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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 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

In vitro antibiotic susceptibility testing often fails to accurately predict in vivo drug efficacies, in part due to differences in the molecular composition between standardized bacteriologic media and physiological environments within the body. Here, we investigate the interrelationship between antibiotic susceptibility and medium composition in Escherichia coli K-12 MG1655 as contextualized through machine learning of transcriptomics data. Application of independent component analysis, a signal separation algorithm, shows that complex phenotypic changes induced by environmental conditions or antibiotic treatment are directly traced to the action of a few key transcriptional regulators, including RpoS, Fur, and Fnr. Integrating machine learning results with biochemical knowledge of transcription factor activation reveals medium-dependent shifts in respiration and iron availability that drive differential antibiotic susceptibility. By extension, the data generation and data analytics workflow used here can interrogate the regulatory state of a pathogen under any measured condition and can be applied to any strain or organism for which sufficient transcriptomics data are available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Considering the Lives of Microbes in Microbial Communities

ABSTRACT Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Yet, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering “the lives of microbes”: we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership

This study elucidates how a cyanobacterial primary producer acclimates to heterotrophic partnership by modulating the expression levels of key metabolic genes. Heterotrophic bacteria can indirectly regulate the physiology of the photoautotrophic primary producers, resulting in physiological changes identified here, such as increased intracellular ROS. Some of the interactions inferred from this model system represent putative principles of metabolic coupling in phototrophic-heterotrophic partnerships. The mechanisms by which microbes interact in communities remain poorly understood. Here, we interrogated specific interactions between photoautotrophic and heterotrophic members of a model consortium to infer mechanisms that mediate metabolic coupling and acclimation to partnership. This binary consortium was composed of a cyanobacterium, Thermosynechococcus elongatus BP-1, which supported growth of an obligate aerobic heterotroph, Meiothermus ruber strain A, by providing organic carbon, O 2 , and reduced nitrogen. Species-resolved transcriptomic analyses were used in combination with growth and photosynthesis kinetics to infer interactions and the environmental context under which they occur. We found that the efficiency of biomass production and resistance to stress induced by high levels of dissolved O 2 increased, beyond axenic performance, as a result of heterotrophic partnership. Coordinated transcriptional responses transcending both species were observed and used to infer specific interactions resulting from the synthesis and exchange of resources. The cyanobacterium responded to heterotrophic partnership by altering expression of core genes involved with photosynthesis, carbon uptake/fixation, vitamin synthesis, and scavenging of reactive oxygen species (ROS). IMPORTANCEThis study elucidates how a cyanobacterial primary producer acclimates to heterotrophic partnership by modulating the expression levels of key metabolic genes. Heterotrophic bacteria can indirectly regulate the physiology of the photoautotrophic primary producers, resulting in physiological changes identified here, such as increased intracellular ROS. Some of the interactions inferred from this model system represent putative principles of metabolic coupling in phototrophic-heterotrophic partnerships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection

Neisseria gonorrhoeae is a Gram-negative diplococcus that is responsible for the sexually transmitted infection gonorrhea, a high-morbidity disease in the United States and worldwide. Over the past several years, N. gonorrhoeae strains resistant to antibiotics used to treat this infection have begun to emerge across the globe. Thus, new treatment strategies are needed to combat this organism. Here, we utilized N. gonorrhoeae transcriptomic data sets, including those obtained from natural infection of the human genital tract, to infer the first global gene coexpression network of this pathogen. Interrogation of this network revealed genes central to the network that are likely critical for gonococcal growth, metabolism, and virulence, including genes encoding hypothetical proteins expressed during mucosal infection. In addition, network analysis revealed overlap in the response of N. gonorrhoeae to incubation with neutrophils and exposure to hydrogen peroxide stress in vitro. Network analysis also identified new targets of the gonococcal global regulatory protein Fur, while examination of the network neighborhood of genes allowed us to assign additional putative categories to several proteins. Collectively, the characterization of the first gene coexpression network for N. gonorrhoeae described here has revealed new regulatory pathways and new categories for proteins and has shown how processes important to gonococcal infection in both men and women are linked. This information fills a critical gap in our understanding of virulence strategies of this obligate human pathogen and will aid in the development of new treatment strategies for gonorrhea.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions

Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics.

