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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Investigating the Effects of Ag, Cu, and Pd Functionalized Chabazite on the Adsorption Affinities of Noble Gases Xe, Kr, and Ar

Separation of the noble gases from air is typically done through a cryogenic distillation process that is both energy intensive and expensive. Notably, Ag-functionalized zeolites and MOFs have a well-documented affinity for Xe and, to a lesser extent, Kr that could serve as an economical alternative to this process on a commercial scale. The mechanism driving the Ag–Xe interaction, however, is still a matter of debate, and the use of other metals in place of Ag is not as thoroughly documented. In this study, Ag, Cu, and Pd functionalized chabazite specimens were prepared, and their affinities for the noble gases Xe, Kr, and Ar were investigated and compared to each other and an unexchanged Na-chabazite. From these analyses, Ag-functionalized chabazite displayed the highest affinity for Xe among these samples, but there was not a similar affinity for Kr or Ar. From the results, a mechanism is proposed such that the strong Ag–Xe interaction contains both an underlying physical and electronic aspect related to the formation of Ag nanoclusters within the chabazite pore geometry that alters the chabazite surface state such that Xe is preferentially adsorbed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Evaluation of polyanionic cyclodextrins as high affinity binding scaffolds for fentanyl

Abstract Cyclodextrins (CDs) have been previously shown to display modest equilibrium binding affinities ( K a ~ 100–200 M -1 ) for the synthetic opioid analgesic fentanyl. In this work, we describe the synthesis of new CDs possessing extended thioalkylcarboxyl or thioalkylhydroxyl moieties and assess their binding affinity towards fentanyl hydrochloride. The optimal CD studied displays a remarkable affinity for the opioid of K a = 66,500 M −1 , the largest value reported for such an inclusion complex to date. One dimensional 1 H Nuclear Magnetic Resonance (NMR) as well as Rotational Frame Overhauser Spectroscopy (2D-ROESY) experiments supported by molecular dynamics (MD) simulations suggest an unexpected binding behavior, with fentanyl able to bind the CD interior in one of two distinct orientations. Binding energies derived from the MD simulations work correlate strongly with NMR-derived affinities highlighting its utility as a predictive tool for CD candidate optimization. The performance of these host molecules portends their utility as platforms for medical countermeasures for opioid exposure, as biosensors, and in other forensic science applications.

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

Characterization of electron spin polarization from positive electron affinity GaAs photocathodes

Negative Electron Affinity (NEA) GaAs photocathodes are widely used to generate spin-polarized electron beams, typically achieving Electron Spin Polarizations (ESPs) in the range of 35%–40%. However, when operated in a Positive Electron Affinity (PEA) state, where a potential barrier inhibits low-energy electrons from escaping into vacuum, measured ESPs can exceed 50%. This effect can occur naturally during photocathode operation, as the NEA surface activation layers can degrade easily over time, increasing the electron affinity. In this work, we investigate and characterize the behavior of enhanced ESPs under PEA conditions. We present experimental measurements of ESP using a retarding-field Mott polarimeter on GaAs photocathodes with controlled and varying electron affinities. These results are complemented by theoretical explanations considering the material band structure, the light excitation profile, and spin depolarization mechanisms.

Electronic band structure↗
DOE OSTI2024

Ni( II )-binding affinity of Cc NikZ-II and its homologs: the role of the HH -prong and variable loop revealed by structural and mutational studies

Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗
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 OSTI2022

Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2

Allosteric activation and silencing of leukocyte β2-integrins transpire through cation-dependent structural changes, which mediate integrin biosynthesis and recycling, and are essential to designing leukocyte-specific drugs. Stepwise addition of Mg 2+ reveals two mutually coupled events for the αXβ2 ligand-binding domain—the αX I-domain—corresponding to allostery establishment and affinity maturation. Electrostatic alterations in the Mg 2+ -binding site establish long-range couplings, leading to both pH- and Mg 2+ -occupancy-dependent biphasic stability change in the αX I-domain fold. The ligand-binding sensorgrams show composite affinity events for the αX I-domain accounting for the multiplicity of the αX I-domain conformational states existing in the solution. On cell surfaces, increasing Mg 2+ concentration enhanced adhesiveness of αXβ2. This work highlights how intrinsically flexible pH- and cation-sensitive architecture endows a unique dynamic continuum to the αI-domain structure on the intact integrin, thereby revealing the importance of allostery establishment and affinity maturation in both extracellular and intracellular integrin events.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Characterization of two affinity matured Anti-Yersinia pestis F1 human antibodies with medical countermeasure potential

