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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Computational Advances in Ionic Liquid Applications for Green Chemistry: A Critical Review of Lignin Processing and Machine Learning Approaches

The valorization and dissolution of lignin using ionic liquids (ILs) is critical for developing sustainable biorefineries and a circular bioeconomy. This review aims to critically assess the current state of computational and machine learning methods for understanding and optimizing IL-based lignin dissolution and valorization processes reported since 2022. The paper examines various computational approaches, from quantum chemistry to machine learning, highlighting their strengths, limitations, and recent advances in predicting and optimizing lignin-IL interactions. Key themes include the challenges in accurately modeling lignin’s complex structure, the development of efficient screening methodologies for ionic liquids to enhance lignin dissolution and valorization processes, and the integration of machine learning with quantum calculations. These computational advances will drive progress in IL-based lignin valorization by providing deeper molecular-level insights and facilitating the rapid screening of novel IL-lignin systems.

09 BIOMASS FUELS↗
DOE OSTI2024

Assessment of the Effect of Deleting the African Swine Fever Virus Gene R298L on Virus Replication and Virulence of the Georgia2010 Isolate

African swine fever (ASF) is a lethal disease of domestic pigs that is currently challenging swine production in large areas of Eurasia. The causative agent, ASF virus (ASFV), is a large, double-stranded and structurally complex virus. The ASFV genome encodes for more than 160 proteins; however, the functions of most of these proteins are still in the process of being characterized. The ASF gene R298L, which has previously been characterized as able to encode a functional serine protein kinase, is expressed late in the virus infection cycle and may be part of the virus particle. There is no description of the importance of the R298L gene in basic virus functions such as replication or virulence in the natural host. Based on its evolution, it is proposed that there are four different phenotypes of R298L of ASFV in nature, which may have potential implications for R298L functionality. We report here that a recombinant virus lacking the R298L gene in the Georgia 2010 isolate, ASFV-G-∆R298L, does not exhibit significant changes in its replication in primary cultures of swine macrophages. In addition, when experimentally inoculated in pigs, ASFV-G-∆R298L induced a fatal form of the disease similar to that caused by the parental virulent ASFV-G. Therefore, deletion of R298L does not significantly affect virus replication and virulence in domestic pigs of the ASFV Georgia 2010 isolate.

Virology↗
DOE OSTI2025

Deletion of the African Swine Fever Virus Gen I196L in the Georgia2010 Isolate Genome Does Not Affect Virus Replication or Virulence in Domestic Pigs

African swine fever (ASF) is a lethal disease of domestic pigs that is currently challenging swine production in large areas of Eurasia and the Caribbean. The causative agent, ASF virus (ASFV), is a large, double-stranded, and structurally complex virus. The ASFV genome encodes for more than 160 proteins; however, the functions of most of them are still in the process of being characterized. Recently, ASFV gene I196L has been reported as being critically involved in disease production in domestic pigs. We report here that a recombinant virus derived from the Georgia 2010 isolate (ASFV-G) lacking the I196L gene, ASFV-G-∆I196L, had the same ability to replicate in primary cultures of swine macrophage and, when experimentally inoculated in pigs, produced a fatal form of the disease similar to that caused by the parental virulent ASFV-G. Therefore, deletion of the I196L gene does not significantly affect virus replication and virulence in domestic pigs of the ASFV Georgia 2010 isolate.

Virology↗
DOE OSTI2024

Physical Yukawa couplings in heterotic string compactifications

One of the challenges of heterotic compactification on a CalabiYau threefold is to determine the physical (27) 3 Yukawa couplings of the resulting four-dimensional $\mathcal{N}$ = 1 theory. In general, the calculation necessitates knowledge of the Ricci-flat metric. However, in the standard embedding, which references the tangent bundle, we can compute normalized Yukawa couplings from the Weil-Petersson metric on the moduli space of complex structure deformations of the Calabi-Yau manifold. In various examples (the Fermat quintic, the intersection of two cubics in $\mathbb{P}$ 5 , and the TianYau manifold), we calculate the normalized Yukawa couplings for (2,1)-forms using the Weil-Petersson metric obtained from the Kodaira-Spencer map. In cases where $h^{1,1}$ = 1 , this is compared to a complementary calculation based on performing period integrals. A third expression for the normalized Yukawa couplings is obtained from a machine learned approximate Ricci-flat metric making use of explicit harmonic representatives. Finally, the excellent agreement between the different approaches opens the door to precision string phenomenology.

Butbaia, Giorgi↗
DOE OSTI2025

Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations

Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale mol­ecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.

