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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Using DNA affinity purification sequencing (DAP-seq) to identify in vitro binding sites of potential Novosphingobium aromaticivorans DSM12444 transcription factors

Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichment. These data will help better understand aromatic metabolism and other features of N. aromaticivorans biology.

DAP-seq↗
DOE OSTI2023

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

We describe our development of ab initio protein-ligand binding pose prediction models based on transformers and binding affinity prediction models based on the neural tangent kernel (NTK). Folding both protein and ligand, the TwoFold models achieve efficient and quality predictions matching state-of-the-art implementations while additionally reconstructing protein structures. In conclusion, solving NTK models points to a new use case for highly optimized linear solver benchmarking codes on HPC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV

The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.

Conti, Simone (ORCID:000000017986567X)↗
DOE OSTI2022

SARS-CoV-2 spike protein variant binding affinity to an angiotensin-converting enzyme 2 fusion glycoproteins

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (Covid-19) pandemic, continues to evolve and circulate globally. Current prophylactic and therapeutic countermeasures against Covid-19 infection include vaccines, small molecule drugs, and neutralizing monoclonal antibodies. SARS-CoV-2 infection is mainly mediated by the viral spike glycoprotein binding to angiotensin converting enzyme 2 (ACE2) on host cells for viral entry. As emerging mutations in the spike protein evade efficacy of spike-targeted countermeasures, a potential strategy to counter SARS-CoV-2 infection is to competitively block the spike protein from binding to the host ACE2 using a soluble recombinant fusion protein that contains a human ACE2 and an IgG1-Fc domain (ACE2-Fc). Here, we have established Chinese Hamster Ovary (CHO) cell lines that stably express ACE2-Fc proteins in which the ACE2 domain either has or has no catalytic activity. The fusion proteins were produced and purified to partially characterize physicochemical properties and spike protein binding. Our results demonstrate the ACE2-Fc fusion proteins are heavily N-glycosylated, sensitive to thermal stress, and actively bind to five spike protein variants (parental, alpha, beta, delta, and omicron) with different affinity. Our data demonstrates a proof-of-concept production strategy for ACE2-Fc fusion glycoproteins that can bind to different spike protein variants to support the manufacture of potential alternative countermeasures for emerging SARS-CoV-2 variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantum efficiency and lifetime study for negative electron affinity GaAs nanopillar array photocathode

Recent studies showed significant improvement in quantum efficiency (QE) by negative electron affinity (NEA) GaAs nanopillar array (NPA) photocathodes over their flat surface peers, particularly at 500 ─ 800 nm waveband. However, the underlying physics is yet to be well understood for further improvement in its performance. In this report, NEA GaAs NPA photocathodes with different dimensions were studied. The diameter of the nanopillars varied from 200 ─ 360 nm, the height varied from 230 ─ 1000 nm and the periodicity varied from 470 ─ 630 nm. The QE and photocathode lifetime were measured. Mie-resonance enhancement was observed at tunable resonance wavelengths. Simulations was also performed to understand the mechanism of photo-absorption and possible ways to further improve the photocathode performance to meet the stringent requirement of the electron sources in large scale electron accelerators. **Acknowledgement** Authored by Jefferson Science Associates, LLC under U.S. DOE contract no. DE-AC05-06OR23177. The U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce this manuscript for U.S. Government purposes. *mrahm008@odu.edu

Rahman, M.↗
DOE OSTI2020

HSolo: Homography from a single affine aware correspondence

The performance of existing robust homography estimation algorithms is highly dependent on the inlier rate of feature point correspondences. In this paper, we present a novel procedure for homography estimation that is particularly well suited for inlier-poor domains. By utilizing the scale and rotation byproducts created by affine aware feature detectors such as SIFT and SURF, we obtain an initial homography estimate from a single correspondence pair. This estimate allows us to filter the correspondences to an inlier-rich subset for use with a robust estimator. Especially at low inlier rates, our novel algorithm provides dramatic performance improvements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Streptavidin Affinity Grids for the Preparation of Biological Samples for Cryogenic Electron Microscopy (CRADA Final Report)

Currently, cryo-EM is the most powerful tool for structural analysis of large biomacromolecules, but there are still problems in that biomacromolecules are denatured at the air-interface and their orientations are limited in a specific orientation. We solved this problem at LBL by developing a streptavidin-coated EM grid. Use of such affinity-binding grids can minimize exposure to air-interface by keeping biomacromolecules bound to streptavidin. It is urgently needed to make such grids readily available to the cryo-EM community, but they are somewhat difficult to make. The goal of the CRADA with Hummingbird company was to mass-produce the streptavidin grids so that they would become readily available to the cryo-EM community. Our contribution to the CRADA was to first help Hummingbird to replicate the manual process that we use, and this was completed successfully.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ising on $\mathbb{S}^2$-- The Affine Conjecture

