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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Deeply conserved synteny resolves early events in vertebrate evolution

Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid–late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Search for charge non-conservation and Pauli exclusion principle violation with the M AJORANA D EMONSTRATOR

Charge conservation and the Pauli exclusion principle result from fundamental symmetries in the standard model of particle physics, and are typically taken as axiomatic. High-precision tests for small violations of these symmetries could point to new physics. Here we consider three models for violation of these processes, which would produce detectable ionization in the high-purity germanium detectors of the M AJORANA D EMONSTRATOR experiment. Using a 37.5 kg yr exposure, we report a lower limit on the electron mean lifetime, improving the previous best limit for the e → v e $\overline{v_e}$ v e decay channel by more than an order of magnitude. Here, we also present searches for two types of violation of the Pauli exclusion principle, setting limits on the probability of an electron to be found in a symmetric quantum state.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1

Nucleic acids from bacteria or viruses induce potent immune responses in infected cells. The detection of pathogen-derived nucleic acids is a central strategy by which the host senses infection and initiates protective immune responses. Cyclic GMP-AMP synthase (cGAS) is a double-stranded DNA sensor. It catalyses the synthesis of cyclic GMP-AMP (cGAMP), which stimulates the induction of type I interferons through the STING-TBK1-IRF-3 signalling axis. STING oligomerizes after binding of cGAMP, leading to the recruitment and activation of the TBK1 kinase. The IRF-3 transcription factor is then recruited to the signalling complex and activated by TBK1. Phosphorylated IRF-3 translocates to the nucleus and initiates the expression of type I interferons. However, the precise mechanisms that govern activation of STING by cGAMP and subsequent activation of TBK1 by STING remain unclear. Here we show that a conserved PLPLRT/SD motif within the C-terminal tail of STING mediates the recruitment and activation of TBK1. Crystal structures of TBK1 bound to STING reveal that the PLPLRT/SD motif binds to the dimer interface of TBK1. Cell-based studies confirm that the direct interaction between TBK1 and STING is essential for induction of IFNβ after cGAMP stimulation. Moreover, we show that full-length STING oligomerizes after it binds cGAMP, and highlight this as an essential step in the activation of STING-mediated signalling. Furthermore, these findings provide a structural basis for the development of STING agonists and antagonists for the treatment of cancer and autoimmune disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors

Polycomb repressive complex 2 (PRC2) mediates trimethylation of histone H3K27 (H3K27me3), an epigenetic hallmark for repressed chromatin. Overactive mutants of the histone lysine methyltransferase subunit of PRC2, Ezh2, are found in various types of cancers. Pyridone-containing inhibitors such as GSK126 compete with S-adenosylmethionine (SAM) for Ezh2 binding and effectively inhibit PRC2 activity. PRC2 from the thermophilic fungus Chaetomium thermophilum (ct) is functionally similar to the human version in several regards and has the added advantage of producing high-resolution crystal structures, although inhibitor-bound structures of human or human/chameleon PRC2 are also available at up to 2.6 Å resolution. We solved crystal structures of both human and ctPRC2 bound to GSK126 and the structurally similar inhibitor GSK343. While the two organisms feature a disparate degree of inhibitor potency, surprisingly, GSK126 binds in a similar manner in both structures. Structure-guided protein engineering of the drug binding pocket allowed us to introduce humanizing mutations into ctEzh2 to produce a ctPRC2 variant that is more susceptible to GSK126 inhibition. Additional analysis indicated that an evolutionarily conserved structural platform dictates a unique mode of GSK126 binding, suggesting a mechanism of drug selectivity. The existing drug scaffold may thus be used to probe the function and cellular regulation of PRC2 in a wide spectrum of organisms, ranging from fungi to humans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unlocking aquifer sustainability through irrigator-driven groundwater conservation

Groundwater depletion caused by intensive pumping for irrigated agriculture is a global threat to economies, food security, and ecosystems. Pumping reductions are required to confront this threat, but their implementation is a “wicked” problem due to interlinked hydrological, social, and economic factors. In the US High Plains Aquifer, an irrigator-led conservation effort known as the Sheridan 6 Local Enhanced Management Area (SD-6 LEMA) is a rare example of successful collective action in agricultural-groundwater systems. In its first decade, the area has exceeded water use reduction goals and decreased depletion rates by over 50% without significantly affecting net income. In this Perspective, we highlight factors underlying the SD-6 LEMA’s effectiveness, and identify transferable governance tenets for other groundwater dependent regions striving for sustainable management of groundwater resources. These tenets include flexibility through multi-year allocations, regulatory oversight to support the irrigators’ plans, and a strong scientific foundation for sustainable agricultural-groundwater systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases

The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an “induced fit” model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Conservation of angular momentum in second harmonic generation from under-dense plasmas

Spin and orbital angular momentum of an optical beam are two independent parameters that exhibit distinct effects on mechanical objects. However, when laser beams with angular momentum interact with plasmas, one can observe the interplay between the spin and the orbital angular momentum. Here, by measuring the helical phase of the second harmonic 2ω radiation generated in an underdense plasma using a known spin and orbital angular momentum pump beam, we verify that the total angular momentum of photons is conserved and observe the conversion of spin to orbital angular momentum. We further determine the source of the 2ω photons by analyzing near field intensity distributions of the 2ω light. The 2ω images are consistent with these photons being generated near the largest intensity gradients of the pump beam in the plasma as predicted by the combined effect of spin and orbital angular momentum when Laguerre-Gaussian beams are used.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Precision conservation for a changing climate

Landscape diversity is critical to enhance agricultural sustainability and resilience. Here, a realistic and achievable route towards adding complexity and biodiversity into agricultural landscapes may be through precision conservation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase

The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Further, our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

3D multi-system Bayesian calibration with energy conservation to study rapidity-dependent dynamics of nuclear collisions

Considerable information about the early-stage dynamics of heavy ion collisions is encoded in the rapidity dependence of measurements. To leverage the large amount of experimental data, we perform a systematic analysis using three-dimensional hydrodynamic simulations of multiple collision systems — large and small, symmetric and asymmetric. Specifically, we perform fully 3D multi-stage hydrodynamic simulations initialized by a parameterized model for rapidity-dependent energy deposition, which we calibrate on the hadron multiplicity and anisotropic flow coefficients. We utilize Bayesian inference to constrain properties of the early- and late-time dynamics of the system, and highlight the impact of enforcing global energy conservation in our 3D model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

On a regularization of a scalar conservation law with discontinuous coefficients

This paper is devoted to a scalar conservation law with a linear flux function involving discontinuous coefficients. It is clear that the delta standing wave should be introduced into the Riemann solution in some nonclassical situation. In order to study the formation of delta standing wave, we consider a regularization of the discontinuous coefficient with the Helmholtz mollifier and then obtain a regularized system which depends on a regularization parameter ε > 0. The regularization mechanism is a nonlinear bending of characteristic curves that prevents their finite-time intersection. It is proved rigorously that the solutions of regularized system converge to the delta standing wave solution in the ε → 0 limit. Compared with the classical method of vanishing viscosity, here it is clear to see how the delta standing wave forms naturally along the characteristics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Variational symmetries, conserved quantities and identities for several equations of mathematical physics

We find variational symmetries, conserved quantities and identities for several equations: envelope equation, Böcher equation, the propagation of sound waves with losses, flow of a gas with losses, and the nonlinear Schrödinger equation with losses or gains, and an electro-magnetic interaction. Most of these equations do not have a variational description with the classical variational principle and we find such a description with the generalized variational principle of Herglotz.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

The charge conserving Poisson-Boltzmann equations: Existence, uniqueness, and maximum principle

The present article is concerned with the charge conserving Poisson-Boltzmann (CCPB) equation in high-dimensional bounded smooth domains. The CCPB equation is a Poisson-Boltzmann type of equation with nonlocal coefficients. First, under the Robin boundary condition, we get the existence of weak solutions to this equation. The main approach is variational, based on minimization of a logarithm-type energy functional. To deal with the regularity of weak solutions, we establish a maximum modulus estimate for the standard Poisson-Boltzmann (PB) equation to show that weak solutions of the CCPB equation are essentially bounded. Then the classical solutions follow from the elliptic regularity theorem. Second, a maximum principle for the CCPB equation is established. In particular, we show that in the case of global electroneutrality, the solution achieves both its maximum and minimum values at the boundary. However, in the case of global non-electroneutrality, the solution may attain its maximum value at an interior point. In addition, under certain conditions on the boundary, we show that the global non-electroneutrality implies pointwise non-electroneutrality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Plasmons in molecules: Microscopic characterization based on orbital transitions and momentum conservation

