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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 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A multiplexed bacterial two-hybrid for rapid characterization of protein–protein interactions and iterative protein design

Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus , as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Promoting multiexciton interactions in singlet fission and triplet fusion upconversion dendrimers

Abstract Singlet fission and triplet-triplet annihilation upconversion are two multiexciton processes intimately related to the dynamic interaction between one high-lying energy singlet and two low-lying energy triplet excitons. Here, we introduce a series of dendritic macromolecules that serve as platform to study the effect of interchromophore interactions on the dynamics of multiexciton generation and decay as a function of dendrimer generation. The dendrimers (generations 1–4) consist of trimethylolpropane core and 2,2-bis(methylol)propionic acid (bis-MPA) dendrons that provide exponential growth of the branches, leading to a corona decorated with pentacenes for SF or anthracenes for TTA-UC. The findings reveal a trend where a few highly ordered sites emerge as the dendrimer generation grows, dominating the multiexciton dynamics, as deduced from optical spectra, and transient absorption spectroscopy. While the dendritic structures enhance TTA-UC at low annihilator concentrations in the largest dendrimers, the paired chromophore interactions induce a broadened and red-shifted excimer emission. In SF dendrimers of higher generations, the triplet dynamics become increasingly dominated by pairwise sites exhibiting strong coupling (Type II), which can be readily distinguished from sites with weaker coupling (Type I) by their spectral dynamics and decay kinetics.

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

Labels as a feature: Network homophily for systematically annotating human GPCR drug-target interactions

Machine learning has revolutionized drug discovery by enabling the exploration of vast, uncharted chemical spaces essential for discovering novel patentable drugs. Despite the critical role of human G protein-coupled receptors in FDA-approved drugs, exhaustive in-distribution drug-target interaction testing across all pairs of human G protein-coupled receptors and known drugs is rare due to significant economic and technical challenges. This often leaves off-target effects unexplored, which poses a considerable risk to drug safety. In contrast to the traditional focus on out-of-distribution exploration (drug discovery), we introduce a neighborhood-to-prediction model termed Chemical Space Neural Networks that leverages network homophily and training-free graph neural networks with labels as features. We show that Chemical Space Neural Networks’ ability to make accurate predictions strongly correlates with network homophily. Thus, labels as features strongly increase a machine learning model’s capacity to enhance in-distribution prediction accuracy, which we show by integrating labeled data during inference. We validate these advancements in a high-throughput yeast biosensing system (3773 drug-target interactions, 539 compounds, 7 human G protein-coupled receptors) to discover novel drug-target interactions for FDA-approved drugs and to expand the general understanding of how to build reliable predictors to guide experimental verification.

Hansson, Frederik G↗
DOE OSTI2021

Electron correlation effects on exchange interactions and spin excitations in 2D van der Waals materials

Despite serious effort, the nature of the magnetic interactions and the role of electron-correlation effects in magnetic two-dimensional (2D) van der Waals materials remains elusive. Using CrI 3 as a model system, we show that the calculated electronic structure including nonlocal electron correlations yields spin excitations consistent with inelastic neutron-scattering measurements. Remarkably, this approach identifies an unreported correlation-enhanced interlayer super-superexchange, which rotates the magnon Dirac lines off, and introduces a gap along the high-symmetry Γ-K-M path. This discovery provides a different perspective on the gap-opening mechanism observed in CrI 3 , which was previously associated with spin–orbit coupling through the Dzyaloshinskii–Moriya interaction or Kitaev interaction. Our observation elucidates the critical role of electron correlations on the spin ordering and spin dynamics in magnetic van der Waals materials and demonstrates the necessity of explicit treatment of electron correlations in the broad family of 2D magnetic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Review of corrosion interactions between different materials relevant to disposal of high-level nuclear waste

Abstract This review covers the corrosion interactions between different materials that are relevant to the disposal of high-level nuclear waste, in particular the waste forms and containers. The materials of interest are borosilicate glass, crystalline ceramics, metal alloys, and any corrosion products that might form. The available data show that these interactions depend on the structure, chemistry, thermodynamic history, and proximity of the materials in contact, as well as the environmental attributes, such as temperature, solution chemistry, and radiation. Several key mechanisms that govern these interactions are highlighted. Scientific gaps and open questions are summarized and discussed.

