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At least 487 records · Page 27

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗

Vibrational properties of heme-nitrosoalkane complexes in comparison with those of their HNO analogs, and reactivity studies towards nitric oxide and Lewis acids

C-Nitroso compounds (RNO, R = alkyl and aryl) are byproducts of drug metabolism and bind to heme proteins, and their heme-RNO adducts are isoelectronic to ferrous nitroxyl (NO-/HNO) complexes. Importantly, heme-HNO compounds are key intermediates in the reduction of NO to N 2 O and nitrite to ammonium in the nitrogen cycle. Ferrous heme-RNO complexes act as stable analogs of these species, potentially allowing for the investigation of the vibrational and electronic properties of unstable heme-HNO intermediates. In this paper, a series of six-coordinate ferrous heme-RNO complexes (where R = iPr and Ph) were prepared using the TPP 2- and 3,5-Me-BAFP 2- co-ligands, and tetrahydrofuran, pyridine, and 1-methylimidazole as the axial ligands (bound trans to RNO). These complexes were characterized using different spectroscopic methods and X-ray crystallography. The complex [Fe(TPP)(THF)(iPrNO)] was further utilized for nuclear resonance vibrational spectroscopy (NRVS), allowing for the detailed assignment of the Fe–N(R)O vibrations of a heme-RNO complex for the first time. The vibrational properties of these species were then correlated with those of their HNO analogs, using DFT calculations. Our studies support previous findings that RNO ligands in ferrous heme complexes do not elicit a significant trans effect. In addition, the complexes are air-stable, and do not show any reactivity of their RNO ligands towards NO. So although ferrous heme-RNO complexes are suitable structural and electronic models for their HNO analogs, they are unsuitable to model the reactivity of heme-HNO complexes. We further investigated the reaction of our heme-RNO complexes with different Lewis acids. Here, [Fe(TPP)(THF)(iPrNO)] was found to be unreactive towards Lewis acids. In contrast, [Fe(3,5-Me-BAFP)(iPrNO) 2 ] is reactive towards all of the Lewis acids investigated here, but in most cases the iron center is simply oxidized, resulting in the loss of the iPrNO ligand. In the case of the Lewis acid B 2 (pin) 2 , the reduced product [Fe(3,5-Me-BAFP)(iPrNH 2 )(iPrNO)] was identified by X-ray crystallography.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modification of wind turbine wakes by large-scale, convective atmospheric boundary layer structures

In this study, we consider the impact of large-scale, convective structures in an unstable atmospheric boundary layer on wind turbine wakes. Simulation data from a high-fidelity large-eddy simulation (LES) of the AWAKEN wind farm site matching unstable atmospheric conditions were analyzed, and both turbine performance and wake behavior were affected based on their location relative to the convective structures. Turbines located in updraft regions of the flow experienced lower inflow velocity and generated less power, but their wakes were observed to recover faster and saw greater turbulent kinetic energy mixing higher in the boundary layer. The opposite effect was found for turbines in the downdraft regions of the convective structures. A simplified model of this wake behavior was also developed based on a two-dimensional k–ε Reynolds-Averaged Navier–Stokes formulation. This simplified model included the effects of vertical transport, but could be efficiently solved as a parabolic system, and was found to capture similar wake modifications observed in the high-fidelity LES computations.

16 TIDAL AND WAVE POWER↗

Energy response characterization of current-mode MeV Cherenkov aerogel detectors

Current-mode Cherenkov aerogel detectors have been used to measure time resolved spectra of MeV radiographic x-ray sources and have been considered to replace gas Cherenkov systems. The simulations of the Cherenkov response of aerogel detectors have uncertainties in how to model the complex structure of aerogels. Data from three sites—the Idaho electron beam, the Los Alamos Site electron beam and microtron sources at Los Alamos—have been used to calibrate the relative energy response of 15 aerogels, varying in density from 10 to 430 mg/cm 3 , from incident electrons with energies from 1 to 12 MeV. Detector simulations need to introduce density variation in the aerogels to match the collected data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Loosely bound composite dark matter

We investigate loosely bound composite states made of dark matter, where the binding energy for constituent particles is considerably less than the constituent mass. We focus on models of nuclear and molecular dark matter, where constituents are separated by length scales larger than the inverse constituent mass, just like nuclei and atoms in the Standard Model. The cosmology, structure, and interactions at underground experiments are described. We find that loosely bound composites can have a very large cross section for scattering with nuclei that scales with nucleon number like ∼ A 4 . For some couplings, these composites produce extremely soft (≪ keV) individual atomic recoils while depositing a large amount of total recoil energy (≫ keV) in a single passage through a detector, implying an interesting new class of signatures for low threshold direct detection.

