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DOE OSTI2025

Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5

Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.

affinity-maturation↗

DOE OSTI2026

Experimental Characterization and Modeling of High Hole Mobility GeSn Quantum Wells: The Role of Alloy Disorder Scattering

Understanding mechanisms influencing electrical transport in material systems not only provides a scientific explanation for observed behavior but also offers insight into ways to enhance transport in devices. This study reports experimental hole mobility of 8 x 10 4 cm 2 V -1 s -1 in a Ge 0.92 Sn 0.08 , the highest recorded mobility for the GeSn system. A study of the material's quality is presented using structural and electrical characterization techniques, with transport data being supported by simulations using an extensive modeling framework. Quantum Hall measurements further indicate the material's high quality and potential spintronic applications, with extracted values of 0.0689$m$ 0 and 13.6 for the effective mass and effective g‐factor, respectively. It is observed that transport is limited by alloy disorder scattering at cryogenic temperatures. A comparative study between the presented structure and similar quantum well heterostructures revealed that the difference in hole mobilities is captured by a disparity in the reduced nominal alloy disorder scattering potential (Δ U alloy = 0.8 eV), that is lower than the value of a fully random alloy (Δ U alloy = 1.4–1.7 eV) potential. The difference in Δ U alloy suggests that heterostructures with similar geometries and alloy compositions can have different alloy disorder scattering, implying that an underlying mechanism, such as short‐range order, may be responsible and warrants further investigation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Influence of Rare Earth Ce Additions on Microstructure and Mechanical Properties of Experimental Pipeline Steels

Herein, the effect of Ce additions ranging from 57 to 263 ppm is evaluated for an experimental pipeline steel. Compared to the Ce-free steel, progressive Ce additions result in a slightly refined microstructure, significantly improve transverse impact properties, and slightly increase strength. All these observations can be attributed to the gradual transformation of Mn sulfide and Mn–Si–Al oxide inclusions to Ce-containing oxide/sulfides. In particular, the inclusions consist exclusively of sub-5 μm spherical Ce 2 O 2 S particles upon near-stoichiometric additions of Ce, considering the oxygen and sulfur impurity level of the steel. In conclusion, the results suggest that Ce is a potentially promising alloying addition for next-generation pipeline steels by replacing overtly deleterious inclusions with potentially beneficial ones.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Toward Real-Time Analysis of Synchrotron Micro-Tomography Data: Accelerating Experimental Workflows with AI and HPC

ynchrotron light sources are routinely used to perform imaging experiments. In this paper, we review the relevant computational stages, identify bottlenecks, and highlight future opportunities to streamline data acquisition for experimental microscopy workflows. We demonstrate our preliminary exploration with an end-to-end scientific workflow on Summit based on micro-computed tomography data. Computational elements include: 1) reconstruction of volumetric image data; 2) denoising with deep neural networks; and 3) non-local means based segmentation and quantitative analysis.

Mcclure, James↗

DOE OSTI2022

A Survey on Sustainable Software Ecosystems to Support Experimental and Observational Science at Oak Ridge National Laboratory

In the search for a sustainable approach for software ecosystems that supports experimental and observational science (EOS) across Oak Ridge National Laboratory (ORNL), we conducted a survey to understand the current and future landscape of EOS software and data. This paper describes the survey design we used to identify significant areas of interest, gaps, and potential opportunities, followed by a discussion on the obtained responses. The survey formulates questions about project demographics, technical approach, and skills required for the present and the next five years. The study was conducted among 38 ORNL participants between June and July of 2021 and followed the required guidelines for human subjects training. We plan to use the collected information to help guide a vision for sustainable, community-based, and reusable scientific software ecosystems that need to adapt effectively to: i) the evolving landscape of heterogeneous hardware in the next generation of instruments and computing (e.g. edge, distributed, accelerators), and ii) data management requirements for data-driven science using artificial intelligence.