X-ray imaging↗
DOE OSTI2024

Pnictogen Bonding at the Core of a Carbene-Stiborane-Gold Complex: Impact on Structure and Reactivity

Our interest in the design of ambiphilic ligands and their coordination to gold has led us to synthesize an indazol-3-ylidene gold chloride complex functionalized at the 4-position of the indazole backbone by a stibine functionality. The antimony center of this new complex cleanly reacts with o-chloranil to afford the corresponding stiborane derivative. Structural analysis indicates that the stiborane coordination environment is best described as a distorted square pyramid whose open face is oriented toward the gold center, allowing for the formation of a long donor–acceptor, or pnictogen, Au → Sb bonding interaction. The presence of this interaction, which has been probed computationally, is also manifested in the enhanced catalytic activity of this complex in the cyclization of N-propargyl-4-fluorobenzamide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structural and Electronic Complexities of a Sulfur‐Bridged Di‐Iron Complex Composed of Mono‐ and Di‐Nitrosyl Units

The delocalized, thermodynamically stable cation, [(N 2 S 2 )Fe(NO)•Fe(NO) 2 ] + , an adduct of mono-nitrosyl and dinitrosyl iron units, is analyzed to address the unusual stability of the sulfur-bridged diiron complex in its three overall redox levels, +, 0, and −. X-ray diffraction and myriad spectroscopic techniques probe products of sequential electron uptake in the corresponding neutral and anionic species. Conundrums include unified blueshifts of the overall 3-band, ν(NO), pattern with added electrons. One-electron reduction changes the anti-ferromagnetically coupled, S = 0, cationic diiron species to the neutral analog, S = ½, with unpaired spin mainly localized on the MNIU, which decreases its ∠Fe–N–O angle by 10 degrees in response to the extra electron density. Subsequent reduction to the anionic species, S = 1, involves a major geometric change at the MNIU, which moves the Fe in {Fe(NO)} 8 out of the N 2 S 2 plane. Site-specific 15 N labeling of nitrosyl in the MNIU confirms the IR analysis and shows rapid NO exchange between the MNIU/DNIU (mono-nitrosyl iron unit/dinitrosyl iron unit) pairs during its synthesis at RT. Mössbauer spectroscopy, S K-edge XAS, and molecular orbital calculations confirm the ability of NO and the versatility of sulfur bridges to buffer and distribute electrons, a key to their major importance in metalloenzymes.

DNIC↗
DOE OSTI2025

Advancing the Performance of Lithium-Rich Oxides in Cooperation with Inherent Complexities: Engineering Domain Structure

The nanodomain structure of lithium- and manganese-rich, composite cathode materials has been systematically altered through synthesis conditions while keeping larger-scale morphological differences to a minimum. Clear changes in electrochemical performance across the samples studied are observed, especially with respect to the anomalous impedance at low states-of-charge. Atomic-scale modeling, coupled to electrochemical measurements and physical characterization, reveals the local consequences of the high-voltage activation charge process as a function of specific domain structures. Furthermore, the results explain the influence of different postactivation structures on the insertion of Li-ions and the associated impedance during discharge. This work adds to our series of studies on lithium- and manganese-rich oxides, demonstrating that the inherent performance of LMRs can be greatly enhanced through rational, highly controlled synthetic strategies based on an understanding of synthesis–structure–property relationships across length scales.

25 ENERGY STORAGE↗
DOE OSTI2024

The hierarchical structure of organic mixed ionic–electronic conductors and its evolution in water

Polymeric organic mixed ionic–electronic conductors underpin several technologies in which their electrochemical properties are desirable. These properties, however, depend on the microstructure that develops in their aqueous operational environment. We investigated the structure of a model organic mixed ionic–electronic conductor across multiple length scales using cryogenic four-dimensional scanning transmission electron microscopy in both its dry and hydrated states. Four-dimensional scanning transmission electron microscopy allows us to identify the prevalent defects in the polymer crystalline regions and to analyse the liquid crystalline nature of the polymer. The orientation maps of the dry and hydrated polymers show that swelling-induced disorder is mostly localized in discrete regions, thereby largely preserving the liquid crystalline order. Therefore, the liquid crystalline mesostructure makes electronic transport robust to electrolyte ingress. Furthermore, this study demonstrates that cryogenic four-dimensional scanning transmission electron microscopy provides multiscale structural insights into complex, hierarchical structures such as polymeric organic mixed ionic–electronic conductors, even in their hydrated operating state.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗
DOE OSTI2026

ODIN: Characterizing the Three-dimensional Structure of Two Protocluster Complexes at z = 3.1

