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DOE OSTI2025

LATTE: open-source, high-performance traveltime computation, tomography and source location in acoustic and elastic media

Traveltime-based tomography and source location are fundamental approaches for imaging subsurface structures and understanding the spatiotemporal distribution of seismicity from local to global scales. We present an open-source, high-performance framework integrating eikonal equation solvers and adjoint-state theory for traveltime computation, velocity tomography, source location and joint tomography-location in 2-D/3-D acoustic and elastic media. We introduce novel regularization schemes based on total generalized p-variation, structural similarity and multitask machine learning to enhance the fidelity and interpretability of inverted models and source locations. Key features of our implementation also include the ability to leverage both absolute-difference and double-difference traveltime misfits for high-fidelity velocity tomography and source parameter estimation; support for traveltime computation and inversion in diverse 2-D/3-D scenarios with arbitrary source and receiver distributions; and a perturbation-based optimal step-size estimation method to reduce computational costs. In addition, our implementation employs shared-memory and distributed-memory parallelization to provide an efficient solution for traveltime computation, tomography, and source location. In conclusion, we validate the efficacy and accuracy of our approach through multiple synthetic data examples.

58 GEOSCIENCES↗

DOE OSTI2024

Cascade CO 2 Insertion in Carbanion Ionic Liquids Driven by Structure Rearrangement

The CO 2 chemisorption in state-of-the-art sorbents based on oxide/hydroxide/amine moieties is driven by strong chemical bonding formation in the carbonate/bicarbonate/carbamate products, which in turn leads to high energy input in sorbent regeneration. In addition, the CO 2 uptake capacity was limited by the active sites’ utilization efficiency, with each active site incorporating one CO 2 molecule or less. In this work, a new concept and generation of sorbent was developed to achieve cascade insertion of multiple CO 2 molecules by leveraging structure rearrangement as the driving force, leading to in situ generation of extra CO 2 -binding sites and significantly reduced energy input for CO 2 release. The designed ionic liquids (ILs) containing carbanions with conjugated and asymmetric structure, deprotonated (methylsulfonyl)acetonitrile ([MSA]) anion, allowed the cascade insertion of two CO 2 molecules via consecutive C–C and O–C bond formations. The proton transfer and structure rearrangement of the carboxylic acid intermediates played critical roles in stabilizing the first integrated CO 2 and generating extra electron-rich oxygen sites for the insertion of the second CO 2 . The structure variation and reaction pathway were confirmed by operando spectroscopy, magnetic resonance spectroscopy (NMR), mass spectroscopy, and computational chemistry. The energy input in sorbent regeneration could be further reduced by harnessing the phase-changing behavior of the carbanion salts in ether solutions upon reacting with CO 2 , avoiding the energy consumption in heating the solvent. In conclusion, the fundamental insights obtained herein provide a promising approach to greatly improve the CO 2 sorption performance via sophisticated molecular-scale structural engineering of the sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Machine learning bridges local static structure with multiple properties in metallic glasses

A long-standing challenge in the metallic glass (MG) community has been how to quantitatively gauge the influence of the intricate local packing environment on the response (such as the propensity for atomic rearrangement) of the atomic configuration to external stimuli. Here we establish this structure–property relation by representing the complex amorphous structure using a single, flexibility-orientated structural quantity. This structural flexibility (SF) couples to a bona fide structural representation, the pair distribution function (PDF) of individual atoms, through a weighting function that reflects what matters in the static atomic configuration to dynamic responses. Machine learning is used, employing microscopic flexibility volume as the supervisory signal, to establish via direct regression an optimized weighting vector, which is proven robust for all quenching rates, deformation conditions, and different compositions in a given (e.g., Cu x Zr 100-x ) alloy system. Additionally, the SF is evaluated solely from the particle positions (PDF), for any structure variation, from the atomic scale up to sample average. Strong correlations are demonstrated between SF and a broad range of properties, including vibrational, diffusional, as well as elastic and plastic relaxation responses.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Elucidating the mechanisms of enhanced lignin bioconversion by an alkali sterilization strategy

