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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 OSTI2021

Endothelial surface translocation of mitochondrial PDCE2 involves the non-canonical secretory autophagy pathway: Putative molecular target for radiation-guided drug delivery

Highlights: • Radiation induces ectopic endothelial surface exposure of mitochondrial PDCE2. • PDCE2 translocation is associated with late-stage inhibition of autophagic flux. • Radiation damage overloads the degradative lysosomal pathway of autophagy. • PDCE2 trafficking occurs via autophagosomes and non-canonical secretory autophagy. • Surface PDCE2 provides a novel target for radiation-guided vascular drug delivery. Radiation has been proposed as a priming agent to induce discriminatory luminal biomarkers for vascular targeting and drug delivery in disorders such as brain arteriovenous malformations and cancers. We previously observed ectopic expression of intracellular proteins such as mitochondrial PDCE2 on irradiated endothelium in animal models. In this study we examined the mechanism of PDCE2 trafficking in human endothelial cells to better understand its suitability as a vascular target. Ionizing radiation induced PDCE2 surface localization in association with accumulation of autophagosome markers (L3CB and p62) indicative of late-stage inhibition of autophagic flux. This effect was abolished in the presence of Rapamycin, an autophagy-inducer, but replicated in the presence of Bafilomycin A, an autophagy blocker. PDCE2 co-localized with lysosomal markers of the canonical degradative autophagy pathway in response to radiation but also with recycling endosomes and SNARE proteins responsible for autophagosome-plasma membrane fusion. These findings demonstrate that radiation-induced blockade of autophagic flux stimulates redirection of intracellular molecules such as PDCE2 to the cell surface via a non-canonical secretory autophagy pathway. Intracellular membrane proteins trafficked in this way could provide a unique pool of radiation biomarkers for therapeutic drug delivery.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A canonical Hamiltonian for open quantum systems

Abstract If an open quantum system is initially uncorrelated from its environment, then its dynamics can be written in terms of a Lindblad-form master equation. The master equation is divided into a unitary piece, represented by an effective Hamiltonian, and a dissipative piece, represented by a hermiticity-preserving superoperator; however, the division of open system dynamics into unitary and dissipative pieces is non-unique. For finite-dimensional quantum systems, we resolve this non-uniqueness by specifying a norm on the space of dissipative superoperators and defining the canonical Hamiltonian to be the one whose dissipator is minimal. We show that the canonical Hamiltonian thus defined is equivalent to the Hamiltonian initially defined by Lindblad, and that it is uniquely specified by requiring the dissipator’s jump operators to be traceless, extending a uniqueness result known previously in the special case of Markovian master equations. For a system weakly coupled to its environment, we give a recursive formula for computing the canonical effective Hamiltonian to arbitrary orders in perturbation theory, which we can think of as a perturbative scheme for renormalizing the system’s bare Hamiltonian.

Physics↗
DOE OSTI2024

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Finite-temperature many-body perturbation theory in the canonical ensemble

Benchmark data are presented for the zeroth- through third-order many-body perturbation corrections to the electronic Helmholtz energy, internal energy, and entropy in the canonical ensemble in a wide range of temperature. They are determined as numerical λ-derivatives of the respective quantities computed by thermal full configuration interaction with a perturbation-scaled Hamiltonian, $\hat{H} = \hat{H}_0 + λ\hat{V}$. Sum-over-states analytical formulas for up to the third-order corrections to these properties are also derived as analytical λ-derivatives. These formulas, which are verified by exact numerical agreement with the benchmark data, are given in terms of the Hirschfelder–Certain degenerate perturbation energies and should be valid for both degenerate and nondegenerate reference states at any temperature down to zero. Further, the results in the canonical ensemble are compared with the same in the grand canonical ensemble.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Streaming Generalized Canonical Polyadic Tensor Decompositions

In this paper, we develop a method which we call OnlineGCP for computing the Generalized Canonical Polyadic (GCP) tensor decomposition of streaming data. GCP differs from traditional canonical polyadic (CP) tensor decompositions as it allows for arbitrary objective functions which the CP model attempts to minimize. This approach can provide better fits and more interpretable models when the observed tensor data is strongly non-Gaussian. In the streaming case, tensor data is gradually observed over time and the algorithm must incrementally update a GCP factorization with limited access to prior data. In this work, we extend the GCP formalism to the streaming context by deriving a GCP optimization problem to be solved as new tensor data is observed, formulate a tunable history term to balance reconstruction of recently observed data with data observed in the past, develop a scalable solution strategy based on segregated solves using stochastic gradient descent methods, describe a software implementation that provides performance and portability to contemporary CPU and GPU architectures and integrates with Matlab for enhanced usability, and demonstrate the utility and performance of the approach and software on several synthetic and real tensor data sets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Probing strangeness canonical ensemble with K - , Φ(1020) and Ξ - production in Au+Au collisions at $\sqrt{^S{NN}}$ = 3 GeV

