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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Finite-temperature many-body perturbation theory for electrons: Algebraic recursive definitions, second-quantized derivation, linked-diagram theorem, general-order algorithms, and grand canonical and canonical ensembles

A comprehensive and detailed account is presented for the finite-temperature many-body perturbation theory for electrons that expands in power series all thermodynamic functions on an equal footing. Algebraic recursions in the style of the Rayleigh–Schrödinger perturbation theory are derived for the grand potential, chemical potential, internal energy, and entropy in the grand canonical ensemble and for the Helmholtz energy, internal energy, and entropy in the canonical ensemble, leading to their sum-over-states analytical formulas at any arbitrary order. For the grand canonical ensemble, these sum-over-states formulas are systematically transformed to sum-over-orbitals reduced analytical formulas by the quantum-field-theoretical techniques of normal-ordered second quantization and Feynman diagrams extended to finite temperature. It is found that the perturbation corrections to energies entering the recursions have to be treated as a nondiagonal matrix, whose off-diagonal elements are generally nonzero within a subspace spanned by degenerate Slater determinants. They give rise to a unique set of linked diagrams—renormalization diagrams—whose resolvent lines are displaced upward, which are distinct from the well-known anomalous diagrams of which one or more resolvent lines are erased. A linked-diagram theorem is introduced that proves the size-consistency of the finite-temperature many-body perturbation theory at any order. General-order algorithms implementing the recursions establish the convergence of the perturbation series toward the finite-temperature full-configuration-interaction limit unless the series diverges. As a result, the normal-ordered Hamiltonian at finite temperature sheds light on the relationship between the finite-temperature Hartree–Fock and first-order many-body perturbation theories.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Electrochemical CO2 Reduction over Metal-/Nitrogen-Doped Graphene Single-Atom Catalysts Modeled Using the Grand-Canonical Density Functional Theory

Renewably driven, electrochemical conversion of carbon dioxide into value-added products is expected to be a critical tool in global decarbonization. However, theoretical studies based on the computational hydrogen electrode largely ignore the nonlinear effects of the applied potential on the calculated results, leading to inaccurate predictions of catalytic behavior or mechanistic pathways. Here, we use grand canonical density functional theory (GC-DFT) to model electrochemical CO2 reduction (CO2R) over metal- and nitrogen-doped graphene catalysts (MNCs) and explicitly include the effects of the applied potential. We used GC-DFT to compute the CO2 to CO reaction intermediate energies at -0.3, -0.7, and -1.2 VSHE catalyzed by MNCs each doped with 1 of the 10 3d block metals coordinated by four pyridinic nitrogen atoms. Our results predict that Sc-, Ti-, Co-, Cu-, and Zn-N4Cs effectively catalyze CO2R at moderate to large reducing potentials (-0.7 to -1.2 VSHE). ZnN4C is a particularly promising electrocatalyst for CO2R to CO both at low and moderate applied potentials based on our thermodynamic analysis. Our findings also explain the observed pH independence of CO production over FeN4C and predict that the rate-determining step of CO2R over FeN4C is not *CO2- formation but rather *CO desorption. Additionally, the GC-DFT-computed density of states analysis illustrates how the electronic states of MNCs and adsorbates change non-uniformly with applied potential, resulting in a significantly increased *CO2- stability relative to other intermediates and demonstrating that the formation of the adsorbed *CO2- anion is critical to CO2R activation. This work demonstrates how GC-DFT paves the way for physically realistic and accurate theoretical simulations of reacting electrochemical systems.

CO2 reduction↗
DOE OSTI2026

Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases

White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic monomericcompounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into ß-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.

dioxygenase↗
DOE OSTI2024

BEAST DB: Grand-Canonical Database of Electrocatalyst Properties

We present BEAST DB, an open-source database comprised of ab initio electrochemical data computed using grand-canonical density functional theory in implicit solvent at consistent calculation parameters. The database contains over 20,000 surface calculations and covers a broad set of heterogeneous catalyst materials and electrochemical reactions. Calculations were performed at self-consistent fixed potential as well as constant charge to facilitate comparisons to the computational hydrogen electrode. This article presents common use cases of the database to rationalize trends in catalyst activity, screen catalyst material spaces, understand elementary mechanistic steps, analyze the electronic structure, and train machine learning models to predict higher fidelity properties. Users can interact graphically with the database by querying for individual calculations to gain a granular understanding of reaction steps or by querying for an entire reaction pathway on a given material using an interactive reaction pathway tool. BEAST DB will be periodically updated, with planned future updates to include advanced electronic structure data, surface speciation studies, and greater reaction coverage.

