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At least 1,441 records · Page 80

Classical combinatorial optimization scaling for random Ising models on 2D heavy-hex graphs

Motivated by near term quantum computing hardware limitations, combinatorial optimization problems that can be addressed by current quantum algorithms and noisy hardware with little or no overhead are used to probe capabilities of quantum algorithms such as the quantum approximate optimization algorithm. In this study, a specific class of near term quantum computing hardware defined combinatorial optimization problems, Ising models on heavy-hex graphs both with and without geometrically local cubic terms, are examined for their classical computational hardness via empirical computation time scaling quantification. Specifically the time-to-solution (TTS) metric using the classical heuristic simulated annealing is measured for finding optimal variable assignments (ground states), as well as the time required for the optimization software Gurobi to find an optimal variable assignment. Because of the sparsity of these Ising models, the classical algorithms are able to find optimal solutions efficiently even for large instances (i.e. 100 000 spin variables). The Ising models both with and without geometrically local cubic terms exhibit average-case linear-time or weakly quadratic scaling when solved exactly using Gurobi, and the Ising models with no cubic terms show evidence of exponential-time TTS scaling when sampled using simulated annealing. These findings point to the necessity of developing and testing more complex, namely more densely connected, optimization problems in order for quantum computing to ever have a practical advantage over classical computing. Our results are another illustration that different classical algorithms can indeed have exponentially different running times, thus making the identification of the best practical classical technique important in any quantum computing vs. classical computing comparison.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software

The open-source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high-pressure limit reaction rate coefficients, and pressure-dependent rate coefficient over multi-well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q-Chem, Psi4). The software outputs high-pressure limit rate coefficients and pressure-dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse-Laplace transform of high-pressure limit rate coefficients into the energy domain, energy corrections based on bond-additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG-Py software suite (https://github.com/ReactionMechanismGenerator/RMG-Py).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Learning dynamical systems from data: An introduction to physics-guided deep learning

Modeling complex physical dynamics is a fundamental task in science and engineering. Traditional physics-based models are first-principled, explainable, and sample-efficient. However, they often rely on strong modeling assumptions and expensive numerical integration, requiring significant computational resources and domain expertise. While deep learning (DL) provides efficient alternatives for modeling complex dynamics, they require a large amount of labeled training data. Furthermore, its predictions may disobey the governing physical laws and are difficult to interpret. Physics-guided DL aims to integrate first-principled physical knowledge into data-driven methods. It has the best of both worlds and is well equipped to better solve scientific problems. Recently, this field has gained great progress and has drawn considerable interest across discipline Here, we introduce the framework of physics-guided DL with a special emphasis on learning dynamical systems. We describe the learning pipeline and categorize state-of-the-art methods under this framework. We also offer our perspectives on the open challenges and emerging opportunities.

97 MATHEMATICS AND COMPUTING↗

Quantum computing universal thermalization dynamics in a (2 + 1)D Lattice Gauge Theory

Simulating non-equilibrium phenomena in strongly-interacting quantum many-body systems, including thermalization, is a promising application of near-term and future quantum computation. By performing experiments on a digital quantum computer consisting of fully-connected optically-controlled trapped ions, we study the role of entanglement in the thermalization dynamics of a Z 2 lattice gauge theory in 2+1 spacetime dimensions. Using randomized-measurement protocols, we efficiently learn a classical approximation of non-equilibrium states that yields the gap-ratio distribution and the spectral form factor of the entanglement Hamiltonian. These observables exhibit universal early-time signals for quantum chaos, a prerequisite for thermalization. Our work, therefore, establishes quantum computers as robust tools for studying universal features of thermalization in complex many-body systems, including in gauge theories.

97 MATHEMATICS AND COMPUTING↗

Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

The unprecedented scientific achievements in combating the COVID-19 pandemic reflect a global response informed by unprecedented access to data. We now have the ability to rapidly generate a diversity of information on an emerging pathogen and, by using high-performance computing and a systems biology approach, we can mine this wealth of information to understand the complexities of viral pathogenesis and contagion like never before. These efforts will aid in the development of vaccines, antiviral medications, and inform policymakers and clinicians. Here we detail computational protocols developed as SARS-CoV-2 began to spread across the globe. They include pathogen detection, comparative structural proteomics, evolutionary adaptation analysis via network and artificial intelligence methodologies, and multiomic integration. These protocols constitute a core framework on which to build a systems-level infrastructure that can be quickly brought to bear on future pathogens before they evolve into pandemic proportions.

Teixeira Prates, Erica↗

A fully-integrated lattice Boltzmann method for fluid–structure interaction

Here we present a fully-integrated lattice Boltzmann (LB) method for fluid–structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid–fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. The LBRMT achieves a spatial convergence rate between first-order and second-order for FSI simulations and is designed for low to intermediate Reynolds number flows with finite inertia at small Mach numbers. With simulations of complex suspensions mixing, we highlight the potential of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.

