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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Theoretical and kinetic modeling study of hydrazine oxidation

The present work constitutes the first theoretical and kinetic modeling study of hydrazine oxidation, which may be important for burnout in ammonia-fueled combustion. The kinetics of the oxidation of N 2 H 4 , N 2 H 3 and tHNNH by molecular oxygen were investigated via a quantum chemistry/canonical transition state theory approach. Geometries and anharmonic frequencies were obtained with density functional theory, and energies from coupled cluster calculations (CCSD(T)) extrapolated to the infinite basis set limit, with corrections for core-valence electron correlation, scalar relativistic effects, and higher level correlation up to lambda coupled cluster, CCSDT(Q) Λ . The key reactions occurred on the N 2 H 4 O 2 potential energy surface, where the results indicated a fast reaction of N 2 H 3 with HO 2 via singlet adducts to yield tHNNH + H 2 O 2 and HNN(H)O + H 2 O, while reaction on the triplet surface proceeds via a bound complex followed by a tight, submerged barrier to yield N 2 H 4 + O 2 . The results were incorporated in a detailed reaction mechanism, which was used to interpret the shock tube results from Michel and Wagner (1965) on the effect of O 2 on hydrazine conversion at 1100–1400 K. The kinetic model captured qualitatively the observed behavior, but underestimated the reaction rate under oxidizing conditions. The hydrazine pyrolysis chemistry dominated conversion at reducing conditions and/or high temperature. At oxidizing conditions and intermediate temperatures (≲ 1400 K), reactions of N 2 -amines with HO 2 and O 2 were important for the oxidation rate.

Ab initio calculations↗
DOE OSTI2022

HȮ 2 + HȮ 2 : High level theory and the role of singlet channels

At low temperatures and high pressures, the HȮ 2 + HȮ 2 reaction is an important reaction in combustion. There are significant unresolved discrepancies between prior theoretical and experimental studies of this reaction. It has generally been presumed to occur as an abstraction on the triplet surface to produce H 2 O 2 + 3 O 2 . Here, we employ a combination of high-level electronic structure theory (the ANL0 composite method or multi-reference methods as appropriate), sophisticated transition state theory (vibrationally adiabatic torsions, variational, and variable reaction coordinate), and master equation analyses to predict the thermal kinetics on the H 2 O 4 surface. Notably, this analysis suggests a significant branching to HȮ 3 + ȮH near 1000 K via reaction on the singlet surface. This channel does not appear to have been considered in prior combustion models. HȮ 3 itself is a metastable complex (bound by only 3 kcal mol -1 ) that rapidly dissociates to ȮH + 3 O 2 . Thus, the net reaction for this channel, HȮ 2 + HȮ 2 → ȮH + ȮH + O 2 , converts two low reactivity HȮ 2 radicals into two highly reactive ȮH radicals. The ramifications of these newly derived rate expressions are highlighted through kinetic modeling studies of H 2 , CH 3 OH, $\textit{n}$-heptane, and isooctane oxidation; all at the high pressures of relevance to combustion devices.

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

The influence of LiH and TiH 2 on hydrogen storage in MgB 2 I: Promotion of bulk hydrogenation at reduced temperature

Mg(BH 4 ) 2 is an attractive hydrogen storage material, owing to its high gravimetric capacity of 14.9 wt %. However, the dehydrogenated material MgB 2 is very difficult to rehydrogenate, requiring excessive pressures and temperatures. Here we report the influence of LiH and TiH 2 on hydrogen storage reactions involving Bulk MgB 2 using XRD, XAS, FTIR and NMR. In ball-milled mixtures of LiH/MgB 2 , the LiH loses crystallinity but remains undissociated, forming a weakly bound complex with MgB 2 . The weak interactions produce minor variations in the local electronic structure at B and Mg, but do not markedly affect the underlying MgB 2 hexagonal crystal structure. No evidence is found for a mixed-metal boride Mg 1-x Li x B 2 in the as-prepared LiH/MgB 2 materials. The presence of LiH dramatically improves the hydrogenation of MgB 2 at 700 bar, forming borohydride 100 °C below the minimum hydrogenation temperature of pure MgB 2 and without the formation of undesirable intermediates such as [B 3 H 8 ] - , [B 10 H 10 ] 2- or [B 12 H 12 ] 2- . Evidence is reported for a mixed-metal borohydride of the type Mg (3-x)/2 Li x (BH 4 ) 3 produced by the hydrogenation. Subsequent desorption is also improved compared to pure Mg(BH 4 ) 2 and LiBH 4 , showing single-step hydrogen release up to ~8 wt% by 380 °C, whereas Mg(BH 4 ) 2 and LiBH 4 still retain significant amounts of hydrogen at this temperature. The material produced by desorption contains both MgB 2 and Mg metal, revealing the original LiH/MgB 2 system is not fully reversible. In contrast to LiH, TiH 2 is essentially inert when ball-milled with MgB 2 , and high-pressure hydrogenation leaves only unreacted TiH 2 and MgB 2 . Thus, added TiH 2 provides no benefit to MgB 2 hydrogenation.

