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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Molecular Insights Into the Ionic Assembly of Poly-Galacturonic Acid Oligomers - Impact of Charge, Ionic Radius, and Polymer Functionalization

Pectin, a major class of matrix polysaccharides present in plant cell walls (PCW), contains widespread anionic saccharides that cross-link in the presence of cations. It modulates important functions such as cell-cell adhesion and determines the PCW's biomechanical properties. It is known that mono-, di-, and tri-valent cations facilitate cross-linking; however, significant knowledge gaps remain in understanding the structure and mechanism of pectin cross-linking. In this study, replica-exchange molecular dynamics (REMD) simulations were employed to elucidate the role of ionic charge, ionic radii, and functional groups on the cross-linking of homogalacturonan (HG), the most abundant pectin molecule. Our enhanced sampling approach in fully solvated environments suggests more effective cross-linking with higher-valent and smaller ions, and that the "zipper" conformation is more favorable than the prevalent "egg-box" conformation. These findings advance our fundamental understanding of pectin matrix structure in PCWs and provide a solid foundation to probe structure-property relationships in pectic polysaccharides.

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

Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Understanding Viscoelasticity of an Entangled Silicone Copolymer via Coarse-Grained Molecular Dynamics Simulations

Entangled dynamics is important for understanding rheological properties of long-chain polymers. For entangled homopolymers, the classic tube-reptation model and its refinements have been successfully applied to quantify properties like diffusion coefficient and zero-rate viscosity. However, the application of such models to copolymers has been limited despite scientific and industrial importance. Here, we study the entangled melt dynamics of poly(dimethyl-co-diphenyl)siloxane random copolymer for a range of mean-composition-ratio ϕ of the diphenyl component via long-term molecular dynamics simulation with a recently developed coarse-grained model. We found that the segmental relaxation is heterogeneous at the monomeric level because of compositional fluctuations. However, at the chain-entanglement level and higher length scales, the viscoelastic response is homogeneous with compositional dependence only through the overall diphenyl fraction ϕ. The relaxation modulus of the entangled copolymer melt conforms to the Likhtman–McLeish model, and the viscosity predicted using our current coarse-grained parameters is in good quantitative agreement with experimental data.

Copolymers↗
DOE OSTI2023

Investigation of the Impact of Lipid Acyl Chain Saturation on Fusion Peptide Interactions with Lipid Bilayers

The interaction of many peptides with lipid bilayer membranes strongly depends on the lipid composition. Here, a study of the impact of unsaturated lipid acyl chains on the interaction of a derivative of the HIV-1 fusion peptide with lipid bilayer vesicles is presented. Lipid bilayer vesicles composed of mixtures of lipids with two saturated acyl chains and lipids and one saturated and one unsaturated acyl chain, but identical head groups, were studied. The dependence of the peptide conformation on the unsaturated lipid content was probed by circular dichroism spectroscopy, while the impact of the peptide on the bilayer structure was determined by small-angle neutron scattering. The impact of the peptide on the lipid bilayer vesicle dynamics was investigated using neutron spin echo spectroscopy. Molecular dynamics simulations were used to characterize the behavior of the systems studied to determine if there were clear differences in their physical properties. The results reveal that the peptide–bilayer interaction is not a simple function of the unsaturated lipid acyl chain content of the bilayer. Instead, the peptide behavior is more consistent with that seen for the bilayer containing only unsaturated lipids, which is supported by lipid-specific interactions revealed by the simulations.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

The constraint method: A new finite element technique

An approch to the finite element method which utilizes families of conforming finite elements based on complete polynomials is presented. Finite element approximations based on this method converge with respect to progressively reduced element sizes as well as with respect to progressively increasing orders of approximation. Numerical results of static and dynamic applications of plates are presented to demonstrate the efficiency of the method. Comparisons are made with plate elements in NASTRAN and the high-precision plate element developed by Cowper and his co-workers. Some considerations are given to implementation of the constraint method into general purpose computer programs such as NASTRAN.

Tsai, C.↗
NASA NTRS1990

Evaluation of an expert system for fault detection, isolation, and recovery in the manned maneuvering unit

The authors explore issues in the specification, verification, and validation of artificial intelligence (AI) based software, using a prototype fault detection, isolation and recovery (FDIR) system for the Manned Maneuvering Unit (MMU). They use this system as a vehicle for exploring issues in the semantics of C-Language Integrated Production System (CLIPS)-style rule-based languages, the verification of properties relating to safety and reliability, and the static and dynamic analysis of knowledge based systems. This analysis reveals errors and shortcomings in the MMU FDIR system and raises a number of issues concerning software engineering in CLIPs. The authors came to realize that the MMU FDIR system does not conform to conventional definitions of AI software, despite the fact that it was intended and indeed presented as an AI system. The authors discuss this apparent disparity and related questions such as the role of AI techniques in space and aircraft operations and the suitability of CLIPS for critical applications.

