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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 OSTI2020

Base pairing, structural and functional insights into N 4 -methylcytidine (m 4 C) and N 4 ,N 4 -dimethylcytidine (m 4 2 C) modified RNA

The N 4 -methylation of cytidine (m 4 C and m 4 2 C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m 4 C and m 4 2 C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m 4 C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m 4 2 C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m 4 2 C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N 4 -position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

A Multi-Physics Study on High-Specific Power Li-O2 Batteries for Electric Aircraft

Commercialization of lithium-air batteries faces many challenges, such as electrolyte decomposition, short cycle life, low energy and power density, etc. However, commercialization of Li-O2 batteries for aeronautics is much more challenging due to additional safety constraints on cyclability and performance (high specific power and specific energy). For this presentation, we will discuss inter-related aspects of physics-based modeling of a pack: cell and battery model calibration. In addition, we will evaluate and present optimal battery designs for high discharge current density, high discharge time, and low battery mass using simulation-based optimization.The Finite Element Model (FEM) used to simulate a Li-O2 cell is based on the work of Bevara [1]. The different aspects of the model are based on: porous electrode theory and concentrated electrolyte theory; quantum tunneling model for the resistance of conformal layer of discharge product (Li2O2) [1]; Butler-Volmer kinetics for electrochemical reaction; Fick's diffusion for oxygen transport; and an oxygen dissolution model is applied at the air/electrolyte interface [2]. The electrolyte properties such as ion conductivity, ion diffusion, oxygen diffusion, and mass density of the electrolyte were taken from Molecular Dynamics (MD) simulations [3]; while the other model parameters, which includes mass of cell components, were calibrated to match experiments at high discharge current densities. The cell mass includes the anode, cathode, separator, electrolyte, and other components (such as current collector). This calibrated model is used to perform parametric studies on cathode thickness, porosity, tortuosity, carbon particle size, electrolyte transport and material properties, partial pressure of oxygen, discharge time, and discharge current density to study optimal designs for high specific power and energy. References:1. Bevara, V. & Andrei, P. (2014), J. Electrochem. Soc. 161 (14), A2068-A2079.2.Mehta, M. & Andrei, P. (2015), J. Power Sources. 286, 299-308.3.Liyana-Arachchi, T.; Haskins, J.; Burke, C.; Diederichsen, K.; McCloskey, B.; & Lawson, J. (2018), J. Phys. Chem. B. 122 (36), 8548 - 8559.4.Choi, W.; Kikumoto, H.; Choudhary, R. & Ooka, R. (2018), Applied Energy, 209, 306-321.

Mehta, Mohit↗
DOE OSTI2020

Isomer-specific spectroscopy of aromatics and their resonance-stabilized radical intermediates

There are many circumstances in which complex gas-phase reaction mixtures must be interrogated and understood, including combustion, plasmas, atmospheres, and molecular clouds. Spectroscopic tools are essential to selective detection and characterization of the widening array of precursors and the reactive intermediates they generate. This research program has focused on the development and implementation of sensitive spectroscopic detection schemes that are isomer-specific and even conformation-specific. In particular, we used an array of laser-based and broadband microwave methods to carry out isomer-specific and conformation-specific spectroscopy on large flexible molecules and reactive intermediates formed by photolysis, pyrolysis, combustion, or electron-driven chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1982

Boundary-fitted coordinate systems for numerical solution of partial differential equations - A review

A comprehensive review of methods of numerically generating curvilinear coordinate systems with coordinate lines coincident with all boundary segments is given. Some general mathematical framework and error analysis common to such coordinate systems is also included. The general categories of generating systems are those based on conformal mapping, orthogonal systems, nearly orthogonal systems, systems produced as the solution of elliptic and hyperbolic partial differential equations, and systems generated algebraically by interpolation among the boundaries. Also covered are the control of coordinate line spacing by functions embedded in the partial differential operators of the generating system and by subsequent stretching transformation. Dynamically adaptive coordinate systems, coupled with the physical solution, and time-dependent systems that follow moving boundaries are treated. References reporting experience using such coordinate systems are reviewed as well as those covering the system development.

