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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Real-Time XFEL Data Analysis at SLAC and NERSC: a Trial Run of Nascent Exascale Experimental Data Analysis

X-ray scattering experiments using Free Electron Lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID-19 viral proteins). XFEL experiments are a challenge to computing in two ways: i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; ii) data collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min -- sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS-NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Furthermore, completing data analysis with 10 mins is a first for XFEL experiments and an important milestone if we are to keep up with data collection trends.

Blaschke, Johannes P.↗
DOE OSTI2022

Overexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulation

The regulation of lipid metabolism in oil seeds is still not fully understood and increasing our knowledge in this regard is of great economic, as well as intellectual, importance. Oilseed rape (Brassica napus) is a major global oil crop where increases in triacylglycerol (TAG) accumulation have been achieved by overexpression of relevant biosynthetic enzymes. In this study, we expressed Arabidopsis phospholipid: diacylglycerol acyltransferase (PDAT1), one of the two major TAG-forming plant enzymes in B. napus DH12075 to evaluate its effect on lipid metabolism in developing seeds and to estimate its flux control coefficient. Despite several-fold increase in PDAT activity, seeds of three independently generated PDAT transgenic events showed a small but consistent decrease in seed oil content and had altered fatty acid composition of phosphoglycerides and TAG, towards less unsaturation. Mass spectrometry imaging of seed sections confirmed the shift in lipid compositions and indicated that PDAT overexpression altered the distinct heterogeneous distributions of phosphatidylcholine (PC) molecular species. Similar, but less pronounced, changes in TAG molecular species distributions were observed. Our data indicate that PDAT exerts a small, negative, flux control on TAG biosynthesis and could have under-appreciated effects in fine-tuning of B. napus seed lipid composition in a tissue-specific manner. This has important implications for efforts to increase oil accumulation in similar crops.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Structure and Dynamics of CO 2 at the Air–Water Interface from Classical and Neural Network Potentials

The accurate description of the structure and dynamics of CO 2 at the instantaneous air–water interface, along with the effects of surface fluctuations on the CO 2 -transport processes, is essential for the development of negative emission technologies aimed at minimizing climate change. In this study, we performed molecular dynamics simulations of CO 2 at the air–water interface using neural network potentials (NNPs) trained on ab initio data generated through density-functional-theory-based molecular dynamics simulations. We compared these results with classical force fields to assess their performance in modeling interfacial CO 2 behavior. Our findings revealed that the asymmetric interactions, coupled with thermal surface fluctuations at the air–water interface, significantly influence CO 2 transport into the aqueous phase. The simulations demonstrate that classical force fields underestimate both the free energy of CO 2 transport and the strength of its interactions at the interface compared with the neural network potentials. In conclusion, the free energy and the interfacial dynamics of CO 2 are primarily influenced by the distribution of water within the instantaneous interfacial water layer, responsible for creating an asymmetric intermolecular interaction environment within the interfacial region.

Ab initio molecular dynamics↗
NASA NTRS1988

Persistence of Antarctic polar stratospheric clouds

The persistence of Polar Stratospheric Clouds (PSCs) observed by the Stratospheric Aerosol Measurement (SAM) 2 satellite sensor over a 9-year period is compared and contrasted. Histograms of the SAM 2 1.0 micron extinction ratio data (aerosol extinction normalized by the molecular extinction) at an altitude of 18 km in the Antarctic have been generated for three 10-day periods in the month of September. Statistics for eight different years (1979 to 1982 and 1984 to 1987) are shown in separate panels for each figure. Since the SAM 2 system is a solar occultation experiment, observations are limited to the edge of the polar night and no measurements are made deep within the vortex where temperatures could be colder. For this reason, use is made of the NMC global gridded fields and the known temperature-extinction relationship to infer additional information on the occurrence and areal coverage of PSCs. Calculations of the daily areal coverage of the 195 K isotherm will be presented for this same period of data. This contour level lies in the range of the predicted temperature for onset of the Type 1 particle enhancement mode at 50 mb (Poole and McCormick, 1988b) and should indicate approximately when formation of the binary HNO3-H2O particles begins.