3D printing↗
DOE OSTI2023

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A history of pore water oxygen isotope evolution in the Cretaceous Travis Peak Formation in East Texas

Oxygen isotope analyses of diagenetic cements can provide detailed evidence of sedimentary burial processes and conditions, as the δ 18 O values of precipitating minerals reflect contemporaneous local δ 18 O water and temperature conditions. Uncertainties in the timing and rates of pore water δ 18 O evolution in sedimentary basins can complicate interpretation of these records. Fracture-bridging (0.5–1 mm) quartz cements observed in sandstones of the Cretaceous Travis Peak Formation in the East Texas basin show clear growth-zoning by cathodoluminescence and contain detailed fluid inclusion records of temperature that make them excellent candidates for interrogating prolonged histories of basin temperature and the evolution of δ 18 O in basin pore water. New secondary ion mass spectrometer (SIMS) δ 18 O quartz isotopic data from fluid inclusion-rich quartz bridges in Travis Peak sandstones record a steady increase of pore water δ 18 O values from ~5 to 7‰ (VSMOW; Vienna Standard Mean Ocean Water) as the sandstone warms from ~130 to 150 °C. To help evaluate whether this trend could be generated solely from local water-rock interactions in response to burial compaction, a one-dimensional closed system isotopic burial model was created to simulate how δ 18 O water values change in a quartz-dominated sandstone during diagenesis. Using both directly measured and inferred rates of Travis Peak compaction, the magnitude of change in δ 18 O water that we calculate from quartz bridge geochemistry cannot be reasonably modeled solely by local quartz mechanical compaction, pressure solution, and cementation processes, necessitating significant fluxes of silica and high-δ 18 O water from outside of the sandstones prior to maximum burial. In conclusion, this indicates that even units which appear surrounded by significant barriers to fluid flow (i.e., mudrock-bounded channel sandstones) may have been infiltrated and diagenetically modified by large fluxes of fluid on geologic time scales.

58 GEOSCIENCES↗
DOE OSTI2014

Photonuclear reaction studies at HIγS: Developing the science of remote detection of nuclear materials

Development of gamma-ray beam interrogation technologies for remote detection of special nuclear materials and isotope analysis requires comprehensive databases of nuclear structure information and gamma-ray induced nuclear reaction observables. Relevant nuclear structure details include the energy, spin and parity of excited states that have significant probability for electromagnetic transition from the ground state, i.e, the angular momentum transferred in the reaction is Δl ≤ 2. This talk will report recent Nuclear Resonance Fluorescence (NRF) measurements to identify and characterize new low-spin states in actinide nuclei at energies from 1 to 4 MeV, which is the energy range most important for remote analysis methods. Here, these measurements are carried out using the nearly mono-energetic linearly polarized gamma-ray beam at the High Intensity Gamma-ray Source (HIγS) at the Triangle Universities Nuclear Laboratory. Also, studies of the (γ, n) reaction on a variety of nuclei with linearly polarized beams at HIγS indicate that this reaction might be used to discern between fissile and non-fissile materials. This work will be described. In addition, an overview will be given of a concept for a next generation laser Compton-backing scattering gamma-ray source to be implemented as an upgrade to increase the beam intensity at HIγS by more than an order of magnitude.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2013

Massive Scale Cyber Traffic Analysis: A Driver for Graph Database Research

We describe the significance and prominence of network traffic analysis (TA) as a graph- and network-theoretical domain for advancing research in graph database systems. TA involves observing and analyzing the connections between clients, servers, hosts, and actors within IP networks, both at particular times and as extended over times. Towards that end, NetFlow (or more generically, IPFLOW) data are available from routers and servers which summarize coherent groups of IP packets flowing through the network. IPFLOW databases are routinely interrogated statistically and visualized for suspicious patterns. But the ability to cast IPFLOW data as a massive graph and query it interactively, in order to e.g.\ identify connectivity patterns, is less well advanced, due to a number of factors including scaling, and their hybrid nature combining graph connectivity and quantitative attributes. In this paper, we outline requirements and opportunities for graph-structured IPFLOW analytics based on our experience with real IPFLOW databases. Specifically, we describe real use cases from the security domain, cast them as graph patterns, show how to express them in two graph-oriented query languages SPARQL and Datalog, and use these examples to motivate a new class of "hybrid" graph-relational systems.