Biological lignin valorization represents an emerging green approach to upgrade lignin for sustainable and economic biorefineries. However, lignin generally exhibits poor water solubility and inhomogeneous distribution in an aqueous medium, significantly limiting its bioconversion efficiency. Herein, we develop a novel alkali sterilization strategy to effectively enhance the dispersion and fermentation performance of lignin substrates. The colloidal particle size and molecular structure variations of lignin during the sterilization were thoroughly investigated to reveal the mechanisms of enhanced fermentation performance. Results showed that alkali sterilization achieved a completely aseptic effect when mixing lignin medium at an initial pH of 12.7 for 24 h. Dynamic light scattering (DLS) analysis demonstrated that the hydrodynamic volume of colloidal lignin particles decreased by 96.3% by alkali sterilization compared with the conventional thermal sterilization. Moreover, lignin characterizations by nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography (GPC) suggested that alkali sterilization modified the lignin molecular structure by generating 50% more hydrophilic carboxyl groups, reducing the weight-average molecular weight (M w ) by 23.0%, and narrowing the molar-mass dispersity (D M ) by 23.8%. The generation of lignin substrates with more uniform distribution and lower molecular weight improved Rhodococcus opacus PD630 cell growth and metabolism. Microbial cell amount, lignin degradation, and lipid production in alkali sterilized medium increased by 309%, 30.3%, and 48.3%, respectively, compared to those in thermally sterilized medium. These results clearly demonstrated that alkali sterilization dramatically improved the lignin bioconversion performance. Furthermore, this work presents a facile and effective sterilization strategy to overcome inhomogeneous lignin distribution in aqueous fermentation media, showing great potentials as a platform technique for promoting biological lignin valorization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Structure and properties of bottlebrush polyelectrolyte complexes

Abstract Structural variation of polyelectrolytes has been shown to play an important role in altering polyelectrolyte complex (PEC) properties in recent years. However, molecular‐level details such as polyelectrolyte architecture remain underdeveloped. Here, we use a combination of ring‐opening metathesis polymerization (ROMP), atom‐transfer radical polymerization (ATRP), and postpolymerization reactions to create densely branched bottlebrushes of poly(dimethylamino ethyl methcacrylate) and poly(tert‐butyl methacrylate) with high molecular weights (MDa), which we then convert into fully charged and densely branched bottlebrushes of poly(trimethylaminoethyl methacrylate) (PTMAEMA) and poly(methacrylic acid) (PAA). We investigate the structure and properties of bottlebrush polyelectrolyte complexes (BPECs) using optical microscopy, rheology, cryogenic transmission electron microscopy (Cryo‐TEM), and small‐angle X‐ray scattering (SAXS). Bottlebrush polyelectrolyte complexes are white solids, which exhibit gel‐like mechanical properties, which we attribute to sidechain interpenetration. Using a combination of Cryo‐TEM and SAXS, we are able to outline the structural development of BPECs, detailing how the network topology, sidechain conformation, and interdigitation spacing changes as a function of salt. Our results provide a foundation for further exploration of branched architectures within polyelectrolyte complexation.

Polymer Science↗

DOE OSTI2023

Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

Summary The fungal pathogen,Magnaporthe oryzae Triticumpathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzaestrains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole‐genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini‐chromosome. Genome assembly of a Zambian strain revealed that its mini‐chromosome was similar to the B71 mini‐chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini‐chromosomes have undergone marked diversification. The maintenance of the mini‐chromosome and rapid genomic changes suggest the mini‐chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.

Plant Sciences↗

DOE OSTI2021

Impacts of Initial Ca/P on Amorphous Calcium Phosphate

Amorphous calcium phosphate (ACP) is a metastable phase in the crystallization pathway of calcium phosphates. Understanding its chemical and structural properties could provide critical insights into biomineralization mechanisms. Of particular interest is the impact of the initial Ca/P on the structure of ACP. Further, the influence of Ca/P on the size, precipitate chemistry, and transformation of ACP is crucial to understanding the metastability of amorphous phosphates. In situ pair distribution function (PDF) analysis results 5 min after mixing show that the Ca-P bonding geometry varies from predominantly monodentate, to mixed monodentate and bidentate, to predominantly bidentate as Ca/P increases from 0.2 to 5.0. This relationship is consistent across a pH range of 6-11. Samples with only monodentate Ca-P geometries transform directly to hydroxylapatite, while samples some or all bidentate geometries form brushite. Regardless of the initial ratio, the Ca/P of precipitates is close to 1.0. In situ small-angle X-ray scattering shows particle size increases with increasing Ca/P. This is the first evidence of structural variations in ACP and is directly linked to system chemistry. Finally, synthesis of ACP with monodentate Ca-P geometries is a promising method to control the crystallization pathway to form hydroxylapatite at circumneutral pH without stabilizing ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Structure and Sulfur: Tuning the Viscoelastic and Surface Properties of Natural Keratin Fibers