We report on the first multi-differential measurement of φ meson and Ξ - hyperon production as well as the φ/K - and φ/Ξ - ratio in Au+Au collisions at $\sqrt{^S{NN}}$ = 3 GeV with the STAR experiment under its fixed target configuration at RHIC. φ mesons and Ξ - hyperons are measured through their hadronic decay channels, φ → K+K - and Ξ - → Λπ - . The transverse kinetic energy spectra of K - , φ and Ξ - are presented in different centrality and rapidity intervals. The total production yields and the ratios within a 4π coverage are calculated and compared to thermal model predictions. A calculation within the grand canonical ensemble framework shows a clear discrepancy from our measurement. Our data favor the canonical ensemble approach employing local strangeness conservation with a small strangeness correlation length (r c ≤ 4.2 fm) in 0–10% central Au+Au collisions at $\sqrt{^S{NN}}$ = 3 GeV.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Grand canonically optimized grain boundary phases in hexagonal close-packed titanium

Grain boundaries (GBs) profoundly influence the properties and performance of materials, emphasizing the importance of understanding the GB structure and phase behavior. As recent computational studies have demonstrated the existence of multiple GB phases associated with varying the atomic density at the interface, we introduce a validated, open-source GRand canonical Interface Predictor (GRIP) tool that automates high-throughput, grand canonical optimization of GB structures. While previous studies of GB phases have almost exclusively focused on cubic systems, we demonstrate the utility of GRIP in an application to hexagonal close-packed titanium. We perform a systematic high-throughput exploration of tilt GBs in titanium and discover previously unreported structures and phase transitions. In low-angle boundaries, we demonstrate a coupling between point defect absorption and the change in the GB dislocation network topology due to GB phase transformations, which has important implications for the accommodation of radiation-induced defects.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis

Photorespiration functions in part to support photosynthetic performance, especially under stress such as high light, yet the underlying mechanisms are poorly understood. To identify modulators of photorespiration under high light, we have isolated genetic suppressors of the photorespiratory mutant hpr1 (hydroxypyruvate reductase 1) from Arabidopsis. A suppressor that partially rescues hpr1 is mapped to GLYR1, which encodes the cytosolic glyoxylate reductase 1 that converts glyoxylate to glycolate. Independent glyr1 mutants also partially rescue hpr1 and another photorespiratory mutant, catalase 2. Our genetic, transcriptomic and metabolic profiling analyses together reveal a connection between cytosolic glyoxylate and a non-canonical photorespiratory route mediated by HPR2, which we name the photorespiratory glyoxylate shunt. This shunt complements the canonical photorespiratory pathway and is especially critical when high photorespiratory fluxes are required and when the major photorespiratory pathway is deficient. Our findings support the metabolic flexibility of photorespiration and may help to improve crop performance under stress.

Light stress↗
DOE OSTI2024

Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism

The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. merolae 's cellular affinity for CO 2 is stronger than the affinity of its rubisco for CO 2 . This finding provided additional evidence that C. merolae operates a CCM while lacking the structures and functions characteristic of CCMs in other organisms. To test how such a CCM could function, we created a mathematical compartmental model of a simple CCM, distinct from those we have seen previously described in detail. The results of our modeling supported the feasibility of this proposed minimal and non-canonical CCM in C. merolae . To facilitate the robust modeling of this process, we measured and incorporated physiological and enzymatic parameters into the model. Additionally, we trained a surrogate machine-learning model to emulate the mechanistic model and characterized the effects of model parameters on key outputs. This parameter exploration enabled us to identify model features that influenced whether the model met the experimentally derived criteria for functional carbon concentration and efficient energy usage. Such parameters included cytosolic pH, bicarbonate pumping cost and kinetics, cell radius, carboxylation velocity, number of thylakoid membranes, and CO 2 membrane permeability. Our exploration thus suggested that a non-canonical CCM could exist in C. merolae and illuminated the essential features generally necessary for CCMs to function.