database↗
DOE OSTI2021

Comparison of the Forward and Reverse Photocycle Dynamics of Two Highly Similar Canonical Red/Green Cyanobacteriochromes Reveals Unexpected Differences

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that exhibit photochromism between two states: a thermally stable dark-adapted state and a metastable light-adapted state with bound linear tetrapyrrole (bilin) chromophores possessing 15Z and 15E configurations, respectively. The photodynamics of canonical red/green CBCRs have been extensively studied; however, the time scales of their excited-state lifetimes and subsequent ground-state evolution rates widely differ and, at present, remain difficult to predict. Here, we compare the photodynamics of two closely related red/green CBCRs that have substantial sequence identity (~68%) and similar chromophore environments: AnPixJg2 from Anabaena sp. PCC 7120 and NpR6012g4 from Nostoc punctiforme. Using broadband transient absorption spectroscopy on the primary (125 fs to 7 ns) and secondary (7 ns to 10 ms) time scales together with global analysis modeling, our studies revealed that AnPixJg2 and NpR6012g4 have comparable quantum yields for initiating the forward ( 15Z P r → 15E P g ) and reverse ( 15E P g → 15Z P r ) reactions, which proceed through monotonic and nonmonotonic mechanisms, respectively. In addition to small discrepancies in the kinetics, the secondary reverse dynamics resolved unique features for each domain: intermediate shunts in NpR6012g4 and a Meta-Gf intermediate red-shifted from the 15Z P r photoproduct in AnPixJg2. Altogether, this study supports the conclusion that sequence similarity is a useful criterion for predicting pathways of the light-induced evolution and quantum yield of generating primary intermediate Φ p within subfamilies of CBCRs, but more studies are still needed to develop a comprehensive molecular level understanding of these processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Stringy canonical forms

Canonical forms of positive geometries play an important role in revealing hidden structures of scattering amplitudes, from amplituhedra to associahedra. In this paper, we introduce “stringy canonical forms”, which provide a natural definition and extension of canonical forms for general polytopes, deformed by a parameter α'. They are defined by real or complex integrals regulated with polynomials with exponents, and are meromorphic functions of the exponents, sharing various properties of string amplitudes. As α'→ 0, they reduce to the usual canonical form of a polytope given by the Minkowski sum of the Newton polytopes of the regulating polynomials, or equivalently the volume of the dual of this polytope, naturally determined by tropical functions. At finite α', they have simple poles corresponding to the facets of the polytope, with the residue on the pole given by the stringy canonical form of the facet. There is the remarkable connection between the α'→ 0 limit of tree-level string amplitudes, and scattering equations that appear when studying the α'→ ∞ limit. We show that there is a simple conceptual understanding of this phenomenon for any stringy canonical form: the saddle-point equations provide a diffeomorphism from the integration domain to the interior of the polytope, and thus the canonical form can be obtained as a pushforward via summing over saddle points. When the stringy canonical form is applied to the ABHY associahedron in kinematic space, it produces the usual Koba-Nielsen string integral, giving a direct path from particle to string amplitudes without an a priori reference to the string worldsheet. We also discuss a number of other examples, including stringy canonical forms for finite-type cluster algebras (with type A corresponding to usual string amplitudes), and other natural integrals over the positive Grassmannian.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Finite temperature auxiliary field quantum Monte Carlo in the canonical ensemble

Finite temperature auxiliary field-based quantum Monte Carlo methods, including determinant quantum Monte Carlo and Auxiliary Field Quantum Monte Carlo (AFQMC), have historically assumed pivotal roles in the investigation of the finite temperature phase diagrams of a wide variety of multidimensional lattice models and materials. Despite their utility, however, these techniques are typically formulated in the grand canonical ensemble, which makes them difficult to apply to condensates such as superfluids and difficult to benchmark against alternative methods that are formulated in the canonical ensemble. Working in the grand canonical ensemble is furthermore accompanied by the increased overhead associated with having to determine the chemical potentials that produce desired fillings. Given this backdrop, in this work, we present a new recursive approach for performing AFQMC simulations in the canonical ensemble that does not require knowledge of chemical potentials. To derive this approach, we exploit the convenient fact that AFQMC solves the many-body problem by decoupling many-body propagators into integrals over one-body problems to which non-interacting theories can be applied. We benchmark the accuracy of our technique on illustrative Bose and Fermi–Hubbard models and demonstrate that it can converge more quickly to the ground state than grand canonical AFQMC simulations. We believe that our novel use of HS-transformed operators to implement algorithms originally derived for non-interacting systems will motivate the development of a variety of other methods and anticipate that our technique will enable direct performance comparisons against other many-body approaches formulated in the canonical ensemble.

