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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Most human body proteins' activity and functionality are related to configurational changes of entire subdomains within the protein crystal structure. The crystal structures build the basis for any calculation that describes the structure or dynamics of a protein, most of the time with strong geometrical restrictions. However, these restrictions from the crystal structure are not present in the solution. The structure of the proteins in the solution may differ from the crystal due to rearrangements of loops or subdomains on the pico to nanosecond time scale (i.e., the internal protein dynamics time regime). This study describes how slow motions on timescales of several tens of nanoseconds can be accessed using neutron scattering. In particular, the dynamical characterization of two major human proteins, an intrinsically disordered protein that lacks a well-defined secondary structure and a classical antibody protein, is addressed by neutron spin echo spectroscopy (NSE) combined with a wide range of laboratory characterization methods. Further insights into protein domain dynamics were achieved using mathematical modeling to describe the experimental neutron data and determine the crossover between combined diffusive and internal protein motions. The extraction of the internal dynamic contribution to the intermediate scattering function obtained from NSE, including the timescale of the various movements, allows further vision into the mechanical properties of single proteins and the softness of proteins in their nearly natural environment in the crowded protein solution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The Galaxy–Galaxy Strong Lensing Cross Section and the Internal Distribution of Matter in ΛCDM Substructure

Abstract Strong gravitational lensing offers a powerful probe of the detailed distribution of matter in lenses, while magnifying and bringing faint background sources into view. Observed strong lensing by massive galaxy clusters, which are often in complex dynamical states, has also been used to map their dark matter (DM) substructures on smaller scales. Deep high-resolution imaging has revealed the presence of strong lensing events associated with these substructures, namely galaxy-scale sub-halos. However, an inventory of these observed galaxy–galaxy strong lensing (GGSL) events is noted to be discrepant with state-of-the-art ΛCDM simulations. Cluster sub-halos appear to be over-concentrated compared to their simulated counterparts yielding an order-of-magnitude higher value of GGSL. In this paper, we explore the possibility of resolving this observed discrepancy by redistributing the mass within observed cluster sub-halos in ways that are consistent within the ΛCDM paradigm of structure formation. Lensing mass reconstructions from data provide constraints on the mass enclosed within apertures and are agnostic to the detailed mass profile within them. Therefore, as the detailed density profile within cluster sub-halos currently remains unconstrained by data, we are afforded the freedom to redistribute the enclosed mass. We investigate if rearranging the mass to a more centrally concentrated density profile helps alleviate the GGSL discrepancy. We report that refitting cluster sub-halos to the ubiquitous ΛCDM-motivated Navarro–Frenk–White profile, and further modifying them to include significant baryonic components, does not resolve this tension. A resolution to this persisting GGSL discrepancy may require more careful exploration of alternative DM models.

Astronomy & Astrophysics↗
DOE OSTI2025

Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution

Morchella species have considerable significance in terrestrial ecosystems, exhibiting a range of ecological lifestyles along the saprotrophism-to-symbiosis continuum. However, the mitochondrial genomes of these ascomycetous fungi have not been thoroughly studied, thereby impeding a comprehensive understanding of their genetic makeup and ecological role. In this study, we analysed the mitogenomes of 30 Morchellaceae species, including yellow, black, blushing and false morels. These mitogenomes are either circular or linear DNA molecules with lengths ranging from 217 to 565 kbp and GC content ranging from 38% to 48%. Fifteen core protein-coding genes, 28–37 tRNA genes and 3–8 rRNA genes were identified in these Morchellaceae mitogenomes. The gene order demonstrated a high level of conservation, with the cox1 gene consistently positioned adjacent to the rnS gene and cob gene flanked by apt genes. Some exceptions were observed, such as the rearrangement of atp6 and rps3 in Morchella importuna and the reversed order of atp6 and atp8 in certain morel mitogenomes. However, the arrangement of the tRNA genes remains conserved. We additionally investigated the distribution and phylogeny of homing endonuclease genes (HEGs) of the LAGLIDADG (LAGs) and GIY-YIG (GIYs) families. A total of 925 LAG and GIY sequences were detected, with individual species containing 19–48HEGs. These HEGs were primarily located in the cox1, cob, cox2 and nad5 introns and their presence and distribution displayed significant diversity amongst morel species. These elements significantly contribute to shaping their mitogenome diversity. Overall, this study provides novel insights into the phylogeny and evolution of the Morchellaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗
DOE OSTI2022

