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Results for “Complexity bounding”

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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Detecting Reactive Products in Carbon Capture Polymers with Chemical Shift Anisotropy and Machine Learning

Aminopolymers are attractive sorbents for CO 2 direct air capture applications due to their high density of amine groups, which can readily react with atmospheric levels of CO 2 to form chemisorbed species. The identity of these chemisorbed species and the functional groups that form upon oxidative degradation depends on both material properties and processing conditions, forming a variety of carbonyl-type sites such as ammonium carbamates, bicarbonates, carbonates, carbamic acids, ureas, and amides. 13 C solid-state nuclear magnetic resonance (NMR) is often used to help elucidate the identity of these reacted species, but it is challenging due to the narrow chemical shift range of carbonyl sites. Herein, we demonstrate the application of a two-dimensional (2D) chemical shift anisotropy (CSA) recoupling pulse sequence (ROCSA) to obtain CSA tensor values at each isotropic chemical shift, overcoming limitations of isotropic peak resolution. CSA tensor values describe the local chemical environment and can readily differentiate between the chemisorbed and degradation products. To aid identification, we also developed a k-nearest neighbor (kNN) classification model to distinguish the functional groups via their CSA tensor parameters. This methodology was demonstrated on poly(ethylenimine) in γ-Al 2 O 3 exposed to CO 2 and showed that the chemisorbed products are ammonium carbamate and a mixed carbamate–carbamic acid species. The sample was analyzed again after desorption at 100 °C inducing mild degradation, and the remaining products were strongly bound carbamate and urea species. In conclusion, the combination of 2D CSA measurements coupled with a kNN classification model enhances the ability to accurately identify chemisorbed or degradation products in complex carbon capture materials.

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

Deep Gaussian process-based cost-aware batch Bayesian optimization for complex materials design campaigns

The accelerating pace and expanding scope of materials discovery demand optimization frameworks that efficiently navigate vast design spaces with complex response surfaces while judiciously allocating limited evaluation resources. We present a cost-aware, batch Bayesian optimization scheme powered by deep Gaussian process (DGP) surrogates and a heterotopic querying strategy. Our DGP surrogate, formed by stacking GP layers, models complex hierarchical relationships among high-dimensional compositional features and captures correlations across multiple target properties, propagating uncertainty through successive layers. We integrate evaluation cost into an upper-confidence-bound acquisition extension, which, together with heterotopic querying, proposes small batches of candidates in parallel, balancing exploration of under-characterized regions with exploitation of high-mean, low-variance predictions across correlated properties. Applied to refractory high-entropy alloys for high-temperature applications, our framework converges to optimal formulations in fewer iterations with cost-aware queries than conventional GP-based BO, highlighting the value of deep, uncertainty-aware, cost-sensitive strategies in materials campaigns.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Puzzles of Exotic Decay Processes

The growing interest in the physics of unstable nuclei, along with their manifestations in laboratory experiments and astrophysical observations, highlights the existence of features in decay processes within complex quantum systems that are not yet fully understood. Furthermore, this paper considers examples of such phenomena, including two-step decay processes, resonance effects, threshold peculiarities, and the interactions between bound and continuum states, as well as the related dynamics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Surface vs Homogeneous Organo-Hafnium Catalyst Ion-Pairing and Ligand Effects on Ethylene Homo- and Copolymerizations

Heterogeneous catalysts have long dominated polyethylene and polypropylene production, but understanding their catalysis is challenged by uncertainties in active site structures and percentages. Surface-bound organometallic catalysts are an emerging strategy to combine successful homogeneous catalysts having well-understood structures, relatively high percentages of active sites, and exceptional control of selectivity, with the attractions of surface catalysts, to transition promising homogeneous systems to large-scale heterogeneous ones. Nevertheless, surface-bound olefin polymerization catalysts typically produce ultrahigh M w ’s but with low activity and comonomer selectivity. Here, we report the systematic synthesis and characterization of a series of pyridylamido–Hf complexes and their corresponding surface catalysts chemisorbed on sulfated alumina (AlS) and zirconia (ZrS). Comparative ethylene homo- and 1-octene copolymerizations reveal similar activity and 1-octene selectivity trends in the homogeneous and heterogeneous systems. For the surface pyridylamido–Hf catalyst series, large variations in activity (up to 10×) and 1-octene incorporation (up to 28×) are achieved by ligand and support manipulation. Interestingly, while the homogeneous catalysts exhibit positive comonomer effects in ethylene/1-octene copolymerization, the surface catalysts behave oppositely. Extended X-ray absorption fine structure (EXAFS) reveals significantly elongated Hf···O bond distances vs typical Hf–O covalent bonds (2.06 vs 1.97 Å). Furthermore, density functional theory (DFT) analysis of the heterolytic ion pair separation enthalpies, olefin insertion energetics, and NBO/Bader charges also suggest electrostatic Hf cation–anionic support binding and catalytic patterns, which are modulated by the ion-pairing energetics and ligand architecture.