Bernholdt, David↗

DOE OSTI2023

Experimental Simulations of Field-Induced Mechanical Abuse Conditions

Mechanical failure of cell components is an important component to understanding safety outcomes for batteries subjected to external loading. Several key parameters governing the mechanical response at the component to the module level are discussed in this chapter. Specifically, nuances associated with experimental measurements of these properties – including development of test methods, fixturing the test articles, ways to minimize errors in measurements, and improving the repeatability of some of these experiments – are examined closely.

Torres-castro, Loraine↗

DOE OSTI2022

A combined experimental and numerical approach that eliminates the non-uniqueness associated with the Johnson-Cook parameters obtained using inverse methods

Abstract Johnson-Cook constitutive model is a commonly used material model for machining simulations. The model includes five parameters that capture the initial yield stress, strain-hardening, strain-rate hardening, and thermal softening behavior of the material. These parameters are difficult to determine using experiments since the conditions observed during machining (such as high strain-rates of the order of $$10^5$$ 10 5 /sec - $$10^6$$ 10 6 /sec) are challenging to recreate in the laboratory. To address this problem, several researchers have recently proposed inverse approaches where a combination of experiments and analytical models are used to predict the Johnson-Cook parameters. The errors between the measured cutting forces, chip thicknesses and temperatures and those predicted by analytical models are minimized and the parameters are determined. In this work, it is shown that only two of the five Johnson-Cook parameters can be determined uniquely using inverse approaches. Two different algorithms, namely, Adaptive Memory Programming for Global Optimization (AMPGO) and Particle Swarm Optimization (PSO), are used for this purpose. The extended Oxley’s model is used as the analytical tool for optimization. For determining a parameter’s value, a large range for each parameter is provided as an input to the algorithms. The algorithms converge to several different sets of values for the five Johnson-Cook parameters when all the five parameters are considered as unknown in the optimization algorithm. All of these sets, however, yield the same chip shape and cutting forces in FEM simulations. Further analyses show that only the strain-rate and thermal softening parameters can be determined uniquely and the three parameters present in the strain-hardening term of the Johnson-Cook model cannot be determined uniquely using the inverse method. A combined experimental and numerical approach is proposed to eliminate this determine all parameters uniquely.

42 ENGINEERING↗

DOE OSTI2025

Cohort-based pan-cancer analysis and experimental studies reveal ISG15 gene as a novel biomarker for prognosis and immunotherapy efficacy prediction

Abstract ISG15, an interferon-stimulated ubiquitin-like protein, plays a multifaceted role in tumorigenesis and immune regulation. This study comprehensively evaluates ISG15 as a prognostic biomarker and predictor of immunotherapy response through pan-cancer bioinformatics analysis and experimental validation. By integrating multiomics data from TCGA, GEO, and clinical cohorts, we found that ISG15 is significantly overexpressed in multiple cancers and generally correlates with poor prognosis. Elevated ISG15 expression is associated with increased immune checkpoint gene expression, particularly PD-L1, and immune infiltration, notably M2-like tumor-associated macrophages. Immunohistochemistry and multiplexed immunofluorescence confirmed a strong positive correlation between ISG15, PD-L1, and M2-TAM infiltration in lung and gastric cancer samples. Functional analysis at the single-cell level revealed significant associations between ISG15 and tumor proliferation, angiogenesis, and immune suppression. Immunotherapy cohort analysis demonstrated that tumors with high ISG15 expression responded favorably to PD-L1 inhibitors but exhibited resistance to CTLA-4 blockade, findings further validated in lung cancer patients receiving anti-PD-1 therapy. These results suggest that ISG15 is a promising biomarker for prognosis and immunotherapy response prediction across cancers. Its integration into clinical decision-making may enhance personalized treatment strategies, improve immunotherapy outcomes, and provide new insights into the tumor immune microenvironment, cancer progression, and potential therapeutic targets for future drug development.

