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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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Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carb
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Structures of Streptococcus pyogenes class A sortase in complex with substrate and product mimics provide key details of target recognition
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Revealing the mechanism of action of a first-in-class covalent inhibitor of $\mathrm{KRASG12C}$ $\mathrm{(ON)}$ and other functional properties of oncogenic $\text{KRAS}$ by 31 P $\mathrm{NMR}$
Individual oncogenic KRAS mutants confer distinct differences in biochemical properties and signaling for reasons that are not well understood. KRAS activity is closely coupled to protein dynamics and is regulated through two interconverting conformations: state 1 (inactive, effector binding deficient) and state 2 (active, effector binding enabled). Here, we use 31 P NMR to delineate the differences in state 1 and state 2 populations present in WT and common KRAS oncogenic mutants (G12C, G12D, G12V, G13D, and Q61L) bound to its natural substrate GTP or a commonly used nonhydrolyzable analog GppNHp (guanosine-5'-[(β,γ)-imido] triphosphate). Our results show that GppNHp-bound proteins exhibit significant state 1 population, whereas GTP-bound KRAS is primarily (90% or more) in state 2 conformation. This observation suggests that the predominance of state 1 shown here and in other studies is related to GppNHp and is most likely nonexistent in cells. We characterize the impact of this differential conformational equilibrium of oncogenic KRAS on RAF1 kinase effector RAS-binding domain and intrinsic hydrolysis. Through a KRAS G12C drug discovery, we have identified a novel small-molecule inhibitor, BBO-8956, which is effective against both GDP- and GTP-bound KRAS G12C. We show that binding of this inhibitor significantly perturbs state 1–state 2 equilibrium and induces an inactive state 1 conformation in GTP-bound KRAS G12C. In the presence of BBO-8956, RAF1–RAS-binding domain is unable to induce a signaling competent state 2 conformation within the ternary complex, demonstrating the mechanism of action for this novel and active-conformation inhibitor.
Class-based separations of mixed solid–liquid systems with condensable solvent washing and extraction: The dilemma of pizza box recycling
As primary feedstocks deplete across the world, raw material extraction becomes increasingly expensive. Awareness of the environmental impact of primary extraction has motivated the development of energy- and reagent-efficient methods for material reuse. This work confronts an emblematic challenge of modern recycling: the soiled pizza box. While the fibers constituting corrugated cardboard are generally recyclable, pizza contaminants such as sauces and oils complicate their reuse, resulting in municipal prohibitions on the recycling of used pizza boxes in cardboard recycling streams and a representative of 275 kg/year per US household of food waste that is directed to landfill. This challenge is common to many materials, and engineering strategies must be developed to tackle complex/mixed feedstocks. To address the mixed composition of the pizza box (and similar materials), an environmentally benign, non-toxic organic solvent is applied to remove and fractionate components from mixed materials. The solvent employed in this process, dimethyl ether (DME), is a condensable hygroscopic gas, which facilitates its removal and recovery for reuse. Further, the results of this study indicate that 1) DME is capable of solubilizing and extracting components from soiled cardboard and other materials, (resulting in cardboard drier than new/unused cardboard) facilitating its recycling, and 2) the DME-soluble components of the system phase separate into aqueous and fatty acid/oil fractions (potentially ~27.5 kg/year per US household). Condensable solvent-driven washing and extraction enable the efficient separation of multiple intermediate product streams, suggesting a pathway to enable technology development necessary for achieving clean production in a circular economy.
