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At least 397 records · Page 22

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗

Deep kernel methods learn better: from cards to process optimization

Abstract The ability of deep learning methods to perform classification and regression tasks relies heavily on their capacity to uncover manifolds in high-dimensional data spaces and project them into low-dimensional representation spaces. In this study, we investigate the structure and character of the manifolds generated by classical variational autoencoder (VAE) approaches and deep kernel learning (DKL). In the former case, the structure of the latent space is determined by the properties of the input data alone, while in the latter, the latent manifold forms as a result of an active learning process that balances the data distribution and target functionalities. We show that DKL with active learning can produce a more compact and smooth latent space which is more conducive to optimization compared to previously reported methods, such as the VAE. We demonstrate this behavior using a simple cards dataset and extend it to the optimization of domain-generated trajectories in physical systems. Our findings suggest that latent manifolds constructed through active learning have a more beneficial structure for optimization problems, especially in feature-rich target-poor scenarios that are common in domain sciences, such as materials synthesis, energy storage, and molecular discovery. The Jupyter Notebooks that encapsulate the complete analysis accompany the article.

97 MATHEMATICS AND COMPUTING↗

Atomistic, macromolecular model of the Populus secondary cell wall informed by solid-state NMR

Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.

09 BIOMASS FUELS↗

Mirror symmetry breaking and lateral stacking shifts in twisted trilayer graphene

Here, we construct a continuum model of twisted trilayer graphene using ab initio density-functional-theory calculations, and we apply it to address twisted trilayer electronic structure. Our model accounts for moiré variation in site energies, hopping between outside layers, and hopping within layers. We focus on the role of a mirror symmetry present in ABA graphene trilayers with a middle layer twist. The mirror symmetry is lost intentionally when a displacement field is applied between layers, and unintentionally when the top layer is shifted laterally relative to the bottom layer. We calculate two band-structure characteristics that are directly relevant to transport measurements, namely the Drude weight and the weak-field Hall conductivity. We relate them via the Hall density to assess the influence of the accidental lateral stacking shifts currently present in all experimental devices on electronic properties. Finally, we comment on the role of the possible importance of accidental lateral stacking shifts for superconductivity in twisted trilayers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

In situ inelastic neutron scattering of mixed CH 4 –CO 2 hydrates

An abundant source of CH 4 can be found in natural hydrate deposits. Recent demonstration of CH 4 recovery from hydrates via CO 2 exchange has revealed the potential as a fuel source that also provides a medium for carbon sequestration. It is vital to understand the structural and dynamic impacts of guest variation in CH 4 , CO 2 , and mixed hydrates and link the results to the stability of various deposits in nature, harvesting methane, and sequestering CO 2 . Molecular vibrations are examined in CH 4 , CO 2 , and mixed CH 4 -CO 2 hydrates at 5 and 190 K and Xe hydrates for comparison. Inelastic neutron scattering (INS) is an ideal spectroscopy technique to observe the dynamic modes in the hydrate structure and enclathrated CH 4 , as it is extremely sensitive to 1 H. The presence of CO 2 in hydrates tightens the lattice. It introduces more active librational modes to the host lattice, while hindering the motion of CH 4 in mixed CH 4 -CO 2 hydrate at 5 K. At 190 K, a large broadening of the CH 4 librational modes indicates disorder in the structure leading to dissociation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Inverse design of cellular structures with the targeted nonlinear mechanical response

Advanced additive manufacturing capabilities have enabled a transformational ability to create sophisticated cellular structures using diverse materials. By altering the topology of the unit cell, the mechanical behavior, such as the stress-strain response during compression, can be modulated. Nevertheless, identifying a printable topology within an enormous design space that would precisely deliver the targeted nonlinear material response is challenging. We propose a data-driven generative framework based on a conditional variational autoencoder (cVAE) architecture that can inverse design the cellular structure based on the intended nonlinear stress-strain response. Trained on a dataset of structure-property pairs, the cVAE learns a compact and expressive latent space that enables efficient mapping from targets to feasible geometries. Two inference modes are explored: (1) decoder-only generation, which enables the exploration of diverse designs conditioned solely on the desired mechanical response, and (2) encoder-decoder generation, which further allows for the incorporation of desired topologies, ensuring the generated structure conforms to both mechanical properties and to desired-topology constraints. The results demonstrate that the model can generate structurally plausible and mechanically accurate designs, with the predicted stress-strain curves closely matching the targets. Even under joint conditioning, the model effectively balances geometric fidelity and functional performance.

