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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17

Including Physics-Informed Atomization Constraints in Neural Networks for Reactive Chemistry

Machine learning interatomic potentials (MLIPs) have emerged as powerful tools for investigating atomistic systems with high accuracy and a relatively low computational cost. However, a common and unaddressed challenge with many current neural network (NN) MLIP models is their limited ability to accurately predict the relative energies of systems containing isolated or nearly isolated atoms, which appear in various reactive processes. To address this limitation, we present a mathematical technique for modifying any existing atom-centered NN architecture to account for the energies of isolated atoms. The result produces a consistent prediction of the atomization energy (AE) of a system using minimal constraints on the model. Using this technique, we build a model architecture that we call hierarchically interacting particle neural network (HIP-NN)-AE, an AE-constrained version of the HIP-NN, as well as ANI-AE, the AE-constrained version of the accurate NN engine for molecular energies (ANI). Our results demonstrate AE consistency of AE-constrained models, which drastically improves the AE predictions for the models. We compare the AE-constrained approach to unconstrained models as well as models from the literature in other scenarios, such as bond dissociation energies, bond dissociation pathways, and extensibility tests. These results show that the constraints improve the model performance in some of these tasks and do not negatively affect the performance on any tasks. The AE constraint approach thus offers a robust solution to the challenges posed by isolated atoms in energy prediction tasks.

74 ATOMIC AND MOLECULAR PHYSICS↗

Particle Markov Chain Monte Carlo Approach to Inference in Transient Surface Kinetics

Here, in this work, we develop a novel Bayesian approach to study the adsorption and desorption of CO onto a Pd(111) surface, a process of great importance in natural sciences. The motivation for this work comes from the recent availability of time-resolved infrared spectroscopy data and the need for model interpretability and uncertainty quantification in chemical processes. The objective is to learn the relevant parameters that characterize the process: coverage with time, rate constants, activation energies, and pre-exponential factors. Our approach consists of three main schemes: (i) a problem design and probabilistic model for the whole system, (ii) a particle Markov chain Monte Carlo sampler to learn the hidden coverages and rate constant parameters, and (iii) two Bayesian formulations to infer the activation energies and pre-exponential factors. The flexibility of the Bayesian framework allows for uncertainty quantification where possible and integration of mathematical constraints in the model to reflect the system physically. We found that our results for the activation energies and pre-exponential factor are in agreement with those reported in the experimental literature, independently, and we provide discussions on the advantages and disadvantages as well as applicability to other systems.

36 MATERIALS SCIENCE↗

Exact-Two-Component Complete Active Space Method with Variational Treatment of Magnetic Field and Spin–Orbit Coupling: Application to X-ray Magnetic Circular Dichroism Spectroscopy

We introduce an exact-two-component complete active space self-consistent-field (X2C-CASSCF) method formulated under the restricted-magnetic-balance condition. This framework allows for the nonperturbative treatment of static magnetic fields using gauge-including atomic orbitals (GIAOs). The GIAO-X2C-CASSCF methodology effectively captures all microstates within the same 2J + 1-degenerate manifold and their splitting in a static magnetic field, which are not accessible through single-reference-based methods. We also present mathematical recursive expressions for evaluating one-electron relativistic integrals by using GIAOs in the presence of a finite magnetic field. Benchmark studies include oxygen and nitrogen K-edge X-ray magnetic circular dichroism spectroscopy (XMCD) for closed-shell organic compounds, as well as L-edge XMCD spectroscopy for the high-spin open-shell transition metal ion Mn 2+ and the tetrahedral Mn(II)O 4 6– complex.

Chemical calculations↗

Physics-Driven Construction of Compact Primitive Gaussian Density Fitting Basis Sets

We present a model-assisted density fitting (MADF) basis set generator, an algorithm for generating primitive atomic Gaussian density fitting (DF) basis sets (DFBSs) from a contracted Gaussian orbital basis set (OBS). The MADF algorithm produces DFBSs suitable for accurate robust DF approximation of 2-particle interactions in mean-field and correlated electronic structures. The algorithm is designed to (a) saturate the OBS product space by a large regularized set of primitive solid-harmonic Gaussian shells with nonuniform distribution of exponents, followed by (b) pruning of the shells according to their contributions to the 2- body energy of a correlated atomic ensemble. Building the DFBS generator model almost exclusively on mathematical and physical principles allows one to limit the number of parameters that control the density fitting error to three, with a single set of parameters sufficient for computations with all basis cardinal numbers, with and without correlation of core electrons, with and without scalar and spin-dependent relativistic effects, spanning almost all of the Periodic Table. Performance assessment included basis sets up to quadruple-ζ quality from several major basis set families, using molecules composed of main-group, d-block, and f-block elements. The resulting DF errors in Hartree−Fock and second-order MP2 energies (with relativistic all-electron treatments, when appropriate) were on the order of 20 and 10 μE h per electron, respectively.