Natural keratin fibers, such as wool, possess a complex hierarchical structure that governs their mechanical properties and surface energy. However, the extent to which these characteristics are influenced by combined contributions of structural variations (e.g., fiber diameter, intermediate filament (IF) packing) and chemical composition (e.g., disulfide bond density) remains poorly understood. In this study, we investigate wool fibers from five sheep breeds (Merino, Polwarth, Cheviot, Eider, and Devon) to elucidate how these factors influence viscoelasticity and surface interactions. Using a multimodal approach integrating interfacial and bulk characterization methods, including inverse gas chromatography (IGC), atomic force microscopy-infrared spectroscopy (AFM-IR), X-ray photoelectron spectroscopy (XPS), uniaxial tensile testing, and synchrotron small-angle X-ray scattering (SAXS), we show that the nanometer-thick 18-methyleicosanoic acid (18-MEA) layer is consistently present across all wool types and plays a key role in governing hydrophobicity and surface heterogeneity. A controlled isothermal treatment at 200 °C, designed to cleave disulfide bonds, results in a nearly 40% reduction in specific surface area across all fiber types, accompanied by a significant decrease in tensile strength and 80% reduction in elongation at break for Merino and Devon wool, but limited influence on the mechanical properties of Eider fibers. Furthermore, rate-dependent tensile testing within the elastic regime reveals distinct viscoelastic responses among the fiber types, suggesting that the sulfur-rich protein matrix surrounding IFs and its structure contribute actively to stress partitioning. Altogether, when combined with conclusions from SAXS measurements of IF spacing, our work offers compelling insights into the role of the keratin-associated protein (KAP) matrix in shaping wool fiber mechanics. Differences in mechanical behavior among wool types, despite similar IF spacing or sulfur content, highlight the importance of matrix composition and cross-linking density, suggesting that the molecular architecture of the KAP network may be a dominant factor in determining fiber performance.

X-ray scattering↗

DOE OSTI2022

Micro- to nano-scale areal heterogeneity in pore structure and mineral compositions of a sub-decimeter-sized Eagle Ford Shale

Mineral and organic matter compositions & pore structures of fine-grained shale influence reservoir properties. To improve the understanding of spatial heterogeneity in core-sized samples, methods of microscale X-ray fluorescence (μXRF) mapping, (ultra-) small-angle x-ray scattering [(U)SAXS] and wide-angle X-ray scattering (WAXS) have been used to determine elemental, pore-structure variations at scales up to ~10 cm on two samples prepared at circular and rectangular orientations from a piece of Eagle Ford Shale outcrop in South Texas, USA. In addition, thin section petrography and field emission-scanning electron microscopy observations, X-ray diffraction (XRD), total organic carbon, and pyrolysis were utilized to investigate the potential spatial heterogeneity of pore types, mineral and organic matter compositions for cm-sized samples at both orientations. Overall, the siliceous-carbonate mineral contents in these two samples (8 cm×8 cm×0.08 cm and 5 cm × 8 cm × 0.08 cm, in terms of width×length×thickness) of carbonate-rich Eagle Ford Shale vary between laminations at mm scales. For the circular sample, porosity and specific surface area (SSA) variations range from 0.82 to 3.04% and 1.51 to 14.1 m 2 /g, respectively. For the rectangular sample, values for porosity and SSA vary from 0.93 to 2.50% and 3.95 to 10.8 m 2 /g. By analyzing six selected sub-samples on each of two samples with (U)SAXS and XRD techniques, nm-sized pores are mainly interparticle ones in the higher calcite regions, where the porosity is also relatively lower, while the lower calcite regions consist of both interparticle and intraparticle pore types with higher porosity. Lastly, the μXRF and (U)SAXS mappings are combined to generate porosity distribution maps to provide more insights about sample heterogeneity related to the laminations and fractures at our observational scales.

58 GEOSCIENCES↗

DOE OSTI2025

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria

Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

PDB↗

DOE OSTI2025

Sub‐5 Ångstrom Porosity Tuning in Calixarene‐Derived Porous Liquids via Supramolecular Complexation Construction

Abstract Sub‐Ångstrom‐level porosity engineering, which is appealing in gas separations, has been demonstrated in solid carbon, polymer, and framework materials but rarely achieved in the liquid phase. In this work, a gas molecular sieving effect in the liquid phase at sub‐5 Ångstrom scale is created via sophisticated porosity tuning in calixarene‐derived porous liquids (PLs). Type II PLs are constructed via supramolecular complexation between the sodium salts of calixarene derivatives and crown ether solvents. The chemical structure variation and assembly behavior of the porous host upon PL construction are monitored by spectroscopy‐, X‐ray‐, and neutron‐scattering techniques. The presence of permanent porosity in calixarene‐derived PLs is verified by pressure swing gas uptake, altered CO 2 physisorption behavior, and molecular simulations. Sub‐5 Ångstrom porosity tuning within the PL phase is achieved by introducing bulky substituted groups on the benzene ring of the calixarene host, which then greatly affects the dynamic motion and transport behavior of CO 2 molecules and the Xe uptake performance. The approach being demonstrated in this work represents a promising pathway to tune and leverage the porosity effect for enhanced gas uptake capacity and selectivity in liquid sorbents.

