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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Shocks and information exchange in de Sitter space

We discuss some implications of recent progress in understanding the black hole information paradox for complementarity in de Sitter space. Extending recent work by two of the authors, we describe a bulk procedure that allows information expelled through the cosmological horizon to be received by an antipodal observer. Generically, this information transfer takes a scrambling time t=H- 1 (S ds ). We emphasize that this procedure relies crucially on selection of the Bunch-Davies vacuum state, interpreted as the thermofield double state that maximally entangles two antipodal static patches. The procedure also requires the presence of an (entangled) energy reservoir, created by the collection of Hawking modes from the cosmological horizon. We show how this procedure avoids a cloning paradox and comment on its implications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Emergent unitarity in de Sitter from matrix integrals

We study Jackiw-Teitelboim gravity with positive cosmological constant as a model for de Sitter quantum gravity. We focus on the quantum mechanics of the model at past and future infinity. There is a Hilbert space of asymptotic states and an infinite-time evolution operator between the far past and far future. This evolution is not unitary, although we find that it acts unitarily on a subspace up to non-perturbative corrections. These corrections come from processes which involve changes in the spatial topology, including the nucleation of baby universes. There is significant evidence that this 1+1 dimensional model is dual to a 0+0 dimensional matrix integral in the double-scaled limit. So the bulk quantum mechanics, including the Hilbert space and approximately unitary evolution, emerge from a classical integral. We find that this emergence is a robust consequence of the level repulsion of eigenvalues along with the double scaling limit, and so is rather universal in random matrix theory.

2D gravity↗
DOE OSTI2023

Generative design of de novo proteins based on secondary-structure constraints using an attention-based diffusion model

We report two generative deep-learning models that predict amino acid sequences and 3D protein structures on the basis of secondary-structure design objectives via either the overall content or the per-residue structure. Both models are robust regarding imperfect inputs and offer de novo design capacity because they can discover new protein sequences not yet discovered from natural mechanisms or systems. The residue-level secondary-structure design model generally yields higher accuracy and more diverse sequences. These findings suggest unexplored opportunities for protein designs and functional outcomes within the vast amino acid sequences beyond known proteins. Our models, based on an attention-based diffusion model and trained on a dataset extracted from experimentally known 3D protein structures, offer numerous downstream applications in the conditional generative design of various biological or engineering systems. Future work could include additional conditioning and an exploration of other functional properties of the generated proteins for various properties beyond structural objectives.

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

De-Risking High-Recovery Brackish Water Desalination via Flow Reversal and Feed Flushing Using Techno-Economic Assessment

Novel desalination technologies have demonstrated enhanced performance and improved financial metrics over existing processes adopted by industry. Establishing quantitative performance targets is essential for achieving financial benefits over the current state of the art. Herein, we demonstrate how WaterTAP, a techno-economic assessment (TEA) tool, can be used to identify minimum performance metrics necessary to achieve financial benefit over using existing processes. This study evaluates the feasibility of increasing water recovery at the Chino Desalter I above 90 % through the addition of a third variable configuration reverse osmosis (VCRO) stage. Sensitivity analyses revealed flow reversal frequency, feed flushing volume (used as a cleaning step), and membrane lifespan are key factors influencing the financial viability of the VCRO process. The TEA analysis demonstrated that the system must achieve a recovery of 84 % and a 1-year membrane lifespan to have a breakeven LCOW, while achieving 90 % recovery can ultimately reduce the LCOW by 16 %. Notably, a trade-off between decreasing frictional losses and increased osmotic pressure across the recovery range, resulted in a stable specific energy consumption across the recovery range, enabling meaningful LCOW reductions without an energy penalty, a key finding that contrasts with conventional RO. This work demonstrates how TEA can guide system design by identifying key performance targets and exploring trade-offs, enabling data-driven decisions to de-risk innovative processes. These findings underscore the importance of leveraging TEA to evaluate scaling mitigation strategies and optimize inland desalination systems for sustainable and cost-effective operation.

14 SOLAR ENERGY↗
DOE OSTI2024

De-risking superhot EGS development through 3D play fairway analysis: Methodology development and application at Newberry Volcano, Oregon, USA

The DErisking Exploration for multiple geothermal Plays in magmatic ENvironments (DEEPEN) project aims to de-risk exploration of geothermal plays in magmatic systems, with a focus on superhot and supercritical geothermal systems. This article presents advancements in geoscientific assessment of superhot enhanced geothermal system (EGS) resources as part of the DEEPEN project, particularly in exploration and identification of these systems. While there exists a general consensus on key components of conventional hydrothermal systems, there has not been a prior consensus on such components for EGS, let alone superhot EGS. The DEEPEN project identified these key components for superhot EGS plays, and used them to modify the traditional geothermal play fairway analysis (PFA) approach to identify favorable areas in superhot EGS plays in 3D. This was done through modeling both favorability and uncertainty separately for each key component of a superhot EGS play, incorporating diverse 3D geoscientific datasets, including geologic features, models produced from direct observations, single inversions, and joint inversions. The PFA is applied to Newberry Volcano as a form of validation. Finally, the results appear to validate the methodology, aligning with expectations derived from conceptual modeling, and highlighting the area targeted for EGS stimulation well NWG 55-29 as favorable, and suggesting potential additional areas worthy of exploration at Newberry.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Validating Modern NRG Oncology Pelvic Nodal and Groupe Francophone de Radiothérapie Urologique Prostate Bed Contouring Guidelines for Post-Prostatectomy Salvage Radiation: A Secondary Analysis of the LOCATE Trial