Approximation↗

Energetics of Cu Adsorption on and Adhesion to Rutile-TiO 2 (100) Studied by Cu Vapor Adsorption Calorimetry

The heat of adsorption of Cu vapor versus coverage was measured on rutile-TiO 2 (100) at 300 and 100 K using single-crystal adsorption calorimetry. At these conditions, Cu nanoparticles nucleate and then grow larger. The average Cu particle size versus Cu coverage was measured using He + low-energy ion scattering spectroscopy. These data were analyzed with the recently introduced spherical cap model (SCM) to provide the heat of Cu adsorption and Cu chemical potential versus Cu particle size, as well as the contact angle (67°) and adhesion energy (2.50 J/m 2 ) at the Cu particle/rutile-TiO 2 (100) interface. The hemispherical cap model (HCM) was used to model the data first, and then those HCM results were converted to the more accurate SCM results using a recently published mathematical approximation whose high accuracy was validated here. Furthermore, the adhesion energy of Cu on rutile-TiO 2 (100) measured here is compared to prior values for Ag and Au on rutile-TiO 2 (100), showing a nearly proportional increase in adhesion energy with metal oxophilicity (per unit area).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Is the Matrix Completion of Reduced Density Matrices Unique?

Reduced density matrices are central to describing observables in many-body quantum systems. In electronic structure theory, the two-particle reduced density matrix (2-RDM) suffices to determine the energy and other key properties. Recent work has used matrix completion, leveraging the low-rank structure of RDMs and approximate theoretical models, to reconstruct the 2-RDM from partial data and thus reduce the computational cost. However, matrix completion is, in general, an under-determined problem. Revisiting Rosina’s theorem (Rosina, M. Queen’s Papers on Pure and Applied Mathematics , 1968, No. 11, 369), we here show that the matrix completion is unique under certain conditions, identifying the subset of 2-RDM elements that enables its exact reconstruction from incomplete information. Building on this, we introduce a hybrid quantum–stochastic algorithm that achieves exact matrix completion, demonstrated through applications to the Fermi–Hubbard model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identifying Topological Defects in Lamellar Phases through Contour Analysis of Complex Wave Fields

Lamellar phases frequently contain structural imperfections that significantly affect their behaviors and properties. Our previous research successfully reconstructed real-space configurations of defective lamellar phases from diffuse scattering patterns, indicating the presence of phase vortices as a potential method for identifying topological defects disrupting the smectic ordering. Here, this report presents a mathematical framework using regularized wave fields to represent defective lamellar structures in real space. Phase singularities, resulting from the interference of random waves and indicating lamellar order disruption, are identified through a contour integral. These wave fields, derived from coherent scattering in reciprocal space, were validated via computational benchmarks analyzing small-angle neutron scattering data from AOT surfactant solutions, facilitating further statistical analysis of the defects. Our study highlights the potential to extract meaningful information about topological defects in lyotropic phases by inversely analyzing experimentally measured two-point static correlations. Our method allows for detailed structural analysis of various lyotropic phases, both particulate and nonparticulate, in their quiescent states and facilitates quantitative investigation of defects’ role in phase transitions. By integrating small-angle scattering, deep learning, and vortex tangle analysis, our comprehensive approach shows promise in addressing complex challenges in the structural analysis of soft matter systems.

