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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

KBase Narrative - SOMATA - Motivating Example

A systems view in the biological context is a useful approach to study complex and potentially interacting systems. In this narrative (accompanying an associated manuscript), we take a systems view of software tools themselves. Instead of using software as a single tool, we demonstrate how users can approach software with the same mindset as the organisms they study; as a complex system that can be optimized based on one’s environment and goals. We demonstrate this idea with an example KBase narrative showing how application parameters in KBase tools can change how a researcher perceives and interacts with bioinformatics tools while conducting a common experimental scenario. In this scenario we are trying to understand how different chemical compounds in a growth media change the metabolic pathways utilized in Escherichia coli.

Cashman, Mikaela↗
DOE OSTI2020

Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production

Response regulators are a critical part of the two-component system of gene expression regulation in bacteria, transferring a signal from a sensor kinase into DNA binding activity resulting in alteration of gene expression. In this study, we investigated a previously uncharacterized response regulator in Francisella novicida, FTN_1452 that we have named BfpR (Biofilm-regulating Francisella protein Regulator, FTN_1452). In contrast to another Francisella response regulator, QseB/PmrA, BfpR appears to be a negative regulator of biofilm production, and also a positive regulator of antimicrobial peptide resistance in this bacterium. The protein was crystallized and X-ray crystallography studies produced a 1.8 Å structure of the BfpR N-terminal receiver domain revealing interesting insight into its potential interaction with the sensor kinase. Structural analysis of BfpR places it in the OmpR/PhoP family of bacterial response regulators along with WalR and ResD. Proteomic and transcriptomic analyses suggest that BfpR overexpression affects expression of the critical Francisella virulence factor iglC, as well as other proteins in the bacterium. We demonstrate that mutation of bfpR is associated with an antimicrobial peptide resistance phenotype, a phenotype also associated with other response regulators, for the human cathelicidin peptide LL-37 and a sheep antimicrobial peptide SMAP-29. F. novicida with mutated bfpR replicated better than WT in intracellular infection assays in human-derived macrophages suggesting that the down-regulation of iglC expression in bfpR mutant may enable this intracellular replication to occur. Response regulators have been shown to play important roles in the regulation of bacterial biofilm production. We demonstrate that F. novicida biofilm formation was highly increased in the bfpR mutant, corresponding to altered glycogen synthesis. Waxworm infection experiments suggest a role of BfpR as a negative modulator of iglC expression with de-repression by Mg 2+ . In this study, we find that the response regulator BfpR may be a negative regulator of biofilm formation, and a positive regulator of antimicrobial peptide resistance in F. novicida.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery

Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation. In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns. Our results suggested soil microbial a-diversity decreased under high C10–C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10–C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile. The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data Needs for Modeling Low-Temperature Non-Equilibrium Plasmas: The LXCat Project, History, Perspectives and a Tutorial

Technologies based on non-equilibrium, low-temperature plasmas are ubiquitous in today’s society. Plasma modeling plays an essential role in their understanding, development and optimization. An accurate description of electron and ion collisions with neutrals and their transport is required to correctly describe plasma properties as a function of external parameters. LXCat is an open-access, web-based platform for storing, exchanging and manipulating data needed for modeling the electron and ion components of non-equilibrium, low-temperature plasmas. The data types supported by LXCat are electron- and ion-scattering cross-sections with neutrals (total and differential), interaction potentials, oscillator strengths, and electron- and ion-swarm/transport parameters. Online tools allow users to identify and compare the data through plotting routines, and use the data to generate swarm parameters and reaction rates with the integrated electron Boltzmann solver. In this review, the historical evolution of the project and some perspectives on its future are discussed together with a tutorial review for using data from LXCat.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Searching for Dark Matter with Superconducting Qubits

Dark matter is an enduring mystery in our quest to understand the fundamental constituents of our universe. Low mass bosons, such the axion or hidden photon, are compelling dark matter candidates. We leverage their potential interactions with electromagnetic fields, whereby the dark matter (of unknown mass) on rare occasion converts into a single photon, to devise a method of detecting these candidates. Current dark matter searches operating at microwave frequencies use a resonant cavity to coherently accumulate the field sourced by the dark matter and a near standard quantum limited (SQL) linear amplifier to read out the cavity signal. To further increase sensitivity to the dark matter signal and enable future searches, sub-SQL detection techniques are required.In this thesis, I report the development of a novel microwave photon counting technique and a new exclusion limit on hidden photon dark matter. We operate a superconducting qubit to make repeated quantum non-demolition measurements of cavity photons and apply a hidden Markov model analysis to reduce the noise to 15.7 dB below the quantum limit, with overall detector performance limited by a residual background of real photons. With the present device, we perform a hidden photon search and constrain the kinetic mixing angle to less than 1.68 x 10-15 in a band around 6.011 GHz (24.86 micro-eV) with an integration time of 8.33 s. This demonstrated noise reduction technique enables future dark matter searches to be sped up by a factor of 1300. By coupling a qubit to an arbitrary quantum sensor, more general sub-SQL metrology is possible with the techniques presented in this work.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Metabolic model-based ecological modeling for probiotic design

The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter ‘probiotic’ treatments intended to alter the composition of the microbiome. Despite so much promise and commercial interest, the factors that contribute to the success or failure of microbiome-targeted treatments remain unclear. We investigate the biotic interactions that lead to successful engraftment of a novel bacterial strain introduced to the microbiome as in probiotic treatments. We use pairwise genome-scale metabolic modeling with a generalized resource allocation constraint to build a network of interactions between taxa that appear in an experimental engraftment study. We create induced sub-graphs using the taxa present in individual samples and assess the likelihood of invader engraftment based on network structure. To do so, we use a generalized Lotka-Volterra model, which we show has strong ability to predict if a particular invader or probiotic will successfully engraft into an individual’s microbiome. Furthermore, we show that the mechanistic nature of the model is useful for revealing which microbe-microbe interactions potentially drive engraftment.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Corrections to vibrational transition probabilities calculated from a three-dimensional model.