79 ASTRONOMY AND ASTROPHYSICS↗

Microscopic scattering approach to in-gap states: Cr adatoms on superconducting 𝛽−Bi 2 ⁢Pd

We develop a microscopic scattering formalism to describe Yu-Shiba-Rusinov (YSR) states due to a single Cr adatom on the Bi-terminated surface of 𝛽−Bi 2 ⁢Pd, by combining ab initio Wannier functions with a real-space Green's function approach in the Bogoliubov–de Gennes formalism. Our framework reproduces key scanning tunneling spectroscopy features, including a single particle-hole asymmetric YSR peak and isotropic 𝑑⁢𝐼/𝑑⁢𝑉 maps around the impurity. Decomposing the YSR states reveals contributions from four nearly degenerate 𝐶 4⁢𝑣 representations, with energy broadening masking their individual signatures. Spin-orbit coupling induces partial spin polarization, while the spatial asymmetry between particle and hole components arises from Cr 𝑑−Bi 𝑝 hybridization. These results highlight the importance of realistic band structures and microscopic modeling for interpreting STM data and provide a foundation for studying impurity chains hosting topological excitations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum Computing for AI-based Design and Optimization of Electric Motors

Knowledge-based artificial intelligence and hierarchical fuzzy logic offer an interpretable framework for electricvehicle motor preliminary design, but their computational burden grows with linguistic granularity and coupled design-space size. This paper presents a reduced quantum reformulation of the hierarchical fuzzy inference of air-gap flux density, a representative level-one motor-design parameter. Starting from the published electric-vehicle motor-design framework, a three-term fuzzy prototype is constructed from the original inference structure. The reduced model is then reformulated as a modular quantum register-oracle system, in which each hierarchical subrelation is encoded as a block oracle and evaluated through superpositionbased candidate-label testing. The proposed modular quantum formulation reproduces the reduced classical prototype after block fusion. A resource analysis shows that the reduced modular system requires seven qubits per block and twenty-two qubits in a straightforward four-block implementation. Finally, a crossovercomplexity model is derived to identify the regime in which quantum candidate search may become favorable relative to hierarchical fuzzy inference. The results show that no quantum advantage should be claimed for the present one-output reduced benchmark, but that a plausible crossover emerges for larger joint candidate spaces and higher linguistic granularity. The work therefore establishes a technically consistent starting point for future quantum-assisted electric-vehicle motor-design optimization.

Kumar, Praveen [ORNL] (ORCID:0000000291877857)↗

Spatio-temporal Fourier Transformer for Long-term Dynamics Prediction (StFT) v1.0

We propose a novel machine learning model spatio-temporal Fourier transformer (StFT) to emulate long-term dynamics of multi-scale and multi-physics systems. Our method StFT overcomes the limitations of rapid error accumulation, particularly in long-term forecasting of systems characterized by complex and coupled dynamics. StFT achieves outstanding accuracy and computational efficiency by effectively capturing multi-scale interactions, and quantify the uncertainties inherent in the predictions. Our model leverages a structured hierarchy of StFT blocks, and explicitly captures dynamics across both macro- and micro- spatial scales. Evaluations conducted on three benchmark datasets (plasma, fluid, and atmospheric dynamics) demonstrate the advantages of our approach over state-of-the-art ML methods.

Bai, Zhe [Lawrence Berkeley National Laboratory (L↗

alchemist-nn

The alchemist-nn code provides a framework for training and running generative AI models for molecular structures.

Rogers, David [Oak Ridge National Laboratory (ORNL↗

Coupled Aero-Hydro-Mechanical Hybrid Simulation Testing of Offshore Wind Turbines Subjected to Operational and Extreme Loading Conditions

Understanding the response of the Offshore Wind Turbine (OWT) subjected to realistic applied loads requires modeling the whole structure including its soil-foundation system. This requires unique and innovative testing facilities. OWT systems experience cyclic and dynamic loading due to wind, wave, current, rotor vibrations (i.e., 1P load) and vibrations caused by the blade shadowing effects (2P/3P loads). These loads are complicated in nature and have varying amplitudes, frequencies, and directions. Investigating the response of the entire OWT system including the soil-foundation system under these complex loading conditions, requires: (1) full understanding of the loading characteristics including: the power take-off mechanical load (1P and 3P), and areo- and hydrodynamic loads that the OWT system is subjected to; (2) testing facility with unique multidirectional loading capabilities that allows for simultaneous application of realistic wind, wave and machine loads, axial gravity loads, and induced overturning moments; and (3) unique and cost-effective testing techniques that allow for accurate analysis of the overall response of the OWT system under realistic conditions such as: Real-Time Hybrid Simulation (RTHS).