97 MATHEMATICS AND COMPUTING↗

Multifidelity computing for coupling full and reduced order models

Hybrid physics-machine learning models are increasingly being used in simulations of transport processes. Many complex multiphysics systems relevant to scientific and engineering applications include multiple spatiotemporal scales and comprise a multifidelity problem sharing an interface between various formulations or heterogeneous computational entities. To this end, we present a robust hybrid analysis and modeling approach combining a physics-based full order model (FOM) and a data-driven reduced order model (ROM) to form the building blocks of an integrated approach among mixed fidelity descriptions toward predictive digital twin technologies. At the interface, we introduce a long short-term memory network to bridge these high and low-fidelity models in various forms of interfacial error correction or prolongation. The proposed interface learning approaches are tested as a new way to address ROM-FOM coupling problems solving nonlinear advection-diffusion flow situations with a bifidelity setup that captures the essence of a broad class of transport processes.

59 BASIC BIOLOGICAL SCIENCES↗

Art and Science of the Cellular Mesoscale

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

59 BASIC BIOLOGICAL SCIENCES↗

EXAFS investigations of temperature-dependent structure in cobalt-59 molecular NMR thermometers

Cobalt-59 nuclei are known for extremely thermally sensitive chemical shifts (δ), which in the long term could yield novel magnetic resonance thermometers for bioimaging applications. In this manuscript, we apply extended X-ray absorption fine structure (EXAFS) spectroscopy for the first time to probe the exact variations in physical structure that produce the exceptional thermal sensitivity of the 59 Co NMR chemical shift. We apply this spectroscopic technique to five Co(III) complexes: [Co(NH3)6]Cl3 (1), [Co(en) 3 ]Cl 3 (2) (en = ethylenediamine), [Co(tn) 3 ]Cl 3 (3) (tn = trimethylenediamine), [Co(tame) 2 ]Cl 3 (4) (tame = 1,1,1-tris(aminomethyl)ethane), and [Co(diNOsar)]Cl 3 (5) (diNOsar = dinitrosarcophagine). The solution-phase EXAFS data reveal increasing Co–N bond distances for these aqueous complexes over a ~50 °C temperature window, expanding by Δr (Co–N) = 0.0256(6) Å, 0.0020(5) Å, 0.0084(5) Å, 0.0006(5) Å, and 0.0075(6) Å for 1–5, respectively. Computational analyses of the structural changes reveal that increased connectivity between the donor atoms encourages complex structural variations. Finally, these results imply that rich temperature-dependent structural variations define 59 Co NMR thermometry in macrocyclic complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hybrid Quantum Vision Transformers for Event Classification in High Energy Physics

Models based on vision transformer architectures are considered state-of-the-art when it comes to image classification tasks. However, they require extensive computational resources both for training and deployment. The problem is exacerbated as the amount and complexity of the data increases. Quantum-based vision transformer models could potentially alleviate this issue by reducing the training and operating time while maintaining the same predictive power. Although current quantum computers are not yet able to perform high-dimensional tasks, they do offer one of the most efficient solutions for the future. In this work, we construct several variations of a quantum hybrid vision transformer for a classification problem in high-energy physics (distinguishing photons and electrons in the electromagnetic calorimeter). We test them against classical vision transformer architectures. Our findings indicate that the hybrid models can achieve comparable performance to their classical analogs with a similar number of parameters.

Unlu, Eyup B. (ORCID:0000000266836463)↗

Rancor-HUNTER: A Virtual Plant and Operator Environment for Predicting Human Performance

Advances in simulation capabilities to model physical systems have outpaced the development of simulations for humans using those physical systems. There is an argument that the infinite span of potential human behaviors inherently render human modeling more challenging than physical systems. Despite this challenge, the need for modeling humans interacting with these complex systems is paramount. As technologies have improved, many of the failure modes originating from the physical systems have been solved. This means the overall proportion of human errors has increased, such that it is not uncommon to be the primary driver of system failure in modern complex systems. Moreover, technologies such as automated systems may introduce emerging contexts that can cause new, unanticipated modes of human error. Therefore, it is now more important than ever to develop models of human behavior to realize overall system error reductions and achieve established safety margins. To support new and novel concepts of operations for the anticipated wave of advanced nuclear reactor deployments, human factors and human reliability analysis researchers need to develop advanced simulation-based approaches. This talk presents a simulation environment suitable to both collect data and then perform Monte Carlo simulations to evaluate human performance and develop better models of human behavior. Specifically, the Rancor Microworld Simulator models a complex energy production system in a simplified manner. Rancor includes computer-based procedures, which serve as a framework to automatically classify human behaviors without manual, subjective experimenter coding during scenarios. This method supports a detailed level of analysis at the task level. It is feasible for collecting large sample sizes required to develop quantitative modelling elements that have historically challenged traditional full-scope simulator study approaches. Additionally, the other portion of this experimental platform, the Human Unimodel for Nuclear Technology to Enhance Reliability (HUNTER), is presented to show how the collected data can be used to evaluate novel scenarios based on the contextual factors, or performance shaping factors, derived from Rancor simulations. Rancor-HUNTER is being used to predict operator performance with new procedures, such as results from control room modernization or new-build situations. Rancor-HUNTER is also proving a useful surrogate platform to model human performance for other complex systems.