Yersinia pestis , the causative agent of plague and a biological threat agent, presents an urgent need for novel medical countermeasures due to documented cases of naturally acquired antibiotic resistance and potential person-to-person spread during a pneumonic infection. Immunotherapy has been proposed as a way to circumvent current and future antibiotic resistance. Here, we describe the development and characterization of two affinity matured human antibodies (αF1Ig AM2 and αF1Ig AM8) that promote survival of mice after exposure to aerosolized Y . pestis . We share details of the error prone PCR and yeast display technology-based affinity maturation process that we used. The resultant matured antibodies have nanomolar affinity for Y . pestis F1 antigen, are produced in high yield, and are resilient to 37°C stress for up to 6 months. Importantly, in vitro assays using a murine macrophage cell line demonstrated that αF1Ig AM2 and αF1Ig AM8 are opsonic. Even more importantly, in vivo studies using pneumonic plague mouse models showed that 100% of the mice receiving 500 μg of IgGs αF1Ig AM2 and αF1Ig AM8 survived lethal challenge with aerosolized Y . pestis CO92. Combined, these results provide evidence of the quality and robustness of αF1Ig AM2 and αF1Ig AM8 and support their development as potential medical countermeasures against plague.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗
DOE OSTI2022

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Characterizing the general chelating affinity of serum protein fetuin for lanthanides

Fetuin is an abundant blood protein that participates in multiple biological processes, including the transport and regulation of calcium. Fetuin is also known to have a high affinity for uranium (as the uranyl dioxo cation) and plutonium, thus it has been suggested as one of the main endogenous chelating biomolecules involved in the transport of actinides following an internal uptake event. Nevertheless, no direct measurements of its affinity for f-elements beside these two actinides have been reported. Here, we investigate the interaction between fetuin and trivalent lanthanides, such as samarium, europium, terbium, and dysprosium, by mass spectrometry and fluorescence spectroscopy. In this work, mass spectrometry results indicated that fetuin has four metal binding sites for the metal ions studied. Upon formation, the metal–protein complexes showed luminescence emission as a result of antenna sensitization of the metal ions, whose photophysics were characterized and exploited to perform direct spectrofluorimetric titrations. Furthermore, the thermodynamic constants were calculated for all complexes, confirming the formation of stable complexes with log $β^{\prime}_4$ values between 26 and 27. In characterizing the affinity of the serum protein fetuin for several f-elements, this study expands upon the initial findings focused on uranyl and plutonium, and contributes to a better understanding of the internal distribution and deposition of lanthanides, potentially representative of trivalent actinides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. Finally, we provide an analysis of the results and discuss insights into determined best practice methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CAML: Commutative Algebra Machine Learning─A Case Study on Protein–Ligand Binding Affinity Prediction

Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein−ligand binding affinities. Specifically, we apply persistent Stanley−Reisner theory, a key concept in combinatorial commutative algebra, to the affinity predictions of protein−ligand binding and metalloprotein−ligand binding. We present three new algorithms, i.e., element-specific commutative algebra, category-specific commutative algebra, and commutative algebra on bipartite complexes, to tackle the complexity of data involved in (metallo) protein−ligand complexes. We show that the proposed CAML outperforms other state-of-theart methods in (metallo) protein−ligand binding affinity predictions, indicating the great potential of commutative algebra learning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Control-Affine Schrödinger Bridge and Generalized Bohm Potential

