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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 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N -formyl of the peptide precursor

Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP via a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which consumes two equivalents of ATP to generate the N–P linkage. We demonstrate that MccB only efficiently processes the precursor heptapeptide that retains the Nformylated initiator Met (fMet). Binding studies and kinetic measurements evidence the role of the N-formyl moiety. Structural data show that the N-formyl peptide binding results in an ordering of residues in the MccB “crossover loop”, which dictates specificity in homologous ubiquitin activating enzymes. The N-formyl peptide exhibits substrate inhibition, and cannot be displaced from MccB by the desformyl counterpart. Such substrate inhibition may be a strategy to avert unwanted McC buildup and avert toxicity in the cytoplasm of producing organisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

On the nonadiabatic collisional quenching of OH(A) by H 2 : a four coupled quasi-diabatic state description

A four-state diabatic potential energy matrix (DPEM), H d , for the description of the nonadiabatic quenching of OH(A 2 Σ + ) by collisions with H 2 is reported. The DPEM is constructed as a fit to adiabatic energies, energy gradients, and derivative couplings obtained exclusively from multireference configuration interaction wave functions. A four-adiabatic-electronic-state representation is used in order to describe all energetically accessible regions of the nuclear coordinate space. Partial permutation-inversion symmetry is incorporated into the representation. Here, the fit is based on electronic structure data at 42 882 points, described by over 1.6 million least squares equations with a root mean square (mean unsigned) error of 178(83) cm –1 . Comparison of ab initio and H d determined minima, saddle points, and energy minimized points on C 2v , C s , C ∞v , and C 1 (noncoplanar) portions of two conical intersection seams are used to establish the accuracy of the H d .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Internal conversion and intersystem crossing dynamics based on coupled potential energy surfaces with full geometry-dependent spin–orbit and derivative couplings. Nonadiabatic photodissociation dynamics of NH 3 (A) leading to the NH(X 3 Σ – , a 1 Δ) + H 2 channel

Here we simulate the photodissociation of NH 3 originating from its first excited singlet state S 1 into the NH 2 + H (radical) and NH + H 2 (molecular) channels. The states considered are the ground singlet state S 0 , the first excited singlet state S 1 and the lowest-lying triplet state T 1 , which permit for the first time a uniform treatment of the internal conversion and intersystem crossing. The simulations are based on a diabatic potential energy matrix (DPEM) of S 0 , S 1 coupled by a conical intersection seam, as well as a potential energy surface (PES) for T 1 coupled by spin-orbit coupling (SOC) to the two singlet states. The DPEM and PES are fitted to ab initio electronic structure data (ESD) including energies, energy gradients, and derivative couplings. The DPEM also defines an adiabatic to diabatic state (AtD) transformation, which is used to transform the singular adiabatic SOC into a smooth function of the nuclear coordinates in the diabatic representation, allowing the diabatic SOC to be fit to an analytical functional form. ESD and SOC data obtained from these surfaces can serve as input for either quantum or semi-classical characterization of the nonadiabatic dynamics. Using the SHARC suite of programs, nonadiabatic simulations based on over 40 000 semi-classical trajectories assess the convergence of our results. The production of NH + H 2 is not direct, but is only achieved through a quasi-statistical dissociation mechanism after internal conversion to the ground electronic state. This leads to a much lower yield comparing with the main NH 2 + H channel. The NH(X 3 Σ_) radical produced through the intersystem crossing from S 0 to T 1 is rare (~0.2%) compared to NH(a 1 Δ) due to the process being spin forbidden.

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

Structural and thermal properties of ultralow thermal conductivity Ba 3 Cu 2 Sn 3 Se 10

The thermal properties of Ba 3 Cu 2 Sn 3 Se 10 were investigated by measurement of the thermal conductivity and heat capacity. The chemical bonding in this diamagnetic material was investigated using structural data from Rietveld refinement and calculated electron localization. This quaternary chalcogenide is monoclinic (P2 1 /c), has a large unit cell with 72 atoms in the primitive cell, and a high local coordination environment. Additionally, the Debye temperature (162 K) and average speed of sound (1666 m s -1 ) are relatively low with a very small electronic contribution to the heat capacity. Ultralow thermal conductivity (0.46 W m -1 K -1 at room temperature) is attributed to the relatively weak chemical bonding and intrinsic anharmonicity, in addition to a large unit cell. This work is part of the continuing effort to explore quaternary chalcogenides with intrinsically low thermal conductivity and identify the features that result in a low thermal conductivity.