We present a detailed study of the 3D morphology of two extended associations of multiple protoclusters at z = 3.1. These protocluster "complexes," designated COSMOS-z3.1-A and COSMOS-z3.1-C, are the most prominent overdensities of z = 3.1 Lyα emitters (LAEs) identified in the COSMOS field by the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey. These protocluster complexes have been followed up with extensive spectroscopy from Keck, Gemini, and DESI. Using a probabilistic method that combines photometrically selected and spectroscopically confirmed LAEs, we reconstruct the 3D structure of these complexes on scales of ≈50 cMpc. We validate our reconstruction method using the IllustrisTNG300-1 cosmological hydrodynamical simulation and show that it consistently outperforms approaches relying solely on spectroscopic data. The resulting 3D maps reveal that both complexes are irregular and elongated along a single axis, emphasizing the impact of sightline on our perception of structure morphology. The complexes consist of multiple density peaks, 10 in COSMOS-z3.1-A and 4 in COSMOS-z3.1-C. The former is confirmed to be a proto-supercluster, similar to Hyperion at z = 2.4 but observed at an even earlier epoch. Multiple "tails" connected to the cores of the density peaks are seen, likely representing cosmic filaments feeding into these extremely overdense regions. The 3D reconstructions further provide strong evidence that Lyα blobs preferentially reside in the outskirts of the highest density regions. Descendant mass estimates of the density peaks suggest that COSMOS-z3.1-A and COSMOS-z3.1-C will evolve to become ultramassive structures by z = 0, with total masses log ( M / M ,⊙ ,) ≳ 15.3 , exceeding that of Coma.

Ramakrishnan, Vandana [Purdue U., West Lafayette] ↗
DOE OSTI2024

Designing multicomponent hydrides with potential high T c superconductivity

While hydrogen-rich materials have been demonstrated to exhibit high T c superconductivity at high pressures, there is an ongoing search for ternary, quaternary, and more chemically complex hydrides that achieve such high critical temperatures at much lower pressures. First-principles searches are impeded by the computational complexity of solving the Eliashberg equations for large, complex crystal structures. Here, we adopt a simplified approach using electronic indicators previously established to be correlated with superconductivity in hydrides. This is used to study complex hydride structures, which are predicted to exhibit promisingly high critical temperatures for superconductivity. In particular, we propose three classes of hydrides inspired by the Fm$\overline{3}$ m RH 3 structures that exhibit strong hydrogen network connectivity, as defined through the electron localization function. The first class [RH 11 X 3 Y] is based on a Pm$\overline{3}$m structure showing moderately high T c , where the T c estimate from electronic properties is compared with direct Eliashberg calculations and found to be surprisingly accurate. The second class of structures [(RH 11 ) 2 X 6 YZ] improves on this with promisingly high density of states with dominant hydrogen character at the Fermi energy, typically enhancing T c . The third class [(R 1 H 11 )(R 2 H 11 )X 6 YZ] improves the strong hydrogen network connectivity by introducing anisotropy in the hydrogen network through a specific doping pattern. These design principles and associated model structures provide flexibility to optimize both T c and the structural stability of complex hydrides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Rare Earth Element-Induced Condensation of the Block V of the Repeats-in-Toxin Domain from CyaA from Bordetella pertussis for Separations

Rare earth elements (REEs) are critical for the development of a range of new technologies. However, the current industrial separation processes of these metals from natural sources, recycled materials, and industrial effluents involve the large consumption of organic solvents, resulting in a sizable environmental footprint. We aim to exploit the high affinity of the block V peptide of the repeats-in-toxin (RTX) domain of the adenylate cyclase protein from Bordetella pertussis for the separation of REEs. This peptide selectively binds with lanthanide (Ln) cations and can undergo Ln-induced phase separation, which can be used in bioseparation processes. Here, we evaluated the self-assembling structures of complexes of the RTX domain peptide folded in the presence of Ln 3+ cations. Size distribution and surface potential measurements of complexes were taken to understand the Ln-induced changes in the complexed peptide. Transmission electron microscopy imaging was used to explore the structures of complexes, while anomalous small-angle X-ray scattering measurements were used to determine the distribution of Ln 3+ ions within the protein-based macrostructures. In the presence of excess Ln 3+ , we observed the formation of coral-like cylindrical structures comprised of Ln 3+ -RTX complexes, with approximately eight trivalent metals per peptide within the nanosized assemblies. These findings provide new insights into the structural organization of assembled RTX domains and their ability to coordinate with REEs, forming nanosized, metal-rich structures that naturally condense, providing a proof-of-concept for protein-based separation processes of these critical materials.

chemical structure↗
DOE OSTI2025

Delineating the Effects of Counterions on the Structural and Vibrational Properties of U(IV) Lindqvist Polyoxometalate Complexes

