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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 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A catalog of the diversity and ubiquity of bacterial microcompartments

Abstract Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which are incompatible with surrounding metabolism. BMCs consist of a selectively permeable shell, composed of three types of structurally conserved proteins, together with sequestered enzymes that vary among functionally distinct BMCs. Genes encoding shell proteins are typically clustered with those for the encapsulated enzymes. Here, we report that the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014, and the number of distinct BMC types has doubled. The new BMC types expand the range of compartmentalized catalysis and suggest that there is more BMC biochemistry yet to be discovered. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, experimental characterization, and development of BMC-based nanoarchitectures for biomedical and bioengineering applications.

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

Analysis of vibronic coupling in a 4f molecular magnet with FIRMS

Vibronic coupling, the interaction between molecular vibrations and electronic states, is a fundamental effect that profoundly affects chemical processes. In the case of molecular magnetic materials, vibronic, or spin-phonon, coupling leads to magnetic relaxation, which equates to loss of magnetic memory and loss of phase coherence in molecular magnets and qubits, respectively. The study of vibronic coupling is challenging, and most experimental evidence is indirect. Here we employ far-infrared magnetospectroscopy to directly probe vibronic transitions in [Yb(trensal)] (where H 3 trensal = 2,2,2-tris(salicylideneimino)trimethylamine). We find intense signals near electronic states, which we show arise due to an “envelope effect” in the vibronic coupling Hamiltonian, which we calculate fully ab initio to simulate the spectra. We subsequently show that vibronic coupling is strongest for vibrational modes that simultaneously distort the first coordination sphere and break the C 3 symmetry of the molecule. With this knowledge, vibrational modes could be identified and engineered to shift their energy towards or away from particular electronic states to alter their impact. Hence, these findings provide new insights towards developing general guidelines for the control of vibronic coupling in molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.

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

Electronic properties and optical spectra of donor–acceptor conjugated organic polymers

Organic semiconductors based on conjugated donor-acceptor (D–A) polymers are a unique platform for electronic, spintronic, and energy-harvesting devices. Understanding the electronic structure of D–A polymers with a small band gap is essential for developing next-generation technologies. Here, we investigate the electronic structure and optical spectra of cyclopentadithiophene-based closed/open-shell D–A polymers using density functional theory and the Bethe–Salpeter equation based on G 0 W 0 approximation. We explored the role of different acceptor units and chemical substitutions on the structural changes and, more importantly, electronic, optical, and dielectric behavior. We found that the computed first exciton peak of the polymers agreed well with the available experimentally measured optical gap. Furthermore, D–A polymers with open-shell character display higher dielectric constant than the closed-shell polymers. We show that the exceptional performance of polycyclopentadithiophene-thiophenylthiadiazoloquinoxaline (PCPDT-TTQ) as a scalable n-type material for Faradaic supercapacitors can be partly ascribed to its elevated dielectric constant. Consequently, these D–A polymers, characterized by their high dielectric constants, exhibit significant potential for various applications, including energy storage, organic electronics, and the production of dielectric films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

C-84 Selective Porphyrin Macrocycle with an Adaptable Cavity Constructed Through Alkyne Metathesis

A bisporphyrin macrocycle was constructed from a porphyrin-based diyne monomer in one step through alkyne metathesis. The fullerene binding studies (C{sub 60}, C{sub 70} and C{sub 84}) showed the highest binding affinity of the macrocycle for C{sub 84}, which is in great contrast to its bisporphyrin four-armed cage analogue that showed the strongest binding with C{sub 70}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch

The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated using theoretical and simulation methods at 4 Torr pressure. SIMION simulations were used to optimize and evaluate conditions for performing turns without loss of signal intensity or ion mobility resolving power. Fundamental considerations indicated that the “race track” effect during ion turns may incur only small losses to the ion mobility resolving power at 4 Torr pressure for the typical plume widths predicted in an optimized SLIM ‘tee’ switch design. The dynamic switching of ions into orthogonal channels was also evaluated using SIMION ion trajectory simulations, and achieved similar performance. Simulation results were in close agreement with experimental results and were used to refine SLIM designs and applied potentials for their use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mechanistic insights into rubidium ion adsorption at the quartz (101) surface from quantum chemical metadynamics

Ion sorption extent and mechanism depend in part on the mineral surface termination, which can be highly complex. Variations in surface functional groups, particularly with defect density and surface roughness, influence mineral reactivity towards solutes. In this work, we investigate the adsorption of a rubidium cation (Rb + ) at pristine and defect quartz (101) surface sites using well-tempered metadynamics, based on simulations with the quantum chemical density-functional tight-binding (DFTB) method. We compare the relative energetics of Rb + adsorption across selected sites for each surface, with nanosecond-level sampling, highlighting similarities between vicinal and geminal silanol sites. We find that the positive Rb + partial atomic charge can increase by as much as 0.5e as it approaches the surface, with implications for modulation of ion adsorption strength and extent at the quartz (101) surface with surface vacancies, silanol coverage, and charge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Approximate models for the study of exponential changed quantities: Application on the plasma waves growth rate or damping