Materials Science↗
DOE OSTI2022

Demonstration of universal control between non-interacting qubits using the Quantum Zeno effect

The Zeno effect occurs in quantum systems when a very strong measurement is applied, which can alter the dynamics in non-trivial ways. Despite being dissipative, the dynamics stay coherent within any degenerate subspaces of the measurement. Here we show that such a measurement can turn a single-qubit operation into a two- or multi-qubit entangling gate, even in a non-interacting system. We demonstrate this gate between two effectively non-interacting transmon qubits. Our Zeno gate works by imparting a geometric phase on the system, conditioned on it lying within a particular non-local subspace. These results show how universality can be generated not only by coherent interactions as is typically employed in quantum information platforms, but also by Zeno measurements.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Orbital structure of the effective pairing interaction in the high-temperature superconducting cuprates

The nature of the effective interaction responsible for pairing in the high-temperature superconducting cuprates remains unsettled. This question has been studied extensively using the simplified single-band Hubbard model, which does not explicitly consider the orbital degrees of freedom of the relevant CuO 2 planes. Here, we use a dynamical cluster quantum Monte Carlo approximation to study the orbital structure of the pairing interaction in the three-band Hubbard model, which treats the orbital degrees of freedom explicitly. We find that the interaction predominately acts between neighboring copper orbitals, but with significant additional weight appearing on the surrounding bonding molecular oxygen orbitals. By explicitly comparing these results to those from the simpler single-band Hubbard model, our study provides strong support for the single-band framework for describing superconductivity in the cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A 9.2-GHz clock transition in a Lu(II) molecular spin qubit arising from a 3,467-MHz hyperfine interaction

Spins in molecules are particularly attractive targets for next-generation quantum technologies, enabling chemically programmable qubits and potential for scale-up via self-assembly. Here, we report observation of one of the largest hyperfine interactions for a molecular system, A iso = 3467±50 MHz, along with an associated clock transition of unprecedented magnitude. This is achieved through chemical control of the degree of s-orbital mixing into the spin-bearing d-orbital associated with a series of spin-½ La(II) and Lu(II) complexes. Increased s-orbital character reduces spin-orbit coupling and enhances the electron-nuclear Fermi contact interaction. Both outcomes are advantageous for quantum applications: the former reduces spin-lattice relaxation, while the latter maximizes the hyperfine interaction that, in turn, generates a 9 gigahertz clock transition, leading to an increase in phase memory time from 1.0±0.4 to 12±1 microseconds for one of the Lu(II) complexes. Furthermore, these findings suggest strategies for development of molecular quantum technologies, akin to trapped ion systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Influence of biogenic emissions from boreal forests on aerosol–cloud interactions

Boreal forest acts as a carbon sink and contributes to the formation of secondary organic aerosols via emission of aerosol precursor compounds. However, these influences on the climate system are poorly quantified. Here we show direct observational evidence that aerosol emissions from the boreal forest biosphere influence warm cloud microphysics and cloud-aerosol interactions in a scale-dependent and highly dynamic manner. Analyses of in situ and ground-based remote-sensing observations from the SMEAR II station in Finland, conducted over eight months in 2014, reveal substantial increases in aerosol load over the forest one to three days after aerosol-poor marine air enters the forest environment. We find that these changes are consistent with secondary organic aerosol formation and, together with water-vapour emissions from evapotranspiration, are associated with changes in the radiative properties of warm, low-level clouds. Here, the feedbacks between boreal forest emissions and aerosol-cloud interactions and the highly dynamic nature of these interactions in air transported over the forest over timescales of several days suggest boreal forests have the potential to mitigate climate change on a continental scale. Our findings suggest that even small changes in aerosol precursor emissions, whether due to changing climatic or anthropogenic factors, may substantially modify the radiative properties of clouds in moderately polluted environments. Emissions from the boreal forest biosphere can substantially increase aerosol load above the forest and influence the radiative properties of clouds, according to analysis of observations from a monitoring station in Finland.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Three-dimensional topological magnetic monopoles and their interactions in a ferromagnetic meta-lattice