08 HYDROGEN↗
DOE OSTI2026

Concordant Mode Approach (CMA): Vibrational Analysis of New and Upgraded Intermolecular Benchmarks for Noncovalent Bonding

The Concordant Mode Approach (CMA) is a novel method that offers tremendous potential for increasing the system size and the level of theory attainable in quantum chemical computations of molecular vibrational frequencies. To investigate the extension of CMA to intermolecular vibrations, computations with coupled cluster singles and doubles with perturbative triples theory [CCSD(T)] using two augmented correlation-consistent polarized-valence triple-ζ basis sets (aug-cc-pVTZ or h-aug-ccpVTZ) were performed on 17 prototypical loosely bound complexes of hydrogen-bonded, dispersion, and mixed character. These Level A results provide new and upgraded benchmarks for noncovalent bonding and a severe test for CMA vibrational analyses. The Level A target frequencies were recovered remarkably well using second-order Møller−Plesset perturbation theory (MP2) with h-aug-cc-pVTZ for generating the underlying (Level B) normal modes of the CMA scheme. Employing this Level B within the lowest-rung CMA-0A method reproduces the 435 benchmark frequencies with a mean absolute error (MAE) of 0.23 cm −1 and a corresponding standard deviation (σ) of 0.84 cm −1 ; strikingly, the corresponding subset of 106 interfragment frequencies exhibits MAE = 0.34 cm −1 and σ = 0.90 cm −1 . Subsequent application of the higher-rung CMA-2A scheme eliminates all outliers and reduces the overall MAE to a minuscule 0.08 cm −1 with the inclusion of only 3.0% of the off-diagonal couplings not accounted for by CMA-0A. Accordingly, the highly efficient CMA methodology proves to be robust even for vibrations on flat potential energy surfaces.

Aromatic compounds↗
DOE OSTI2020

Electron Redistribution within the Nitrogenase Active Site FeMo-cofactor During Reductive Elimination of H2 to Achieve N=N Triple-Bond Activation

Nitrogen fixation by nitrogenase begins with accumulation of four reducing equivalents at the active-site FeMo-cofactor (FeMo-co), generating a state (denoted E4(4H)) with two [Fe-H-Fe] bridging hydrides. Recently, photolytic reductive elimination (re) of the E4(4H) hydrides showed that enzymatic re of E4(4H) hydride yields an H2-bound complex (E4(H2,2H)), in a process corresponding to a formal 2-electron reduction of the metal-ion core of FeMo-co. The resulting electron-density redistribution from Fe-H bonds to the metal ions themselves enables N2 to bind with concomitant H2 release, a process illuminated here by QM/MM molecular dynamics simulations. What is the nature of this redistribution? Although E4(H2,2H) hasn’t been trapped, cryogenic photolysis of E4(4H) provides a means to address this question. Photolysis of E4(4H) causes hydride-re with release of H2, generating doubly-reduced FeMo-co (denoted E4(2H)*), the extreme limit of the electron-density redistribution upon formation of E4(H2,2H). Here we examine the doubly-reduced FeMo-co core of the E4(2H)* limiting-state by 1H, 57Fe, and 95Mo ENDOR to illuminate the partial electron-density redistribution upon E4(H2,2H) formation during catalysis, complementing these results with corresponding DFT computations. Inferences from the E4(2H)* ENDOR results as extended by DFT computations include: (i) the Mo-site participates negligibly, and overall it is unlikely that Mo changes valency throughout the catalytic cycle; (ii) two distinctive E4(4H) 57Fe signals are suggested as associated with ‘anchors’ of one bridging hydride, two others with anchors of the second, with NBO-analysis identifying one anchor of each hydride as a major recipient of electrons released upon breaking Fe-H bonds.

