preconditioning techniques. The proposed kernel approximation for the integration of the electronic equations of motion makes it possible to apply extended Lagrangian first-principles molecular dynamics simulations to a broader range of problems, including reactive chemical systems with numerically sensitive and unsteady charge solutions. This can be achieved without requiring exact full calculations of the inverse Jacobian kernel in each time step or relying on iterative non-linear self-consistent field optimization of the electronic ground state prior to the force evaluations as in regular direct Born–Oppenheimer molecular dynamics. We note the low-rank approximation of the Jacobian is directly related to Broyden’s class of quasi-Newton algorithms and Jacobian-free Newton–Krylov methods and provides a complementary formulation for the solution of nonlinear systems of equations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Sparsity of the electron repulsion integral tensor using different localized virtual orbital representations in local second-order Møller–Plesset theory

Utilizing localized orbitals, local correlation theory can reduce the unphysically high system-size scaling of post-Hartree–Fock (post-HF) methods to linear scaling in insulating molecules. The sparsity of the four-index electron repulsion integral (ERI) tensor is central to achieving this reduction. For second-order Møller–Plesset theory (MP2), one of the simplest post-HF methods, only the (ia|jb) ERIs are needed, coupling occupied orbitals i, j and virtuals a, b. In this paper, we compare the numerical sparsity (called the “ragged list”) and two other approaches revealing the low-rank sparsity of the ERI. The ragged list requires only one set of (localized) virtual orbitals, and we find that the orthogonal valence virtual-hard virtual set of virtuals originally proposed by Subotnik et al. gives the sparsest ERI tensor. To further compress the ERI tensor, the pair natural orbital (PNO) type representation uses different sets of virtual orbitals for different occupied orbital pairs, while the occupied-specific virtual (OSV) approach uses different virtuals for each occupied orbital. Here, our results indicate that while the low-rank PNO representation achieves significant rank reduction, it also requires more memory than the ragged list. The OSV approach requires similar memory to that of the ragged list, but it involves greater algorithmic complexity. An approximation (called the “fixed sparsity pattern”) for solving the local MP2 equations using the numerically sparse ERI tensor is proposed and tested to be sufficiently accurate and to have highly controllable error. A low-scaling local MP2 algorithm based on the ragged list and the fixed sparsity pattern is therefore promising.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tree tensor network hierarchical equations of motion based on time-dependent variational principle for efficient open quantum dynamics in structured thermal environments

In this work, we introduce an efficient method, TTN-HEOM, for exactly calculating the open quantum dynamics for driven quantum systems interacting with highly structured bosonic baths by combining the tree tensor network (TTN) decomposition scheme with the bexcitonic generalization of the numerically exact hierarchical equations of motion (HEOM). The method yields a series of quantum master equations for all core tensors in the TTN that efficiently and accurately capture the open quantum dynamics for non-Markovian environments to all orders in the system–bath interaction. These master equations are constructed based on the time-dependent Dirac–Frenkel variational principle, which isolates the optimal dynamics for the core tensors given the TTN ansatz. The dynamics converges to the HEOM when increasing the rank of the core tensors, a limit in which the TTN ansatz becomes exact. We introduce TENSO, tensor equations for non-Markovian structured open systems, as a general-purpose Python code to propagate the TTN-HEOM dynamics. We implement three general propagators for the coupled master equations: two fixed-rank methods that require a constant memory footprint during the dynamics and one adaptive-rank method with a variable memory footprint controlled by the target level of computational error. We exemplify the utility of these methods by simulating a two-level system coupled to a structured bath containing one Drude–Lorentz component and eight Brownian oscillators, which is beyond what can presently be computed using the standard HEOM. Our results show that the TTN-HEOM is capable of simulating both dephasing and relaxation dynamics of driven quantum systems interacting with structured baths, even those of chemical complexity, with an affordable computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tensor decompositions for count data that leverage stochastic and deterministic optimization