36 MATERIALS SCIENCE↗

Insights into Prismatic Loop Formation in Irradiated Fe–Cr Alloys from Hypothesis-Driven Active Learning and Causal Analysis

Neutron and electron irradiation experimental studies conducted on body-centered cubic Fe and Fe–Cr alloys have established two prismatic dislocation loop populations, which have Burgers vectors of either a/2$\langle$111$\rangle$ or a$\langle$100$\rangle$. Here, the loop formation depends on factors such as dose (D), dose rate (D rt ), temperature (T), chromium content (Cr%), and other alloying elements. Hence, it is important to understand how irradiation-induced dislocation loops evolve conditional upon the loop characteristics, such as loop density (DD), average loop size d̅, and irradiation parameters (D, D rt , T, and irradiation type), which is still an active area of research. To understand these complex structure–property relationships, machine learning (ML) is employed in a three-step approach. This includes imputing missing data with a k-nearest neighbor, generating functionalized features, and assessing feature importance with random forest classification and regression. Physics-based features are incorporated in a hypothesis-driven active learning scheme to overcome data unavailability challenges. Insights obtained from ML models (i) to categorize dislocation loop types, show the highest correlation with d̅; (ii) Log(DD), obtained through mathematical formulations involving D, Cr%, d̅, and T (e.g., Log(DD) ~ D + exp(-Cr%) + 1/d̅ and log(DD) ~ D + exp(-Cr%) + 1/T). Hypothesis-driven active learning is able to predict Log(DD) in which the experimental date is not known. Causal models verify cause–effect relationships for dislocation loop classification and irradiation factors in FeCr alloys.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multiscale Modeling and Experimental Insights into High-Temperature Soil Biodegradation Dynamics of Semi-Crystalline Poly(Lactic Acid) Nonwoven Fabrics

This study investigates the biodegradation of semi-crystalline poly(lactic acid) (PLA) nonwovens (NWs) in soil at 58 °C using both experimental and mathematical modeling approaches. The model utilizes a system of parabolic diffusion-reaction partial differential equations (PDEs) to elucidate chemical transformations over time and in space. It accounts for phenomena such as the diffusion of water and lactic acid monomers through the polymer matrix and into the surrounding soil, along with their microbial breakdown. It also accounts for the initial PLA crystallinity and predicts its evolution in time. The model is solved numerically for a single filament, and the results were used to shed light on PLA NW transformations observed in soil over a 180-day incubation period. Various characterization techniques, including scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and Raman spectroscopy, were employed to assess morphological changes, crystallinity, and molecular changes in the NWs throughout the experiment. By comparing the experimental data with the model predictions, the hydrolysis rate coefficient was found to be 3.37 × 10 -7 s -1 , while the rate of microbial degradation of lactic acid monomers was faster, of the order of 9.63 × 10 -7 s -1 . The findings highlight the significant role of crystallinity in the biodegradation process. The PLA degradation ceases when no amorphous material remains, and the crystallinity reaches 0.8, as observed in the experiments by day 120. Furthermore, this research contributes to a deeper understanding of PLA biodegradation dynamics and offers insights for effectively managing biodegradable materials in environmental settings.

Diffusion−reaction modeling↗

Degrees of Rate Control in Interconnected Reaction Networks

Overall reactions in interconnected networks exhibit net, forward, and reverse rates that are governed by both constitutive elementary steps in the pathway of interest and branching elementary steps that lead to alternative products. Accordingly, steps in branching pathways exhibit negative net, forward, and reverse degrees of rate control, as they reduce reaction flux to the desired product. We here contextualize the forward and reverse degrees of rate control in terms of kinetic resistances (inverse of rates) and leverage the additive nature of kinetic resistance to decouple kinetic driving forces contributed by constitutive elementary steps and branching points (nodal species) in interconnected networks. Regardless of the network connectivity, forward and reverse degrees of rate control are shown to converge at equilibrium. Away from equilibrium, we identify two critical features of interconnected networks: stoichiometric regularity─condition where all stoichiometric numbers are unity─and pathway symmetry around nodal species─condition where branching pathways share the same rate constants, stoichiometry, and species concentrations/activities─that result in (i) equal forward, reverse, and consequently net degrees of rate control and (ii) forward and reverse degrees of rate control that exhibit constant offsets, respectively, across all extents of reaction. Furthermore, our discourse further provides a mathematical description for the influence of stoichiometric irregularity and pathway asymmetry on forward and reverse degrees of rate control. Altogether, the presented work details the effects of network (inter)connectivity and stoichiometry on reaction kinetics and, in doing so, establishes general protocols for capturing these effects as additive terms in the formulation of forward and reverse degrees of rate control.