36 MATERIALS SCIENCE↗

On the statistical theory of self-gravitating collisionless dark matter flow: Scale and redshift variation of velocity and density distributions

The statistics of velocity and density fields are crucial for cosmic structure formation and evolution. Here, this paper extends our previous work on the two-point second-order statistics for the velocity field [Phys. Fluids 35, 077105 (2023)] to one-point probability distributions for both density and velocity fields. The scale and redshift variation of density and velocity distributions are studied by a halo-based non-projection approach. First, all particles are divided into halo and out-of-halo particles so that the redshift variation can be studied via generalized kurtosis of distributions for halo and out-of-halo particles, respectively. Second, without projecting particle fields onto a structured grid, the scale variation is analyzed by identifying all particle pairs on different scales $r$. We demonstrate that: (i) Delaunay tessellation can be used to reconstruct the density field. The density correlation, spectrum, and dispersion functions were obtained, modeled, and compared with the N-body simulation; (ii) the velocity distributions are symmetric on both small and large scales and are non-symmetric with a negative skewness on intermediate scales due to the inverse energy cascade on small scales with a constant rate $\varepsilon_u$; (iii) On small scales, the even order moments of pairwise velocity $\Delta u_L$ follow a two-thirds law $\propto{(-\varepsilon_ur)}^{2/3}$, while the odd order moments follow a linear scaling $\langle(\Delta u_L)^{2n+1}\rangle=(2n+1)\langle(\Delta u_L)^{2n}\rangle\langle\Delta u_L\rangle\propto{r}$; (iv) The scale variation of the velocity distributions was studied for longitudinal velocities $u_L$ or $u_L^{'}$, pairwise velocity (velocity difference) $\Delta u_L$=$u_L^{'}$-$u_L$ and velocity sum $\Sigma u_L$=$u^{'}_L$+$u_L$. Fully developed velocity fields are never Gaussian on any scale, despite that they can initially be Gaussian; (v) On small scales, $u_L$ and $\Sigma u_L$ can be modeled by a $X$ distribution to maximize the entropy of the system. The distribution of $\Delta u_L$ can be different; (vi) On large scales, $\Delta u_L$ and $\Sigma u_L$ can be modeled by a logistic or a $X$ distribution, while $u_L$ has a different distribution; (vii) the redshift variation of the velocity distributions follows the evolution of the $X$ distribution involving a shape parameter $\alpha(z)$ decreasing with time.

79 ASTRONOMY AND ASTROPHYSICS↗

Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions

Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSFs) or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from golden eagles Aquila chrysaetos from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During the summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.

54 ENVIRONMENTAL SCIENCES↗

Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology

Abstract The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum . The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

59 BASIC BIOLOGICAL SCIENCES↗

Description of the Three-Dimensional Large-Scale Forcing Data from the 3D Constrained Variational Analysis (VARANAL3D)

This technical report introduces a Three-Dimensional Constrained Variational Analysis (3DCVA) (Tang and Zhang 2015) and its product of three-dimensional large-scale forcing data to drive single-column models (SCM), cloud-resolving models (CRM), and large-eddy simulation (LES) models, and to evaluate model results. The 3DCVA algorithm is an extension of the original 1D constrained variational analysis (1DCVA) (Zhang and Lin 1997, Zhang et al. 2001). The three-dimensional structure of the forcing data allows studies of spatial variation of the large-scale forcing fields and tests of physical parameterizations across scales. In the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility, the 3D forcing data are assigned the datastream name varanal3d. In this technical report, 3DCVA will be used to refer to the algorithm, while VARANAL3D will be used to refer to the data product.

