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At least 181 records · Page 10

Transferable predictions of energetic and structural properties for refractory solid solution alloys across chemical compositions

We present a data-efficient approach to train graph neural networks (GNNs) on density functional theory (DFT) data for accurate and transferable predictions of energetic and structural properties of refractory solid solution alloys in the niobium-tantalum-vanadium (Nb-Ta-V) chemical space. We start by training the GNN model only on DFT data that describes refractory binary alloys niobium-tantalum (Nb-Ta), niobium-vanadium (Nb-V), and tantalum-vanadium (Ta-V) to predict formation enthalpy and root mean squared displacement. Once trained, the GNN predictions are tested on DFT data describing refractory ternary alloys Nb-Ta-V. While, unsurprisingly, direct transferability from binary to ternary is not sufficiently accurate, augmenting the training with only 1% of the available ternary data (uniformly distributed across the entire range of chemical compositions) improves significantly the quality of the GNN predictions. For comparison, we assess the transferability in the opposite direction by training GNN models on ternary Nb-Ta-V data and making predictions on binaries Nb-Ta, Nb-V, and Ta-V, which exhibits notably higher predictive errors. The proposed methodology, which favors transferability from lower-component to higher-component alloys, offers an efficient path towards avoiding the curse of dimensionality incurred when collecting DFT data for discovery and design of multi-component disordered alloys.

Density functional theory calculations↗

Liquid-phase mega-electron-volt ultrafast electron diffraction

The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure–function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast electron diffraction instrument for the study of structural dynamics in solution. Limitations posed by the shallow penetration depth of electrons and the resulting information loss due to multiple scattering and the technical challenge of delivering liquids to vacuum were overcome through the use of MeV electrons and a gas-accelerated thin liquid sheet jet. To demonstrate the capabilities of this instrument, the structure of water and its network were resolved up to the 3rd hydration shell with a spatial resolution of 0.6 Å; preliminary time-resolved experiments demonstrated a temporal resolution of 200 fs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Processability and Material Behavior of NiTi Shape Memory Alloys Using Wire Laser-Directed Energy Deposition (WL-DED)

Utilizing additive manufacturing (AM) techniques with shape memory alloys (SMAs) like NiTi shows great promise for fabricating highly flexible and functionally superior 3D metallic structures. Compared to methods relying on powder feedstocks, wire-based additive manufacturing processes provide a viable alternative, addressing challenges such as chemical composition instability, material availability, higher feedstock costs, and limitations on part size while simplifying process development. This study presented a novel approach by thoroughly assessing the printability of Ni-rich Ni55.94Ti (Wt. %) SMA using the wire laser-directed energy deposition (WL-DED) technique, addressing the existing knowledge gap regarding the laser wire-feed metal additive manufacturing of NiTi alloys. For the first time, the impact of processing parameters—specifically laser power (400–1000 W) and transverse speed (300–900 mm/min)—on single-track fabrication using NiTi wires in the WL-DED process was examined. An optimal range of process parameters was determined to achieve high-quality prints with minimal defects, such as wire dripping, stubbing, and overfilling. Building upon these findings, we printed five distinct cubes, demonstrating the feasibility of producing nearly porosity-free specimens. Notably, this study investigated the effect of energy density on the printed part density, impurity pick-up, transformation temperature, and hardness of the manufactured NiTi cubes. The results from the cube study demonstrated that varying energy densities (46.66–70 J/mm3) significantly affected the quality of the deposits. Lower to intermediate energy densities achieved high relative densities (>99%) and favorable phase transformation temperatures. In contrast, higher energy densities led to instability in melt pool shape, increased porosity, and discrepancies in phase transformation temperatures. These findings highlighted the critical role of precise parameter control in achieving functional NiTi parts and offer valuable insights for advancing AM techniques in fabricating larger high-quality NiTi components. Additionally, our research highlighted important considerations for civil engineering applications, particularly in the development of seismic dampers for energy dissipation in structures, offering a promising solution for enhancing structural performance and energy management in critical infrastructure.