Observations of gas-phase products from the nitrate-radical-initiated oxidation of four monoterpenes

Abstract. Chemical ionization mass spectrometry with the nitrate reagent ion (NO3- CIMS) was used to investigate the products of the nitrate radical (NO3) initiated oxidation of four monoterpenes in laboratory chamber experiments. α-Pinene, β-pinene, Δ-3-carene, and α-thujene were studied. The major gas-phase species produced in each system were distinctly different, showing the effect of monoterpene structure on the oxidation mechanism and further elucidating the contributions of these species to particle formation and growth. By comparing groupings of products based on the ratios of elements in the general formula CwHxNyOz, the relative importance of specific mechanistic pathways (fragmentation, termination, and radical rearrangement) can be assessed for each system. Additionally, the measured time series of the highly oxidized reaction products provide insights into the ratio of relative production and loss rates of the high-molecular-weight products of the Δ-3-carene system. The measured effective O:C ratios of reaction products were anticorrelated with new particle formation intensity and number concentration for each system; however, the monomer : dimer ratios of products had a small positive trend. Gas-phase yields of oxidation products measured by NO3- CIMS correlated with particle number concentrations for each monoterpene system, with the exception of α-thujene, which produced a considerable amount of low-volatility products but no particles. Species-resolved wall loss was measured with NO3- CIMS and found to be highly variable among oxidized reaction products in our stainless steel chamber.

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

Multi‐scale simulation of rock compaction through breakage models with microstructure evolution

Abstract. Regional subsidence due to fluid depletion includes the interaction among multiple physical processes. Specifically, rock compaction is governed by coupled hydro-mechanical feedbacks involving fluid flow, effective stress change and pore collapse. Although poroelastic models are often used to explain the delay between depletion and subsidence, recent evidence indicates that inelastic effects could alter the rock microstructure, thus exacerbating coupling effects. Here, a constitutive law built within the framework of Breakage Mechanics is proposed to account for the inherent connection between rock microstructure, hydraulic conductivity, and pore compaction. Furthermore, it is embedded into a 1-D hydromechanical coupled finite element analysis (FEA) to explore the effects of micro-structure rearrangement on the development of reservoir compaction. Numerical examples with the proposed model are compared with simulations under constant hydraulic conductivity to illustrate the model capability to capture the non-linear processes of reservoir compaction induced by fluid depletion.

Buscarnera, Giuseppe↗
DOE OSTI2022

Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O 2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1965

Theory of Intramolecular Relaxation Processes

A master equation is derived to describe internal relaxation processes in molecular systems with a relatively small number of degrees of freedom. It is an inhomogeneous equation, taking into account nondiagonal elements of the coarse‐grained density matrix which prove to be the most relevant ones for the problem under consideration. Various relaxational time scales, inherent in a molecular system, can thus be shown to exist. Relaxation mechanisms and equilibrium states on these time scales can be determined. The general character and different types of solutions of the master equation are investigated. The theory is applied to internal vibrational relaxation and intramolecular rearrangement (isomerization) reactions.

Hofacker, G. Ludwig↗
NASA NTRS1966

Four-fermion interaction Lagrangians

Pauli exclusion principle and Fierz rearrangement theorem shown to limit arbitrariness of Lorentz invariant interaction Lagrangian for self-coupled Dirac field

LAGRANGE EQUATION↗