Li, Errui [Department of Chemistry University of T↗

DOE OSTI2025

Sub-5 Ångstrom Porosity Tuning in Calixarene-Derived Porous Liquids via Supramolecular Complexation Construction

Sub-Ångstrom-level porosity engineering, which is appealing in gas separations, has been demonstrated in solid carbon, polymer, and framework materials but rarely achieved in the liquid phase. In this work, a gas molecular sieving effect in the liquid phase at sub-5 Ångstrom scale is created via sophisticated porosity tuning in calixarene-derived porous liquids (PLs). Type II PLs are constructed via supramolecular complexation between the sodium salts of calixarene derivatives and crown ether solvents. The chemical structure variation and assembly behavior of the porous host upon PL construction are monitored by spectroscopy-, X-ray-, and neutron-scattering techniques. The presence of permanent porosity in calixarene-derived PLs is verified by pressure swing gas uptake, altered CO 2 physisorption behavior, and molecular simulations. Sub-5 Ångstrom porosity tuning within the PL phase is achieved by introducing bulky substituted groups on the benzene ring of the calixarene host, which then greatly affects the dynamic motion and transport behavior of CO 2 molecules and the Xe uptake performance. Further, the approach being demonstrated in this work represents a promising pathway to tune and leverage the porosity effect for enhanced gas uptake capacity and selectivity in liquid sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Extending a 10‐node composite tetrahedral finite element for solid mechanics

Abstract We propose to extend the composite tetrahedral finite element first introduced by Thoutireddy et al. (2002) and recently reformulated by Ostien et al. (2016). We generalize the gradient operator and mass matrix to curved domains through analytical expressions weighted by subtetrahedra Jacobians. Optimal integration weights are constructed to increase the accuracy of Gaussian quadrature. We preserve the variational structure of the formulation through a new five‐field functional with additional, independent fields for the Jacobian and the pressure. This approach not only obviates volumetric locking but also yields symmetry. A deleterious soft mode, common to both the quadratic and composite tetrahedral element with constant pressure formulations is effectively stabilized through a novel convex energy penalty function. Numerous numerical examples spanning a patch test to the impact of a Taylor bar demonstrate the accuracy, robustness, and convergence of the extended composite tetrahedral element for application to structural metals.

Foulk III, James W.↗

DOE OSTI2021

In Operando Angle‐Resolved Photoemission Spectroscopy with Nanoscale Spatial Resolution: Spatial Mapping of the Electronic Structure of Twisted Bilayer Graphene

To pinpoint the electronic and structural mechanisms that affect intrinsic and extrinsic performance limits of 2D material devices, it is of critical importance to resolve the electronic properties on the mesoscopic length scale of such devices under operating conditions. Herein, angle‐resolved photoemission spectroscopy with nanoscale spatial resolution (nanoARPES) is used to map the quasiparticle electronic structure of a twisted bilayer graphene device. The dispersion and linewidth of the Dirac cones associated with top and bottom graphene layers are determined as a function of spatial position on the device under both static and operating conditions. The analysis reveals that microscopic rotational domains in the two graphene layers establish a range of twist angles from 9.8° to 12.7°. Application of current and electrostatic gating lead to strong electric fields with peak strengths of 0.75 V/μm at the rotational domain boundaries in the device. These proof‐of‐principle results demonstrate the potential of nanoARPES to link mesoscale structural variations with electronic states in operating device conditions and to disentangle such extrinsic factors from the intrinsic quasiparticle dispersion.

Majchrzak, Paulina↗

DOE OSTI2021

TUMME: Tsinghua University Minnesota Master Equation program

We report that TUMME is a program for assembling and solving master equations for gas-phase chemical kinetics based on chemically significant eigenmodes. TUMME has interfaces to the Gaussian, Polyrate, and/or MSTor output files that allow the master equation code to obtain the microcanonical flux coefficients needed for the coefficient matrix of the master equation. The flux coefficients for reactions with barriers can be calculated by multi-structural variational transition state theory with small-curvature tunneling (MS-VTST/SCT) or by simpler approximations to this such as conventional transition state theory without tunneling (also called RRKM theory). The flux coefficients for barrierless reactions are provided by a hard-sphere model. TUMME is written in double precision with Python 3; quadruple and octuple precision are also available for some subtasks in C++. The Python code can run in serial or parallel (MP or MPI), and the C++ code can run on a single processor or on multiple processors with OpenMP.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