Mccormick, M. Patrick↗
NASA NTRS1975

Molecular hydrogen in the galaxy and galactic gamma rays

Recent surveys of 2.6 mm CO emission and 100 MeV gamma-radiation in the galactic plane reveal a striking correlation suggesting that both emissions may be primarily proportional to the line-of-sight column density of H2 in the inner galaxy. Both the gamma ray and CO data suggest a prominent ring or arm consisting of cool clouds of H2 at a galactocentric distance of approximately 5 kpc with a mean density of approximately 4 atoms/cu cm. The importance of H2 in understanding galactic gamma ray observations is also reflected in the correlation of galactic latitude distribution of gamma rays and dense dust clouds. A detailed calculation of the gamma ray flux distribution in the 0 deg to 180 deg range using the CO data to obtain the average distribution of molecular clouds in the galaxy shows that most of the enhancement in the inner galaxy is due to pion-decay radiation and the 5 kpc ring plays a major role. Detailed agreement with the gamma ray data is obtained with the additional inclusion of contributions from bremsstrahlung and Compton radiation of secondary electrons and Compton radiation from the intense radiation field near the galactic center.

Stecker, F. W.↗
NASA NTRS1994

Numerical Simulation of Cylindrical, Self-field MPD Thrusters with Multiple Propellants

A two-dimensional, two-temperature, single fluid MHD code was used to predict the performance of cylindrical, self-field magnetoplasmadynamic (MPD) thrusters operated with argon, lithium, and hydrogen propellants. A thruster stability equation was determined relating maximum stable J(sup 2)/m values to cylindrical thruster geometry and propellant species. The maximum value of J(sup 2)/m was found to scale as the inverse of the propellant molecular weight to the 0.57 power, in rough agreement with limited experimental data which scales as the inverse square root of the propellant molecular weight. A general equation which relates total thrust to electromagnetic thrust, propellant molecular weight, and J(sup 2)/m was determined using reported thrust values for argon and hydrogen and calculated thrust values for lithium. In addition to argon, lithium, and hydrogen, the equation accurately predicted thrust for ammonia at sufficiently high J(sup 2)/m values. A simple algorithm is suggested to aid in the preliminary design of cylindrical, self-field MPD thrusters. A brief example is presented to illustrate the use of the algorithm in the design of a low power MPD thruster.

Lapointe, Michael R.↗
DOE OSTI2021

First principles reactive simulation for equation of state prediction

The high cost of density functional theory (DFT) has hitherto limited the ab initio prediction of the equation of state (EOS). In this article, we employ a combination of large scale computing, advanced simulation techniques, and smart data science strategies to provide an unprecedented ab initio performance analysis of the high explosive pentaerythritol tetranitrate (PETN). Comparison to both experiment and thermochemical predictions reveals important quantitative limitations of DFT for EOS prediction and thus the assessment of high explosives. In particular, we find that DFT predicts the energy of PETN detonation products to be systematically too high relative to the unreacted neat crystalline material, resulting in an underprediction of the detonation velocity, pressure, and temperature at the Chapman–Jouguet state. The energetic bias can be partially accounted for by high-level electronic structure calculations of the product molecules. Furthermore we demonstrate a modeling strategy for mapping chemical composition across a wide parameter space with limited numerical data, the results of which suggest additional molecular species to consider in thermochemical modeling.