54 ENVIRONMENTAL SCIENCES↗

Description of the Three-Dimensional Large-Scale Forcing Data from the 3D Constrained Variational Analysis (VARANAL3D)

This technical report introduces a Three-Dimensional Constrained Variational Analysis (3DCVA) (Tang and Zhang 2015) and its product of three-dimensional large-scale forcing data to drive single-column models (SCM), cloud-resolving models (CRM), and large-eddy simulation (LES) models, and to evaluate model results. The 3DCVA algorithm is an extension of the original 1D constrained variational analysis (1DCVA) (Zhang and Lin 1997, Zhang et al. 2001). The three-dimensional structure of the forcing data allows studies of spatial variation of the large-scale forcing fields and tests of physical parameterizations across scales. In the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility, the 3D forcing data are assigned the datastream name varanal3d. In this technical report, 3DCVA will be used to refer to the algorithm, while VARANAL3D will be used to refer to the data product.

54 ENVIRONMENTAL SCIENCES↗

Confinement and Processing Can Alter the Morphology and Periodicity of Bottlebrush Block Copolymers in Thin Films

Bottlebrush block copolymers (BBCPs) are intriguing architectural variations on linear BCPs with highly tunable structure. Confinement can have a significant impact on polymer assembly, giving rise to changes in morphology, assembly kinetics, and properties like the glass transition. Given that confinement leads to significant changes in the persistence length of bottlebrush homopolymers, it is reasonable to expect that BBCPs will see significant changes in their structure and periodicity relative to the bulk morphology. Understanding how confinement influences assembly will be important for designing BBCPs for thin film applications including membranes, integrated photonic structures, and potentially BCP lithography. In this work, in order to study the effects of confinement on BBCP conformation and morphology, a blade coating was used to prepare films with continuous variation in film thickness. Unlike thin films of linear BCPs, islands/holes were not observed, and instead mixtures of parallel and perpendicular morphologies emerge after annealing. The lamellar periodicity ($L_0$) of the morphologies is found to be thickness dependent, increasing $L_0$ with decreasing film thickness for blade coated films. Films coated out of tetrahydrofuran (THF) resulted in a single well-defined lamellar periodicity, verified through atomic force microscopy (AFM) and grazing incidence small-angle X-ray scattering (GISAXS), which increases dramatically from the bulk value (30.6 nm) and continues to increase as the film thickness decreases. The largest observed $L_0$ was 65.5 nm, and this closely approaches the estimated upper limit of 67 nm corresponding to a fully extended backbone in a bilayer arrangement. Films coated out of propylene glycol methyl ether acetate (PGMEA) resulted in a mixture of perpendicular lamellae and a smaller, likely cylindrical morphology. The lamellar portion of the film shows the same thickness dependence as the lamellae observed in the THF coated films. The scaling of the lamellar $L_0$ with respect to film thickness follows predictions for confined semiflexible polymers with weak excluded volume interactions and can be related to models for confinement of DNA. Spin coated films shows the same reduction in periodicity, although at very different film thicknesses. This result suggests that the material has shallow free-energy barriers to transitioning between different $L_0$ and morphologies, a property that could be taken advantage of for patterning diverse structures with a single material.

36 MATERIALS SCIENCE↗

Self-Limitations of Heat Release in Coupled Core-Shell Spinel Ferrite Nanoparticles: Frequency, Time, and Temperature Dependencies

We explored a series of highly uniform magnetic nanoparticles (MNPs) with a core-shell nanoarchitecture prepared by an efficient solvothermal approach. In our study, we focused on the water dispersion of MNPs based on two different CoFe 2 O 4 core sizes and the chemical nature of the shell (MnFe 2 O 4 and spinel iron oxide). We performed an uncommon systematic investigation of the time and temperature evolution of the adiabatic heat release at different frequencies of the alternating magnetic field (AMF). Our systematic study elucidates the nontrivial variations in the heating efficiency of core-shell MNPs concerning their structural, magnetic, and morphological properties. In addition, we identified anomalies in the temperature and frequency dependencies of the specific power absorption (SPA). We conclude that after the initial heating phase, the heat release is governed by the competition of the Brown and Néel mechanism. In addition, we demonstrated that a rational parameter sufficiently mirroring the heating ability is the mean magnetic moment per MNP. Our study, thus, paves the road to fine control of the AMF-induced heating by MNPs with fine-tuned structural, chemical, and magnetic parameters. Importantly, we claim that the nontrivial variations of the SPA with the temperature must be considered, e.g., in the emerging concept of MF-assisted catalysis, where the temperature profile influences the undergoing chemical reactions.