Thompson, J. F.↗
DOE OSTI2020

Pilgrim : A thermal rate constant calculator and a chemical kinetics simulator

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. Finally, this algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

High‐Performance Rechargeable Lithium‐Chlorine Batteries with ALD Conformal Starburst Porous Graphene Positive Electrodes

Abstract Rechargeable alkali metal‐chlorine batteries are emerging as a promising high‐energy‐density solution. However, they confront significant challenges, including the primary issue stemming from the weak binding affinity of cathode materials for Cl 2 , which leads to a sluggish and inadequate supply of Cl 2 during the redox reactions, resulting in a shortened cycle life and low Coulombic efficiency (CE), particularly when operating at ultrahigh specific capacity outputs. Herein, an Al 2 O 3 ‐skinned heterostructured starburst porous graphene with conformal metasurfaces (Al 2 O 3 @rGO) is reported, crafted from a hierarchical porous starburst graphene arranged in a unique layered structure by the PTFE microemulsion skin effect, leveraging subsequent fluidized bed atomic layer deposition (FBALD) of Al 2 O 3 groups. Al 2 O 3 @rGO features superhydrophilicity, effective adsorption, fast kinetics from stable dynamic respiratory interface, high electrical and thermal conductivity anisotropy, intelligent thermal management and safe operation over a wide temperature range. Consequently, the Li‐Cl 2 @Al 2 O 3 @rGO battery achieves an ultrahigh discharge specific capacity of 5000 mAh g −1 at ≈100% CE, and even delivers stable cycling over 200 cycles with 2000 mAh g −1 at an average CE of 99.8% under low temperature environment of ‐40 °C. The scalable heterostructure approach offers a sustainable perspective of the development of functionalized metamaterials and metasurfaces for next‐generation safe and energy‐dense batteries and broader applications.

Chemistry↗
DOE OSTI2024

Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state

Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54 ± 11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.

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

The TESS-Keck Survey. III. A Stellar Obliquity Measurement of TOI-1726 c

We report the measurement of a spectroscopic transit of TOI-1726c, one of two planets transiting a G-type star with V = 6.9 in the Ursa Major Moving Group (∼400 Myr). With a precise age constraint from cluster membership, TOI-1726 provides a great opportunity to test various obliquity excitation scenarios that operate on different timescales. By modeling the Rossiter–McLaughlin (RM) effect, we derived a sky-projected obliquity of −1{sub −32}{sup +35{sup ∘}}. This result rules out a polar/retrograde orbit and is consistent with an aligned orbit for planet c. Considering the previously reported, similarly prograde RM measurement of planet b and the transiting nature of both planets, TOI-1726 tentatively conforms to the overall picture that compact multitransiting planetary systems tend to have coplanar, likely aligned orbits. TOI-1726 is also a great atmospheric target for understanding differential atmospheric loss of sub-Neptune planets (planet b 2.2 R {sub ⊕} and c 2.7 R {sub ⊕} both likely underwent photoevaporation). The coplanar geometry points to a dynamically cold history of the system that simplifies any future modeling of atmospheric escape.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Complex Relationship between Side-Chain Polarity, Conductivity, and Thermal Stability in Molecularly Doped Conjugated Polymers

Molecularly doped conjugated polymers with polar side chains are an emerging class of conducting materials exhibiting enhanced and thermally stable conductivity. In this work, we study the electronic conductivity (σ) and the corresponding thermal stability of two polythiophene derivatives comprising oligoethylene glycol side chains: one having oxygen attached to the thiophene ring (poly(3-(methoxyethoxyethoxy)thiophene) (P3MEET)) and the other having a methylene spacer between the oxygen and the thiophene ring (poly(3-(methoxyethoxyethoxymethyl)thiophene) (P3MEEMT)). Thin films were vapor-doped with fluorinated derivatives of tetracyanoquinodimethane (FnTCNQ, n = 4, 2, 1) to determine the role of dopant strength (electron affinity) in maximum achievable σ. Specifically, when vapor doping with F 4 TCNQ, P3MEET achieved a substantially higher σ of 37.1 ± 10.1 S/cm compared to a σ of 0.82 ± 0.06 S/cm for P3MEEMT. Structural characterization using a combination of X-ray and optical spectroscopy reveals that the higher degree of conformational order of polymer chains in the amorphous domain upon doping with F 4 TCNQ in P3MEET is a major contributing factor for the higher σ of P3MEET. Additionally, vapor-doped P3MEET exhibited superior thermal stability compared to P3MEEMT, highlighting that the presence of polar side chains alone does not ensure higher thermal stability. Molecular dynamics simulations indicate that the dopant–side-chain nonbond energy is lower in the P3MEET:F 4 TCNQ mixture, suggesting more favorable dopant–side-chain interaction, which is a factor in improving the thermal stability of a polymer/dopant pair. Our results reveal that additional factors such as polymer ionization energy and side-chain–dopant interaction should be taken into account for the design of thermally stable, highly conductive polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Extracting the Quantum Hall Conductance from a Single Bulk Wave Function