Herein we conducted a full investigation into the fundamental structural and vibrational properties of uranium(IV) Peacock−Weakley-type lacunary Lindqvist (W 10 ) polyoxometalate (POM) complexes. We recently demonstrated the importance of the secondary lattice elements in tuning the distortion of the D 4d symmetry in W 10 POM complexes, and here, we synthesized eight UW 10 complexes with different alkali metal counterions and evaluated how the composition and packing of counterion species affected complex structural and vibrational properties. Single-crystal X-ray diffraction analysis on complexes 1−8 revealed changes in structural distortion parameters as a function of differences in counterion configurations, while far-infrared and Raman spectra for 1−8 also demonstrated that vibrational mode frequencies were sensitive to changes in counterion composition and packing. To more effectively compare different counterion configurations, we developed counterion effective ionic radius (eIR) as a new structural parameter, and comparisons between structural distortion parameters and eIR values strongly suggested that modulation by the secondary lattice elements can affect structural and vibrational manifolds within POM complexes. Partial least squares (PLS) analysis was used to quantitatively evaluate correlations observed within this investigation, and PLS statistical models showed a strong correlation between counterion eIR and both structural distortion parameters and vibrational mode frequencies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

CASM Monte Carlo: Calculations of the thermodynamic and kinetic properties of complex multicomponent crystals

Monte Carlo techniques play a central role in statistical mechanics approaches that connect macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo techniques for the study of multicomponent crystalline materials within the Clusters Approach to Statistical Mechanics (CASM) software suite, and demonstrates their use in model systems to calculate free energies and kinetic coefficients, study phase transitions, and construct phase diagrams from first principles. Many crystal structures are complex, with multiple sublattices occupied by differing sets of chemical species, along with the presence of vacancies or interstitial species. This imposes constraints on concentration variables, the form of thermodynamic potentials, and the values of kinetic transport coefficients. The framework used by CASM to formulate thermodynamic potentials and kinetic transport coefficients accounting for arbitrarily complex crystal structures is presented and demonstrated with examples of increasing complexity. Additionally, an overview of the capabilities of the CASM software specific to Monte Carlo methods is given, and a new CASM software package is introduced, casm-flow, which helps automate the setup, submission, management, and analysis of Monte Carlo simulations.

Cluster expansion↗
DOE OSTI2025

Structure and ultrafast dynamics of tri-nuclear Ag-/Tl–Pt 2 POP 4 complexes in solution

The energetics and dynamics of ion assembly in solution has broad influence in nanomaterials and inorganic synthesis. To investigate the fundamental processes involved, we present a time-resolved x-ray solution scattering (TR-XSS) study of the trinuclear silver and thallium complexes of the diplatinum ion PtPOP [Pt 2 (H 2 P 2 O 5 )$_4^{4−}$] in aqueous solution. These complexes, their structural properties, and their electronic structure are not well understood and afford a unique opportunity to study the metal–metal bond formation that influences molecular and material assembly in solution. We present model-independent analysis of the observed dynamics as well as an analysis incorporating time-resolved structural refinements of key bond lengths with $<$100 fs time resolution. We find that upon photoexcitation, the Pt atoms contract ∼0.25 Å toward the center of both the Ag- and the Tl-PtPOP complexes, as previously observed for the PtPOP anion. For the AgPtPOP system, an ultrafast Ag-Pt bond expansion of ∼0.2 Å is observed, whereas in contrast, the TlPtPOP system exhibits a Tl-Pt bond contraction of ∼0.3 Å upon photoexcitation. For both complexes, the change in electronic state leads to coherent (“wave-packet”) oscillations along the metal–Pt coordinates. Based on these structural dynamics, we propose an electronic structure model that describes the metal–metal bonding behavior in both the ground and excited state for both complexes.

Lenzen, Philipp [Technical Univ. of Denmark, Lyngb↗
DOE OSTI2025

Local rare-earth dopant structure in a complex-oxide/semiconductor heterojunction: Molecular beam epitaxy grown Yb-doped SrTiO3 on Si(001)

We have investigated the structural and electronic properties of Yb-doped SrTiO3/Si(001) grown by molecular beam epitaxy. Other rare-earth donor dopants that result in n-type conductivity typically substitute for Sr at the A-sites in the perovskite lattice. In contrast, Yb has been found to substitute predominantly for Ti at the perovskite B-sites based on data from atomically resolved scanning transmission electron microscopy and spectroscopy, as well as extended x-ray absorption fine structure. Yb exhibits two distinct charge states as determined by x-ray absorption spectroscopy and associated modeling, +2.7 and +2.1. These aliovalent substitutional dopants are compensated by donor electrons from oxygen vacancies that form during epitaxial film growth. An atom beam flux mismatch was present during film depositions because it was assumed that Yb would occupy A-sites, leading to a flux matching formula given by Yb + Sr = Ti. However, the formation of YbTi rather than YbSr results in Sr vacancies and extraneous (i.e. non-lattice) Ti atoms in the films, or on the film surfaces. The presence of these defects, together with oxygen vacancies, leads to deep-level electron traps that were detected by resonant photoemission and much higher sheet resistance than that associated with, for instance, La-doped films.

Chambers, Scott A. (ORCID:000000025415043X)↗