We used the patterns of recurrence on {sup 18}F-fluciclovine positron emission tomography (PET)–computed tomography (CT) in patients enrolled in the LOCATE trial after prostatectomy to evaluate how well the most recent NRG Oncology and Groupe Francophone de Radiothérapie Urologique (GFRU) contouring recommendations encompassed all sites of recurrence in the prostate fossa and pelvic nodes in comparison to former Radiation Therapy Oncology Group (RTOG) recommendations.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

A late glacial paleoenvironmental and climate record from the Sierra de Juarez, Baja California

Ciénegas are desert wetlands that are strongly correlated with the stability of the hydrologic cycle in arid landscapes. However, these environments are particularly vulnerable to climate change, drought, water diversion, and fire suppression which all have contributed to the degradation of ciénegas along the U.S.-Mexican borderlands. Therefore, identifying the timing of precipitation patterns in this region is of particular interest because of its relationship to many ecological responses of the landscape such as groundwater recharge and fire. Here, we present the first-ever fire paleoenvironmental record from Ciénega Chimeneas, a ciénega complex in the Sierra de Juárez of Baja California. We explore how changes in the amount and seasonality of moisture affected ciénega complexes and fire activity from across the southwestern North American region over the past 45,000 years. Further, our record suggests that during the late glacial period, 41,000–21,000 cal yr BP, the increase of Larrea and Quercus indicate an increase in summer precipitation. Subsequently, when summer precipitation increased, pollen preservation and pollen accumulation rates (PAR) also increased. Increased vegetation allowed for increased fire activity during the late glacial period. Regionally, most of the comparison sites also indicated wet conditions during the full glacial period. However, around 21,000 cal yr BP, effective moisture decreased resulting in a dramatic change in the vegetation assemblage. Specifically, the summer wet taxa disappeared, while pollen preservation and PAR decreased, suggesting a dry period until ~14,000 cal yr BP. Little fire activity is recorded after 21,000 cal yr BP, likely due to the absence of fuels. At ~14,000 cal yr BP, Larrea and Quercus reappear suggesting increased summer precipitation. However, the appearance of Cyperaceae and increases in grasses suggest increased winter precipitation. We suggest that the combination of summer wet and winterwet taxa ~14,000 cal yr BP represents an increase in ENSO conditions, while the summer moisture controls remained relatively constant.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Controlling Hydrocarbon (De)Hydrogenation Pathways with Bifunctional PtCu Single-Atom Alloys

The conversions of surface-bound alkyl groups to alkanes and alkenes are important steps in many heterogeneously catalyzed reactions. On the one hand, while Pt is ubiquitous in industry because of its high activity toward C–H activation, many Pt-based catalysts tend to overbind reactive intermediates, which leads to deactivation by carbon deposition and coke formation. On the other hand, Cu binds intermediates more weakly than Pt, but activation barriers tend to be higher on Cu. We examine the reactivity of ethyl, the simplest alkyl group that can undergo hydrogenation and dehydrogenation via β-elimination, and show that isolated Pt atoms in Cu enable low-temperature hydrogenation of ethyl, unseen on Cu, while avoiding the decomposition pathways on pure Pt that lead to coking. Lastly, we confirm the predictions of our theoretical model and experimentally demonstrate that the selectivity of ethyl (de)hydrogenation can be controlled by changing the surface coverage of hydrogen.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Nicotine-Inspired, De Novo-Designed SARS-CoV-2 Main Protease Inhibitors Reveal Unique Chemistry for Covalently Conjugating Both Cysteine and Histidine Residues in the Catalytic Dyad

Anecdotal reports about smokers with low SARS-CoV-2 infection rates prompted a search for nicotine and its pyrolysis products as SARS-CoV-2 main protease (M Pro ) inhibitors. From this search, 3-vinylpyridine was discovered as a weak binder for the M Pro S1 subsite and was used subsequently as a de novo starting point for covalent inhibitor design that quickly yielded a highly potent inhibitor, SR-A-174, with an IC 50 value of 60 nM. Representing a novel class of M Pro inhibitors, SR-A-174 features an N,N -diaryl-α,α-dichloroacetamide scaffold that facilitated rapid exploration of alternative covalent warheads and various N-substituents, leading to the identification of multiple inhibitors with potent antiviral activity. Eight such M Pro inhibitor structures were determined, all demonstrating covalent binding to catalytic Cys145 of M Pro . In six determined structures, binding is dominated by the covalent bond plus van der Waals contacts, which contrasts with the extensive hydrogen bond networks formed with peptidomimetic inhibitors such as nirmatrelvir. Strikingly, two N,N -diaryl-α,α-dichloroacetamide inhibitors exhibit an unprecedented dual covalent modification mode of the catalytic dyad, forming bonds to both Cys145 and His41 with a concomitant loss of both chlorides and displacing the inhibitors from the S1 subsite. This dyad-targeting reactivity suggests a novel route for bioconjugation of both cysteine and histidine.