Dabbaghi, Hediyeh↗

Accelerating structural dynamics simulations with localised phenomena through matrix compression and projection‐based model order reduction

In this work, a novel approach is introduced for accelerating the solution of structural dynamics problems in the presence of localised phenomena, such as cracks. For this category of problems, conventional projection-based Model Order Reduction (MOR) methods are either limited with respect to the range of system configurations that can be represented or require frequent solutions of the Full Order Model (FOM) to update the low-dimensional spaces, in which solutions are represented. In the proposed approach, low-dimensional spaces, constructed for the healthy structure, are enriched with appropriately selected columns of the flexibility matrix of the system. It can be shown that these spaces contain the solution to the original problem for the static case, while their dimension is much smaller. In order to allow their online construction for arbitrary localised features, the full flexibility matrix of the system should be available. To this end, a hierarchical representation is used for the matrices involved, allowing to compute the flexibility matrix efficiently and with reduced memory requirements. The resulting method offers significant speedups, without sacrificing the flexibility and accuracy of the full order model. The performance and limitations of the approach are studied through a series of examples in structural dynamics.

fracture mechanics↗

Protein remote homology detection and structural alignment using deep learning

Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring the hardness and high-pressure behavior of osmium and ruthenium-doped rhenium diboride solid solutions

Rhenium diboride (ReB 2 ) exhibits high differential strain due to its puckered boron sheets that impede shear deformation. Here, we demonstrate the use of solid solution formation to enhance the Vickers hardness and differential strain of ReB 2 . ReB 2 -structured solid solutions (Re 0.98 Os 0.02 B 2 and Re 0.98 Ru 0.02 B 2 , noted as “ReOsB 2 ” and “ReRuB 2 ”) were synthesized via arc-melting from the pure elements. In-situ high-pressure radial x-ray diffraction was performed in the diamond anvil cell to study the incompressibility and lattice strain of ReOsB 2 and ReRuB 2 up to ~56 GPa. Both solid solutions exhibit higher incompressibility and differential strain than pure ReB 2 . However, while all lattice planes are strengthened by doping osmium (Os) into the ReB 2 structure, only the weakest ReB 2 lattice plane is enhanced with ruthenium (Ru). These results are in agreement with the Vickers hardness measurements of the two systems, where higher hardness was observed in ReOsB 2 . The combination of high-pressure studies with experimentally observed hardness data provides lattice specific information about the strengthening mechanisms behind the intrinsic hardness enhancement of the ReB 2 system.

36 MATERIALS SCIENCE↗

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗

Interplay of surface energy and rheology in biopolymer soil enhancement

Biopolymers such as xanthan gum (XG) and locust bean gum (LBG) hold great potential as eco-friendly alternative soil binders. In this work, we investigated the impact of XG/LBG mixtures on the unconfined compressive strength (UCS) of sand. The high strength of dry biopolymer/sand arises from the cohesion between solid polymer films and sand particles which supported by work of adhesion calculation and soil mechanics measurement. LBG exhibits much lower sand reinforcement efficacy because polymers unevenly distributed within sand matrix. The formation of a core-shell structure in LBG/sand is an interplay of surface free energy and viscoelastic properties of polymer solutions. This structure is altered when LBG mixed with XG at varying ratios as those physical properties changed due to the complexity of polymer chains association. By probing these factors, we aim to elucidate the role of surface energies and polymer physics in governing the strength of the sand/polymer network, thereby contributing to a more comprehensive understanding polymer-sand interface. The low strength of gels (G’ ∼10Pa) cannot solely account for the increased UCS of wet sand over 10 kPa. Instead, the high strength of biopolymer/sand is more likely derived from the granular particles with biopolymers as solid glue.

36 MATERIALS SCIENCE↗

Deciphering the Solvation Structure of Aqueous ZnCl 2 Solutions from X-ray Absorption Spectra Using the Interpretable Graph Neural Network

Machine learning (ML) provides powerful pathways for predicting spectroscopic observables from atomic structures, but its broader impact depends on making model predictions interpretable in terms of physical and chemical principles. Here, we introduce a physics-guided graph neural network (GNN) model that predicts Zn K-edge X-ray spectroscopy (XAS) spectra of aqueous ZnCl 2 solutions. Training data are generated from ab initio XAS calculations on molecular dynamics snapshots obtained using a machine learning interatomic potential. The GNN reproduces experimental spectra across concentrations from dilute (<0.1 m) to highly concentrated (30 m, “water-in-salt”) regimes and scales efficiently to large, disordered liquid systems beyond the reach of conventional ab initio approaches. Gradient-based attribution analysis reveals that the model learns physically meaningful structure-spectrum relationships. Ligand-specific attributions reflect orbital hybridization patterns and the origin of the excitations derived from the density functional theory. Bond-length attributions recover spectral shifts consistent with multiple-scattering theory. Finally, this work bridges data-driven prediction with electronic-structure theory, establishing a general paradigm for interpretable ML that links atomic structure, electronic structure, and spectroscopic observables.