Shen, Tong (ORCID:0000000206292468)↗
DOE OSTI2025

A non-canonical fungal peroxisome PTS-1 signal, SYM, and its evolutionary aspects

Abstract Proteins localized to peroxisomes, particularly those expressed under specific conditions or in low abundance, are often undetected by routine proteomics methods due to detection sensitivity limits. In silico identification and experimental validation of peroxisomal targeting signals (PTSs) offer a reliable alternative. We demonstrate that SYM, a non-canonical plant PTS-1 signal, functions similarly inAspergillus nidulans, as GFP tagged with a SYM C-terminal tripeptide localizes to peroxisomes. One of two nativeA. nidulansproteins with C-terminal SYM tripeptide shows weak peroxisomal localization alongside cytoplasmic presence, indicating that only a subset of proteins with non-canonical signals access peroxisomes.In silicoanalysis of 1,010 fungal genomes identified diverse SYM-proteins with variable functions, suggesting that non-canonical PTS-1 signals may evolve spontaneously. Two-thirds of SYM-proteins are predicted to localize to specific intracellular compartments other than the peroxisome. We propose that despite their predicted localization, these proteins possessing SYM as a non-canonical peroxisomal signal might also have peroxisomal presence. Among SYM-proteins, pectinesterases, known plant pathogen virulence factors, were frequent. Notably, 25% of fungal pectinesterases harbor non-canonical PTS-1 signals, suggesting that partial peroxisomal localization of pectinesterases has evolved convergently. This suggests that partial peroxisomal localization may enhance protein functional flexibility, contributing to the organism’s adaptability.

Science & Technology - Other Topics↗
DOE OSTI2019

Degenerate Hamiltonian operator in higher-order canonical gravity — The problem and a remedy

Different routes towards canonical formulation of a classical theory result in different canonically equivalent Hamiltonians, while their quantum counterparts are related through appropriate unitary transformation. However, for higher-order theory of gravity although two Hamiltonians emerging from the same action differing by total derivative terms are related through canonical transformation, the difference transpires while attempting canonical quantization, which is predominant in non-minimally coupled higher-order theory of gravity. We follow Dirac’s constraint analysis to formulate phase-space structures, in the presence (case-I) and absence (case-II) of total derivative terms. While the coupling parameter plays no significant role as such for case-I, quantization depends on its form explicitly in case-II, and as a result unitary transformation relating the two is not unique. We also find certain mathematical inconsistencies in case-I, for modified Gauss–Bonnet-Dilatonic coupled action, in particular. Thus, we conclude that total derivative terms indeed play a major role in the quantum domain and should be taken care of a-priori, for consistency.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Wave function methods for canonical ensemble thermal averages in correlated many-fermion systems

We present a wave function representation for the canonical ensemble thermal density matrix by projecting the thermofield double state against the desired number of particles. Furthermore, the resulting canonical thermal state obeys an imaginary-time evolution equation. Starting with the mean-field approximation, where the canonical thermal state becomes an antisymmetrized geminal power (AGP) wave function, we explore two different schemes to add correlation: by number-projecting a correlated grand-canonical thermal state and by adding correlation to the number-projected mean-field state. As benchmark examples, we use number-projected configuration interaction and an AGP-based perturbation theory to study the hydrogen molecule in a minimal basis and the six-site Hubbard model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Canonical Transformation to Eliminate Resonant Perturbations. I

We study dynamical systems that admit action-angle variables at leading order, which are subject to nearly resonant perturbations. If the frequencies characterizing the unperturbed system are not in resonance, the long-term dynamical evolution may be integrated by orbit-averaging over the high-frequency angles, thereby evolving the orbit-averaged effect of the perturbations. It is well known that such integrators may be constructed via a canonical transformation, which eliminates the high-frequency variables from the orbit-averaged quantities. An example of this algorithm in celestial mechanics is the von Zeipel transformation. However, if the perturbations are inside or close to a resonance, i.e., the frequencies of the unperturbed system are commensurate; these canonical transformations are subject to divergences. We introduce a canonical transformation that eliminates the high-frequency phase variables in the Hamiltonian without encountering divergences. This leads to a well-behaved symplectic integrator. We demonstrate the algorithm through two examples: a resonantly perturbed harmonic oscillator and the gravitational three-body problem in mean motion resonance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Clebsch canonization of Lie–Poisson systems