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

A biophysical framework for double-drugging kinases

Selective orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as “double-drugging”, has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Förster resonance energy transfer, coupled-enzyme assays, and X-ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a conformational equilibrium shift is the main principle governing cooperativity. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X-ray crystal structures of the double-drugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe a fully closed conformation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light on the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of double-drugging strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Large gradients via correlation in random parameterized quantum circuits

Scaling of variational quantum algorithms to large problem sizes requires efficient optimization of random parameterized quantum circuits. For such circuits with uncorrelated parameters, the presence of exponentially vanishing gradients in cost function landscapes is an obstacle to optimization by gradient descent methods. In this work, we prove that reducing the dimensionality of the parameter space by utilizing circuit modules containing spatially or temporally correlated gate layers can allow one to circumvent the vanishing gradient phenomenon. Here, examples are drawn from random separable circuits and asymptotically optimal variational versions of Grover's algorithm based on the quantum alternating operator ansatz. In the latter scenario, our bounds on cost function variation imply a transition between vanishing gradients and efficient trainability as the number of layers is increased toward $\mathcal{O}\left({2}^{n/2}\right)$, the optimal oracle complexity of quantum unstructured search.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Complexity-calibrated benchmarks for machine learning reveal when prediction algorithms succeed and mislead

Abstract Recurrent neural networks are used to forecast time series in finance, climate, language, and from many other domains. Reservoir computers are a particularly easily trainable form of recurrent neural network. Recently, a “next-generation” reservoir computer was introduced in which the memory trace involves only a finite number of previous symbols. We explore the inherent limitations of finite-past memory traces in this intriguing proposal. A lower bound from Fano’s inequality shows that, on highly non-Markovian processes generated by large probabilistic state machines, next-generation reservoir computers with reasonably long memory traces have an error probability that is at least $$\sim 60\%$$ ∼ 60 % higher than the minimal attainable error probability in predicting the next observation. More generally, it appears that popular recurrent neural networks fall far short of optimally predicting such complex processes. These results highlight the need for a new generation of optimized recurrent neural network architectures. Alongside this finding, we present concentration-of-measure results for randomly-generated but complex processes. One conclusion is that large probabilistic state machines—specifically, large $$\epsilon$$ ϵ -machines—are key to generating challenging and structurally-unbiased stimuli for ground-truthing recurrent neural network architectures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Unraveling the Intermediate Reaction Complexes and Critical Role of Support-Derived Oxygen Atoms in CO Oxidation on Single-Atom Pt/CeO 2

CeO 2 -supported Pt single-atom catalysts have been extensively studied due to their relevance in automobile emission control and for the fundamental understanding of CeO 2 -based catalysts. Though CeO 2 -supported Pt nanoparticles are often more active than their single-atom counterparts, the former could easily redisperse to Pt single atom under oxidizing diesel conditions. Therefore, to maximize the reactivity of every Pt atom, it is important to fully understand the reaction mechanism of CeO 2 -supported Pt single atoms. Here, we report a CO oxidation study on a Pt/CeO 2 single-atom catalyst, where we can account for all of the neighbors using in situ and operando spectroscopy techniques and microcalorimetric measurements. Coupled with density functional theory calculations, we present a comprehensive picture of the dynamics of the surface species, the role of surface intermediates, and explain the observed reaction kinetics. We started with a catalyst containing exclusively single atoms and used in situ/operando spectroscopy to provide evidence for their stability during the reaction and to identify the Pt 1 complexes before and during the reaction and their binding to CO. The results reveal that in the precatalyst, Pt is present as Pt(O) 4 on the CeO 2 (111) step edge sites, but during CO oxidation, we find that two Pt 1 complexes coexist, representing two states of the same active site in the reaction cycle. The dominant state/complex remains Pt(O) 4 , which adsorbs CO very weakly as shown by CO microcalorimetry. The second, minority state/complex, Pt(CO)(O) 3 is generated through the reaction of Pt(O) 4 with CO, and CO is bound strongly to Pt 1 . Labile oxygen adatoms from the CeO 2 surface play a major role in the regeneration of Pt(O) 4 either directly from Pt(O) 3 or by reaction with the strongly adsorbed CO in Pt(CO)(O) 3 . We show that the formation of an oxygen vacancy and generation of a labile O* are not barrierless, which explains the long lifetime of Pt(CO)(O) 3 and its detectability despite being a minority complex. The results help to develop a comprehensive view of the dynamic evolution of Pt 1 complexes along the reaction cycle and provide mechanistic insights to guide the design of Pt-based single-atom catalysts.