25 ENERGY STORAGE↗

Strong Enhancement of Nanoconfined Water Mobility by a Structure Breaking Salt

For the majority of the water present on earth, the two most important factors influencing its behavior are confinement, in either inorganic or organic matrixes, and the presence of solutes. Here, we investigate the effect of confinement in 3 nm pores on water diffusivity in aqueous solutions with archetypical solutes, a structure making (kosmotrope) NaCl and a structure breaking (chaotrope) KCl, up to 1.0 M in concentration. The water diffusivity in bulk aqueous solutions in such a concentration range is known to decrease very slightly in the presence of NaCl and increase very slightly in the presence of KCl. However, here we observe the water diffusivity in confined H 2 O–KCl increases by a factor of 2 compared to the pure water diffusivity in the same confinement. This unusually strong cumulative effect of confinement and a structure breaking additive may have profound implications for the mobility and transport of aqueous species in nature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling the Morphology of PEDOT:PSS Blend Films with Pre-Deposition Solution Composition and Deposition Technique

Understanding the relationships between morphology, fabrication processes, and thermoelectric performance in conducting polymers is essential to the development of high- efficiency organic thermoelectrics as an alternative to commonly used rare metals. Altering the film fabrication process of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) with the addition of high boiling solvents to the precast solution improves the electrical conductivity and significantly increases its Seebeck value. Neutron scattering monitors the changes in the atomic, nanoscale, and mesoscale morphologies of PEDOT:PSS thin films with the addition of dimethyl sulfoxide (DMSO) to the aqueous solution prior to film formation and with varying fabrication procedures. The neutron scattering results show a decrease in the deuterated PSS domain size along with systematic variations in PEDOT fibril assemblies in the final blend film with the addition of DMSO to the pre-deposition solution. These structural modifications indicate that the increase in conductivity of PEDOT:PSS blends with addition of DMSO reported in the literature can be ascribed to the disruption of solvated PEDOT assemblies by the DMSO, forming smaller PSS domains in the pre-deposition solution and allowing smoother film formation. These improvements are observed significantly with the addition of just 1% DMSO but continue to modestly improve with the addition of up to 5% DMSO to the PEDOT:PSS blend pre-deposition solution. The fact that the variations in the measured morphology are independent of whether the films were deposited by spin or ultrasonic spray casting methods emphasizes the crucial importance of the structure of the blend in the pre-deposition solution in determining the final thin film blend morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding plasma turbulence through exact coherent structures

Plasma turbulence is a key challenge in understanding transport phenomena in magnetically confined plasmas. This work presents a generalized framework to analyze plasma turbulence that utilizes periodic orbit theory. In periodic orbit theory, doubly periodic solutions (coherent structures) of the governing equation(s) serve as building blocks of the considered turbulent dynamics. To illustrate the concept and method, the particularly simple Kuramoto–Sivashinsky (referred to here as LMRT for the original authors: LaQuey, Mahajan, Rutherford, and Tang) trapped-ion mode toy model is used. By applying numerical optimization techniques to the LMRT equation, we extract coherent spacetime patterns that represent the library of allowable fundamental structures of the equation. These structures provide a framework to systematically describe turbulence as a composition of recurrent solutions, revealing an underlying order within chaotic plasma motion. Although illustrated here using the simplified LMRT model for clarity, this framework provides a general strategy that can be extended to more complex and realistic models of plasma turbulence, including gyrokinetic systems. This offers a new method for predicting and potentially controlling transport processes in fusion plasmas by providing a bridge between nonlinear dynamical systems theory and plasma physics in the form of a generalized framework with which to analyze and understand spatially extended nonlinear partial differential equations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗

Subtle Molecular Changes Largely Modulate Chiral Helical Assemblies of Achiral Conjugated Polymers by Tuning Solution-State Aggregation