We propose a systematic procedure called the Clebsch canonization for obtaining a canonical Hamiltonian system that is related to a given Lie–Poisson equation via a momentum map. We describe both coordinate and geometric versions of the procedure, the latter apparently for the first time. We also find another momentum map so that the pair of momentum maps constitute a dual pair under a certain condition. The dual pair gives a concrete realization of what is commonly referred to as collectivization of Lie–Poisson systems. It also implies that solving the canonized system by symplectic Runge–Kutta methods yields so-called collective Lie–Poisson integrators that preserve the coadjoint orbits and hence the Casimirs exactly. We give a couple of examples, including the Kida vortex and the heavy top on a movable base with controls, which are Lie–Poisson systems on $\mathfrak{so}$ (2,1)* and ($\mathfrak{se}$ (3) ⋉ $\mathbb{R}^3$)* and, respectively.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Nonnegative canonical tensor decomposition with linear constraints: nnCANDELINC

Abstract There is an emerging interest for tensor factorization applications in big‐data analytics and machine learning. To speed up the factorization of extra‐large datasets, organized in multidimensional arrays (also known as tensors), easy to compute compression‐based tensor representations, such as, Tucker and tensor train formats, are used to approximate the initial large‐tensor. Further, tensor factorization is used to extract latent features that can facilitate discoveries of new mechanisms and signatures hidden in the data, where the explainability of the latent features is of principal importance. Nonnegative tensor factorization extracts latent features that are naturally sparse and parts of the data, which makes them easily interpretable. However, to take into account available domain knowledge and subject matter expertise, often additional constraints need to be imposed, which lead us to canonical decomposition with linear constraints (CANDELINC), a canonical polyadic decomposition with rank deficient factors. In CANDELINC, Tucker compression is used as a preprocessing step, which lead to a larger residual error but to more explainable latent features. Here, we propose a nonnegative CANDELINC (nnCANDELINC) accomplished via a specific nonnegative Tucker decomposition; we refer to as minimal or canonical nonnegative Tucker. We derive several results required to understand the specificity of nnCANDELINC, focusing on the difficulties of preserving the nonnegative rank of a tensor to its Tucker core and comparing the real valued to nonnegative case. Finally, we demonstrate nnCANDELINC performance on synthetic and real‐world examples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Scattering amplitudes and simple canonical forms for simple polytopes

We provide an efficient recursive formula to compute the canonical forms of arbitrary d-dimensional simple polytopes, which are convex polytopes such that every vertex lies precisely on d facets. For illustration purposes, we explicitly derive recursive formulae for the canonical forms of Stokes polytopes, which play a similar role for a theory with quartic interaction as the Associahedron does in planar bi-adjoint φ 3 theory. As a by-product, our formula also suggests a new way to obtain the full planar amplitude in φ 4 theory by taking suitable limits of the canonical forms of constituent Stokes polytopes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

A canonical purification for the entanglement wedge cross-section

In AdS/CFT we consider a class of bulk geometric quantities inside the entanglement wedge called reflected minimal surfaces. The areas of these surfaces are dual to the entanglement entropy associated to a canonical purification (the GNS state) that we dub the reflected entropy. From the bulk point of view, we show that half the area of the reflected minimal surface gives a reinterpretation of the notion of the entanglement wedge cross-section. We prove some general properties of the reflected entropy and introduce a novel replica trick in CFTs for studying it. The duality is established using a recently introduced approach to holographic modular flow. We also consider an explicit holographic construction of the canonical purification, introduced by Engelhardt and Wall; the reflected minimal surfaces are simply RT surfaces in this new spacetime. We contrast our results with the entanglement of purification conjecture, and finally comment on the continuum limit where we find a relation to the split property: the reflected entropy computes the von Neumann entropy of a canonical splitting type-I factor introduced by Doplicher and Longo.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

On the canonical formulation of gauge field theories and Poincaré transformations

We address the Hamiltonian formulation of classical gauge field theories while putting forward results some of which are not entirely new, though they do not appear to be well known. We refer in particular to the fact that neither the canonical energy momentum vector ( P μ ) nor the gauge invariant energy momentum vector ( P inv μ ) do generate space-time translations of the gauge field by means of the Poisson brackets: In a general gauge, one has to consider the so-called kinematical energy momentum vector and, in a specific gauge (like the radiation gauge in electrodynamics), one has to consider the Dirac brackets rather than the Poisson brackets. Similar arguments apply to rotations and to Lorentz boosts and are of direct relevance to the “nucleon spin crisis” since the spin of the proton involves a contribution which is due to the angular momentum vector of gluons and thereby requires a proper treatment of the latter. We conclude with some comments on the relationships between the different approaches to quantization (canonical quantization based on the classical Hamiltonian formulation, Gupta-Bleuler, path integrals, BRST, covariant canonical approaches).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