Steensma, Anne K. [Michigan State Univ., East Lans↗
DOE OSTI2022

Comparison of the canonical transformation and energy functional formalisms for ab initio calculations of self-localized polarons

In materials with strong electron-phonon (e-ph) interactions, charge carriers can distort the surrounding lattice and become trapped, forming self-localized (small) polarons. We recently developed an ab initio approach based on canonical transformations to efficiently compute the formation and energetics of small polarons A different approach based on a Landau-Pekar energy functional has been proposed in the recent literature. Here in this work, we analyze and compare these two methods in detail. We show that the small polaron energy is identical in the two formalisms when using the same polaron wave function. We also show that our canonical transformation formalism can predict polaron band structures and can properly treat zero- and finite-temperature lattice vibration effects, although at present using a fixed polaron wave function. Conversely, the energy functional approach can compute the polaron wave function, but as we show here, it neglects lattice vibrations and cannot address polaron self-localization and thermal band narrowing. Taken together, this work relates two different methods developed recently to study polarons from first-principles, highlighting their merits and shortcomings and discussing them both in a unified formalism.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Curvature-slope correlation of nuclear symmetry energy and its imprints on the crust-core transition, radius, and tidal deformability of canonical neutron stars

Background: The nuclear symmetry energy E sym (ρ) encodes information about the energy necessary to make nuclear systems more neutron-rich. While its slope parameter L at the saturation density ρ 0 of nuclear matter has been relatively well constrained by recent astrophysical observations and terrestrial nuclear experiments, its curvature K sym characterizing the E sym (ρ) around 2ρ 0 remains largely unconstrained. Over 520 calculations for E sym (ρ) using various nuclear theories and interactions in the literature have predicted several significantly different K sym –L correlations. Purpose: If a unique K sym –L correlation of E sym (ρ) can be firmly established, it will enable us to progressively better constrain the high-density behavior of E sym (ρ) using the available constraints on its slope parameter L. Here, we investigate if and by how much the different K sym –L correlations may affect neutron star observables. Method: A meta-model of nuclear Equation of States (EOSs) with three representative K sym –L correlation functions is used to generate multiple EOSs for neutron stars. We then examine effects of the K sym –L correlation on the crust-core transition density and pressure as well as the radius and tidal deformation of canonical neutron stars. Results: The K sym –L correlation affects significantly both the crust-core transition density and pressure. It also has strong imprints on the radius and tidal deformability of canonical neutron stars especially at small L values. The available data from LIGO/VIRGO and NICER set some useful limits for the slope L but can not distinguish the three representative K sym –L correlations considered.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Understanding protein-complex assembly through grand canonical maximum entropy modeling

Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are far more protein complexes that are yet to be solved because of their dynamic associations with one another. Nevertheless, it is possible to infer these protein complexes through a physical model. However, it is often not clear to physicists what kind of data from biology is necessary for such a modeling endeavor. Here, we aim to model these clusters of coarse-grained protein assemblies from multiple subunits through the constraints of interactions among the subunits and the chemical potential of each subunit. We obtained the constraints on the interactions among subunits from the known protein structures. We inferred the chemical potential that dictates the particle number distribution of each protein subunit from the knowledge of protein abundance from experimental data. Guided by the maximum entropy principle, we formulated an inverse statistical mechanical method to infer the distribution of particle numbers from the data of protein abundance as chemical potentials for a grand canonical multicomponent mixture. Using grand canonical Monte Carlo simulations, we captured a distribution of high-order clusters in a protein complex of succinate dehydrogenase with four known subunits. The complexity of hierarchical clusters varies with the relative protein abundance of each subunit in distinctive cell types such as lung, heart, and brain. When the crowding content increases, we observed that crowding stabilizes emergent clusters that do not exist in dilute conditions. We, therefore, proposed a testable hypothesis that the hierarchical complexity of protein clusters on a molecular scale is a plausible biomarker of predicting the phenotypes of a cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Geodesic-based relaxation for deep canonical correlation analysis

Deep canonical correlation analysis (DCCA) is often applied to paired data samples from diverse sources to extract meaningful common information. However, when the data sources are heterogeneous, some of the useful information may be complementary but not exactly common. In spite of this fact, existing techniques learn maximally correlated representations from multiple views and are formulated so that they aim to yield identical latent subspaces for each view. This approach is sub-optimal in estimating the true signal subspaces for heterogeneous data sources. We propose a residual relaxation for deep canonical correlation analysis (RDCCA) based on a subspace distance metric, which generalizes the existing problem formulation and extracts representations that are better estimates of the actual, non-identical subspaces. We demonstrate that when using such a relaxation, the learned representations are closer to the true ones and that RDCCA outperforms CCA and DCCA in scenarios with heterogeneous data.