36 MATERIALS SCIENCE↗

Characterization of MoS 2 films via simultaneous grazing incidence X-ray diffraction and grazing incidence X-ray fluorescence (GIXRD/GIXRF)

Physical vapor deposited (PVD) molybdenum disulfide (nominal composition MoS 2 ) is employed as a thin film solid lubricant for extreme environments where liquid lubricants are not viable. The tribological properties of MoS 2 are highly dependent on morphological attributes such as film thickness, orientation, crystallinity, film density, and stoichiometry. These structural characteristics are controlled by tuning the PVD process parameters, yet undesirable alterations in the structure often occur due to process variations between deposition runs. Nondestructive film diagnostics can enable improved yield and serve as a means of tuning a deposition process, thus enabling quality control and materials exploration. Grazing incidence X-ray diffraction (GIXRD) for MoS 2 film characterization provides valuable information about film density and grain orientation (texture). However, the determination of film stoichiometry can only be indirectly inferred via GIXRD. The combination of density and microstructure via GIXRD with chemical composition via grazing incidence X-ray fluorescence (GIXRF) enables the isolation and decoupling of film density, composition, and microstructure and their ultimate impact on film layer thickness, thereby improving coating thickness predictions via X-ray fluorescence. We have augmented an existing GIXRD instrument with an additional X-ray detector for the simultaneous measurement of energy-dispersive X-ray fluorescence spectra during the GIXRD analysis. This combined GIXRD/GIXRF analysis has proven synergetic for correlating chemical composition to the structural aspects of MoS 2 films provided by GIXRD. We present the usefulness of the combined diagnostic technique via exemplar MoS 2 film samples and provide a discussion regarding data extraction techniques of grazing angle series measurements.

MoS2↗

Real-time tracking of structural evolution in 2D MXenes using theory-enhanced machine learning

In situ Electron Energy Loss Spectroscopy (EELS) combined with Transmission Electron Microscopy (TEM) has traditionally been pivotal for understanding how material processing choices affect local structure and composition. However, the ability to monitor and respond to ultrafast transient changes, now achievable with EELS and TEM, necessitates innovative analytical frameworks. Here, we introduce a machine learning (ML) framework tailored for the real-time assessment and characterization of in operando EELS Spectrum Images (EELS-SI). We focus on 2D MXenes as the sample material system, specifically targeting the understanding and control of their atomic-scale structural transformations that critically influence their electronic and optical properties. This approach requires fewer labeled training data points than typical deep learning classification methods. By integrating computationally generated structures of MXenes and experimental datasets into a unified latent space using Variational Autoencoders (VAE) in a unique training method, our framework accurately predicts structural evolutions at latencies pertinent to closed-loop processing within the TEM. This study presents a critical advancement in enabling automated, on-the-fly synthesis and characterization, significantly enhancing capabilities for materials discovery and the precision engineering of functional materials at the atomic scale.