Lukoyanov, Dmitriy↗
DOE OSTI2025

Bulky Phosphine Ligands Promote Palladium-Catalyzed Protodeboronation

The Suzuki-Miyaura cross-coupling reaction is plagued by protodeboronation, an undesirable side reaction with water that consumes the boronic acid derivatives required for the cross-coupling reaction. Meticulous mechanistic studies have previously established protodeboronation to be highly sensitive to the nature of the boronic reagent and reaction conditions. Particularly, the presence of bases, which are essential for the Suzuki-Miyaura coupling, is known to catalyze protodeboronation. However, protodeboronation catalyzed by palladium-phosphine complexes, the benchmark catalyst system for Suzuki-Miyaura cross-coupling, has been understudied compared to its base-catalyzed counterpart. Here, we demonstrate, using automated high-throughput experimentation, comprehensive computational mechanistic analyses and kinetic modeling, that protodeboronation is accelerated by palladium(II) complexes bound to bulky phosphine ligands. While sterically hindered ligands are typically used to facilitate difficult cross-couplings, these ligands can instead paradoxically impede cross-coupling product formation, requiring careful and judicious consideration when choosing ligands for Suzuki-Miyaura cross-couplings.

Ser, Cher Tian [University of Toronto, ON (Canada)↗
DOE OSTI2025

NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor NUB1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system with human components and revealed that NUB1 uses the intrinsic instability of FAT10 to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin-independent and p97-independent manner. Using hydrogen–deuterium exchange, structural modeling and site-directed mutagenesis, we identified the formation of an intricate complex with FAT10 that activates NUB1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic NUB1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These findings identified a previously unknown mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.

Arkinson, Connor↗
DOE OSTI2023

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro -1,2-diguaiacylpropane-1,3-diol ( erythro -DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans . The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro -DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C 1 reaction product, and we further demonstrated that both enantiomers of erythro -DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.

09 BIOMASS FUELS↗
NASA NTRS1979

Gaseous NH4Cl revisited - A computational investigation of the potential surface and properties

An investigation of the potential surface and properties of the ground state of gaseous NH4Cl is presented. The calculations, which utilize a good basis set and include investigation of the valence correlation effects, result in a description of gaseous NH4Cl as a weakly bound complex with NH3 and HCl structures essentially equivalent to those of the isolated fragments. The charge distributions within the fragments are modifed in the complex, however, and there is a small amount of charge transfer. The results are in reasonable agreement with estimate of D sub 0, super 0 from high temperature mass spectroscopic investigations and vibrational frequencies from matrix experiments. The equilibrium constant for the reversible reaction NH4Cl yields NH3 + HCl indicates that the homogeneous formation of NH4Cl does not represent a significant chemical sink for HCl in the upper atmosphere

Raffenetti, R. C.↗
NASA NTRS1989

Computational solution of chemistry problems

AB initio quantum chemical techniques have been used to investigate weakly bound complexes of H2O and SO2. An energy gradient program was used to locate stable structures for the H2O, SO2 complexes, and SCF calculations were carried out to determine the binding energies of complexes with multiple water molecules. A 4-31G basis set was used for most potential energy searches. More accurate basis sets including a generally contracted basis set with d orbitals on the sulfur were used for geometry and binding energy verification. For single water complexes, five different stable geometries were located with binding energies between 4 and 11 Kcal mol(-1), suggesting a binding shell for H2O around SO2 and a mechanism for the formation of an SO2-containing water droplet. Calculations on one of the complexes utilizing a larger double zeta basis and d functions on the sulfur atom lead to adjusted binding energies in the range 3 to 8 Kcal mol(-1). Very little charge transfer between SO2 and H2O was present. Addition of more than one H2O was found to be energetically favorable although the addition of the fourth water in certain geometries did not increase the stability of the complex. An alternative mechanism for the tropospheric gas phase production of acid rain is suggested.

Ake, Robert L.↗
NASA NTRS1991

Tunable far infrared laser spectrometers

The state of the art in far infrared (FIR) spectroscopy is reviewed. The development of tunable, coherent FIR radiation sources is discussed. Applications of tunable FIR laser spectrometers for measurement of rotational spectra and dipole moments of molecular ions and free radicals, vibration-rotation-tunneling spectra of weakly bound complexes, and vibration-rotation spectra of linear carbon clusters are presented. A detailed description of the Berkeley tunable FIR laser spectrometers is presented.

Blake, G. A.↗
NASA NTRS1990

Newton modified barrier method in constrained optimization

In this paper, we develop and investigate the Newton method for solving constrained (non-smooth) optimization problems. This approach is based on the modified barrier functions (MBF) theory and on the global converging step-size version of the Newton method for smooth unconstrained optimization. Due to the excellent properties of the MBF near primal-dual solution, the Newton modified barrier method (NMBM) has a better rate of convergence, better complexity bound, and is much more stable in the final stage of the computational process than the methods which are based on the classical barrier functions (CBF).