In this work, we propose a new formula that extracts the quantum Hall conductance from a single (2+1)⁢ D gapped wave function. The formula applies to general many-body systems that conserve particle number, and is based on the concept of modular flow, i.e., unitary dynamics generated from the entanglement structure of the wave function. The formula is shown to satisfy all formal properties of the Hall conductance: it is odd under time reversal and reflection, even under charge conjugation, universal and topologically rigid in the thermodynamic limit. Further evidence for relating the formula to the Hall conductance is obtained from conformal field theory arguments. Finally, we numerically check the formula by applying it to a noninteracting Chern band where excellent agreement is obtained.

2-dimensional systems↗
NASA NTRS1980

Head-up transition behavior of pilots with and without head-up display in simulated low-visibility approaches

To quantify head-up transition behavior with and without a flightpath type head-up display, eight rated B-727 pilots each flew 31 manual and coupled approaches in a simulator with B-727 dynamics and collimated model board external scene. Data were also obtained on the roll played by the head-up display in the coupled-to-manual transition. Various wind shears, low visibilities, and ceilings were tested along with unexpected misalignment between the runway and head-up display symbology. The symbolic format used was a conformal scene. Every pilot except one stayed head-up, flying with the display after descending below the ceiling. Without the display and as altitude decreased, the number of lookups from the instrument panel decreased and the duration of each one increased. No large differences in mean number or duration of transitions up or down were found during the head-up display runs comparing the no-misalignment with the lateral instrument landing system offset misalignment runs. The head-up display led to fewer transitions after the pilot made a decision to land or execute a missed approach. Without the display, pilots generally waited until they had descended below the ceiling to look outside the first time, but with it several pilots looked down at their panel at relatively high altitudes (if they looked down at all). Manual takeover of control was rapid and smooth both with and without the display which permitted smoother engine power changes.

Haines, R. F.↗
NASA NTRS1984

Spokes in Saturn's rings - Dynamical and reflectance properties

The results and implications of dynamical and reflectance studies of spokes in the Voyager 2 low-resolution ring movie are presented. The spoke of greater interest (Spoke 1) can be traced from its first appearance on the morning and to its terminal dispersion on the evening side. Orbital velocities, reflectances, and reflectance profiles are reported. The behavior of Spoke 1 conforms to the plasma cloud model of spoke formation and evolution proposed by Goertz and Morfill (1983). A second spoke observed in the ring movie provides corroborating support for the observed behavior of Spoke 1.

Eplee, R. E., Jr.↗
DOE OSTI2021

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments

Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO 3 ·nH 2 O systems, where M 2+ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Finally, water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.

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

Regulation of the EphA2 receptor intracellular region by phosphomimetic negative charges in the kinase-SAM linker

Eph receptor tyrosine kinases play a key role in cell-cell communication. Lack of structural information on the entire multi-domain intracellular region of any Eph receptor has hindered understanding of their signaling mechanisms. Here, we use integrative structural biology to investigate the structure and dynamics of the EphA2 intracellular region. EphA2 promotes cancer malignancy through a poorly understood non-canonical form of signaling involving serine/threonine phosphorylation of the linker connecting its kinase and SAM domains. We show that accumulation of multiple linker negative charges, mimicking phosphorylation, induces cooperative changes in the EphA2 intracellular region from more closed to more extended conformations and perturbs the EphA2 juxtamembrane segment and kinase domain. In cells, linker negative charges promote EphA2 oligomerization. We also identify multiple kinases catalyzing linker phosphorylation. Our findings suggest multiple effects of linker phosphorylation on EphA2 signaling and imply that coordination of different kinases is necessary to promote EphA2 non-canonical signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coupling sensor to enzyme in the voltage sensing phosphatase

Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), resembling that of voltage-gated cation channels, and a lipid phosphatase domain (PD). The mechanism by which voltage turns on enzyme activity is unclear. Structural analysis and modeling suggest several sites of VSD-PD interaction that could couple voltage sensing to catalysis. Voltage clamp fluorometry reveals voltage-driven rearrangements in three sites implicated earlier in enzyme activation—the VSD-PD linker, gating loop and R loop—as well as the N-terminal domain, which has not yet been explored. N-terminus mutations perturb both rearrangements in the other segments and enzyme activity. Our results provide a model for a dynamic assembly by which S4 controls the catalytic site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