A phase-field fracture formulation for generalized standard materials: The interplay between thermomechanics and damage

Accurately modeling fracture of ductile materials poses open challenges in the field of computational mechanics due to the multiphysics nature of their failure processes. Integrating the interplay between thermodynamics and damage into ductile fracture models is vital for predicting critical failure modes. Here, in this paper, we develop a versatile phase-field (PF) framework for modeling ductile fracture, taking into account finite-strain elasto-plasticity. The framework stems from a variational formulation of constitutive relations for generalized standard materials (GSMs), whose response is described by a Helmholtz free energy and a dissipation pseudo-potential. Its variational structure is based on a minimum principle for a functional that expresses the sum of power densities for reversible and irreversible processes. By minimizing this functional with a constraint on a von Mises yield function, we derive the evolution equation for the equivalent plastic strain and an associative flow rule. This constrained optimization problem is analytically solved for a wide class of thermo-viscoplasticity models. The key innovations of the current work include (i) a cubic plastic degradation function that accounts for a non-vanishing damage-dependent yield stress, (ii) closed-form expressions of the Helmholtz free energy and dissipation pseudo-potential for three thermo-viscoplasticity models, (iii) an extended Johnson–Cook plasticity model with a nonlinear hardening law, and (iv) a plastic work heat source that depends on the plastic degradation function and a variable Taylor–Quinney (TQ) coefficient. The capabilities of the proposed framework are tested with the aid of four ductile fracture problems, including the Sandia Fracture Challenge. In each of these problems, we examine the evolution of relevant field variables such as the PF order parameter, the equivalent plastic strain, the temperature, and the internal power dissipation density, in addition to the overall structural response quantified by the force–displacement curve. These numerical studies demonstrate that the proposed framework effectively represents ductile fracture, yielding computational results that exhibit good agreement with experimental data.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Inhibition of asphaltene aggregation using deep eutectic solvents: COSMO-RS calculations and experimental validation

Asphaltene precipitation/deposition adversely affects various oil and gas processes, such as oil recovery, transportation, and petroleum processing. The resulting increase in viscosity of crude oil decreases distillate yields creating unstable phase separation. Deep eutectic solvents (DESs) have recently gained interest as inhibitors of asphaltene aggregation. The goal of the present study is to derive the mechanism of inhibition of petroleum asphaltene aggregation by a novel screening of DESs. An archipelago-based chemical structure of asphaltene was adopted for performing quantum chemical calculations. The structure was used in the conductor-like screening model for real solvents (COSMO-RS) model to screen potential DESs for asphaltene precipitation. It was found that DESs containing thymol were the most promising of the 153 DES combinations screened. The COSMO-RS predictions were validated experimentally using solubility data of asphaltene in DESs. Among the studied DESs, thymol-diphenyl ether provided the highest solubility for asphaltene, which was further validated using the experimental and the COSMO-RS predicted data. In addition, to characterize the structural interactions between asphaltene and DESs, Fourier transform infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) measurements were performed. It was found that strong interaction between asphaltene and the DESs is responsible for the higher asphaltene dispersion. Finally, the present approach opens pathways to rationally design and understand the impact of structural variation of DESs based on their interactions with asphaltene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Enhanced Carbon Dioxide Capture Using a Mixed Amino Acid Salt Solution

This study investigated the carbon dioxide (CO 2 ) absorption and desorption performance of a mixed amino acid solution (containing glycine (G), alanine (A), proline (P), and lysine (L), GAPL). These four amino acids were intentionally selected to reflect the chemical and structural variations (pK a and steric hindrance of amino groups) of amino acids. The single cycle CO 2 capture experiment showed that the GAPL salt solution had 19% higher CO 2 absorption (0.91 mol CO 2 /mol amino acids) compared to the absorption calculated by adding the proportional capacities of G, A, P, and L (0.77 mol CO 2 /mol amino acids). 13 C NMR data delineated the effects of individual amino acids on carbamate and bicarbonate/carbonate formation and elucidated the distribution of captured CO 2 in the GAPL salt solution. The recirculation experiment concluded that the GAPL salt solution had much better CO 2 capture performance than the conventional monoethanolamine process. Less than 10% of the absorption and cyclic capacity of the GAPL salt solution was lost after ten cycles of CO 2 capture. Furthermore, this study demonstrated an approach that blended amino acid solutions can be tailored and designed as new, efficient reagents to massively capture CO 2 in a technically feasible, economically viable, and environmentally friendly manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