Understanding the solution-state aggregate structure and the consequent hierarchical assembly of conjugated polymers is crucial for controlling multiscale morphologies during solid thin-film deposition and the resultant electronic properties. However, it remains challenging to comprehend detailed solution aggregate structures of conjugated polymers, let alone their chiral assembly due to the complex aggregation behavior. Herein, we present solution-state aggregate structures and their impact on hierarchical chiral helical assembly using an achiral diketopyrrolopyrrole-quaterthiophene (DPP-T4) copolymer and its two close structural analogues wherein the bithiophene is functionalized with methyl groups (DPP-T2M2) or fluorine atoms (DPP-T2F2). Combining in-depth small-angle X-ray scattering analysis with various microscopic solution imaging techniques, we find distinct aggregate in each DPP solution: (i) semicrystalline 1D fiber aggregates of DPP-T2F2 with a strongly bound internal structure, (ii) semicrystalline 1D fiber aggregates of DPP-T2M2 with a weakly bound internal structure, and (iii) highly crystalline 2D sheet aggregates of DPP-T4. These nanoscopic aggregates develop into lyotropic chiral helical liquid crystal (LC) mesophases at high solution concentrations. Intriguingly, the dimensionality of solution aggregates largely modulates hierarchical chiral helical pitches across nanoscopic to micrometer scales, with the more rigid 2D sheet aggregate of DPP-T4 creating much larger pitch length than the more flexible 1D fiber aggregates. Combining relatively small helical pitch with long-range order, the striped twist-bent mesophase of DPP-T2F2 composed of highly ordered, more rigid 1D fiber aggregate exhibits an anisotropic dissymmetry factor (g-factor) as high as 0.09. This study can be a prominent addition to our knowledge on a solution-state hierarchical assembly of conjugated polymers and, in particular, chiral helical assembly of achiral organic semiconductors that can catalyze an emerging field of chiral (opto)electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transactive Energy Systems: The Market-based Coordination of Distributed Energy Resources

This paper synthesizes a unifying framework that captures a large class of transactive energy systems studied in the literature. The framework consists of four key elements: agent preferences, control decisions, information structure, and solution concept. Among them, agent preference specifies the preferred outcome by each agent and models the conflict of interest in decision making. Control decision specifies the set of decisions for each agent to maximize its payoff. Information structure describes the information available to each agent before it makes a decision. Solution concept encodes the rationality assumptions of each agent in the system. These elements are important in identifying and distinguishing different transactive energy systems. In this paper, we use them to analyze a number of important ones, including the competitive equilibrium, Stackelberg game, reverse Stackelberg game, and mechanism design. Each class of these problems is formulated as a special case of the proposed transactive energy systems. Their connections and differences are discussed. Available tools and results for each category of problems are surveyed.

Li, Sen↗

Effect of Solvent Quality on Structure and Dynamics of Lignin in Solution

The conversion of lignin into useful chemicals and monomers requires that different linkages connecting monomers are exposed to the catalytic sites. As most conversion processes are expected to occur in the liquid phase, it is important to understand the structure and dynamics of lignin in solution. Here, we have examined the structure and dynamics of hardwood- and softwood-derived lignin model compounds with 61 monomers in methanol/water solution.

09 BIOMASS FUELS↗

Effect of water models on structure and dynamics of lignin in solution

Lignin, a major biomass component, can be an excellent source for different monomers in the polymer industry. However, the complex and heterogeneous structure of lignin poses a significant challenge for designing energy-efficient processes for depolymerization. As many proposed depolymerization processes are solvothermal, it is essential to understand the structure and dynamics of lignin in solution, in particular aqueous solution. Here, we utilize molecular dynamics simulations to understand the effect of water models on the structure and dynamics of different model lignin oligomers (softwood and hardwood) as a function of temperature. We have examined three different water models: TIP3P, TIP4P/Ew, and flexible SPC/Fw. We find that the diffusion constant of lignin oligomers in an aqueous solution differs significantly depending on the water model used. The diffusion constant of lignin in the TIP3P water model is almost twice as large as that in SPC/Fw and TIP4P/Ew. The softwood and hardwood oligomers adopt an extended structure in TIP3P water compared to SPC/Fw and TIP4P/Ew. Given the different levels of sensitivity of transport and structural properties of aqueous lignin on water models, it is important to take these into account when discussing results from a specific water model.

09 BIOMASS FUELS↗

Reactor for hydrothermal growth of structured materials

Design, fabrication, and usage of a reactor are presented for synthesis of structured materials from a liquid-phase precursor by heating. The structured materials are particles, membranes or films of micro-porous molecular sieve crystals such as zeolite and meso-porous materials. The precursor solution and structured materials in the reactor are uniformly heated by a planar heater with characteristic heat transfer dimension in the range of 3 mm to 10 cm. A planar heater having width and length at least three times of the characteristic heat transfer dimension provides at least one surface of uniform temperature distribution for heating purposes. Heating is conducted over a temperature range of 20 to 300° C. The planar heater can be heated by electrical power of by thermal fluid.

36 MATERIALS SCIENCE↗