We review the recent construction \cite{brower2024isingmodelmathbbs2} of the 2d Ising model on a triangulated sphere $\mathbb{S}^2$. Surprisingly, this led to a precise map of the lattice couplings to the target geometry in order to reach the conform field theory (CFT) in the continuum limit. For the integrable 2d Ising CFT, the map was found analytically \cite{Brower_2023}. Here we conjecture how this might be generalized. The discrete geometry is implemented by the piecewise flat triangulation introduced by Regge in 1960 for the Einstein Hilbert action \cite{Regge1961GeneralRW}. Then following our Ising example, we posit the existence of a smooth map of lattice couplings in affine parameters consistent with quantum correlators. A sequence of theoretical investigations and numerical simulations are recommended to test this conjecture. They begin with non-integrable CFT's -- the 2d $\phi^4$ theory on $\mathbb{S}^2$; the 3d Ising model on $\mathbb{S}^3$ and $\mathbb{R} \times \mathbb{S}^2$; QED3 on $\mathbb{R} \times \mathbb{S}^{2} $ as an intermediate step to 4d non-Abelian lattice gauge theory on $\mathbb{R} \times \mathbb{S}^3$.

Brower, Richard C. [Boston U.] (ORCID:000000028185↗
DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H……N between the -COOH and -NH2 groups, and two N-H……O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H……N-H……O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Using DNA Affinity Purification sequencing (DAP-seq) to identify in vitro binding sites of transcription factors potentially involved in aromatic degradation

The genome-wide binding sites of 44 transcription factors from the aromatic metabolizing Alphaproteobacterium Novosphingobium aromaticivorans were identified using DNA Affinity Purification sequencing (DAP-seq). We report 32 of these transcription factors have at least one area of enrichment. These data will be valuable for better understanding of aromatic metabolism.

aromatic metabolism↗
DOE OSTI2020

Selective high-affinity polydentate ligands and methods of making such

This invention provides novel polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each bind different region son the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Selective high-affinity polydentate ligands and methods of making such

This invention provides novel polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each bind different region son the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

DeNardo, Sally J.↗
DOE OSTI2022

Selective high-affinity polydentate ligands and methods of making such

This invention provides novel polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each bind different region son the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Affinity and Treatment of LDR Organics in Low Activity Waste by Cementitious Materials – 26109

The physiochemical interactions between organic contaminants, minerals, and polymer additives in grout/cementitious materials are being identified. This research supports a proposed Resource Conservation and Recovery Act (RCRA) treatment variance relevant to the Land Disposal Restriction (LDR) organics present in Hanford tank waste. It provides the technical basis to address the aspects documented by the Environmental Protection Agency in a draft memo necessary to establish that organics can be immobilized/stabilized in a cementitious matrix. The organic species may interact with cementitious minerals, including slag, fly ash, cement, and other components/dopants like activated carbon. A list of 132 reasonably expected LDR organics associated with Hanford tank waste (RPP-RPT-63493, Rev 1a) was screened by functional groups, octanol-water partitioning coefficients, and detection frequency in Hanford tank waste samples. A subset of 15 compounds spanning the identified properties was tested using sorption and leachate tests. These compounds were subjected to traditional batch sorption tests and leaching tests on/from Cast Stone cementitious material with and without activated carbon (a potential organic adsorption additive). The interactions between organic compounds were observed in traditional batch sorption and modified TCLP leachate tests for surrogate Cast Stone material with and without activated carbon addition. Specifically, phthalic acid (negatively charged) and 4-chloroaniline (polar) sorbed strongly to unmodified Cast Stone, while a group of three phenolic compounds (2,4,6-Trichlorophenol, Pentachlorophenol, o-Cresol) sorbed to and were retained by Cast Stone with a 1% activated carbon amendment. Mixtures of these compounds demonstrated visible retention of the organics within the matrix with a quantifiable affinity of the organics to the cement. This novel testing supports the notion that organics within Hanford tank waste would be retained onto the cement phase with the addition of simple materials easily added to the formulation as part of the treatment process. To further provide additional support to this claim, models employing Flory-Huggins theory in conjunction with macromolecular and organic molecule solubility parameters and species activity coefficients are being utilized to better understand these interactions. Within this context, Van Krevelen (VK) and Hansen organic and polymer solubility parameters were used to inform the Flory-Huggins interaction parameter, allowing for a quantifiable method of evaluating polymer-solvent compatibility and, by extension, interactions with proposed binding additives (e.g., activated carbon). These models and measurement should test the hypothesis for our systems understanding and applicability of Flory-Huggins theory, and whether the prediction of organics in the polymer phase versus the aqueous phase can be confidently made using this strategy. The estimation of the organic molecular activity coefficient in these high salt-saturated aqueous systems is another factor that will be assessed. This project aims to predict and understand complicated organic interactions in these heterogenous systems, guiding optimal treatment and stabilization methodologies.