Many physical phenomena that concern the research these days are basically complicated because of being multi-parametric. Thus, their study and understanding meets with big if not unsolved obstacles. Such complicated and multi-parametric is the plasmatic state as well, where the plasma and the physical quantities that appear along with it have chaotic behavior. Many of those physical quantities change exponentially and at most times they are stabilized by presenting wavy behavior. Mostly in the transitive state rather than the steady state, the exponentially changing quantities (Growth, Damping etc) depend on each other in most cases. Thus, it is difficult to distinguish the cause from the result. The present paper attempts to help this difficult study and understanding by proposing mathematical exponential models that could relate with the study and understanding of the plasmatic wavy instability behavior. Such instabilities are already detected, understood and presented in previous publications of our laboratory. In other words, our new contribution is the study of the already known plasmatic quantities by using mathematical models (modeling and simulation). These methods are both useful and applicable in the chaotic theory. In addition, our ambition is to also conduct a list of models useful for the study of chaotic problems, such as those that appear into the plasma, starting with this paper's examples.

36 MATERIALS SCIENCE↗
DOE OSTI2014

High spatial resolution mapping of deposition layers on plasma facing materials by laser ablation microprobe time-of-flight mass spectroscopy

A laser ablation microprobe time-of-flight mass spectroscopy (LAM-TOF-MS) system with high spatial resolution, ∼20 nm in depth and ∼500 μm or better on the surface, is developed to analyze the composition distributions of deposition layers on the first wall materials or first mirrors in tokamak. The LAM-TOF-MS system consists of a laser ablation microprobe combined with a TOF-MS and a data acquisition system based on a LabVIEW program software package. Laser induced ablation combined with TOF-MS is an attractive method to analyze the depth profile of deposited layer with successive laser shots, therefore, it can provide information for composition reconstruction of the plasma wall interaction process. In this work, we demonstrate that the LAM-TOF-MS system is capable of characterizing the depth profile as well as mapping 2D composition of deposited film on the molybdenum first mirror retrieved from HL-2A tokamak, with particular emphasis on some of the species produced during the ablation process. The presented LAM-TOF-MS system provides not only the 3D characterization of deposition but also the removal efficiency of species of concern.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Non-invasive airway health measurement using synchrotron x-ray microscopy of high refractive index glass microbeads

Cystic fibrosis (CF) is caused by a gene defect that compromises the ability of the mucociliary transit (MCT) system to clear the airways of debris and pathogens. To directly characterise airway health and the effects of treatments we have developed a synchrotron X-ray microscopy method that non-invasively measures the local rate and patterns of MCT behaviour. Although the nasal airways of CF mice exhibit the CF pathophysiology, there is evidence that nasal MCT is not altered in CF mice1. The aim of this experiment was to determine if our non-invasive local airway health assessment method could identify differences in nasal MCT rate between normal and CF mice, information that is potentially lost in bulk MCT measurements. Experiments were performed on the BL20XU beamline at the SPring-8 Synchrotron in Japan. Mice were anaesthetized, a small quantity of micron-sized marker particles were delivered to the nose, and images of the nasal airways were acquired for 15 minutes. The nasal airways were treated with hypertonic saline or mannitol to increase surface hydration and MCT. Custom software was used to locate and track particles and calculate individual and bulk MCT rates. No statistically significant differences in MCT rate were found between normal and CF mouse nasal airways or between treatments. However, we hope that the improved sensitivity provided by this technique will accelerate the ability to identify useful CF lung disease-modifying interventions in small animal models, and enhance the development and efficacy of proposed new therapies.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

CalE6 from Micromonospora echinospora is a (pyridoxal 50 phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. Here, we report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Evolutionary strategy for inverse charge measurements of dielectric particles

Here, we report a computational strategy to obtain the charges of individual dielectric particles from experimental observation of their interactions as a function of time. This strategy uses evolutionary optimization to minimize the difference between trajectories extracted from the experiment and simulated trajectories based on many-particle force fields. The force fields include both Coulombic interactions and dielectric polarization effects that arise due to particle-particle charge mismatch and particle-environment dielectric contrast. The strategy was applied to systems of free falling charged granular particles in a vacuum, where electrostatic interactions are the only driving forces that influence the particles' motion. We show that when the particles' initial positions and velocities are known, the optimizer requires only an initial and final particle configuration of a short trajectory in order to accurately infer the particles' charges; when the initial velocities are unknown and only the initial positions are given, the optimizer can learn from multiple frames along the trajectory to determine the particles' initial velocities and charges. While the results presented here offer a proof-of-concept demonstration of the proposed ideas, the proposed strategy could be extended to more complex systems of electrostatically charged granular matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Physics of picosecond pulse laser ablation