SARS-CoV-2↗
DOE OSTI2023

Thermally Significant Fluid Seepage Through Thick Sediment on the Juan de Fuca Plate Entering the Cascadia Subduction Zone

We use heat flux measurements colocated with seismic reflection profiles over a buried basement high on the Juan de Fuca plate ∼25 km seaward of the deformation front offshore Oregon to test for the presence of hydrothermal circulation in the oceanic crust. We also revisit heat flux data crossing a buried basement high ∼25 km seaward of the deformation front ∼150 km north, offshore Washington. Seafloor heat flux is inversely correlated with sediment thickness, consistent with vigorous hydrothermal circulation in the basement aquifer homogenizing temperatures at the top of the basement. Heat flux immediately above the summit of the basement highs is greater than expected solely from conduction. Fluid seepage at rates of ∼2.6–5.4 cm yr −1 in a 1–1.5 km-wide conduit through ∼800–1,300 m thick sediment sections above these basement highs can explain these observations. Observations of thermally significant fluid seepage through sediment >225 m thick on oceanic crust are unprecedented. High sediment permeability, high fluid overpressure in the basement, or a combination of both is required to drive fluid seepage at the observed rates. We infer that rapid seepage occurs because the basement highs rise above the low permeability basal sediment with their tops protruding into the base of high permeability Nitinat or Astoria Fan sediment. Seepage from basement highs penetrating into the submarine fans can affect the thermal state of crust entering the subduction zone.

58 GEOSCIENCES↗
DOE OSTI2021

Role of backbone strain in de novo design of complex α/β protein structures

Abstract We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

De novo design of knotted tandem repeat proteins

De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (3 1 ) and pentafoil (5 1 ) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein’s structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Circular olefin copolymers made de novo from ethylene and α-olefins

Ethylene/α-olefin copolymers are produced in huge scale and widely used, but their after-use disposal has caused plastic pollution problems. Their chemical inertness made chemical re/upcycling difficult. Ideally, PE materials should be made de novo to have a circular closed-loop lifecycle. However, synthesis of circular ethylene/α-olefin copolymers, including high-volume, linear low-density PE as well as high-value olefin elastomers and block copolymers, presents a particular challenge due to difficulties in introducing branches while simultaneously installing chemical recyclability and directly using industrial ethylene and α-olefin feedstocks. Here we show that coupling of industrial coordination copolymerization of ethylene and α-olefins with a designed functionalized chain-transfer agent, followed by modular assembly of the resulting AB telechelic polyolefin building blocks by polycondensation, affords a series of ester-linked PE-based copolymers. These new materials not only retain thermomechanical properties of PE-based materials but also exhibit full chemical circularity via simple transesterification and markedly enhanced adhesion to polar surfaces.

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

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

De novo design of miniprotein antagonists of cytokine storm inducers

Cytokine release syndrome (CRS), commonly known as cytokine storm, is an acute systemic inflammatory response that is a significant global health threat. Interleukin-6 (IL-6) and interleukin-1 (IL-1) are key pro-inflammatory cytokines involved in CRS and are hence critical therapeutic targets. Current antagonists, such as tocilizumab and anakinra, target IL-6R/IL-1R but have limitations due to their long half-life and systemic anti-inflammatory effects, making them less suitable for acute or localized treatments. Here we present the de novo design of small protein antagonists that prevent IL-1 and IL-6 from interacting with their receptors to activate signaling. The designed proteins bind to the IL-6R, GP130 (an IL-6 co-receptor), and IL-1R1 receptor subunits with binding affinities in the picomolar to low-nanomolar range. X-ray crystallography studies reveal that the structures of these antagonists closely match their computational design models. In a human cardiac organoid disease model, the IL-1R antagonists demonstrated protective effects against inflammation and cardiac damage induced by IL-1β. These minibinders show promise for administration via subcutaneous injection or intranasal/inhaled routes to mitigate acute cytokine storm effects.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Overlapping qubits from non-isometric maps and de Sitter tensor networks

The emergence of a local effective theory from a more fundamental theory of quantum gravity with seemingly fewer degrees of freedom is a major puzzle of theoretical physics. A recent approach to this problem is to consider general features of the Hilbert space maps relating these theories. In this work, we construct approximately local observables, or overlapping qubits, from such non-isometric maps. We show that local processes in effective theories can be spoofed with a quantum system with fewer degrees of freedom, with deviations from actual locality identifiable as features of quantum gravity. For a concrete example, we construct two tensor network models of de Sitter space-time, demonstrating how exponential expansion and local physics can be spoofed for a long period before breaking down. Our results highlight the connection between overlapping qubits, Hilbert space dimension verification, degree-of-freedom counting in black holes, holography, and approximate locality in quantum gravity.

Quantum information↗