From a stochastic control perspective, the Schrödinger bridge is a density-valued continuous curve parameterized by time that connects a given pair of initial and terminal probability densities via minimum effort controlled Brownian motion. The control-affine Schrödinger bridge extends this idea to a generic control-affine Itô diffusion, possibly with an additive state cost. Here, in this letter, we recast the necessary conditions of optimality for the control-affine Schrödinger bridge problem as a two point boundary value problem for a quantum mechanical Schrödinger PDE with complex potential. This complex-valued potential is a generalization of the real-valued Bohm potential in quantum mechanics. Our derived potential is akin to the optical potential in nuclear physics where the real part of the potential encodes elastic scattering (transmission of wave function), and the imaginary part encodes inelastic scattering (absorption of wave function). The key takeaway is that the process noise that drives the evolution of probability densities induces an absorbing medium in the evolution of wave function. These results make new connections between control theory and non-equilibrium statistical mechanics through the lens of quantum mechanics.

Markov processes↗
DOE OSTI2020

The emergence of small-scale self-affine surface roughness from deformation

Most natural and man-made surfaces appear to be rough on many length scales. There is presently no unifying theory of the origin of roughness or the self-affine nature of surface topography. One likely contributor to the formation of roughness is deformation, which underlies many processes that shape surfaces such as machining, fracture, and wear. Using molecular dynamics, we simulate the biaxial compression of single-crystal Au, the high-entropy alloy Ni 36.67 Co 30 Fe 16.67 Ti 16.67 , and amorphous Cu 50 Zr 50 and show that even surfaces of homogeneous materials develop a self-affine structure. By characterizing subsurface deformation, we connect the self-affinity of the surface to the spatial correlation of deformation events occurring within the bulk and present scaling relations for the evolution of roughness with strain. These results open routes toward interpreting and engineering roughness profiles.

42 ENGINEERING↗
DOE OSTI2024

Exploring Architectural-Aware Affinity Policies in Modern HPC Runtimes

Modern commodity and High-Performance Computing (HPC) systems are evolving with complex CPU architectures. These architectures now feature higher core and NUMA domain counts and implement features such as hyperthreading. When considering significant differences in hardware configurations, library availability, and hardware-tailored system/software stacks, which could substantially vary from one system to another, performance portability is hard to achieve. Throughout the years, this trend resulted in an increasingly high burden on application developers to fine-tune their workloads for each architecture. This work explores how hardware-dependent aspects such as locality/process/thread affinity affect performance in modern CPU architectures. We focus our study on the Global Memory and Threading (GMT) distributed runtime system as a representative of Partitioned Global Address Space (PGAS) software stacks commonly adopted for productivity. In particular, to appreciate performance implications, we evaluate GMT’s thread affinity policies, and, introduce two new ones which exploit architectural awareness. Finally, we explore alternative NUMA configurations via different process bindings and perform a scalability study on three HPC clusters with varying CPU architectures and NUMA layouts. Our analysis indicates that more complex architectures are more affected by affinity and binding policies and highlights the importance of setting proper runtime configurations to achieve superior performance.

Di Dio Lavore, Ian↗
DOE OSTI2022

Reversible domain closure modulates GlnBP ligand binding affinity

Glutamine binding protein (GlnBP) is an Escherichia Coli periplasmic binding protein, which binds and carries glutamine to the inner membrane ATP-binding cassette (ABC) transporter. GlnBP binds the ligand with affinity around 0.1μM measured by isothermal titration calorimetry (ITC) and ligand binding stabilizes protein structure shown by its increase in thermodynamic stability. However, the molecular determinant of GlnBP ligand binding is not known. Electrostatic and hydrophobic interaction between GlnBP and glutamine are critical factors. We propose that the freedome of closure movement is also vital for ligand binding. In order to approve this hypothesis, we generate a series of mutants with different linker length that has different magnitude of domain closure. Mutants show different ligand binding affinity, which indicates that the propensity of domain closure determines the ligand binding affinity. Ligand binding triggers gradual ensemble conformational change. Structural changes upon ligand binding are monitored by combination of small angle x-ray scattering (SAXS) and NMR spectroscopy. Detailed structure characterization of GlnBP contributes to a better understanding of ligand binding and provides the structural basis for biosensor design.

59 BASIC BIOLOGICAL SCIENCES↗