There is growing interest to extend low-rank matrix decompositions to multi-way arrays, or tensors. One fundamental low-rank tensor decomposition is the canonical polyadic decomposition (CPD). The challenge of fitting a low-rank, nonnegative CPD model to Poisson-distributed count data is of particular interest. Several popular algorithms use local search methods to approximate the maximum likelihood estimator (MLE) of the Poisson CPD model. Here, this work presents two new algorithms that extend state-of-the-art local methods for Poisson CPD. Hybrid GCP-CPAPR combines Generalized Canonical Decomposition (GCP) with stochastic optimization and CP Alternating Poisson Regression (CPAPR), a deterministic algorithm, to increase the probability of converging to the MLE over either method used alone. Restarted CPAPR with SVDrop uses a heuristic based on the singular values of the CPD model unfoldings to identify convergence toward optimizers that are not the MLE and restarts within the feasible domain of the optimization problem, thus reducing overall computational cost when using a multi-start strategy. We provide empirical evidence that indicates our approaches outperform existing methods with respect to converging to the Poisson CPD MLE.

CPAPR↗

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗

Zero-truncated Poisson regression for sparse multiway count data corrupted by false zeros

Abstract We propose a novel statistical inference methodology for multiway count data that is corrupted by false zeros that are indistinguishable from true zero counts. Our approach consists of zero-truncating the Poisson distribution to neglect all zero values. This simple truncated approach dispenses with the need to distinguish between true and false zero counts and reduces the amount of data to be processed. Inference is accomplished via tensor completion that imposes low-rank tensor structure on the Poisson parameter space. Our main result shows that an $N$-way rank-$R$ parametric tensor $\boldsymbol{\mathscr{M}}\in (0,\infty )^{I\times \cdots \times I}$ generating Poisson observations can be accurately estimated by zero-truncated Poisson regression from approximately $IR^2\log _2^2(I)$ non-zero counts under the nonnegative canonical polyadic decomposition. Our result also quantifies the error made by zero-truncating the Poisson distribution when the parameter is uniformly bounded from below. Therefore, under a low-rank multiparameter model, we propose an implementable approach guaranteed to achieve accurate regression in under-determined scenarios with substantial corruption by false zeros. Several numerical experiments are presented to explore the theoretical results.

97 MATHEMATICS AND COMPUTING↗

Environment-imposed selection rules for nuclear-spin conversion of H 2 in molecular crystals

Nuclear-spin conversion in molecular hydrogen is governed by strict symmetry rules that typically require magnetic fields or catalytic surfaces to break. Here we demonstrate that the intrinsic tensor composition of a non-magnetic molecular crystal field can impose and relax these rules without external fields. High-resolution infrared spectra of H 2 in crystalline CO 2 reveal large rank-2 (quadrupolar) crystal-field splittings of the 𝑚 sublevels, while nuclear-spin conversion occurs only through 𝛥𝑚 = 0 channels. Replacing CO 2 with polar N 2 O introduces rank-1 (dipole) components that partially open 𝛥⁢𝑚 ≠ 0 pathways, while incorporation of paramagnetic NO 2 fully lifts the restriction. Furthermore, these results establish a direct correspondence between crystal-field tensor rank and nuclear-spin dynamics, introducing a general symmetry-based framework for designing and controlling spin-isomer populations and quantum-state connectivity in molecular solids.

McLane, Nathan [University of Maryland, College Pa↗

Symmetry analysis of tensors in the honeycomb lattice of edge-sharing octahedra

In this work, we obtain the most general forms of rank-2 and rank-3 tensors allowed by the crystal symmetries of the honeycomb lattice of edge-sharing octahedra for crystals belonging to different crystallographic point groups, including the monoclinic point group 2/$\textit{m}$ and the trigonal (or rhombohedral) point group $\bar{3}$. Our results are relevant for two-dimensional materials, such as α-RuCl 3 , CrI 3 , and the honeycomb iridates. We focus on the magnetic-field-dependent thermal conductivity tensor $κ_{ij}$ (H), which describes a system’s longitudinal and thermal Hall responses, for the cases when the magnetic field is applied along high-symmetry directions, perpendicular to the plane and in the plane. We highlight some unexpected results, such as the equality of fully longitudinal components to partially transverse components in rank-3 tensors for