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

SAXS-guided unbiased coarse-grained Monte Carlo simulation for identification of self-assembly nanostructures and dimensions

Recent studies have shown that solvated amphiphiles can form nanostructured self-assemblies called dynamic binary complexes (DBCs) in the presence of ions. Since the nanostructures of DBCs are directly related to their viscoelastic properties, it is important to understand how the nanostructures change under different solution conditions. However, it is challenging to obtain a three-dimensional molecular description of these nanostructures by utilizing conventional experimental characterization techniques or thermodynamic models. To this end, we combined the structural data from small angle X-ray scattering (SAXS) experiments and thermodynamic knowledge from coarse-grained Monte Carlo (CGMC) simulations to identify the detailed three-dimensional nanostructure of DBCs. Specifically, unbiased CGMC simulations are performed with SAXS-guided initial conditions, which aids us to sample accurate nanostructures in a computationally efficient fashion. As a result, an elliptical bilayer nanostructure is obtained as the most probable nanostructure of DBCs whose dimensions are validated by scanning electron microscope (SEM) images. Then, utilizing the obtained molecular model of DBCs, here we could also explain the pH tunability of the system. Overall, our results from SAXS-guided unbiased CGMC simulations highlight that using potential energy combined with SAXS data, we can distinguish otherwise degenerate nanostructures resulting from the inherent ambiguity of SAXS patterns.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Towards non-contact pollution monitoring in sewers with hyperspectral imaging

Monitoring water quality in sewers is challenging, particularly because state-of-the-art technologies require contact with the raw wastewater. The presence of fat, oil, grease, and solids makes automated grab sampling difficult and causes sensor fouling. To overcome these limitations, non-contact methods based on light reflectance, such as hyperspectral imaging (HSI), are gaining attention. However, HSI has never been tested for raw wastewater. To assess its accuracy for measuring pollution, we developed a laboratory setup and performed targeted experiments with a combination of raw and diluted wastewater, as well as synthetic turbidity stock solutions. We measured seven pollution variables: chemical oxygen demand, turbidity, dissolved organic compounds, ammonium, total nitrogen, phosphate, and sulphates. We used automated pixel selection and partial least squares regression to retrieve pollution information from the hyperspectral images. Our results, based on 144 samples, suggest that HSI can estimate pollution levels with a precision in the range of state-of-the-art absorbance spectrophotometric methods. Additionally, we found that the combination of pixel and wavelength selection, enabled by the hyperspectral data structure, significantly influences the performance of partial least square modelling. Overall, our findings indicate that HSI is a promising technology for non-contact monitoring of water quality in raw wastewater.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

In situ studies of reversible solid–gas reactions of ethylene responsive silver pyrazolates

Solid–gas reactions and in situ powder X-ray diffraction investigations of trinuclear silver complexes {[3,4,5-(CF 3 ) 3 Pz]Ag} 3 and {[4-Br-3,5-(CF 3 ) 2 Pz]Ag} 3 supported by highly fluorinated pyrazolates reveal that they undergo intricate ethylene-triggered structural transformations in the solid-state producing dinuclear silver–ethylene adducts. Despite the complexity, the chemistry is reversible producing precursor trimers with the loss of ethylene. Less reactive {[3,5-(CF 3 ) 2 Pz]Ag} 3 under ethylene pressure and low-temperature conditions stops at an unusual silver–ethylene complex in the trinuclear state, which could serve as a model for intermediates likely present in more common trimer–dimer reorganizations described above. Complete structural data of three novel silver–ethylene complexes are presented together with a thorough computational analysis of the mechanism.