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

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2023

Natural attenuation of uranium in a fluvial Wetland: Importance of hydrology and speciation

A nuclear fuel fabrication facility released 43,500 kg of uranium into a riparian wetland located on the Savannah River Site between 1955 and 1988. Studies were undertaken to evaluate hydrological and geochemical processes influencing uranium accumulation in the wetland. Gamma-radiation-mapping surveys were conducted by systematically walking over the contaminated wetland with backpacks equipped with global positioning systems and NaI gamma detectors. Based on maps compiled from >700,000 gamma spectra and eight sediment uranium depth profiles, it was determined that 94% of the released uranium remained in the wetland. The uranium in the wetland is concentrated in five multi-hectare areas along the stream, accounting for ~11% of the land area adjacent to the stream. While land type (upland or wetland) and topography provided a reasonable first approximation of where much of the uranium was deposited, hydrological watershed modeling revealed that the stream velocity was especially slow through many of the hot spots. Here, using autoradiography combined with SEM/EDX measurements of contaminated sediments, surprisingly few hot particles were detected. Instead, uranium was evenly distributed throughout the sampled sediment, suggesting that dissolved uranium had bound to sediment particles that became suspended and later deposited in low energy (low flow velocity) portions of the stream. EXAFS suggested that U atoms were present as individual ions in disordered complexes within the sediment. Furthermore, linear combination analyses suggested that the predominant component of the U(VI) was adsorbed to sediment minerals (~70%) and a minor component (~30%) was associated with organic matter phases. Furthermore, these studies show that wetlands can be extraordinarily effective at binding and retaining uranium, thereby providing a natural barrier to the transport of uranium out of a watershed. However, significant anthropogenic or climatic changes to wetlands, such as those associated with flooding, forest fires, or land use, may disrupt the complex hydrological and biogeochemical balance necessary to maintain long-term immobilization of uranium.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Changes in Sedimentary Phosphorus Burial Following Artificial Eutrophication of Lake 227, Experimental Lakes Area, Ontario, Canada

Lake 227 of the Experimental Lakes Area (ELA) in Ontario, Canada has been fertilized with phosphorus (P) since 1969, which resulted in a rapid transition from oligotrophic to eutrophic conditions. Sediment cores collected from the oxygenated epilimnion and the mostly anoxic hypolimnion of this unique lake contain a historical record of the changes in sediment P speciation and burial rates across the trophic transition. To elucidate these changes, results of chemical extractions were combined with 210 Pb sediment dating, and with 31 P NMR, Mössbauer and XANES spectroscopies. Prior to 1969, organic P (P Org ) was the major sedimentary P sink in Lake 227. Eutrophication of the lake coincided with marked increases in the burial rate of total P (TP), as well as in the relative contribution of the NaHCO 3 -extractable P pool (humic-bound P, P Hum ). Together, P Hum and P Org account for ≥70% of total P burial in the sediments deposited since artificial fertilization started. The P Hum fraction likely comprises phosphate complexes with humic substances. The strong linear correlation between P and iron (Fe) extracted by NaHCO 3 implies a close association of the two elements in the humic fraction. Mössbauer and XANES spectra further indicate that most Fe in the post-1969 sediments remained in the Fe(III) oxidation state, which is attributed to the stabilization of reducible Fe by organic matter, in part via the formation of phosphate-Fe(III)-humic complexes. Importantly, our results show that the eutrophication experimentation of Lake 227 caused the accumulation of a large reservoir of reactive sediment P, which may continue to fuel internal P loading to the water column once artificial fertilization is terminated.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Spectroscopic factors in dripline nuclei

Single-nucleon knockout reaction studies of the proton-dripline nuclei 9 C and 13 O suggest an appreciable suppression of spectroscopic factors. In this work, we calculate the one-neutron and one-proton spectroscopic factors for the mirror pair 9 C – 9 Li and 13 O using two variants of the continuum shell model: the complex-energy Gamow shell model and the real-energy shell model embedded in the continuum. Furthermore, our results indicate that the continuum effects strongly suppress the spectroscopic factors of well-bound orbits in the dripline systems but have less impact on the spectroscopic factors of weakly bound states.