99 GENERAL AND MISCELLANEOUS↗

Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa

Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.

59 BASIC BIOLOGICAL SCIENCES↗

Fracture Shearing in the Eau Claire Formation

This data set consists of Computed Tomographic (CT) data for five sheared Eau Claire Formation core samples with complex and heterogeneous lithology. Each sample was prefractured, housed in a specially adapted core holder, and sheared in incremental fashion. CT scans were taken before and after each shearing event.

Computed Tomography↗

Benchmarking boron carbide equation of state using computation and experiment

Boron carbide ( B 4 C ) is of both fundamental scientific and practical interest due to its structural complexity and how it changes upon compression, as well as its many industrial uses and potential for use in inertial confinement fusion (ICF) and high-energy density physics experiments. Here, we report the results of a comprehensive computational study of the equation of state (EOS) of B 4 C in the liquid, warm dense matter, and plasma phases. Our calculations are cross-validated by comparisons with Hugoniot measurements up to 61 megabar from planar shock experiments performed at the National Ignition Facility (NIF). Our computational methods include path integral Monte Carlo, activity expansion, as well as all-electron Green's function Korringa-Kohn-Rostoker and molecular dynamics that are both based on density functional theory. We calculate the pressure-internal energy EOS of B 4 C over a broad range of temperatures ( ~ 6 × 10 3 – 5 × 10 8 K) and densities (0.025–50 g / cm 3 ). We assess that the largest discrepancies between theoretical predictions are ≲ 5 % near the compression maximum at 1– 2 × 10 6 K. This is the warm-dense state in which the K shell significantly ionizes and has posed grand challenges to theory and experiment. By comparing with different EOS models, we find a Purgatorio model (LEOS 2122) that agrees with our calculations. The maximum discrepancies in pressure between our first-principles predictions and LEOS 2122 are ~ 18 % and occur at temperatures between 6 × 10 3 – 2 × 10 5 K, which we believe originate from differences in the ion thermal term and the cold curve that are modeled in LEOS 2122 in comparison with our first-principles calculations. To account for potential differences in the ion thermal term, we have developed three new equation-of-state models that are consistent with theoretical calculations and experiment. We apply these new models to 1D hydrodynamic simulations of a polar direct-drive NIF implosion, demonstrating that these new models are now available for future ICF design studies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Multiscale Characterization of Additive Manufacturing Components with Computed Tomography, 3D X-ray Microscopy, and Deep Learning

Additive manufacturing (AM) facilitates the creation of complex-geometry parts, driving advancements in lightweight aerospace components, high-efficiency engine cooling channels, and customized medical implants. However, ensuring the quality and reliability of AM parts remains challenging due to internal defects, surface irregularities, porosity, and residual trapped powder, which are often inaccessible to traditional inspection methods. Recent developments in X-ray computed tomography (XCT) and 3D X-ray microscopy (XRM), particularly systems equipped with resolution-at-a-distance (RaaD™) capabilities, enable high-resolution, non-destructive evaluation of AM components across multiple scales, from sub-micrometer to macroscopic levels. This paper explores modern XCT and XRM techniques for multiscale characterization of AM parts, focusing on their ability to detect and analyze defects such as porosity, cracks, inclusions, and surface roughness, while offering insights into defect formation mechanisms, material properties, and process-induced variations. The integration of deep learning (DL) frameworks, including Simurgh, DeepRecon, and DeepScout, enhances XCT/XRM workflows by reducing scan times, improving resolution recovery, and enabling accurate defect detection even with limited projection data. These DL-based methods overcome limitations of traditional reconstruction techniques, enabling faster, more reliable characterization of dense materials like Inconel 718 and novel alloys such as AlCe. Applications include process parameter optimization, high-throughput quality control, and multistage AM process evaluation, with DL-enhanced workflows accelerating analysis times from weeks to days. Correlative imaging approaches further validate XCT and XRM data against scanning electron microscopy (SEM) images of physically sectioned samples, confirming the accuracy of DL-based reconstructions and enabling comprehensive defect analysis. While challenges remain in generalizing DL models to diverse materials and imaging conditions, improvements in resolution, noise reduction, and defect detection highlight the transformative potential of these methods. This multiscale and correlative approach enables precise identification and correlation of microstructural features with the overall performance of AM components. By integrating advanced XCT, XRM, and DL techniques, this paper demonstrates a significant leap forward in AM characterization, offering valuable insights into the relationships between processing parameters, microstructure, and part performance, and driving innovations that enhance the quality and reliability of AM products for demanding industrial applications.