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

Delocalization error poisons the density-functional many-body expansion

The many-body expansion is a fragment-based approach to large-scale quantum chemistry that partitions a single monolithic calculation into manageable subsystems. This technique is increasingly being used as a basis for fitting classical force fields to electronic structure data, especially for water and aqueous ions, and for machine learning. Here, we show that the many-body expansion based on semilocal density functional theory affords wild oscillations and runaway error accumulation for ion–water interactions, typified by F − (H 2 O) N with N ≳ 15. We attribute these oscillations to self-interaction error in the density-functional approximation. The effect is minor or negligible in small water clusters, explaining why it has not been noticed previously, but grows to catastrophic proportion in clusters that are only moderately larger. This behavior can be counteracted with hybrid functionals but only if the fraction of exact exchange is ≳50%, whereas modern meta-generalized gradient approximations including ωB97X-V, SCAN, and SCAN0 are insufficient to eliminate divergent behavior. Other mitigation strategies including counterpoise correction, density correction (i.e., exchange–correlation functionals evaluated atop Hartree–Fock densities), and dielectric continuum boundary conditions do little to curtail the problematic oscillations. In contrast, energy-based screening to cull unimportant subsystems can successfully forestall divergent behavior. These results suggest that extreme caution is warranted when the many-body expansion is combined with density functional theory.

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

QuaSiMo: A composable library to program hybrid workflows for quantum simulation

Abstract A composable design scheme is presented for the development of hybrid quantum/classical algorithms and workflows for applications of quantum simulation. The proposed object‐oriented approach is based on constructing an expressive set of common data structures and methods that enables programming of a broad variety of complex hybrid quantum simulation applications. The abstract core of the scheme is distilled from the analysis of the current quantum simulation algorithms. Subsequently, it allows synthesis of new hybrid algorithms and workflows via the extension, specialisation, and dynamic customisation of the abstract core classes defined by the proposed design. The design scheme is implemented using the hardware‐agnostic programming language QCOR into the QuaSiMo library. To validate the implementation, the authors test and show its utility on commercial quantum processors from IBM and Rigetti, running some prototypical quantum simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

dCache – Efficient Message Encoding For Inter-Service Communication in dCache: Evaluation of Existing Serialization Protocols as a Replacement for Java Object Serialization

As a well established, large-scale distributed storage system, dCache is used to manage and serve huge amounts of data collected by high energy physics, astrophysics and photon science experiments. Based on a microservices-like architecture, dCache is built as a modular distributed system, where each component provides a different core functionality. These services communicate by passing serialized messages to each other, a core behavior whose performance properties can consequently affect the entire system.This paper compares and evaluates different data serialization protocols in computer science with the objective of replacing and improving upon Java Object Serialization (JOS), which has increasingly presented itself as no longer being sufficiently performant for encoding messages. The criteria for choosing a new framework are collected, analyzed and formalized. The primary motivation for replacing Java serialization for encoding dCache messages is increasing the general speed of message-passing and thereby reducing the round-trip time for user requests. Emphasis is also placed on schema evolution capabilities and framework usability. Approaches for generalizing (de)serialization speed and size measurements based on data structure complexity are introduced, criteria for measuring documentation, learning curve, maintainability and introduction effort are defined. Finally, several selected serialization protocols are evaluated and compared accordingly, concluding with a recommendation for a suitable JOS replacement.

Morschel, Lea↗
DOE OSTI2015

Constant-complexity stochastic simulation algorithm with optimal binning

At the molecular level, biochemical processes are governed by random interactions between reactant molecules, and the dynamics of such systems are inherently stochastic. When the copy numbers of reactants are large, a deterministic description is adequate, but when they are small, such systems are often modeled as continuous-time Markov jump processes that can be described by the chemical master equation. Gillespie’s Stochastic Simulation Algorithm (SSA) generates exact trajectories of these systems, but the amount of computational work required for each step of the original SSA is proportional to the number of reaction channels, leading to computational complexity that scales linearly with the problem size. The original SSA is therefore inefficient for large problems, which has prompted the development of several alternative formulations with improved scaling properties. We describe an exact SSA that uses a table data structure with event time binning to achieve constant computational complexity with respect to the number of reaction channels for weakly coupled reaction networks. We present a novel adaptive binning strategy and discuss optimal algorithm parameters. We compare the computational efficiency of the algorithm to existing methods and demonstrate excellent scaling for large problems. This method is well suited for generating exact trajectories of large weakly coupled models, including those that can be described by the reaction-diffusion master equation that arises from spatially discretized reaction-diffusion processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Point-in-convex polygon and point-in-convex polyhedron algorithms with O(1) complexity using space subdivision