Immunology↗

DOE OSTI2022

Effect of second Si–O vibrational overtones/combinations on quantifying water in silicate and silica minerals using infrared spectroscopy, and an experimental method for its removal

Infrared spectroscopy (IR) is the most widely used analytical tool to quantify trace water in silicate and silica minerals. A prerequisite for highly accurate IR measurements of trace water is a good understanding of the effect of the second Si–O vibrational overtones/combination bands (2nd Si–O VOCBs) on the water peaks. Silicate and silica minerals can be divided as isolated (Q 0 ), paired (Q 1 ), ring (Q 2 ), chain (Q 1 or Q 2 ), sheet (Q 3 ) and framework (Q 4 ) structures according to the polymerization of their SiO 4 tetrahedral units, and the 2nd Si–O VOCBs of these different structural types attain different vibrational features which are expected to affect the water peaks to different extents. Here, we selected olivine (Q 0 ) and α-quartz (Q 4 ) as two endmember-like structural examples, performed extensive IR measurements on both pristine and heat-treated thin sections prepared for these two minerals, and explored the vibrational features of the 2nd Si–O VOCBs. In this work, we have found that the 2nd Si–O VOCBs are well separated from the water peaks in olivine, but severely overlap with the water peaks in α-quartz, confirming the different roles that the 2nd Si–O VOCBs play in quantifying trace water in silicate and silica minerals with different structural polymerizations. To remove the influence of the 2nd Si–O VOCBs (or any other species rather than water), an experimental protocol has been successfully developed, as approved by some fundamental equations and verified by the data of α-quartz in the literature. This development should lead to significant accuracy improvement in quantifying trace amounts of water in Earth and planetary materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Thermo-mechanical modeling and experimental validation for multilayered metallic microstructures

This paper presents thermo-mechanical modeling on multilayered metallic microstructures consisting of two bilayers that enable 3D deployment once being Joule heated. Additionally, a representative design of such microstructures, as well as their working principle is introduced. Furthermore, a mathematical model is derived using Euler–Bernoulli beam theory, and analytical solutions describing out-of-plane displacement of the multilayered microstructures when uniformly heated, which is validated by finite element analysis. Parametric analysis on thermal load and dimensional change of beam shows a good agreement between the analytical solutions and results given by finite element analysis. The phases of the near-equiatomic NiTi layer are analyzed by EDS and XRD, which prove to be austenite during the Joule heating process. The mechanical properties of austenite NiTi are incorporated into the analytical solutions that provides a good estimation of 3D deployment of microstructures made of NiTi and aluminum. The experimental results provide an approximately 7 µm out-of-plane deployment by applying a uniform temperature increase of 132 K, and parametric analysis on the dimension of top aluminum beam offers another promising approach to larger 3D deployment. The proposed mathematical model provides an efficient tool for predicting the out-of-plane deployment of such multilayered microstructures.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Contrasting stream nitrate and sulfate response to recovery from experimental watershed acidification

Improvements in air quality have led to ecosystem recovery from acidic deposition, but the mechanisms and trajectories of this recovery are not fully understood. Here, we present long-term stream response and recovery data for paired watersheds at the Bear Brook Watershed in Maine (BBWM) during declining ambient SO 4 and NO 3 in precipitation. East Bear (EB) received ambient deposition from 1989 to 2018; West Bear (WB) received artificially elevated N+S from 1989 to 2016. The WB treatment was discontinued after 2016, the beginning of the recovery from both the experimental N+S and ambient decline. Stream SO 4 in WB gradually declined after the treatment ended, from ~147 µeq L -1 in 2010-16 to ~126 µeq L -1 in 2017-18. The declining S inputs induced desorption of SO 4 from soil phase surfaces, with stream loss far exceeding precipitation input. At the current rate of recovery, it will be many decades before the WB stream returns to pre-treatment SO 4 concentrations. In contrast, NO 3 is only weakly adsorbed in soil, and WB stream NO 3 concentrations rapidly declined from ~39 µeq L -1 in 2010-16 to ~5 µeq L -1 in 2017-18, comparable to the N-limited EB stream. The acid anions are strongly coupled to base cation chemistry in streams, and there was a distinct hysteretic response of Ca and Mg to the chronic acidification, as (Ca+Mg) increased rapidly during the initial years, followed by declining values due to depletion of the soil exchange complex. This 30-year monitoring study (1989-2019) provides insights into recovery mechanisms from acidic deposition and highlights the role of abiotic processes in soil that mediate nutrient cycling and retention. Finally, documenting the rapid response of N alongside the slower recovery for S identifies the temporal resolution necessary for other whole-watershed recovery studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Experimentally simulated sea level rise destabilizes carbon-mineral associations in temperate tidal marsh soil