This study investigates the physical processes involved in picosecond pulse (20-28 ps FWHM) laser ablation of Al 6061, 316L stainless steel, and undoped crystalline Si ($\langle$100$\rangle$) over a range of laser wavelength (355 nm and 1064 nm) and fluence (0.1-40 J/cm 2 ). Experimental measurements of material ablation rate show enhanced removal at the 355 nm wavelength, primarily due to laser-plasma interaction (LPI) within the ablative plume that approaches an order of magnitude increase over the measured removal at 1064 nm. A transition in the ablation rate at 355 nm is identified around ~10 J/cm 2 above which the removal efficiency increases by a factor of two to three. Multi-physics radiation hydrodynamic simulations, considering LPI effects and utilizing a novel mixed-phase equation of state model, show that the transition in ablation efficiency is due to the onset of melt ejection through cavitation, where laser-driven shock heating sets the depth of melt penetration and the ensuing release wave from the ablation surface drives cavitation through the imposition of tensile strain within the melt. High-speed pump-probe imaging of the ejecta and ejecta collection studies, as well as scanning electron microscopy of the ablation craters, support the proposed cavitation mechanism in the higher fluence range. The ablation process is vitally influenced by LPI effects and the thermophysical properties of the material.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Oscillation-like diffusion of two-dimensional liquid dusty plasmas on one-dimensional periodic substrates with varied widths

The long-time diffusion of two-dimensional dusty plasmas on a one-dimensional periodic substrate with varying widths is investigated using Langevin dynamical simulations. When the substrate is narrow and the dust particles form a single row, the diffusion is the smallest in both directions. In this study, we find that as the substrate width gradually increases to twice its initial value, the long-time diffusion of the two-dimensional dusty plasmas first increases, then decreases, and finally increases again, giving an oscillation-like diffusion with varying substrate widths. When the width increases to a specific value, the dust particles within each potential well arrange themselves in a stable zigzag pattern, greatly reducing the diffusion and leading to the observed oscillation in the diffusion with the increase in the width. In addition, the long-time oscillation-like diffusion is consistent with the number of dust particles that are hopping across the potential wells of the substrate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Determining best practices for using genetic algorithms in molecular discovery

Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this tutorial, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selection method, mutation rate, and convergence criteria, on key GA performance metrics. Here, we show that using a self-termination method with a minimum Spearman’s rank correlation coefficient of 0.8 between generations maintained for 50 consecutive generations along with a population size of 32, a 50% elitism rate, three-way tournament selection, and a 40% mutation rate provides the best balance of finding the overall champion, maintaining good coverage of elite targets, and improving relative speedup for general use in molecular design GAs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Strain effects on Auger–Meitner recombination in silicon

We study the effects of compressive and tensile biaxial strain on direct and phonon-assisted Auger–Meitner recombination (AMR) in silicon using first-principles calculations. We find that the application of strain has a non-trivial effect on the AMR rate. For most AMR processes, the application of strain increases the AMR rate. However, the recombination rate for the AMR process involving two holes and one electron is suppressed by 38% under tensile strain. We further analyze the specific phonon contributions that mediate the phonon-assisted AMR mechanism, demonstrating the increased anisotropy under strain. In conclusion, our results indicate that the application of tensile strain increases the lifetime of minority electron carriers in p-type silicon and can be leveraged to improve the efficiency of silicon devices.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Influence of Coulomb effects on the resolving power of multireflection mass-spectrometer systems

General theoretical approaches to the modelling of Coulomb effects in short ion bunches, developed previously by the authors, are applied in this paper to the calculation of multireflection mass-spectrometer systems. A separate module of the MASIM 3D applied software package is designed. An adaptive computational procedure for calculating the 'mirror potential' induced by an ion bunch on the surface of field-forming electrodes is proposed. The dynamics of ion bunches in a time-of-flight reflectron-type mass analyser is calculated and the limitations on the resolving power, caused by resonant Coulomb effects of self-bunching and coalescence in the groups of particles with close masses, are revealed on the basis of numerical experiments. (laser applications and other topics in quantum electronics)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Efficient quantum algorithm for dissipative nonlinear differential equations

Significance Nonlinear differential equations appear in many domains and are notoriously difficult to solve. Whereas previous quantum algorithms for general nonlinear differential equations have complexity exponential in the evolution time, we give the first quantum algorithm for dissipative nonlinear differential equations that is efficient provided the dissipation is sufficiently strong relative to nonlinear and forcing terms and the solution does not decay too rapidly. We also establish a lower bound showing that differential equations with sufficiently weak dissipation have worst-case complexity exponential in time, giving an almost tight classification of the quantum complexity of simulating nonlinear dynamics. Furthermore, numerical results for the Burgers equation suggest that our algorithm may potentially address complex nonlinear phenomena even in regimes with weaker dissipation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