17 WIND ENERGY↗

Predicting Fuel Properties and Emissions for Advanced Biofuels for Diesel Engines (CRADA Final Report)

The project will investigate variations in biofuel composition and optimize performance in combustion for conventional and future compression ignition engines. It will evaluate a variety of bio-derived molecules in the diesel range that can be produced using technology in ExxonMobil’s portfolio as well as fuels that cover the range of potential molecular structures for robust model development. Changes in fuel/air premixing and stratification in advanced engines could alter the relationship between fuel properties and performance in comparison to current generation spray combustion approaches. NREL experience in fuel and combustion modeling will enable development of general rules for predicting performance of a wide range of biofuel options.

33 ADVANCED PROPULSION SYSTEMS↗

Zentropy Theory for Transformative Functionalities of Magnetic and Superconducting Materials

The proposed research developed the zentropy theory through applications to complex magnetic materials and superconductors under the hypothesis that the emergent properties of complex magnetic materials and superconductors can be predicted by statistical mechanics of ergodic microstates with their partition functions computed from DFT-predicted free energies. The key objective is to develop approaches to systematically determine the types and number of microstates and the supercell size in DFT-based calculations through convergency of macroscopic functionalities, with the incorporation of our mixed-space approach accounting for the interactions between periodic supercells. In addition to use scientific intuitions to guide the design of important microstates, the key innovation of the proposed research is to integrate the domain knowledge and the material-property-descriptor database (MPDD) with 4 million microstates, which is supported by our deep neural network machine learning models (SIPFENN: structure-informed prediction of formation energy using neural networks) and integrated with our high throughput DFT Tool Kit (DFTTK). For complex magnetic materials, one of the objectives is to develop approaches to calculate short-range ordering from the statistical distribution of each microstate. For superconductors, the divergency of quasiparticle effective mass at a quantum critical point will be investigated, and the superconducting and non-superconducting microstates will be delineated through analysis of electronic band structure, density of states, charge density, and Fermi surface.

36 MATERIALS SCIENCE↗

Microscopic Scattering Approach to In-Gap States

We develop a microscopic scattering formalism to describe Yu-Shiba-Rusinov (YSR) states due to a single Cr adatom on the Bi-terminated surface of beta Bi2Pd, by combining ab initio Wannier functions with a real-space Green's function approach in the Bogoliubov-de Gennes formalism[1]. Our framework reproduces key scanning tunneling spectroscopy features, including a single particle-hole asymmetric YSR peak and isotropic dIdV maps around the impurity. Decomposing the YSR states reveals contributions from four nearly degenerate C4v representations, with energy broadening masking their individual signatures. Spin-orbit coupling induces partial spin polarization, while the spatial asymmetry between particle and hole components arises from Cr d-Bi p hybridization. These results highlight the importance of realistic band structures and microscopic modeling for interpreting STM data for magnetic in-gap states on superconductors. Further advances examining layered 2D material surfaces, such as NbSe2, will be described[2]. For this system the superconducting properties are obtained from a full anisotropic Eliashberg calculation of the superconducting order parameter along with the charge density wave gap. Additional features associated with proposals to measure the dynamics of these individual YSR states will be presented. [1] arXiv:2507.08740 [2] arXiv:2507.11856

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NoRA: A Tensor Network Ansatz for Volume-Law Entangled Equilibrium States of Highly Connected Hamiltonians

Motivated by the ground state structure of quantum models with all-to-all interactions such as mean-field quantum spin glass models and the Sachdev-Ye-Kitaev (SYK) model, we propose a tensor network architecture which can accomodate volume law entanglement and a large ground state degeneracy. We call this architecture the non-local renormalization ansatz (NoRA) because it can be viewed as a generalization of MERA, DMERA, and branching MERA networks with the constraints of spatial locality removed. We argue that the architecture is potentially expressive enough to capture the entanglement and complexity of the ground space of the SYK model, thus making it a suitable variational ansatz, but we leave a detailed study of SYK to future work. We further explore the architecture in the special case in which the tensors are random Clifford gates. Here the architecture can be viewed as the encoding map of a random stabilizer code. We introduce a family of codes inspired by the SYK model which can be chosen to have constant rate and linear distance at the cost of some high weight stabilizers. We also comment on potential similarities between this code family and the approximate code formed from the SYK ground space.