6 ≤ A ≤ 19↗
DOE OSTI2024

Convex optimization of contour deformations

We discuss various formal aspects of contour deformations used to alleviate sign problems; most importantly, relating these contour deformations to a certain convex optimization problem. As a consequence of this connection we describe a general method for proving upper bounds on the average phase achievable by the contour deformation method. Using this method we show that Abelian lattice Yang-Mills in two spacetime dimensions possesses, for many values of the complex coupling, an exponential sign problem that cannot be removed via any contour deformation. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

The universal suppressor mutation restores membrane budding defects in the HSV-1 nuclear egress complex by stabilizing the oligomeric lattice

Nuclear egress is an essential process in herpesvirus replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress–budding at the inner nuclear membrane–is coordinated by the nuclear egress complex (NEC). Composed of the viral proteins UL31 and UL34, NEC deforms the membrane around the capsid as the latter buds into the perinuclear space. NEC oligomerization into a hexagonal membrane-bound lattice is essential for budding because NEC mutants designed to perturb lattice interfaces reduce its budding ability. Previously, we identified an NEC suppressor mutation capable of restoring budding to a mutant with a weakened hexagonal lattice. Using an established in-vitro budding assay and HSV-1 infected cell experiments, we show that the suppressor mutation can restore budding to a broad range of budding-deficient NEC mutants thereby acting as a universal suppressor. Cryogenic electron tomography of the suppressor NEC mutant lattice revealed a hexagonal lattice reminiscent of wild-type NEC lattice instead of an alternative lattice. Further investigation using x-ray crystallography showed that the suppressor mutation promoted the formation of new contacts between the NEC hexamers that, ostensibly, stabilized the hexagonal lattice. This stabilization strategy is powerful enough to override the otherwise deleterious effects of mutations that destabilize the NEC lattice by different mechanisms, resulting in a functional NEC hexagonal lattice and restoration of membrane budding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Covariance operator estimation: Sparsity, lengthscale, and ensemble Kalman filters

This paper investigates covariance operator estimation via thresholding. For Gaussian random fields with approximately sparse covariance operators, we establish non-asymptotic bounds on the estimation error in terms of the sparsity level of the covariance and the expected supremum of the field. We prove that thresholded estimators enjoy an exponential improvement in sample complexity compared with the standard sample covariance estimator if the field has a small correlation lengthscale. As an application of the theory, we study thresholded estimation of covariance operators within ensemble Kalman filters.

Covariance operator estimation↗
DOE OSTI2020

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗
DOE OSTI2022

Electronically-coupled redox centers in trimetallic cobalt complexes

Synthesis and isolation of molecular building blocks of metal–organic frameworks (MOFs) can provide unique opportunities for characterization that would otherwise be inaccessible due to the heterogeneous nature of MOFs. Herein, we report a series of trinuclear cobalt complexes incorporating dithiolene ligands, triphenylene-2,3,6,7,10,11-hexathiolate (THT) (1 3+ ), and benzene hexathiolate (BHT) (2 3+ ), with 1,1,1,-tris(diphenylphosphinomethyl)ethane (triphos) employed as the capping ligand. Single crystal X-ray analyses of 1 3+ and 2 3+ display three five-coordinate cobalt centers bound to the triphos and dithiolene ligands in a distorted square pyramidal geometry. Cyclic voltammetry studies of 1 3+ and 2 3+ reveal three redox features associated with the formation of mixed valence states due to the sequential reduction of the redox-active metal centers (Co III/II ). Using this electrochemical data, the comproportionality values were determined for 1 and 2 (log K c = 1.4 and 1.5 for 1, and 4.7 and 5.8 for 2), suggesting strong resonance-stabilized coupling of the metal centers, with stronger electronic coupling observed for complex 2 compared to that for complex 1. Cyclic voltammetry studies were also performed in solvents of varying polarity, whereupon the difference in the standard potentials (ΔE 1/2 ) for 1 and 2 was found to shift as a function of the polarity of the solvent, indicating a negative correlation between the dielectric constant of the electrochemical medium and the stability of the mixed valence species. Spectroelectrochemical studies of in situ generated multi-valent (MV) states of complexes 1 and 2 display characteristic NIR intervalence charge transfer (IVCT) bands, and analysis of the IVCT transitions for complex 2 suggests a weakly coupled class II multi-valent species and relatively large electronic coupling factors (1700 cm –1 for the first multi-valent state of 2 2+ , and 1400 and 4000 cm –1 for the second multi-valent state of 2 + ). Here, density functional theory (DFT) calculations indicate a significant deviation in relative energies of the frontier orbitals of complexes 1 3+ , 2 3+ , and 3 + that contrasts those calculated for the analogous trinuclear cobalt dithiolene complexes employing pentamethylcyclopentadienyl (Cp*) as the capping ligand (Co 3 Cp* 3 THT and Co 3 Cp* 3 BHT, respectively), and may be a result of the cationic nature of complexes 1 3+ , 2 3+ , and 3 + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