Jolin, Will [Savannah River National Laboratory (S↗
DOE OSTI2026

Affine Transformations to Enable Machine Learning for Semi-Quantitative EDS Analysis

Energy Dispersive X-ray Spectroscopy (EDS) is an essential technique for determining elemental concentrations and distributions within microstructures, critical for materials discovery, optimization, and qualification. However, most published EDS data is qualitative because current quantitative EDS analysis methods require extensive calibration and post-processing, limiting their practicality and widespread adoption. This work seeks to establish a framework for accelerated EDS characterization and spectrum analysis that can leverage ML to analyze correlations between various elemental compositions and resulting EDS spectra. The complex physics and data result in a high-dimensional problem that grows exponentially with the number of elements in the system and the complexity of the spectrum analysis. ML provides a way to compute and optimize the results of this highly dimensional problem in a flexible way to tailor it to the user’s specific needs and material system. However, the framework emphasizes transparency through a strictly mathematical affine transformation, so the analysis remains understandable and reviewable to facilitate adoption by the scientific community. While currently implemented methods are simplistic and unvalidated, further development and demonstration of this framework could enable high-throughput, accurate, and accessible EDS characterization.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Computing the Critical Temperature of the Affine-Transformed $D=3$ Ising Model Using Masked Autoregressive Flow

The simple Ising model provides a rich environment to build and study lattice field theories. As part of an ongoing project to construct a conformal field theory (CFT) on an arbitrarily curved manifold, in this work we develop methods to measure the critical temperature $β_c$ of the affine-transformed Ising model on the face-centered cubic (FCC) lattice. The main challenge in this endeavor is finding a computationally efficient and accurate method of interpolating and extrapolating Monte Carlo observables with respect to coupling coefficients and temperature. Herein, we compare two such methods. A traditional statistical approach uses the multiple histogram (MH) method, while a newer machine learning approach uses a masked autoregressive flow (MAF) to estimate the underlying probability density function of a set of observables. While the MH method is specifically designed to interpolate and extrapolate Monte Carlo observables, we find that MAF is a viable alternative for measuring $β_c$ with a computational cost that scales more favorably. Furthermore, we comment on additional advantages of MAF relevant to our work, such as extrapolating in system volume.

Svenson, Kai [Texas U.]↗
DOE OSTI2020

Tunable Dopants with Intrinsic Counterion Separation Reveal the Effects of Electron Affinity on Dopant Intercalation and Free Carrier Production in Sequentially Doped Conjugated Polymer Films

Carrier mobility in doped conjugated polymers is limited by Coulomb interactions with dopant counterions. This complicates studying the effect of the dopant’s oxidation potential on carrier generation because different dopants have different Coulomb interactions with polarons on the polymer backbone. In this work, dodecaborane (DDB)-based dopants are used, which electrostatically shield counterions from carriers and have tunable redox potentials at constant size and shape. DDB dopants produce mobile carriers due to spatial separation of the counterion, and those with greater energetic offsets produce more carriers. Neutron reflectometry indicates that dopant infiltration into conjugated polymer films is redox-potential-driven. Remarkably, X-ray scattering shows that despite their large 2-nm size, DDBs intercalate into the crystalline polymer lamellae like small molecules, indicating that this is the preferred location for dopants of any size. These findings elucidate why doping conjugated polymers usually produces integer, rather than partial charge transfer: dopant counterions effectively intercalate into the lamellae, far from the polarons on the polymer backbone. Finally, it is shown that the IR spectrum provides a simple way to determine polaron mobility. Overall, higher oxidation potentials lead to higher doping efficiencies, with values reaching 100% for driving forces sufficient to dope poorly crystalline regions of the film.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