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

Identification of novel organic polar materials: A machine learning study with importance sampling

Recent advances in the synthesis of polar molecular materials have produced practical alternatives to ferroelectric ceramics, opening up exciting new avenues for their incorporation into modern electronic devices. However, in order to realize the full potential of polar polymer and molecular crystals for modern technological applications, it is paramount to assemble and evaluate all the available data for such compounds, identifying descriptors that could be associated with an emergence of ferroelectricity. In this paper, we utilized data-driven approaches to judiciously shortlist candidate materials from a wide chemical space that could possess ferroelectric functionalities. A machine learning study with importance sampling was employed to address the challenge of having a limited amount of available data on already-known organic ferroelectrics. Sets of molecular- and crystal-level descriptors were combined with a Random Forest Regression algorithm in order to predict the spontaneous polarization of the shortlisted compounds. First-principles simulations were performed to further validate the predictions obtained from the machine learning model.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Unsymmetric Pentacene- and Pentacenequinone-Fused Porphyrins: Understanding the Effect of Cross- and Linear-Conjugation

Unsymmetric pentacenequinone-fused (cross-conjugated) and pentacene-fused (linear-conjugated) porphyrins were designed and synthesized. The cross-conjugated (AM 1 –AM 3 ) and linear-conjugated (AM 5 –AM 7 ) porphyrins displayed strikingly different sets of optical and electronic properties, both of which are unusual and nontypical of porphyrins. MCD, DFT, and TDDFT calculations suggest that multiple charge transfer states exist in both π-conjugated systems, which contributes to the complex absorption and MCD spectra of these molecular systems. The general Gouterman’s four-orbital model used to explain porphyrin spectroscopy led to contradicting theoretical and experimental data, and is thus not applicable for these molecular systems. The “2 + 4” and “3 + 3” active spaces have been deduced and have proven effective to interpret the absorption and MCD spectra of the pentacenequinone-fused (cross-conjugated) and pentacene-fused (linear-conjugated) porphyrins, respectively. Spectroelectrochemistry of AM 5 –AM 7 revealed broad and intense IR absorptions in the range of 1500–2500 nm, illustrating the exceptional ability of these pentacene-fused systems to accommodate positive charges. A pronounced metal effect was observed for pentacene-fused porphyrins. While pentacene-fused Ni(II) porphyrin (AM 6 ) demonstrated an abnormal ability to stabilize pentacene with a half-life of >28.3 days, the half-life of the free base and Zn(II) counterparts were normal, similar to those of pentacene analogues. This work provides important and useful information on guiding new material designs.

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

Eu(III) and Cm(III) Complexation by the Aminocarboxylates NTA, EDTA, and EGTA Studied with NMR, TRLFS, and ITC—An Improved Approach to More Robust Thermodynamics

The complex formation of Eu(III) and Cm(III) was studied via tetradentate, hexadentate, and octadentate coordinating ligands of the aminopolycarboxylate family, viz., nitrilotriacetate (NTA 3- ), ethylenediaminetetraacetate (EDTA 4- ), and ethylene glycol-bis(2-aminoethyl ether)-N,N,N',N'-tetraacetate (EGTA 4- ), respectively. Based on the complexones’ pK a values obtained from 1 H nuclear magnetic resonance (NMR) spectroscopic pH titration, complex formation constants were determined by means of the parallel-factor-analysis-assisted evaluation of Eu(III) and Cm(III) time-resolved laser-induced fluorescence spectroscopy (TRLFS). This was complemented by isothermal titration calorimetry (ITC), providing the enthalpy and entropy of the complex formation. This allowed us to obtain genuine species along with their molecular structures and corresponding reliable thermodynamic data. The three investigated complexones formed 1:1 complexes with both Eu(III) and Cm(III). Besides the established Eu(III)–NTA 1:1 and 1:2 complexes, we observed, for the first time, the existence of a Eu(III)–NTA 2:2 complex of millimolar metal and ligand concentrations. Demonstrated for thermodynamic studies on Eu(III) and Cm(III) interaction with complexones, the utilized approach is commonly applicable to many other metal–ligand systems, even to high-affinity ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Directed gas phase preparation of ethynylallene (H 2 CCCHCCH; X 1 A') via the crossed molecular beam reaction of the methylidyne radical (CH; X 2 Π) with vinylacetylene (H 2 CCHCCH; X 1 A')