A Feynman-Kac based numerical method for the exit time probability of a class of transport problems
The exit time probability, which gives the likelihood that an initial condition leaves a prescribed region of the phase space of a dynamical system at, or before, a given time, is arguably one of the most natural and important transport problems. In this work, we present an accurate and efficient numerical method for computing this probability for systems described by non-autonomous (time-dependent) stochastic differential equations (SDEs) or their equivalent Fokker-Planck partial differential equations. The method is based on the direct approximation of the Feynman-Kac formula that establishes a link between the adjoint Fokker-Planck equation and the forward SDE. The Feynman-Kac formula is approximated using the Gauss-Hermite quadrature rules and piecewise cubic Hermite interpolating polynomials, and a GPU accelerated matrix representation is used to compute the entire time evolution of the exit time probability using a single pass of the algorithm. The method is unconditionally stable, exhibits second order convergence in space, first order convergence in time, and it is straightforward to parallelize. Applications are presented to the advection diffusion of a passive tracer in a fluid flow exhibiting chaotic advection, and to the runaway acceleration of electrons in a plasma in the presence of an electric field, collisions, and radiation damping. Benchmarks against analytical solutions as well as comparisons with explicit and implicit finite difference standard methods for the adjoint Fokker-Planck equation are presented.
Preparation and characterization of MnIIMnIII complexes with relevance to class Ib ribonucleotide reductases
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An emerging class of carbon materials: Synthesis and applications of carbon flowers
Porous carbon materials are widely applied in energy storage, gas adsorption, and catalysis applications because of their advantageous properties, such as high surface areas, tunable surface properties, chemical stability, high conductivity, and low cost. Recently, a flower-shaped carbon material, referred to as carbon flowers (CFs), has received attention as an emerging porous carbon material because of its unique shape. In this review, we summarize the synthetic strategies, characterization techniques, and formation mechanisms of CFs from various precursors. We also review the applications of CFs and their pros and cons. Last, we discuss challenges and perspectives for future development of CFs.
A class of solutions of the two-dimensional Toda lattice equation
In this study, a method is proposed to systematically generate solutions of the two-dimensional Toda lattice equation in terms of previously known solutions ϕ(x,y) of the two-dimensional Laplace's equation. The solitonic solution of Nakamura's [J. Phys. Soc. Jpn. 52 (1983) 380] is shown to correspond to one particular choice of ϕ(x,y).
POLARIS-LC: A Multi-Class traffic Flow Model in Lagrangian Coordinates for Large-Scale Simulation
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A new class of entropy stabilized oxides: Commensurately modulated A[subscript 6]B[subscript 2]O[sub
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A flexible class of priors for orthonormal matrices with basis function-specific structure
Statistical modeling of high-dimensional matrix-valued data motivates the use of a low-rank representation that simultaneously summarizes key characteristics of the data and enables dimension reduction. Low-rank representations commonly factor the original data into the product of orthonormal basis functions and weights, where each basis function represents an independent feature of the data. However, the basis functions in these factorizations are typically computed using algorithmic methods that cannot quantify uncertainty or account for basis function correlation structure a priori. While there exist Bayesian methods that allow for a common correlation structure across basis functions, empirical examples motivate the need for basis function-specific dependence structure. We propose a prior distribution for orthonormal matrices that can explicitly model basis function-specific structure. The prior is used within a general probabilistic model for singular value decomposition to conduct posterior inference on the basis functions while accounting for measurement error and fixed effects. We discuss how the prior specification can be used for various scenarios and demonstrate favorable model properties through synthetic data examples. Finally, we apply our method to two-meter air temperature data from the Pacific Northwest, enhancing our understanding of the Earth system’s internal variability.
Estimating multi-class dynamic origin-destination demand through a forward-backward algorithm on computational graphs
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First-in-class SAM-competitive G9a inhibitor FLAV-27 as a disease-modifying therapy for Alzheimer disease
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A class of three-dimensional gyroviscous magnetohydrodynamic models
A Hamiltonian and action principle formalism for deriving three-dimensional gyroviscous magnetohydrodynamic models is presented. The uniqueness of the approach in constructing the gyroviscous tensor from first principles and its ability to explain the origin of the gyromap and the gyroviscous terms are highlighted. The procedure allows for the specification of free functions, which can be used to generate a wide range of gyroviscous models. Through the process of reduction, the noncanonical Hamiltonian bracket is obtained and briefly analysed.