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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 OSTI2024

Mechanisms in the Synthesis of S -Alcohols with 1,4-NADH Biomimetic Co-factor N-Benzyl-1,4-dihydronicotinamide using Horse Liver Alcohol Dehydrogenase: A Hybrid Computational Study

The enantioselective reduction of prochiral ketones catalyzed by horse liver alcohol dehydrogenase (HLADH), was investigated via a hybrid computational approach, for molecular reactions involved in chiral synthesis of S-alcohols, when the natural co-factor, 1,4-dihyronicotinamide adenine dinucleotide, 1,4-NADH, was replaced with biomimetic co-factor, N-benzyl-1,4-dihydronicotinamide, 1. We surmised that different hydride and proton transfer mechanisms were involved using co-factor, 1. An alternative mechanism, where the hydride transfer step occurred, via an η 1 -keto-S-η 2 -5,6-1,4-dihydronicotinamide-Zn(II) complex, was previously investigated with a model of the HLADH-Zn(II) catalytic site (J. Organometal. Chem. 2021, 943, 121810). Presently, we studied canonical and alternative mechanisms compared to models of the entire enzyme structure. We disproved the η 2 -Zn(II) complex, and discovered a canonical hydride transfer from biomimetic 1,4-NADH, 1, to the Zn(II) bound prochiral ketone substrate, followed by a new proton relay, consisting of a water chain connecting His51 to Ser48 that accomplished the S-alkoxy anion's protonation to yield the final S-alcohol product. The HLADH catalysis, with biomimetic co-factor, 1, that replaced the ribose group, the 5'-diphosphate groups, and the adenine nucleotide with a N-benzyl group, has provided a new paradigm for the design of other structures of 1,4-NADH biomimetic co-factors, including their economic value in biocatalysis reactions.

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

Projector‐Based Quantum Embedding Study of Iron Complexes

Projection‐based embedding theory (PBET) is used to calculate and assess the challenging spin‐crossover energies for a selection of small Fe‐containing systems by embedding the metal center into the frozen potential of the ligands. MP2, CCSD, and CCSD(T) are embedded in potentials from the SCAN and r 2 SCAN functionals and compared with the canonical values for the constituent methods and previously reported reference values. Considering the PBET calculations as a correction for the underlying DFT, the embedding calculations are able to provided improvement for most cases. In some cases, the PBET methods are able to compensate for limitations in the wave function methods and produce results similar to more rigorous calculations from the literature. For the systems with spin‐crossover energies near zero, the current methodology fails to provide consistent improvement. In conclusion, the isolated recalculation of the electronic structure around the metal center when embedded into a DFT treatment of the ligand field shows promise as a pragmatic and lower cost treatment compared to the canonical treatment of the whole system of the difficult class of spin‐crossover complexes.

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

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Constraints on a generalization of geometric quantum mechanics from neutrino and B0-$$ \overline{B^0} $$ oscillations

Abstract Nambu Quantum Mechanics, proposed in Phys. Lett. B536, 305 (2002), is a deformation of canonical Quantum Mechanics in which the manifold over which the “phase” of an energy eigenstate time evolves is modified. This generalization affects oscillation and interference phenomena through the introduction of two deformation parameters that quantify the extent of deviation from canonical Quantum Mechanics. In this paper, we constrain these parameters utilizing atmospheric neutrino oscillation data, andB 0 -$$ \overline{B^0} $$ B 0 ¯ oscillation data from Belle. Surprisingly, the bound from atmospheric neutrinos is stronger than the bound from Belle. Various features of Nambu Quantum Mechanics are also discussed.

Physics↗
DOE OSTI2021

Non-perturbative geometries for planar $ \mathcal{N} $ = 4 SYM amplitudes

There is a remarkable well-known connection between the G(4, n) cluster algebra and n-particle amplitudes in $ \mathcal{N} $ = 4 SYM theory. For n ≥ 8 two long-standing open questions have been to find a mathematically natural way to identify a finite list of amplitude symbol letters from among the infinitely many cluster variables, and to find an explanation for certain algebraic functions, such as the square roots of four-mass-box type, that are expected to appear in symbols but are not cluster variables. In this letter we use the notion of “stringy canonical forms” to construct polytopal realizations of certain compactifications of (the positive part of) the configuration space Conf n (P k–1 ) ≅ G(k, n)/T that are manifestly finite for all k and n. Some facets of these polytopes are naturally associated to cluster variables, while others are naturally associated to algebraic functions constructed from Lusztig’s canonical basis. For (k, n) = (4, 8) the latter include precisely the expected square roots, revealing them to be related to certain “overpositive” functions of the kinematical invariants.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Sign flip triangulations of the amplituhedron

We present new triangulations of the m = 4 amplituhedron relevant for scattering amplitudes in planar N = 4 super-Yang-Mills, obtained directly from the combinatorial definition of the geometry. Using the “sign flip” characterization of the amplituhedron, we reproduce the canonical forms for the all-multiplicity next-tomaximally helicity violating (NMHV) and next-to-next-to-maximally helicity violating (N2MHV) tree-level as well as the NMHV one-loop cases, without using any input from traditional amplitudes methods. Our results provide strong evidence for the equivalence of the original definition of the amplituhedron [1] and the topological one [2], and suggest a new path forward for computing higher loop amplitudes geometrically. In particular, we realize the NMHV one-loop amplituhedron as the intersection of two amplituhedra of lower dimensionality, which is reflected in the novel structure of the corresponding canonical form.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