Kuschel, Maurice↗
DOE OSTI2021

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Abstract Background Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na V 1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified. Methods To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior. Results Mice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and Na V 1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits. Conclusions This work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene, SCN1A . We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Canonical Transformation of Potential Model Hamiltonian Mechanics to Geometrical Form I

Using the methods of symplectic geometry, we establish the existence of a canonical transformation from potential model Hamiltonians of standard form in a Euclidean space to an equivalent geometrical form on a manifold, where the corresponding motions are along geodesic curves. The advantage of this representation is that it admits the computation of geodesic deviation as a test for local stability, shown in recent previous studies to be a very effective criterion for the stability of the orbits generated by the potential model Hamiltonian. We describe here an algorithm for finding the generating function for the canonical transformation and describe some of the properties of this mapping under local diffeomorphisms. We give a convergence proof for this algorithm for the one-dimensional case, and provide a precise geometric formulation of geodesic deviation which relates the stability of the motion in the geometric form to that of the Hamiltonian standard form. We apply our methods to a simple one-dimensional harmonic oscillator and conclude with a discussion of the relation of bounded domains in the two representations for which Morse theory would be applicable.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Electrocatalytic Reduction of CO 2 to CO over Ag(110) and Cu(211) Modeled by Grand-Canonical Density Functional Theory

We report the results of modeling CO 2 reduction (CO 2 R) to CO over Ag(110) and Cu(211) surfaces at different applied potentials using grand-canonical density functional theory (GC-DFT), a method specifically designed to accurately model electrochemical systems. In addition to demonstrating GC-DFT’s ability to accurately model electrochemical processes, we also compare it with the computational hydrogen electrode (CHE) approach. GC-DFT predicts that the geometries of these reacting systems strongly depend on the applied potential and the Helmholtz free energies vary nonlinearly with the applied potential, which contradicts a central assumption of the CHE approach. The CHE approach neglects the change in the number of electrons on the electrode surface at different applied potentials, which reduces its accuracy as the potential changes from the potential of zero charge. Our results further demonstrate that the grand free energies of the reaction intermediates not only depend on the value of the applied potential but also on the metal surface type, adsorption site, and adsorbate. GC-DFT’s ability to predict the effect of the applied potential on adsorbate geometry enables it to evaluate different possible reaction mechanisms at different applied potentials. For instance, GC-DFT predicts that the first step of CO2R likely switches from proton-coupled electron transfer to sequential electron transfer and then proton transfer at more reducing potentials, a result that cannot be determined by the CHE because it assumes that all electron transfers are coupled to proton transfers and neglects the effect of the applied potential on the adsorbate geometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Dynamical tuning of the chemical potential to achieve a target particle number in grand canonical Monte Carlo simulations

We present a method to facilitate Monte Carlo simulations in the grand canonical ensemble given a target mean particle number. The method imposes a fictitious dynamics on the chemical potential, to be run concurrently with the Monte Carlo sampling of the physical system. Corrections to the chemical potential are made according to time-averaged estimates of the mean and variance of the particle number, with the latter being proportional to thermodynamic compressibility. Here, we perform a variety of tests, and in all cases find rapid convergence of the chemical potential—inexactness of the tuning algorithm contributes only a minor part of the total measurement error for realistic simulations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Cell-Edge Detection via Selective Cooperation and Generalized Canonical Correlation

Improving the uplink quality of service for users located around the boundaries between cells is a key challenge in cellular systems. Existing approaches relying on power control throttle the rates of cell-center users, while multi-user detection requires accurate channel estimates for the cell-edge users, which is another challenge due to their low received signal-to-noise ratio (SNR). Utilizing the fact that cell-edge user signals are weak but common (received at roughly equal power) at different base stations (BSs), this paper establishes a connection between cell-edge user detection and generalized canonical correlation analysis (GCCA). It puts forth a GCCA-based method that leverages selective BS cooperation to recover the cell-edge user signal subspace even at low SNR. The cell-edge user signals can then be extracted from the resulting mixture via algebraic signal processing techniques. The paper includes theoretical analysis showing why GCCA recovers the correct subspace containing the cell-edge user signals under mild conditions. The proposed method can also identify the number of cell-edge users in the system, i.e., the common subspace dimension. Simulations reveal significant performance improvement relative to various multiuser detection techniques. Cell-edge detection performance is further studied as a function of how many / which BSs are selected, and it is shown that using the closest three BS is always the best choice.

base station cooperation↗