Rushby, John↗
NASA NTRS1991

Transformation of two and three-dimensional regions by elliptic systems

A reliable linear system is presented for grid generation in 2-D and 3-D. The method is robust in the sense that convergence is guaranteed but is not as reliable as other nonlinear elliptic methods in generating nonfolding grids. The construction of nonfolding grids depends on having reasonable approximations of cell aspect ratios and an appropriate distribution of grid points on the boundary of the region. Some guidelines are included on approximating the aspect ratios, but little help is offered on setting up the boundary grid other than to say that in 2-D the boundary correspondence should be close to that generated by a conformal mapping. It is assumed that the functions which control the grid distribution depend only on the computational variables and not on the physical variables. Whether this is actually the case depends on how the grid is constructed. In a dynamic adaptive procedure where the grid is constructed in the process of solving a fluid flow problem, the grid is usually updated at fixed iteration counts using the current value of the control function. Since the control function is not being updated during the iteration of the grid equations, the grid construction is a linear procedure. However, in the case of a static adaptive procedure where a trial solution is computed and used to construct an adaptive grid, the control functions may be recomputed at every step of the grid iteration.

Mastin, C. Wayne↗
NASA NTRS1994

NASA Technology Applications Team: Commercial applications of aerospace technology

The Research Triangle Institute (RTI) is pleased to report the results of NASA contract NASW-4367, 'Operation of a Technology Applications Team'. Through a period of significant change within NASA, the RTI Team has maintained its focus on helping NASA establish partnerships with U.S. industry for dual use development and technology commercialization. Our emphasis has been on outcomes, such as licenses, industry partnerships and commercialization of technologies that are important to NASA in its mission of contributing to the improved competitive position of U.S. industry. RTI's ongoing commitment to quality and customer responsiveness has driven our staff to continuously improve our technology transfer methodologies to meet NASA's requirements. For example, RTI has emphasized the following areas: (1) Methodology For Technology Assessment and Marketing: RTI has developed an implemented effective processes for assessing the commercial potential of NASA technologies. These processes resulted from an RTI study of best practices, hands-on experience, and extensive interaction with the NASA Field Centers to adapt to their specific needs; (2) Effective Marketing Strategies: RTI surveyed industry technology managers to determine effective marketing tools and strategies. The Technology Opportunity Announcement format and content were developed as a result of this industry input. For technologies with a dynamic visual impact, RTI has developed a stand-alone demonstration diskette that was successful in developing industry interest in licensing the technology; and (3) Responsiveness to NASA Requirements: RTI listened to our customer (NASA) and designed our processes to conform with the internal procedures and resources at each NASA Field Center and the direction provided by NASA's Agenda for Change. This report covers the activities of the Research Triangle Institute Technology Applications Team for the period 1 October 1993 through 31 December 1994.

Source record↗
NASA NTRS1994

NASA Technology Applications Team: Commercial applications of aerospace technology

The Research Triangle Institute (RTI) Team has maintained its focus on helping NASA establish partnerships with U.S. industry for dual use development and technology commercialization. Our emphasis has been on outcomes, such as licenses, industry partnerships and commercialization of technologies, that are important to NASA in its mission of contributing to the improved competitive position of U.S. industry. The RTI Team has been successful in the development of NASA/industry partnerships and commercialization of NASA technologies. RTI ongoing commitment to quality and customer responsiveness has driven our staff to continuously improve our technology transfer methodologies to meet NASA's requirements. For example, RTI has emphasized the following areas: (1) Methodology For Technology Assessment and Marketing: RTI has developed and implemented effective processes for assessing the commercial potential of NASA technologies. These processes resulted from an RTI study of best practices, hands-on experience, and extensive interaction with the NASA Field Centers to adapt to their specific needs. (2) Effective Marketing Strategies: RTI surveyed industry technology managers to determine effective marketing tools and strategies. The Technology Opportunity Announcement format and content were developed as a result of this industry input. For technologies with a dynamic visual impact, RTI has developed a stand-alone demonstration diskette that was successful in developing industry interest in licensing the technology. And (3) Responsiveness to NASA Requirements: RTI listened to our customer (NASA) and designed our processes to conform with the internal procedures and resources at each NASA Field Center and the direction provided by NASA's Agenda for Change. This report covers the activities of the Research Triangle Institute Technology Applications Team for the period 1 October 1993 through 31 December 1994.