A new Wilson line-based action for gluodynamics

We perform a canonical transformation of fields that brings the Yang-Mills action in the light-cone gauge to a new classical action, which does not involve any triple-gluon vertices. The lowest order vertex is the four-point MHV vertex. Higher point vertices include the MHV and $\overline{\mathrm{MHV}}$ vertices, that reduce to the corresponding amplitudes in the on-shell limit. In general, any n -leg vertex has 2 ≤ m ≤ n - 2 negative helicity legs. The canonical transformation of fields can be compactly expressed in terms of path-ordered exponentials of fields and their functional derivative. We apply the new action to compute several tree-level amplitudes, up to 8-point NNMHV amplitude, and find agreement with the standard methods. The absence of triple-gluon vertices results in fewer diagrams required to compute amplitudes, when compared to the CSW method and, obviously, considerably fewer than in the standard Yang-Mills action.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Measurement of correlations among net-charge, net-proton, and net-kaon multiplicity distributions in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV

Correlations among conserved quantum numbers, such as the net-electric charge, the net-baryon, and the net-strangeness in heavy-ion collisions, are crucial for exploring the QCD phase diagram. In this paper, these correlations are investigated using net-proton number (as a proxy for the net-baryon), net-kaon number (for the net-strangeness), and net-charged particle number in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV with the ALICE detector. The observed correlations deviate from the Poissonian baseline, with a more pronounced deviation at LHC energies than at RHIC. Theoretical calculations of the Thermal-FIST hadron resonance gas model, HIJING, and EPOS LHC event generators are compared with experimental results, where a significant impact of resonance decays is observed. Thermal-FIST calculations under the grand canonical and canonical ensembles highlight significant differences, underscoring the role of local charge conservation in explaining the data. Recent lattice QCD studies have demonstrated that the magnetic field generated by spectator protons in heavy-ion collisions affects susceptibility ratios, in particular those related to the net-electric charge and the net-baryon numbers. The experimental findings are in qualitative agreement with the expectations of lattice QCD.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Off-shell Partition Functions in 3d Gravity

We explore three-dimensional gravity with negative cosmological constant via canonical quantization. We focus on chiral gravity which is related to a single copy of PSL(2,R) Chern-Simons theory and is simpler to treat in canonical quantization. Its phase space for an initial value surface Σ is given by the appropriate moduli space of Riemann surfaces. We use geometric quantization to compute partition functions of chiral gravity on three-manifolds of the form Σ×S 1 , where Σ can have asymptotic boundaries. Most of these topologies do not admit a classical solution and are thus not amenable to a direct semiclassical path integral computation. We use an index theorem that expresses the partition function as an integral of characteristic classes over phase space. In the presence of n asymptotic boundaries, we use techniques from equivariant cohomology to localize the integral to a finite-dimensional integral over $\overline{M}$ g,n , which we evaluate in low genus cases. Higher genus partition functions quickly become complicated since they depend in an oscillatory way on Newton's constant. There is a precise sense in which one can isolate the non-oscillatory part which we call the fake partition function. We establish that there is a topological recursion that computes the fake partition functions for arbitrary Riemann surfaces Σ. As a result, there is a scaling limit in which the model reduces to JT gravity and our methods give a novel way to compute JT partition functions via equivariant localization.

Classical and Quantum Gravity↗
DOE OSTI2024

Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers

Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here, in this work, we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel “dimer of dimers” mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Strigolactones: diversity, perception, and hydrolysis

Abstract Strigolactones (SLs) are a unique and novel class of phytohormones that regulate numerous processes of growth and development in plants. Besides their endogenous functions as hormones, SLs are exuded by plant roots to stimulate critical interactions with symbiotic fungi but can also be exploited by parasitic plants to trigger their seed germination. In the past decade, since their discovery as phytohormones, rapid progress has been made in understanding the SL biosynthesis and signaling pathway. Of particular interest are the diversification of natural SLs and their exact mode of perception, selectivity, and hydrolysis by their dedicated receptors in plants. Here we provide an overview of the emerging field of SL perception with a focus on the diversity of canonical, non-canonical, and synthetic SL probes. Moreover, this review offers useful structural insights into SL perception, the precise molecular adaptations that define receptor-ligand specificities, and the mechanisms of SL hydrolysis and its attenuation by downstream signaling components.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantum multi-programming for Grover’s search

Quantum multi-programming is a method utilizing contemporary noisy intermediate-scale quantum computers by executing multiple quantum circuits concurrently. Despite early research on it, the research remains on quantum gates or small-size quantum algorithms without correlation. In this paper, we propose a quantum multi-programming (QMP algorithm for Grover's search. Our algorithm decomposes Grover's algorithm by the partial diffusion operator and executes the decomposed circuits in parallel by QMP. We proved that this new algorithm increases the rotation angle of the Grover operator which, as a result, increases the success probability. The new algorithm is implemented on IBM quantum computers and compared with the canonical Grover's algorithm and other variations of Grover's algorithms. So, the empirical tests validate that our new algorithm outperforms other variations of Grover's algorithms as well as the canonical Grover's algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Order Parameter Engineering for Random Systems