Polyak, R.↗
NASA NTRS1992

The Extrapolation of Elementary Sequences

We study sequence extrapolation as a stream-learning problem. Input examples are a stream of data elements of the same type (integers, strings, etc.), and the problem is to construct a hypothesis that both explains the observed sequence of examples and extrapolates the rest of the stream. A primary objective -- and one that distinguishes this work from previous extrapolation algorithms -- is that the same algorithm be able to extrapolate sequences over a variety of different types, including integers, strings, and trees. We define a generous family of constructive data types, and define as our learning bias a stream language called elementary stream descriptions. We then give an algorithm that extrapolates elementary descriptions over constructive datatypes and prove that it learns correctly. For freely-generated types, we prove a polynomial time bound on descriptions of bounded complexity. An especially interesting feature of this work is the ability to provide quantitative measures of confidence in competing hypotheses, using a Bayesian model of prediction.

Laird, Philip↗
NASA NTRS2013

Thermal Design and Analysis of the Supersonic Flight Dynamics Test Vehicle for the Low Density Supersonic Decelerator Project

The thermal design and analysis of the experimental Supersonic Flight Dynamics Test (SFDT) vehicle is presented. The SFDT vehicle is currently being designed as a platform to help demonstrate key technologies for NASA's Low Density Supersonic Decelerator (LDSD) project. The LDSD project is charged by NASA's Office of the Chief Technologist (OCT) with the task of advancing the state of the art in Mars Entry, Descent, and Landing (EDL) systems by developing and testing three new technologies required for landing heavier payloads on Mars. The enabling technologies under development consist of a large 33.5 meter diameter Supersonic Ringsail (SSRS) parachute and two different types of Supersonic Inflatable Aerodynamic Decelerator (SIAD) devices - a robotic class, SIAD-R, that inflates to a 6 meter diameter torus, and an exploration class, SIAD-E, that inflates to an 8 meter diameter isotensoid. As part of the technology development effort, the various elements of the new supersonic decelerator system must be tested in a Mars-like environment. This is currently planned to be accomplished by sending a series of SFDT vehicles into Earth's stratosphere. Each SFDT vehicle will be lifted to a stable float altitude by a large helium carrier balloon. Once at altitude, the SFDT vehicles will be released from their carrier balloon and spun up via spin motors to provide trajectory stability. An onboard third stage solid rocket motor will propel each test vehicle to supersonic flight in the upper atmosphere. After main engine burnout, each vehicle will be despun and testing of the deceleration system will begin: first an inflatable decelerator will be deployed around the aeroshell to increase the drag surface area, and then the large parachute will be deployed to continue the deceleration and return the vehicle back to the Earth's surface. The SFDT vehicle thermal system must passively protect the vehicle structure and its components from cold temperatures experienced during the ascent phase of the mission as well as from the extreme heat fluxes produced during the supersonic test phase by the main motor plume and aeroheating. The passive thermal design approach for the SFDT vehicle relies upon careful and complex bounding analysis of all three modes of heat transfer - conduction, convection, and radiation - coupled with a tightly managed transient power dissipation timeline for onboard electronics components throughout all mission phases.

thermal desktop↗
NASA NTRSDate not supplied

Resilient Autonomy in the Face of Adversity

The NASA Resilient Autonomy Project developed a software framework that implemented a Run Time Assurance (RTA) architecture that leveraged ASTM International’s F3269 Industry Standard for safely bounding complex behavior in aircraft. This framework was called the Expandable Variable Autonomy Architecture, or EVAA. EVAA was developed during the height of the Covid-19 lockdown that caused the Resilient Autonomy team to pivot from flight test to distributed simulator testing. EVAA was developed to be platform and mission agnostic where platform specifics were behind a hardware abstraction layer that EVAA called a Coupler. EVAA was able to host multiple safety monitors that could resolve individual safety hazards. EVAA was able to resolve priority conflicts when multiple safety hazards needed to be resolved simultaneously and was able to resolve highly complex situations in a safe manner that could exceed human capabilities.

Ethan Williams↗
DOE OSTI2022

General bounds on holographic complexity

We prove a positive volume theorem for asymptotically AdS spacetimes: the maximal volume slice has nonnegative vacuum-subtracted volume, and the vacuum-subtracted volume vanishes if and only if the spacetime is identically pure AdS. Under the Complexity=Volume proposal, this constitutes a positive holographic complexity theorem. The result features a number of parallels with the positive energy theorem, including the assumption of an energy condition that excludes false vacuum decay (the AdS weak energy condition). Our proof is rigorously established in broad generality in four bulk dimensions, and we provide strong evidence in favor of a generalization to arbitrary dimensions. Our techniques also yield a holographic proof of Lloyd’s bound for a class of bulk spacetimes. We further establish a partial rigidity result for wormholes: wormholes with a given throat size are more complex than AdS-Schwarzschild with the same throat size.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