There are many space subdivision and space partitioning techniques used in many algorithms to speed up computations. They mostly rely on orthogonal space subdivision, resp. using hierarchical data structures, e.g. BSP trees, quadtrees, octrees, kd-trees, bounding volume hierarchies etc. However in some applications a non-orthogonal space subdivision can offer new ways for actual speed up. In the case of convex polygon in E{sup 2} a simple Point-in-Polygon test is of the O(N) complexity and the optimal algorithm is of O(log N) computational complexity. In the E{sup 3} case, the complexity is O(N) even for the convex polyhedron as no ordering is defined. New Point-in-Convex Polygon and Point-in-Convex Polyhedron algorithms are presented based on space subdivision in the preprocessing stage resulting to O(1) run-time complexity. The presented approach is simple to implement. Due to the principle of duality, dual problems, e.g. line-convex polygon, line clipping, can be solved in a similarly.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Multistate, multichannel coupled diabatic state representations of adiabatic states coupled by conical intersections. CH 2 OH photodissociation

In this work, a coupled diabatic state representation, H d , of the 1, 2, 3 2 A states of CH 2 OH suitable for the description of the three channel, three state photodissociation process CH 2 OH(1 2 A) + hv → CH 2 OH(2, 3 2 A) → CH 2 O(X, A) + H, cis-CHOH + H, trans-CHOH + H, is reported. The representation is based on electronic structure data (energies, energy gradients, and derivative couplings) obtained exclusively from multireference configuration interaction single and double excitation wave functions. Diabat shifting is employed to improve the representation’s agreement with accurate experimental energetics. A careful analysis of the numerous minima, saddle points, and conical intersection seams is reported. The computed T 0 (3 2 A) ~ 35 220 cm -1 is in excellent agreement with the experimental estimate of 35 053 cm -1 , and the computed channel dissociation energies, D 0 , for CH 2 O 9453 (10 160), cis-HCOH 30 310.2 (29 923), and trans-HCOH 28 799 (28 391) cm -1 are in good accord with the measured values given parenthetically. Lastly, these accurate energetics over a wide range of nuclear configurations strongly support the ability of this H d to enable quality simulations of nonadiabatic dynamics.

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

Permutation invariant polynomial neural network based diabatic ansatz for the ( E + A ) × ( e + a ) Jahn–Teller and Pseudo-Jahn–Teller systems

In this work, the permutation invariant polynomial neural network (PIP-NN) approach is employed to construct a quasi-diabatic Hamiltonian for system with non-Abelian symmetries. It provides a flexible and compact NN-based diabatic ansatz from the related approach of Williams, Eisfeld, and co-workers. The example of $H^3_+$ is studied, which is an (E + A) × (e + a) Jahn–Teller and Pseudo-Jahn–Teller system. The PIP-NN diabatic ansatz is based on the symmetric polynomial expansion of Viel and Eisfeld, the coefficients of which are expressed with neural network functions that take permutation-invariant polynomials as input. This PIP-NN-based diabatic ansatz not only preserves the correct symmetry but also provides functional flexibility to accurately reproduce ab initio electronic structure data, thus resulting in excellent fits. Further, the adiabatic energies, energy gradients, and derivative couplings are well reproduced. A good description of the local topology of the conical intersection seam is also achieved. Therefore, this diabatic ansatz completes the PIP-NN based representation of DPEM with correct symmetries and will enable us to diabatize even more complicated systems with complex symmetries.