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Singular value decomposition and similarity renormalization group evolution of nuclear interactions

One of the main challenges for ab initio nuclear many-body theory is the growth of computational and storage costs as calculations are extended to heavy, exotic, and structurally complex nuclei. Here, we investigate the factorization of nuclear interactions as a means to address this issue. We perform Singular Value Decompositions of nucleon-nucleon interactions in partial wave representation and study the dependence of the singular value spectrum on interaction characteristics like regularization scheme and resolution scales. We develop and implement the Similarity Renormalization Group (SRG) evolution of the factorized interaction, and demonstrate that this SVD-SRG approach accurately preserves two-nucleon observables. We find that low-resolution interactions allow the truncation of the SVD at low rank, and that a small number of relevant components is sufficient to capture the nuclear interaction and perform an accurate SRG evolution, while the Coulomb interaction requires special consideration. The rank is uniform across all partial waves, and almost independent of the basis choice in the tested cases. This suggests an interpretation of the relevant singular components as mere representations of a small set of abstract operators that can describe the interaction and its SRG flow. Following the traditional workflow for nuclear interactions, we discuss how the transformation between the center-of-mass and laboratory frames creates redundant copies of the partial wave components when implemented in matrix representation, and we discuss strategies for mitigation. Lastly, we test the low-rank approximation to the SRG-evolved interactions in many-body calculations using the In-Medium SRG. By including nuclear radii in our analysis, we verify that the implementation of the SRG using the singular vectors of the interaction does not spoil the evolution of other observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Development of a machine-learning-based ionic-force correction model for quantum molecular dynamic simulations of warm dense matter

In this work Δ learning is used to map orbital-free density functional theory (OF-DFT) ionic forces to the corresponding Kohn-Sham (KS) DFT ionic forces. The development of the approximate force difference in terms of the ion positions is constructed and serves as a stand in for the ground truth force difference. Descriptor vectors for ion configurations are constructed using all distance between ions in conjunction with an indexing based on a nearest neighbor ranking. It is demonstrated that such a scheme of descriptors can uniquely describe an ionic configuration up to a rotation and reflection when no ambiguity in the nearest neighbor ranking exists. How to handle the case when an ambiguity exists in the nearest neighbor ranking is discussed. As a proof of principle, the model is trained and tested on warm dense hydrogen at temperatures between 1 and 15 eV. Once tested, the model was used to perform molecular dynamic simulations of warm dense hydrogen. Furthermore, the resulting energies and pressures are within 1% and 2% of their respective target KS values.

36 MATERIALS SCIENCE↗

Tensorized Feature Spaces for Feature Explosion

In this paper 1 1 This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-000R22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan) This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-000R22725., we present a novel framework that uses tensor factorization to generate richer feature spaces for pixel classification in hyperspectral images. In particular, we assess the performance of different tensor rank decomposition methods as compared to the traditional kernel-based approaches for the hyperspectral image classification problem. We propose Orion, which takes as input a hyperspectral image tensor and a rank and outputs an enhanced feature space from the factor matrices of the decomposed tensor. Our method is a feature explosion technique that inherently maps low dimensional input space in $\mathbb{R}^{K}$ to high dimensional space in $\mathbb{R}^{R}$ , where $R\gg K$ , say in the order of 1000x, like a kernel. We show how the proposed method exploits the multi-linear structure of hyperspectral three dimensional tensor. We demonstrate the effectiveness of our method with experiments on three publicly available hyperspectral datasets with labeled pixels and compare their classification performance against traditional linear and non-linear supervised learning methods such as SVM with Linear, Polynomial, RBF kernels, and the Multi-Layer Perceptron model. Finally, we explore the relationship between the rank of the tensor decomposition and the classification accuracy using several hyperspectral datasets with ground truth.

Pasricha, Ravdeep Singh↗