10 SYNTHETIC FUELS↗

High-Nickel Cathodes with Mechanical and Interfacial Robustness via Tailored Concentration Gradients for Stable Li-Ion Batteries

Here, we have developed a versatile mathematical framework integrated with an automated reactor system to design and reify highly customizable full concentration gradient (FCG) in high-nickel cathodes for advanced Li-ion batteries. This method provides precise and independent control of the average composition, slope, and curvature of FCGs, enabling the optimization of structural and mechanical properties of the cathode materials. We have showcased this method with Ni 0.8 Co 0.1 Mn 0.1 (OH) 2 precursors of controlled FCGs, which unlocked an optimized cathode with excellent cycling stability without crack formation after repeated cycles. This work opens up new possibilities for the design and manufacturing of advanced cathode materials, enabling safer, high-performance batteries.

25 ENERGY STORAGE↗

Topological Data Analysis for Particulate Gels

Soft gels, formed via the self-assembly of particulate materials, exhibit intricate multiscale structures that provide them with flexibility and resilience when subjected to external stresses. Here, this work combines particle simulations and topological data analysis (TDA) to characterize the complex multiscale structure of soft gels. Our TDA analysis focuses on the use of the Euler characteristic, which is an interpretable and computationally scalable topological descriptor that is combined with filtration operations to obtain information on the geometric (local) and topological (global) structure of soft gels. We reduce the topological information obtained with TDA using principal component analysis (PCA) and show that this provides an informative low-dimensional representation of the gel structure. We use the proposed computational framework to investigate the influence of gel preparation (e.g., quench rate, volume fraction) on soft gel structure and to explore dynamic deformations that emerge under oscillatory shear in various response regimes (linear, nonlinear, and flow). Our analysis provides evidence of the existence of hierarchical structures in soft gels, which are not easily identifiable otherwise. Moreover, our analysis reveals direct correlations between topological changes of the gel structure under deformation and mechanical phenomena distinctive of gel materials, such as stiffening and yielding. In summary, we show that TDA facilitates the mathematical representation, quantification, and analysis of soft gel structures, extending traditional network analysis methods to capture both local and global organization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Unified Analytical Method Greenness Score ( uAMGS ) Quantifies How Microscopic Imaging Is Greener Than Conventional Liquid Chromatography

Green chemistry is a set of principles for assessing, developing, and implementing methods that are safer, more efficient, and less detrimental to the environment. The analytical method greenness score (AMGS) is one of many metrics that attempt to evaluate traditional liquid chromatography (LC) based on the energy consumption of the instrument and the safety, health risks, and environmental impact of the solvents employed. Unfortunately, in practice, the AMGS is primarily focused on traditional separation methods in the pharmaceutical industry and is not amenable to cutting-edge separation science, including miniaturization. To broaden this scope, the unified Analytical Method Greenness Score (uAMGS) is presented here, which clarifies and expands on the underlying mathematics and incorporates both dimensional and uncertainty analysis, enabling its application to a broader range of analytical techniques. The uAMGS is used to compare the greenness of two distinct methods: single-molecule microscopy (SMM) and high-performance liquid chromatography (HPLC), which were used to collect equivalent data. uAMGS determines that SMM is significantly greener than HPLC due primarily to decreased solvent consumption. Overall, the uAMGS should allow chemists ranging from undergraduates to industrial PhDs to assess the greenness of a wide range of separations.

chemical separations↗

How Does Escherichia coli Allocate Proteome?

Microorganisms are shown to actively partition their intracellular resources, such as pro- teins, for growth optimization. Recent experiments have begun to reveal molecular com- ponents unpinning the partition; however, it remains unclear quantitatively how individual parts orchestrate to yield precise resource allocation that is both robust and dynamic. Here we developed a coarse-grained mathematical framework that centers on guanosine pentaphosphate (ppGpp)-mediated regulation, and used it to systematically uncover the design principles of proteome allocation in Escherichia coli. Our results showed that cellular ability of resource partition lies in an ultrasensitive, negative feedback control- ling topology with the ultrasensitivity arising from zero-order amino acid kinetics and the negative feedback from ppGpp-controlled ribosome synthesis. In addition, together with the time-scale separation between slow ribosome kinetics and fast turnovers of ppGpp and amino acids, the network topology confers the organism an optimization mechanism which mimics sliding mode control, a nonlinear optimization strategy that is widely used in man-made systems. We further showed that such a controlling mechanism is robust against parameter variations and molecular fluctuations, and is also efficient for biomass production over time. Furthermore, this work elucidates the fundamental controlling mechanism of E. coli proteome allocation, thereby providing insights into quantitative microbial physiology as well as the design of synthetic gene networks.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Design of Peptide Materials Based on Supramolecular Cohesion