Corrections to the collision-induced vibration transition probability calculated by Hansen and Pearson from a three-dimensional semiclassical model are examined. These corrections come from the retention of higher order terms in the expansion of the interaction potential and the use of the actual value of the deflection angle in the calculation of the transition probability. It is found that the contribution to the transition cross section from previously neglected potential terms can be significant for short range potentials and for the large relative collision velocities encountered at high temperatures. The correction to the transition cross section obtained from the use of actual deflection angles will not be appreciable unless the change in the rotational quantum number is large.

Stallcop, J. R.↗
NASA NTRS1973

Molecular collisions. 11: Semiclassical approximation to atom-symmetric top rotational excitation

In a paper of this series a distorted wave approximation to the T matrix for atom-symmetric top scattering was developed which is correct to first order in the part of the interaction potential responsible for transitions in the component of rotational angular momentum along the symmetry axis of the top. A semiclassical expression for this T matrix is derived by assuming large values of orbital and rotational angular momentum quantum numbers.

Russell, D.↗
NASA NTRS1973

Molecular collisions 21: Semiclassical approximation to atom-symmetric top rotational excitation

A distorted wave approximation to the T matrix for atom-symmetric top scattering was developed. The approximation is correct to first order in the part of the interaction potential responsible for transitions in the component of rotational angular momentum along the symmetry axis of the top. A semiclassical expression for this T matrix is derived by assuming large values of orbital and rotational angular momentum quantum numbers.

Russell, D.↗
NASA NTRS1974

Collisionless relaxation in spiral galaxy models

The increase in random kinetic energy of stars by rapidly fluctuating gravitational fields (collisionless or violent relaxation) in disk galaxy models is investigated for three interaction potentials of the stars corresponding to (1) point stars, (2) rod stars of length 2 kpc, and (3) uniform density spherical stars of radius 2 kpc. To stabilize the galaxy against the large scale bar forming instability, a fixed field corresponding to a central core or halo component of stars was added with the stars containing at most 20 percent of the total mass of the galaxy. Considerable heating occurred for both the point stars and the rod stars, whereas the use of spherical stars resulted in a very low heating rate. The use of spherical stars with the resulting low heating rate will be desirable for the study of large scale galactic stability or density wave propagation, since collective heating effects will no longer mask the phenomena under study.

Hohl, F.↗
NASA NTRS1975

Vibration-translation energy transfer in anharmonic diatomic molecules. 2: The vibrational quantum number dependence

A semiclassical model of the inelastic collision between a vibrationally excited anharmonic oscillator and a structureless atom was used to predict the variation of thermally averaged vibration-translation rate coefficients with temperature and initial-state quantum number. Multiple oscillator states were included in a numerical solution for collinear encounters. The results are compared with CO-He experimental values for both ground and excited initial states using several simplified forms of the interaction potential. The numerical model was also used as a basis for evaluating several less complete but analytic models. Two computationally simple analytic approximations were found that successfully reproduced the numerical rate coefficients for a wide range of molecular properties and collision partners. Their limitations were also identified. The relative rates of multiple-quantum transitions from excited states were evaluated for several molecular types.

Mckenzie, R. L.↗
NASA NTRS1974

Semiclassical S-matrix theory of vibrationally inelastic collisions between two diatomic molecules

We derive a semiclassical S matrix for vibrationally inelastic collisions between two diatomic molecules, assuming a collinear geometry. Our theory incorporates a quantum mechanical superposition principle with classical dynamics and, as such, is an extension of the atom-diatomic molecule theory of Miller. The several approximations to the S matrix differ in the complexity with which the interference between various classical trajectories is treated. We report numerical calculations for H2-D2 and D2-D2 collisions based on two different interaction potentials. The cruder approximations yield transition probabilities which agree with exact quantum mechanical results to within a factor of 2. More sophisticated approximations to the S matrix yield excellent quantitative agreement with the quantum calculations.

Cohen, S. C.↗
NASA NTRS1976

Vibration-translation energy transfer in anharmonic diatomic molecules. II - The vibrational quantum-number dependence

A semiclassical model of the inelastic collision between a vibrationally excited anharmonic oscillator and a structureless atom is used to predict the variation of thermally averaged vibrational-translational rate coefficients with temperature and initial-state quantum number. Multiple oscillator states are included in a numerical solution for collinear encounters. The results are compared with CO-He experimental values for both ground and excited initial states using several simplified forms of the interaction potential. The numerical model is also used as a basis for evaluating several less complete, but analytic, models. Two computationally simple analytic approximations are found that successfully reproduce the numerical rate coefficients for a wide range of molecular properties and collision partners. Their limitations are identified, and the relative rates of multiple-quantum transitions from excited states are evaluated for several molecular types.

Mckenzie, R. L.↗