Additive manufacturing↗

Iron‐Catalyzed Intermolecular C−H Amination Assisted by an Isolated Iron‐Imido Radical Intermediate

Here we report the use of a base metal complex [( tBu pyrpyrr 2 )Fe(OEt 2 )] (1-OEt 2 ) ( tBu pyrpyrr 2 2− =3,5-tBu 2 -bis(pyrrolyl)pyridine) as a catalyst for intermolecular amination of C sp3 −H bonds of 9,10-dihydroanthracene (2 a) using 2,4,6-trimethyl phenyl azide (3 a) as the nitrene source. The reaction is complete within one hour at 80 °C using as low as 2 mol % 1-OEt 2 with control in selectivity for single C−H amination versus double C−H amination. Catalytic C−H amination reactions can be extended to other substrates such as cyclohexadiene and xanthene derivatives and can tolerate a variety of aryl azides having methyl groups in both ortho positions. Under stoichiometric conditions the imido radical species [( tBu pyrpyrr 2 )Fe{=N(2,6-Me 2 -4-tBu-C 6 H 2 )] (1-imido) can be isolated in 56 % yield, and spectroscopic, magnetometric, and computational studies confirmed it to be an S = 1 Fe IV complex. Complex 1-imido reacts with 2 a to produce the ferrous aniline adduct [( tBu pyrpyrr 2 )Fe{NH(2,6-Me 2 -4-tBu-C 6 H 2 )(C 14 H 11 )}] (1-aniline) in 45 % yield. Lastly, it was found that complexes 1-imido and 1-aniline are both competent intermediates in catalytic intermolecular C−H amination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive Mesh Refinement Simulations for Turbulent Reacting Flow

With the increased availability of exascale computing hardware, detailed simulations of realistic devices can be performed at practically relevant time and length scales. Insights into the multiscale driving mechanisms in compressible reacting flow systems with complex geometry, such as combustors, can be used for design optimization and technology improvements. However, to effectively perform these simulations, advanced numerical algorithms must be used to maintain solution accuracy without incurring undue computational costs. PeleC, part of the Pele suite of codes, leverages block-structured adaptive mesh refinement (AMR) through the AMReX library to capture fine-scale flow features in compressible reacting flows. In this talk, we discuss recent improvements to the numerical algorithms, particularly in regard to describing flows at complex boundary structures, and PeleC's performance on exascale computing hardware. We will demonstrate that PeleC is well-suited for modern, extreme-scale, heterogenous compute platforms.

combustion↗

Computationally Guided and Experimentally Validated Design of Custom Chelators for Critical Mineral Recovery

Selective, high throughput separation of target critical metals from complex environments such as fly ash leachates and mining process streams presents a significant challenge for economical production. Custom chelators and sorbents are an attractive technology for selective metal extraction, however it can be difficult to predict their performance, and significant experimental efforts are often required to develop chelating technologies. Here, we present a computational strategy focused on modelling chelator-metal binding interactions and benchmark these results versus experimental data. A computational pipeline combining forcefield, semiempirical, and meta-GGA methods with a thermodynamic framework optimized for error cancellation has been developed to predict binding energies of chelator complexes towards critical mineral recovery applications. This approach, originally validated on [2.2.2] cryptates binding mono- and divalent cations, demonstrated robust predictive capabilities with an R2 of 0.850 against experimental aqueous binding energies. The workflow includes metadynamics for exploring high-dimensional potential energy surfaces and a cluster-continuum model for accurate yet computationally efficient solvation modeling. Error cancellation between solvation energies of free and chelator-coordinated ions enables faster convergence, even with finite cluster sizes. Initial studies on the cryptates revealed consistent metal-ligand coordination patterns, with systematic variations influenced by ion size and charge, highlighting key structural features linked to binding selectivity. Further studies of a proprietary chelator have resulted in identification of previously unreported selectivity towards economically significant metals, which in-house experiments have confirmed, demonstrating the feasibility of this approach. By applying this methodology to new chelators targeting critical minerals such as lithium, cobalt, nickel and other strategic metals, we aim to accelerate the discovery of next-generation chelators for efficient recovery, recycling, and separation processes. This computational framework serves as the backbone of a high-throughput design pipeline tailored for sustainable resource utilization and may be applied to a wide range of systems to meet experimental needs.

computational materials↗