In solid state physics, electronic excitations are often classified as plasmons or single-particle excitations. The former class of states refers to collective oscillations of the electron density. The random-phase approximation allows for a quantum-theoretical treatment and a characterization on a microscopic level as a coherent superposition of a large number of particle-hole transitions with the same momentum transfer. However, small systems such as molecules or small nanoclusters lack the basic properties (momentum conservation and uniform exchange interaction) responsible for the formation of plasmons in the solid-state case. Despite an enhanced interest in plasmon-based technologies and an increasing number of studies regarding plasmons in molecules and small nanoclusters, their definition on a microscopic level of theory remains ambiguous. In this work, we analyze the microscopic properties of molecular plasmons in comparison with the homogeneous electron gas as a model system. Subsequently, the applicability of the derived characteristics is validated by analyzing the electronic excitation vectors with respect to orbital transitions for two linear polyenes within second order versions of the algebraic diagrammatic construction scheme for the polarization propagator.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

A fast conservative spectral solver for the nonlinear Boltzmann collision operator

We present a conservative spectral method for the fully nonlinear Boltzmann collision operator based on the weighted convolution structure in Fourier space developed by Gamba and Tharkabhushnanam. This method can simulate a broad class of collisions, including both elastic and inelastic collisions as well as angularly dependent cross sections in which grazing collisions play a major role. The extension presented in this paper consists of factorizing the convolution weight on quadrature points by exploiting the symmetric nature of the particle interaction law, which reduces the computational cost and memory requirements of the method to O(M{sup 2}N{sup 4}logN) from the O(N{sup 6}) complexity of the original spectral method, where N is the number of velocity grid points in each velocity dimension and M is the number of quadrature points in the factorization, which can be taken to be much smaller than N. We present preliminary numerical results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Hydrodynamic and kinetic models for spin-1/2 electron-positron quantum plasmas: Annihilation interaction, helicity conservation, and wave dispersion in magnetized plasmas

We discuss the complete theory of spin-1/2 electron-positron quantum plasmas, when electrons and positrons move with velocities mach smaller than the speed of light. We derive a set of two fluid quantum hydrodynamic equations consisting of the continuity, Euler, spin (magnetic moment) evolution equations for each species. We explicitly include the Coulomb, spin-spin, Darwin and annihilation interactions. The annihilation interaction is the main topic of the paper. We consider the contribution of the annihilation interaction in the quantum hydrodynamic equations and in the spectrum of waves in magnetized electron-positron plasmas. We consider the propagation of waves parallel and perpendicular to an external magnetic field. We also consider the oblique propagation of longitudinal waves. We derive the set of quantum kinetic equations for electron-positron plasmas with the Darwin and annihilation interactions. We apply the kinetic theory to the linear wave behavior in absence of external fields. We calculate the contribution of the Darwin and annihilation interactions in the Landau damping of the Langmuir waves. We should mention that the annihilation interaction does not change number of particles in the system. It does not related to annihilation itself, but it exists as a result of interaction of an electron-positron pair via conversion of the pair into virtual photon. A pair of the non-linear Schrodinger equations for the electron-positron plasmas including the Darwin and annihilation interactions is derived. Existence of the conserving helicity in electron-positron quantum plasmas of spinning particles with the Darwin and annihilation interactions is demonstrated. We show that the annihilation interaction plays an important role in the quantum electron-positron plasmas giving the contribution of the same magnitude as the spin-spin interaction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

A new class of ensemble conserving algorithms for approximate quantum dynamics: Theoretical formulation and model problems

We develop two classes of quasi-classical dynamics that are shown to conserve the initial quantum ensemble when used in combination with the Feynman-Kleinert approximation of the density operator. These dynamics are used to improve the Feynman-Kleinert implementation of the classical Wigner approximation for the evaluation of quantum time correlation functions known as Feynman-Kleinert linearized path-integral. As shown, both classes of dynamics are able to recover the exact classical and high temperature limits of the quantum time correlation function, while a subset is able to recover the exact harmonic limit. A comparison of the approximate quantum time correlation functions obtained from both classes of dynamics is made with the exact results for the challenging model problems of the quartic and double-well potentials. It is found that these dynamics provide a great improvement over the classical Wigner approximation, in which purely classical dynamics are used. In a special case, our first method becomes identical to centroid molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