Physics↗

HamLib: A library of Hamiltonians for benchmarking quantum algorithms and hardware

In order to characterize and benchmark computational hardware, software, and algorithms, it is essential to have many problem instances on-hand. This is no less true for quantum computation, where a large collection of real-world problem instances would allow for benchmarking studies that in turn help to improve both algorithms and hardware designs. To this end, here we present a large dataset of qubit-based quantum Hamiltonians. The dataset, called HamLib (for Hamiltonian Library), is freely available online and contains problem sizes ranging from 2 to 1000 qubits. HamLib includes problem instances of the Heisenberg model, Fermi-Hubbard model, Bose-Hubbard model, molecular electronic structure, molecular vibrational structure, MaxCut, Max- k -SAT, Max- k -Cut, QMaxCut, and the traveling salesperson problem. The goals of this effort are (a) to save researchers time by eliminating the need to prepare problem instances and map them to qubit representations, (b) to allow for more thorough tests of new algorithms and hardware, and (c) to allow for reproducibility and standardization across research studies.

97 MATHEMATICS AND COMPUTING↗

Gas jet targets for direct reaction studies

The study of direct reactions is of broad interest in nuclear physics, providing constraint to models of nuclear structure evolution and data to better understand the creation of the elements. In many cases, however, the data of interest are hindered by backgrounds and poor resolution from contaminants in either the beam, the target, or both. The use of a gas jet can overcome some of these issues through clever engineering, providing a reaction target that is chemically pure and thin enough to significantly reduce the impact on experimental resolution. This Perspective will discuss the effort to design, construct, and operate gas jet targets for direct reaction studies in the rare isotope era.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Dynamic ecosystem assembly and escaping the “fire trap” in the tropics: insights from FATES_15.0.0

Abstract. Fire is a fundamental part of the Earth system, with impacts on vegetation structure, biomass, and community composition, the latter mediated in part via key fire-tolerance traits, such as bark thickness. Due to anthropogenic climate change and land use pressure, fire regimes are changing across the world, and fire risk has already increased across much of the tropics. Projecting the impacts of these changes at global scales requires that we capture the selective force of fire on vegetation distribution through vegetation functional traits and size structure. We have adapted the fire behavior and effects module, SPITFIRE (SPread and InTensity of FIRE), for use with the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a size-structured vegetation demographic model. We test how climate, fire regime, and fire-tolerance plant traits interact to determine the biogeography of tropical forests and grasslands. We assign different fire-tolerance strategies based on crown, leaf, and bark characteristics, which are key observed fire-tolerance traits across woody plants. For these simulations, three types of vegetation compete for resources: a fire-vulnerable tree with thin bark, a vulnerable deep crown, and fire-intolerant foliage; a fire-tolerant tree with thick bark, a thin crown, and fire-tolerant foliage; and a fire-promoting C4 grass. We explore the model sensitivity to a critical parameter governing fuel moisture and show that drier fuels promote increased burning, an expansion of area for grass and fire-tolerant trees, and a reduction of area for fire-vulnerable trees. This conversion to lower biomass or grass areas with increased fuel drying results in increased fire-burned area and its effects, which could feed back to local climate variables. Simulated size-based fire mortality for trees less than 20 cm in diameter and those with fire-vulnerable traits is higher than that for larger and/or fire-tolerant trees, in agreement with observations. Fire-disturbed forests demonstrate reasonable productivity and capture observed patterns of aboveground biomass in areas dominated by natural vegetation for the recent historical period but have a large bias in less disturbed areas. Though the model predicts a greater extent of burned fraction than observed in areas with grass dominance, the resulting biogeography of fire-tolerant, thick-bark trees and fire-vulnerable, thin-bark trees corresponds to observations across the tropics. In areas with more than 2500 mm of precipitation, simulated fire frequency and burned area are low, with fire intensities below 150 kW m−1, consistent with observed understory fire behavior across the Amazon. Areas drier than this demonstrate fire intensities consistent with those measured in savannas and grasslands, with high values up to 4000 kW m−1. The results support a positive grass–fire feedback across the region and suggest that forests which have existed without frequent burning may be vulnerable at higher fire intensities, which is of greater concern under intensifying climate and land use pressures. The ability of FATES to capture the connection between fire disturbance and plant fire-tolerance strategies in determining biogeography provides a useful tool for assessing the vulnerability and resilience of these critical carbon storage areas under changing conditions across the tropics.

54 ENVIRONMENTAL SCIENCES↗