Peptide materials offer a broad platform to design biomimetic soft matter, and filamentous networks that emulate those in extracellular matrices and the cytoskeleton are among the important targets. Given the vast sequence space, a combination of computational approaches and readily accessible experimental techniques is required to design peptide materials efficiently. Here, we report here on a strategy that utilizes this combination to predict supramolecular cohesion within filaments of peptide amphiphiles, a property recently linked to supramolecular dynamics and consequently bioactivity. Using established coarse-grained simulations on 10,000 randomly generated peptide sequences, we identified 3500 likely to self-assemble in water into nanoscale filaments. Atomistic simulations of small clusters were used to further analyze this subset of sequences and identify mathematical descriptors that are predictive of intermolecular cohesion, which was the main purpose of this work. We arbitrarily selected a small cohort of these sequences for chemical synthesis and verified their fiber morphology. With further characterization, we were able to link the latent heat associated with fiber to micelle transitions, an indicator of cohesion and potential supramolecular dynamicity within the filaments, to calculated hydrogen bond densities in the simulation clusters. Based on validation from in situ synchrotron X-ray scattering and differential scanning calorimetry, we conclude that the phase transitions can be easily observed by very simple polarized light microscopy experiments. We are encouraged by the methodology explored here as a relatively low-cost and fast way to design potential functions of peptide materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin

The lanmodulin (LanM) protein has emerged as an effective means for rare earth element (REE) extraction and separation from complex feedstocks without the use of organic solvents. Whereas the binding of LanM to individual REEs has been well characterized, little is known about the thermodynamics of mixed metal binding complexes (i.e., heterogeneous ion complexes), which limits the ability to accurately predict separation performance for a given metal ion mixture. In this paper, we employ the law of mass action to establish a theory of perfect cooperativity for LanM-REE complexation at the two highest-affinity binding sites. The theory is then used to derive an equation that explains the nonintuitive REE binding behavior of LanM, where separation factors for binary pairs of ions vary widely based on the ratio of ions in the aqueous phase, a phenomenon that is distinct from single-ion-binding chemical chelators. We then experimentally validate this theory and perform the first quantitative characterization of LanM complexation with heterogeneous ion pairs using resin-immobilized LanM. Importantly, the resulting homogeneous and heterogeneous constants enable accurate prediction of the equilibrium state of LanM in the presence of mixtures of up to 10 REEs, confirming that the perfect cooperativity model is an accurate mechanistic description of REE complexation by LanM. We further employ the model to simulate separation performance over a range of homogeneous and heterogeneous binding constants, revealing important insights into how mixed binding differentially impacts REE separations based on the relative positioning of the ion pairs within the lanthanide series. In addition to informing REE separation process optimization, these results provide mathematical and experimental insight into competition dynamics in other ubiquitous and medically relevant, cooperative binding proteins, such as calmodulin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Induced Polarization of Clayey Rocks and Soils: Non‐Linear Complex Conductivity Models

Abstract The past decades have witnessed the increased applications of induced polarization (IP) method in the critical zone studies with ubiquitous clay minerals. Although IP outperforms traditional electrical and electromagnetic methods through its unique ability to measure quadrature conductivity, the nonlinearity that quadrature conductivity behaves with salinities and frequencies greatly tortures IP practitioners, as (a) salinity‐dependency makes the quadrature conductivity a varyingly unstable parameter to quantitatively estimate hydraulic properties and clay content; (b) frequency‐dependent Cole‐Cole and Debye/Warburg decomposition models, although mathematically sound, physically mingle the properties of pore water and clay minerals and are empirical in nature. From basic principles, we demonstrate that quadrature conductivity remains a hybrid property involving both clay and water, and develop relevant models to distinguish them. Our models are validated by theories, experiments, simulations, and comparisons, all of which proclaim considerable advantages over previous models and offer the prospect of quantitative applications.

58 GEOSCIENCES↗