How sea level rise (SLR) alters carbon (C) dynamics in tidal salt marsh soils is unresolved. Changes in hydrodynamics could influence organo-mineral associations, influencing dissolved organic carbon (DOC) fluxes. As SLR increases the duration of inundation, we hypothesize that lateral DOC export will increase due to reductive dissolution of C-bearing iron (Fe) oxides, destabilizing soil C stocks and influencing greenhouse gas emissions. To test this, soil cores (0–8 cm depth) were collected from the high marsh of a temperate salt marsh that currently experiences changes in water level and soil redox oscillation due to spring-neap tides. Mesocosms experimentally simulated SLR by continuously inundating high marsh soils and were compared to mesocosms with Control conditions, where the water level oscillated on a spring-neap cycle. Porewater DOC, lateral DOC, and porewater reduced Fe (Fe 2+ ) concentrations were significantly higher in SLR treatments (1.7 ± 0.5 mM, 0.63 ± 0.14 mM, and 0.15 ± 0.11 mM, respectively) than Control treatments (1.2 ± 0.35 mM, 0.56 ± 0.15 mM, and 0.08 ± 01 mM, respectively Solid phase analysis with Fe extended X-ray absorption fine-structure spectroscopy further revealed that SLR led to > 3 times less Fe oxide-C coprecipitates than Control conditions In addition, the overall global warming potential (GWP) decreased under SLR due to suppressed CO 2 emissions. Our data suggest that SLR may increase lateral C export of current C stocks by dissolving C-bearing Fe oxides but decrease the overall GWP from emissions of soil trace gases. Finally, these findings have implications for understanding the fate of SOC dynamics under future SLR scenarios.

dissolved organic carbon↗

DOE OSTI2025

Experimental Realization of One-Dimensional Helium

Abstract As the spatial dimension is lowered, locally stabilizing interactions are reduced, leading to the emergence of strongly fluctuating phases of matter without classical analogues. Realizing 1D platforms has been elusive, due to their inherent lack of stability, with a few notable exceptions such as spin chains and ultracold low-density gasses. The inability of such systems to exhibit long range order is essential to their universal description in terms of the Tomonaga-Luttinger liquid theory. Here we report on the experimental observation of a one-dimensional quantum liquid of $$^4$$ 4 He using nanoengineering to confine it within a porous material preplated with a noble gas to enhance dimensional reduction. The resulting excitations of the confined $$^4$$ 4 He, confirmed by neutron scattering, are qualitatively different than three- and two-dimensional superfluid helium, and consistent with Quantum Monte Carlo calculations. The results can be analyzed in terms of a mobile impurity in an otherwise linear Luttinger liquid allowing for the extraction of the microscopic parameters describing the emergent quantum liquid.