The gas-phase bimolecular reaction of the methylidyne (CH; X 2 Π) radical with vinylacetylene (H 2 CCHCCH; X 1 A') was conducted at a collision energy of 20.3 kJ mol –1 under single collision conditions exploiting the crossed molecular beam experimental results merged with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations. The laboratory data reveal that the bimolecular reaction proceeds barrierlessly via indirect scattering dynamics through long-lived C 5 H 5 reaction intermediate(s) ultimately dissociating to C 5 H 4 isomers along with atomic hydrogen with the latter predominantly originating from the vinylacetylene reactant as confirmed by the isotopic substitution experiments in the D1-methylidyne–vinylacetylene reaction. Combined with ab initio calculations of the potential energy surface (PES) and statistical Rice–Ramsperger–Kassel–Marcus (RRKM) calculations, the experimental determined reaction energy of –146 ± 26 kJ mol –1 along with the distribution minimum of T(θ) at 90° and isotopic substitution experiments suggest ethynylallene (p1; ΔrG = –230 ± 4 kJ mol –1 ) as the dominant product. The ethynylallene (p1) may be formed with extensive rovibrational excitation, which would result in a lower maximum translational energy. Further, AIMD simulations reveal that the reaction dynamics leads to p1 (ethynylallene, 75%) plus atomic hydrogen with the dominant initial complex being i1 formed by methylidyne radical addition to the double C[double bond, length as m-dash]C bond in vinylacetylene. Altogether, combining the crossed molecular beam experimental results with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations, ethynylallene (p1) is expected to represent the dominant product in the reaction of the methylidyne (CH; X 2 Π) radical with vinylacetylene (H 2 CCHCCH; X 1 A').

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

Phase‐Change‐Memory Process at the Limit: A Proposal for Utilizing Monolayer Sb 2 Te 3

Abstract One central task of developing nonvolatile phase change memory (PCM) is to improve its scalability for high‐density data integration. In this work, by first‐principles molecular dynamics, to date the thinnest PCM material possible (0.8 nm), namely, a monolayer Sb 2 Te 3 , is proposed. Importantly, its SET (crystallization) process is a fast one‐step transition from amorphous to hexagonal phase without the usual intermediate cubic phase. An increased spatial localization of electrons due to geometrical confinement is found to be beneficial for keeping the data nonvolatile in the amorphous phase at the 2D limit. The substrate and superstrate can be utilized to control the phase change behavior: e.g., with passivated SiO 2 (001) surfaces or hexagonal Boron Nitride, the monolayer Sb 2 Te 3 can reach SET recrystallization in 0.54 ns or even as fast as 0.12 ns, but with unpassivated SiO 2 (001), this would not be possible. Besides, working with small volume PCM materials is also a natural way to lower power consumption. Therefore, the proposed PCM working process at the 2D limit will be an important potential strategy of scaling the current PCM materials for ultrahigh‐density data storage.

2D limit↗
NASA NTRS1992

Analysis of sonic boom data to quantify distortions of shock profiles

Researchers at Penn State have been examining some sonic boom waveforms recorded during overflights by the Air Force which have become available to NASA and its contractors. The quality of the digitized data and the supporting meteorological data was such that one could test the applicability of molecular relaxation theories. In the late sixties, it had been supposed that the finite rise times in the absence of turbulence had neglected the vibrational relaxation of nitrogen molecules. Bass et al. have demonstrated that molecular relaxation definitely gives the correct order of magnitude of the observed rise times. However, the Air Force data in conjunction with the recent steady-state shock profile model theory of Kang and Pierce give the first opportunity to make a detailed quantitative assessment of the molecular relaxation hypothesis. Currently an investigation is ongoing to establish a method of quantifying the distortion of a sonic boom wave from a classic N-wave shape using the Air Force data taken at Edwards AFB in 1987. Using the premise that energy will be conserved approximately for a sonic boom wave both before and after the boom passes through the Earth's turbulent boundary layer, a classic undistorted waveform is constructed from the distorted signature received at the ground. A correlation between the mean-squared deviation of the distorted and undistorted waveforms and the distance the boom travels through the turbulence is sought.

Gionfriddo, Thomas A.↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2021

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