Source record↗
NASA NTRS2009

Computational Study on Full-length Human Ku70 with Double Stranded DNA: Dynamics, Interactions and Functional Implications

The Ku70/80 heterodimer is the first repair protein in the initial binding of double-strand break (DSB) ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. In this study we constructed a full-length human Ku70 structure based on its crystal structure, and performed 20 ns conventional molecular dynamic (CMD) simulations on this protein and several other complexes with short DNA duplexes of different sequences. The trajectories of these simulations indicated that, without the topological support of Ku80, the residues in the bridge and C-terminal arm of Ku70 are more flexible than other experimentally identified domains. We studied the two missing loops in the crystal structure and predicted that they are also very flexible. Simulations revealed that they make an important contribution to the Ku70 interaction with DNA. Dislocation of the previously studied SAP domain was observed in several systems, implying its role in DNA binding. Targeted molecular dynamic (TMD) simulation was also performed for one system with a far-away 14bp DNA duplex. The TMD trajectory and energetic analysis disclosed detailed interactions of the DNA-binding residues during the DNA dislocation, and revealed a possible conformational transition for a DSB end when encountering Ku70 in solution. Compared to experimentally based analysis, this study identified more detailed interactions between DNA and Ku70. Free energy analysis indicated Ku70 alone is able to bind DNA with relatively high affinity, with consistent contributions from various domains of Ku70 in different systems. The functional implications of these domains in the processes of Ku heterodimerization and DNA damage recognition and repair can be characterized in detail based upon this analysis.

Hu, Shaowen↗
NASA NTRS2022

Structures of the Nitrogenase Complex Prepared Under Catalytic Turnover Conditions

The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here, we report cryo–electron microscopy structures of the nitrogenase complex prepared under enzymatic turnover conditions. We observe that asymmetry governs all aspects of the nitrogenase mechanism, including ATP hydrolysis, protein-protein interactions, and catalysis. Conformational changes near the catalytic iron-molybdenum cofactor are correlated with the nucleotide-hydrolysis state of the enzyme.

Hannah L. Rutledge↗
NASA NTRS1995

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

NASA Discipline Exobiology↗
DOE OSTI2021

A Constrained Data Assimilation Algorithm Based on GSI Hybrid 3D-EnVar and Its Application

Abstract Data assimilation (DA) at mesoscales is important for severe weather forecasts, yet the techniques of data assimilation at this scale remain a challenge. This study introduces dynamical constraints in the Gridpoint Statistical Interpolation (GSI) three-dimensional ensemble variational (3D-EnVar) data assimilation algorithm to enable the use of high-resolution surface observations of precipitation to improve atmospheric analysis at mesoscales. The constraints use the conservations of mass and moisture. Mass constraint suppresses the unphysical high-frequency oscillation, while moisture conservation constrains the atmospheric states to conform with the observed high-resolution precipitation. We show that the constrained data assimilation (CDA) algorithm significantly reduced the spurious residuals of the mass and moisture budgets compared to the original data assimilation (ODA). A case study is presented for a squall line over the Southern Great Plains on 20 May 2011 during Midlatitude Continental Convective Clouds Experiment (MC3E) of the Atmospheric Radiation Measurement (ARM) program by using ODA or CDA analysis as initial condition of forecasts. The state variables, and the location and intensity of the squall line are better simulated in the CDA experiment. Results show how surface observation of precipitation can be used to improve atmospheric analysis through data assimilation by using the dynamical constraints of mass and moisture conservations.

Wang, Jia↗
DOE OSTI2023

Patterns in interactions of variably acetylated xylans with hydrophobic cellulose surfaces

The recalcitrance of plant cell wall lignocellulosic biomass to deconstruction is a major hurdle to sustainable biofuel/bioproduct economy. A multitude of interactions stabilize lignocellulosic biomass structure. Among these, tight packing of hemicellulose-cellulose is partly responsible for biomass recalcitrance. Here, unrestrained molecular dynamics simulations are employed to understand the influence of the nature and pattern of naturally-occuring acetyl decorations of the xylan backbone on interactions with the (100) hydrophobic cellulose surface. Periodically O2-acetylated xylan (2AcX) assume twofold helical screw conformations that are stabilized by a combination of multiple hydrophobic contacts and hydrogen bonds with the hydrophobic cellulose surface. In contrast, acetylation at the O3 position in xylan obstructs interactions, thereby adopting threefold helical screw conformations that potentially preferably interact with lignin rather than cellulose. Fully acetylated xylan desorbs from the surface implying a minimum number of unsubstituted residues on the xylan backbone is required for interaction with the surface. Here, the substituted residues must form ~ 20% fewer contacts than the unsubstituted residues to sustain stable twofold helical screw xylan conformations on the cellulose surface. Thus, specific roles of macromolecular conformations of cellulose and hemicellulose in influencing the supramolecular interactions and function of plant cell walls have been determined.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