Sokol, Paul E.↗

DOE OSTI2021

Mutual Diffusion Coefficients of Na 2 SO 4 at C = 0.02989 mol·dm -3 and 298.15 K by Using Rayleigh Interferometry with Free Diffusion Boundary Conditions: Experimental Test of the Effect of the C 3/2 Concentration Dependence of Refractive Index at Low Concentration

Rayleigh interferometry is one of the most precise and accurate methods for the experimental determination of the mutual diffusion coefficients of both electrolytes and non-electrolytes in liquid solutions. For binary solutions at moderate and high concentrations where the concentration dependences of both diffusion coefficient and refractive index can be assumed to be linear or almost linear and the concentration difference ΔC between a pair of solutions undergoing free diffusion is not large compared to their average concentration, and by using proper combinations of the interference fringe positions as they vary with time, under these conditions diffusion coefficients are obtained that are independent of the size of ΔC. However, this situation becomes more complicated at low concentrations for electrolyte solutions where the concentration dependences of both the diffusion coefficient and refractive index are non-linear, with C 1/2 dependence for the diffusion coefficient and C 3/2 dependence for the refractive index. As a test of these effects on calculated mutual diffusion of electrolyte solutions at low concentrations as measured by Rayleigh interferometry, apparent mutual diffusion coefficients D v,a (volume-fixed reference frame) were measured for fixed average concentrations C=(0.02989 ± 0.00001) mol·dm –3 of Na 2 SO 4 (aq) at 298.15 K while varying ΔC/C from 0.66673 to 2, a threefold variation. The dependence of the diffusion coefficient on ΔC/C was found to be linear, yielding D v = 1.041 6 × 10 –9 m 2 ·s –1 for an infinitely small concentration difference between the diffusing solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Adsorption of Tracer Gases in Geological Media: Experimental Benchmarking

The interaction of xenon with containment barriers can play a crucial role in the detection of underground nuclear explosions. Independent field experiments and laboratory-derived models have observed depressed surface level xenon concentrations and subsequently predicted geological capture rates. This work sought to experimentally verify those predictions by analyzing xenon transport though a two-bulb diffusion apparatus adapted for the study of geologic media. Novel to this work is the timescale over which these experiments were carried out, allowing the system to reach equilibrium, rather than relying on numerical models to treat the equilibrium concentration of each gas as a fit coefficient.

Byers, Maggie↗

DOE OSTI2023

Thermodynamics and Kinetics of Refractory Multi-principal Element Alloys: An Experimental and Modeling Comparison

Here, the search for structural alloys capable of ultrahigh temperature performance has led to the exploration of refractory multi-principal element alloys (RMPEAs). In this work, experimental results for solidification segregation and homogenization of two RMPEAs, NbTaTiW and MoNbTaTi, are compared to simulations using the Scheil and DICTRA modules in Thermo-Calc®. Scheil calculations accurately predict the observed solidification segregation, while DICTRA predicts general trends and can provide a minimum time to achieve homogenization at a given temperature.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Experimental and Modeling Review of the Plutonium-Zirconium (Pu-Zr) System: Lost in Translation and Over Time?

This article presents a review of the phase equilibria of the Pu-Zr system and discusses the contradictory reports on the experimental phase diagram and misinterpretations that have led to confusion over time. In addition, a review of the few Pu-Zr CALPHAD (CALculation of PHAse Diagrams) assessments is presented with emphasis on the heat of formation of the bcc phase, highlighting a disagreement between CALPHAD and ab initio calculations. Based on the information gathered in this study, a critical re-assessment of the Pu-Zr system involving the ζ (Pu 28 Zr), θ (Pu 4 Zr), kinetically hindered κ (PuZr 2 ), and once observed ι phases is called for.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Theoretical and experimental constraints for the equation of state of dense and hot matter

Abstract This review aims at providing an extensive discussion of modern constraints relevant for dense and hot strongly interacting matter. It includes theoretical first-principle results from lattice and perturbative QCD, as well as chiral effective field theory results. From the experimental side, it includes heavy-ion collision and low-energy nuclear physics results, as well as observations from neutron stars and their mergers. The validity of different constraints, concerning specific conditions and ranges of applicability, is also provided.

Kumar, Rajesh (ORCID:0000000327463956)↗