Topological magnetic monopoles (TMMs), also known as hedgehogs or Bloch points, are three-dimensional (3D) nonlocal spin textures that are robust to thermal and quantum fluctuations due to the topology protection. Although TMMs have been observed in skyrmion lattices, spinor Bose–Einstein condensates, chiral magnets, vortex rings and vortex cores, it has been difficult to directly measure the 3D magnetization vector field of TMMs and probe their interactions at the nanoscale. Here, we report the creation of 138 stable TMMs at the specific sites of a ferromagnetic meta-lattice at room temperature. We further develop soft x-ray vector ptycho-tomography to determine the magnetization vector and emergent magnetic field of the TMMs with a 3D spatial resolution of 10 nm. This spatial resolution is comparable to the magnetic exchange length of transition metals, enabling us to probe monopole-monopole interactions. We find that the TMM and anti-TMM pairs are separated by 18.3±1.6 nm, while the TMM and TMM, anti-TMM and anti-TMM pairs are stabilized at comparatively longer distances of 36.1±2.4 nm and 43.1±2.0 nm, respectively. We also observe virtual TMMs created by magnetic voids in the meta-lattice. This work demonstrates that ferromagnetic meta lattices could be used as a platform to create and investigate the interactions and dynamics of TMMs. Furthermore, we expect that soft x-ray vector ptycho-tomography can be broadly applied to quantitatively image 3D vector fields in magnetic and anisotropic materials at the nanoscale.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Dipole ladders with large Hubbard interaction in a moiré exciton lattice

Two-dimensional semiconductor moiré superlattices have emerged as a powerful platform for engineering correlated electronic phenomena. On the other hand, optical excitation creates charge neutral interlayer excitons with an out-of-plane electric dipole. Strong onsite dipole–dipole interaction promises the formation of correlated bosonic states, akin to the Mott states of electrons, but has not yet been demonstrated. Here we report a large interaction between excitons occupying the same moiré lattice site—characterized by the Hubbard U parameter—and consequent dipole ladders with spin- and electron-filling dependence in WSe 2 /WS 2 moiré superlattices. Photoluminescence measurements show successive peaks emerging with an energy separation of around 34 meV above the ground state as the exciton density is increased. This corresponds to the sequential injection of excitons into a single site with an energy cost to overcome the large exciton Hubbard U, forming a dipole ladder. Based on findings of local magnetic moments at two holes per moiré cell, we show that excitons can also fill a second moiré orbital, establishing the two-orbital nature of the moiré potential landscape. Our results show that the Bose–Hubbard model with possible exciton crystal phases can be investigated in interacting opto-moiré quantum matter.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The CNK–HYP scaffolding complex promotes RAF activation by enhancing KSR–MEK interaction

The RAS–MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1–BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR–MEK interaction, which in turn enhances RAF–KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR–MEK–CNK–HYP complex reveals a ring-like arrangement of the CNK–HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR–MEK interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tuning interfacial Dzyaloshinskii-Moriya interactions in thin amorphous ferrimagnetic alloys

Skyrmions can be stabilized in magnetic systems with broken inversion symmetry and chiral interactions, such as Dzyaloshinskii-Moriya interactions (DMI). Further, compensation of magnetic moments in ferrimagnetic materials can significantly reduce magnetic dipolar interactions, which tend to favor large skyrmions. Tuning DMI is essential to control skyrmion properties, with symmetry breaking at interfaces offering the greatest flexibility. However, in contrast to the ferromagnet case, few studies have investigated interfacial DMI in ferrimagnets. Here we present a systematic study of DMI in ferrimagnetic CoGd films by Brillouin light scattering. We demonstrate the ability to control DMI by the CoGd cap layer composition, the stack symmetry and the ferrimagnetic layer thickness. The DMI thickness dependence confirms its interfacial nature. In addition, magnetic force microscopy reveals the ability to tune DMI in a range that stabilizes sub-100 nm skyrmions at room temperature in zero field. Our work opens new paths for controlling interfacial DMI in ferrimagnets to nucleate and manipulate skyrmions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Quantile-specific heritability of sibling leptin concentrations and its implications for gene-environment interactions

“Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g., leptin) is high or low relative to its distribution. Leptin concentrations are strongly related to adiposity, whose heritability is quantile dependent. Whether inheritance of leptin concentrations is quantile dependent, and whether this explains the greater heritability in women than men in accordance with their greater adiposity, and explains other gene-environment interactions, remains to be determined. Therefore, leptin and leptin receptor concentrations from 3068 siblings in 1133 sibships from the Framingham Heart Study Third Generation Cohort were analyzed. Free leptin index (FLI) was calculated as the ratio of leptin to soluble leptin receptor concentrations. Full-sib (β FS ) regression slopes were robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples. The analyses showed β FS increased significantly with increasing percentiles of the offspring’s age- and sex-adjusted leptin distribution (P linear = 0.0001), which was accelerated at the higher concentrations (P quadratic = 0.0003). β FS at the 90th percentile (0.418 ± 0.066) was 4.7-fold greater than at the 10th percentile (0.089 ± 0.032, P difference = 3.6 × 10 –6 ). Consistent with quantile-dependent expressivity, the β FS was greater in female sibs, which was attributable to their higher leptin concentrations. Reported gene-environment interactions involving adiposity and LEP , LEPR , MnSOD , PPARγ , PPARγ2 , and IRS-1 polymorphisms were consistent with quantile-dependent expressivity of leptin concentrations. β FS for leptin receptor concentrations and free leptin index also increased significantly with increasing percentiles of their distributions (P linear = 0.04 and P linear = 8.5 × 10 –6 , respectively). In conclusion, inherited genetic and shared environmental effects on leptin concentrations were quantile dependent, which likely explains male–female differences in heritability and some gene-environment interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Aerosol-boundary layer interaction modulated entrainment process

Abstract Aerosol-boundary layer interactions play an important role in affecting atmospheric thermodynamics and air pollution. As a key factor in dictating the development of the boundary layer, the entrainment process in the context of aerosol-boundary layer interactions is still poorly understood. Using comprehensive field observations made at a superstation in Beijing, we gain insight into the response of the entrainment process to aerosols. We found that high aerosol loading can significantly suppress the entrainment rate, breaking the conventional linear relationship between sensible heat fluxes and entrainment fluxes. Related to aerosol vertical distributions, aerosol heating effects can alter vertical heat fluxes, leading to a strong interaction between aerosols and the entrainment process in the upper boundary layer. Such aerosol-entrainment coupling can inhibit boundary layer development and explains the great sensitivity of observed entrainment rates to aerosols than can traditional calculations. The notable impact of aerosols on the entrainment process raises holistic thinking about the dynamic framework of the boundary layer in a polluted atmosphere, which may have a significant bearing on the dispersion of air pollutants and the land-atmosphere coupling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Layer-resolved many-electron interactions in delafossite PdCoO2 from standing-wave photoemission spectroscopy

Abstract When a three-dimensional material is constructed by stacking different two-dimensional layers into an ordered structure, new and unique physical properties can emerge. An example is the delafossite PdCoO 2 , which consists of alternating layers of metallic Pd and Mott-insulating CoO 2 sheets. To understand the nature of the electronic coupling between the layers that gives rise to the unique properties of PdCoO 2 , we revealed its layer-resolved electronic structure combining standing-wave X-ray photoemission spectroscopy and ab initio many-body calculations. Experimentally, we have decomposed the measured VB spectrum into contributions from Pd and CoO 2 layers. Computationally, we find that many-body interactions in Pd and CoO 2 layers are highly different. Holes in the CoO 2 layer interact strongly with charge-transfer excitons in the same layer, whereas holes in the Pd layer couple to plasmons in the Pd layer. Interestingly, we find that holes in states hybridized across both layers couple to both types of excitations (charge-transfer excitons or plasmons), with the intensity of photoemission satellites being proportional to the projection of the state onto a given layer. This establishes satellites as a sensitive probe for inter-layer hybridization. These findings pave the way towards a better understanding of complex many-electron interactions in layered quantum materials.

36 MATERIALS SCIENCE↗