The chemical short-range order (CSRO) in crystalline materials influences the properties, and its effect is significant in the context of multicomponent materials. Here, we propose a scheme for the CSRO parameter or Δ-parameter in terms of the number of like and unlike bonds in the multicomponent systems. The OPERA or Order Parameter Engineering for RAndom Systems scheme for semi-canonical and canonical ensembles is proposed. The proposed framework of Δ-parameter with OPERA framework can generate the single-phase supercell with desired CSRO without explicit energy calculations and provides a computationally efficient scheme for exploration of the CSRO. We demonstrate the applicability of the Δ-parameter as a scalar quantity for describing the CSRO in multicomponent alloys and oxides (FCC-CoCrNi, BCC-MoNbTaW, and (CoCuMgNiZn)O).

36 MATERIALS SCIENCE↗
DOE OSTI2025

Fundamental microscopic properties as predictors of large-scale quantities of interest: Validation through grain boundary energy trends

Correlations between fundamental microscopic properties computable from first principles, which we term canonical properties, and complex large-scale quantities of interest (QoIs) provide an avenue to predictive materials discovery. Here, we propose that such correlations can be efficiently discovered through simulations utilizing approximate interatomic potentials (IPs), which serve as an ensemble of “synthetic materials”. As a proof of principle we build a regression model relating canonical properties to the symmetric tilt grain boundary (GB) energy curves in face-centered cubic crystals, characterized by the scaling factor in the universal lattice matching model of Runnels et al. (2016), which we take to be our QoI. Our analysis recovers known correlations of GB energy to other properties and discovers new ones. We also demonstrate, using available density functional theory (DFT) GB energy data, that the regression model constructed from IP data is consistent with DFT results, confirming the assumption that the IPs and DFT belong to same statistical pool and thereby validating the approach. Regression models constructed in this fashion can be used to predict large-scale QoIs based on first-principles data and provide a general method for training IPs for QoIs beyond the scope of first-principles calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Stochastic symplectic reduced-order modeling for model-form uncertainty quantification in molecular dynamics simulations in various statistical ensembles

Here, this work focuses on the representation of model-form uncertainties in molecular dynamics simulations in various statistical ensembles. In prior contributions, the modeling of such uncertainties was formalized and applied to quantify the impact of, and the error generated by, pair-potential selection in the microcanonical ensemble (NVE). In this work, we extend this formulation and present a linear-subspace reduced-order model for the canonical (NVT) and isobaric (NPT) ensembles. The symplectic reduced-order basis is randomized on the tangent space of the Stiefel manifold to provide topological relationships and capture model-form uncertainty. Using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), we assess the relevance of these stochastic reduced-order atomistic models on canonical problems involving a Lennard-Jones fluid and an argon crystal melt.

42 ENGINEERING↗
DOE OSTI2020

Grain boundary structure search by using an evolutionary algorithm with effective mutation methods

Grain boundaries (GBs) accommodate the misorientation between adjacent grains in a polycrystalline material. GBs are geometrically described by the macroscopic and microscopic degrees of freedom. Besides, at the atomistic level, GBs exhibit complicated behaviors under varying thermodynamic conditions. The complexity of atomistic GB structures demands stochastic searching for possible states. The effectiveness of stochastic search methods relies on techniques to recreate and select atomistic structures. In this work, we developed a new mutation operator that can induce direct and collective atomistic structure changes to boost the search efficiency of exploring GB structures with evolutionary algorithms (EA). We implemented the mutation methods along with innovative selection, crossover, boundary condition preprocessing methods to form an EA-based package to explore GB structures in grand canonical ensembles with atomistic simulations. We used this package to study the [001] symmetric tilt grain boundaries (STGBs) in FCC copper (Cu), the [110] STGBs in BCC tungsten (W), and the $[1\bar{2}10]$ STGBs in HCP magnesium (Mg). The results show that our design and implementation based on new mutation procedures, selection, and boundary conditions provide a high-quality search of atomistic GB structures in the grand canonical ensemble for different crystal lattices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Pilgrim : A thermal rate constant calculator and a chemical kinetics simulator

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. Finally, this algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Reducing the complexity of finite-temperature auxiliary-field quantum Monte Carlo

The auxiliary-field quantum Monte Carlo (AFMC) method is a powerful and widely used technique for ground-state and finite-temperature simulations of quantum many-body systems. Here we introduce several algorithmic improvements for finite-temperature AFMC calculations of dilute fermionic systems that reduce the computational complexity of most parts of the algorithm. This is principally achieved by reducing the number of single-particle states that contribute at each configuration of the auxiliary fields to a number that is of the order of the number of fermions. Our methods are applicable for both the canonical and grand-canonical ensembles. We demonstrate the reduced computational complexity of the methods for the homogeneous unitary Fermi gas.

67.85.Lm↗