47 OTHER INSTRUMENTATION↗

Alloying multiple halide perovskites on the same sublattice in search of stability and target band gaps

Single-component halide perovskites (HPs) rarely satisfy all the necessary criteria for optoelectronic applications, such as achieving an optimal band gap while maintaining high chemical and structural stability. Alloying halide perovskites has emerged as a promising strategy, not only to enhance stability but also to fine-tune their electronic and optical properties. In this work, we explore multiple degrees of freedom in alloy design, considering different substitution sublattices sites (A, B, or X in ABX3 perovskites), various chemical species (isovalent and hetero-valent elements), and multi-component compositions on a given sublattice. Using first-principles calculations based on density functional theory (DFT), we investigate how compositional variations influence the electronic (band gap) and structural properties (mixing enthalpy) of HP alloys. Our approach employs the polymorphous cell model, allowing full local relaxation which breaks local symmetry while preserving global cubic symmetry—an essential framework for accurately modeling HPs. Our results reveal that X-site mixing (halogen substitution) primarily affects the valence band maximum, allowing target band gap engineering. Additionally, variations in halogen radii introduce internal strain through octahedral distortions, influencing the mixing enthalpy. A-site substitution, while not directly contributing to the band edge states, modifies structural stability via volume effects, indirectly impacting the band gap. B-site alloying plays a dominant role in band gap modulation, leading to either positive or negative band gap bowing. Specifically, isovalent B-site mixing (Sn–Pb) induces strong positive bowing, where the alloy band gap is smaller than the average gap of parent compounds, whereas hetero-valent mixing (Cd–Pb) results in pronounced negative bowing. As an aside, we investigate the competition between the excess energy of disordered alloys vs. that of long-range ordered double perovskites of the same compositions, seeking examples of ordered phases emerging from disordered alloys. Furthermore, our findings provide fundamental insights into the electronic and structural behavior of HP alloys, offering valuable design principles for the development of stable and efficient materials for next-generation photovoltaic and optoelectronic devices.

14 SOLAR ENERGY↗

Closed‐Loop Recycling of Poly(pentylene Adipate‐ co ‐Terephthalate) via Amine‐Catalyzed Methanolysis

Advancing circularity through effective chemical recycling strategies is essential for enabling the sustainable use of emerging biodegradable polyesters in film applications. In this context, poly(pentylene adipate-co-terephthalate) with a 40/60 adipate-to-terephthalate ratio (PPeAT60), a significantly stiffer and partially biobased copolyester recently reported by our team, offers improved mechanical performance and processability compared to commercial poly(butylene adipate-co-terephthalate), while providing a platform to evaluate advanced recycling approaches for film applications. Here, this study describes depolymerization of PPeAT60 through amine-catalyzed methanolysis, followed by the repolymerization of the recovered monomers. The resulting repolymerized material exhibited a molar mass distribution, chemical structure, and thermal stability comparable to the virgin polymer, confirming the technical feasibility of the methanolysis-based recycling route. Both polymers displayed nearly identical melting, glass transition, and decomposition temperatures, crystallinity, and modulus, demonstrating full structural and mechanical reproducibility after recycling. Variations in crystallization kinetics, elongation at break, and barrier properties likely arise from trace impurities (<1%) introduced during processing acting as nucleating and stress-inducing agents. Overall, these results demonstrate that PPeAT60 retains its key properties after chemical recycling, establishing methanolysis as a promising platform for recycling of this partially biobased polymer that may be able to replace both conventional polyolefins and PBAT in flexible packaging applications.

09 BIOMASS FUELS↗

Engineering highly stable variants of Corynactis californica green fluorescent proteins

Fluorescent proteins (FPs) are versatile biomarkers that facilitate effective detection and tracking of macromolecules of interest in real time. Engineered FPs such as superfolder green fluorescent protein (sfGFP) and superfolder Cherry (sfCherry) have exceptional refolding capability capable of delivering fluorescent readout in harsh environments where most proteins lose their native functions. Our recent work on the development of a split FP from a species of strawberry anemone, Corynactis californica, delivered pairs of fragments with up to threefold faster complementation than split GFP. We present the biophysical, biochemical, and structural characteristics of five full-length variants derived from these split C. californica GFP (ccGFP). These ccGFP variants are more tolerant under chemical denaturation with up to 8 kcal/mol lower unfolding free energy than that of the sfGFP. It is likely that some of these ccGFP variants could be suitable as biomarkers under more adverse environments where sfGFP fails to survive. A structural analysis suggests explanations of the variations in stabilities among the ccGFP variants.

59 BASIC BIOLOGICAL SCIENCES↗