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

Flexible, integrated modeling of tokamak stability, transport, equilibrium, and pedestal physics

The STEP (Stability, Transport, Equilibrium, and Pedestal) integrated-modeling tool has been developed in OMFIT to predict stable, tokamak equilibria self-consistently with core-transport and pedestal calculations. STEP couples theory-based codes to integrate a variety of physics, including magnetohydrodynamic stability, transport, equilibrium, pedestal formation, and current-drive, heating, and fueling. The input/output of each code is interfaced with a centralized ITER-Integrated Modelling & Analysis Suite data structure, allowing codes to be run in any order and enabling open-loop, feedback, and optimization workflows. This paradigm simplifies the integration of new codes, making STEP highly extensible. STEP has been verified against a published benchmark of six different integrated models. Core-pedestal calculations with STEP have been successfully validated against individual DIII-D H-mode discharges and across more than 500 discharges of the H98,y2 database, with a mean error in confinement time from experiment less than 19%. STEP has also reproduced results in less conventional DIII-D scenarios, including negative-central-shear and negative-triangularity plasmas. Predictive STEP modeling has been used to assess performance in several tokamak reactors. Simulations of a high-field, large-aspect-ratio reactor show significantly lower fusion power than predicted by a zero-dimensional study, demonstrating the limitations of scaling-law extrapolations. STEP predictions have found promising scenarios for an EXhaust and Confinement Integration Tokamak Experiment, including a high-pressure, 80%-bootstrap-fraction plasma. ITER modeling with STEP has shown that pellet fueling enhances fusion gain in both the baseline and advanced-inductive scenarios. Finally, STEP predictions for the SPARC baseline scenario are in good agreement with published results from the physics basis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer

Improved understanding of the relationship among structure, dynamics, and function for the enzyme phenylalanine hydroxylase (PAH) can lead to needed new therapies for phenylketonuria, the most common inborn error of amino acid metabolism. PAH is a multidomain homo-multimeric protein whose conformation and multimerization properties respond to allosteric activation by the substrate phenylalanine (Phe); the allosteric regulation is necessary to maintain Phe below neurotoxic levels. A recently introduced model for allosteric regulation of PAH involves major domain motions and architecturally distinct PAH tetramers [Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL, Jr (2013) Arch Biochem Biophys 530(2):73–82]. Herein, we present, to our knowledge, the first X-ray crystal structure for a full-length mammalian (rat) PAH in an autoinhibited conformation. Chromatographic isolation of a monodisperse tetrameric PAH, in the absence of Phe, facilitated determination of the 2.9 Å crystal structure. The structure of full-length PAH supersedes a composite homology model that had been used extensively to rationalize phenylketonuria genotype–phenotype relationships. Small-angle X-ray scattering (SAXS) confirms that this tetramer, which dominates in the absence of Phe, is different from a Phe-stabilized allosterically activated PAH tetramer. The lack of structural detail for activated PAH remains a barrier to complete understanding of phenylketonuria genotype–phenotype relationships. Nevertheless, the use of SAXS and X-ray crystallography together to inspect PAH structure provides, to our knowledge, the first complete view of the enzyme in a tetrameric form that was not possible with prior partial crystal structures, and facilitates interpretation of a wealth of biochemical and structural data that was hitherto impossible to evaluate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal structure and stability of gyrase–fluoroquinolone cleaved complexes from Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) infects one-third of the world’s population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone–gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone–enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. Lastly, these concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis

Enzymes that generate ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products have garnered significant interest, given their ability to produce large libraries of chemically diverse scaffolds. Such RiPP biosynthetic enzymes are predicted to bind their corresponding peptide substrates through sequence-specific recognition of the leader sequence, which is removed after the installation of posttranslational modifications on the core sequence. The conservation of the leader sequence within a given RiPP class, in otherwise disparate precursor peptides, further supports the notion that strict sequence specificity is necessary for leader peptide engagement. Here, we demonstrate that leader binding by a biosynthetic enzyme in the lasso peptide class of RiPPs is directed by a minimal number of hydrophobic interactions. Biochemical and structural data illustrate how a single leader-binding domain can engage sequence-divergent leader peptides using a conserved motif that facilitates hydrophobic packing. We report the presence of this simple motif in noncognate peptides results in low micromolar affinity binding by binding domains from several different lasso biosynthetic systems. We also demonstrate that these observations likely extend to other RiPP biosynthetic classes. The portability of the binding motif opens avenues for the engineering of semisynthetic hybrid RiPP products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