Joslyn, Cliff A.↗
DOE OSTI2017

"Who Has Plots?": Contextualizing Scientific Software, Practice, and Visualizations

We present that software is an integral element of the work of science yet it is not commonly an object of inquiry in studies of scientific infrastructures. This paper presents findings from an ethnographic study of a cosmology group's collaborative scientific software production. We demonstrate how these cosmologists use plots to simultaneously test their software and analyze data while interrogating multiple layers of infrastructural components. We broaden perspectives on scientific software development using a sociotechnical, software studies lens to examine this work of scientific discovery as a creative and embodied, yet exacting and methodical, activity that requires a 'human in the loop'. Here, we offer a new reading of scientific software practices to convey how creating scientific software is often really the act of doing science itself--an intervention we believe is necessary to more successfully support scientific software sharing and infrastructure production.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Gnu-RL: A Precocial Reinforcement Learning Solution for Building HVAC Control Using a Differentiable MPC Policy

Reinforcement learning (RL) was first demonstrated to be a feasible approach to controlling heating, ventilation, and air conditioning (HVAC) systems more than a decade ago. However, there has been limited progress towards a practical and scalable RL solution for HVAC control. While one can train an RL agent in simulation, it is not cost-effective to create a model for each thermal zone or building. Likewise, existing RL agents generally take a long time to learn and are opaque to expert interrogation, making them unattractive for real-world deployment. To tackle these challenges, we propose Gnu-RL: a novel approach that enables practical deployment of RL for HVAC control and re- quires no prior information other than historical data from exist- ing HVAC controllers. To achieve this, Gnu-RL adopts a recently- developed Differentiable Model Predictive Control (MPC) policy, which encodes domain knowledge on planning and system dynam- ics, making it both sample-efficient and interpretable. Prior to any interaction with the environment, a Gnu-RL agent is pre-trained on historical data using imitation learning, which enables it to match the behavior of the existing controller. Once it is put in charge of controlling the environment, the agent continues to improve its policy end-to-end, using a policy gradient algorithm. We evaluate Gnu-RL on both an EnergyPlus model and a real- world testbed. In both experiments, our agents were directly de- ployed in the environment after offline pre-training on expert demonstration. In the simulation experiment, our approach saved 6.6% energy compared to the best published RL result for the same environment, while maintaining a higher level of occupant comfort. Next, Gnu-RL was deployed to control the HVAC of a real-world conference room for a three-week period. Our results show that Gnu-RL saved 16.7% of cooling demand compared to the existing controller and tracked temperature set-point better.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2016

Vacuum Ultraviolet Photoionization of Complex Chemical Systems

Tunable vacuum ultraviolet (VUV) radiation coupled to mass spectrometry is applied to the study of complex chemical systems in this paper. The identification of novel reactive intermediates and radicals is revealed in flame, pulsed photolysis, and pyrolysis reactors, leading to the elucidation of spectroscopy, reaction mechanisms, and kinetics. Mass-resolved threshold photoelectron photoion coincidence measurements provide unprecedented access to vibrationally resolved spectra of free radicals present in high-temperature reactors. Photoionization measurements in water clusters, nucleic acid base dimers, and their complexes with water provide signatures of proton transfer in hydrogen-bonded and π-stacked systems. Experimental and theoretical methods to track ion–molecule reactions and fragmentation pathways in intermolecular and intramolecular hydrogen-bonded systems in sugars and alcohols are described. Photoionization of laser-ablated molecules, clusters, and their reaction products inform thermodynamics and spectroscopy that are relevant to astrochemistry and catalysis. Finally, new directions in coupling VUV radiation to interrogate complex chemical systems are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

3D Nanocrystallography and the Imperfect Molecular Lattice

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

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

Determining the Length Scale of Transport Impedances in Li-Ion Electrodes: Li(Ni 0.33 Mn 0.33 Co 0.33 )O 2

Battery cathodes are complex multiscale, multifunctional materials. The length scale at which the dominant impedance arises may be difficult to determine even with the most advanced experimental characterization efforts, and thus modeling can play an important role in analysis. Discharge and voltage relaxation curves, interrogated with theory, are used to distinguish between transport impedance that arise on the scale of the active crystal and on the scale of agglomerates (secondary particles) comprised of nanoscale crystals. Model-selection algorithms are applied to determine that the agglomerate scale is dominant in the Li Ni 0.33 Mn 0.33 Co 0.33 O 2 electrode studied here. Furthermore, conditions where the agglomerate and crystal-scale models yield distinct simulation results are demonstrated, providing approaches that can be applied to other systems.

25 ENERGY STORAGE↗
DOE OSTI2023

Review—Fundamental Uranium Electrochemistry and Spectroscopy in Molten Salt Systems

Uranium is a key element used for nuclear energy production. Some advanced reactor designs, specifically molten salt reactors, will continue to use uranium as the fissile material for energy production. These new technologies require an intimate understanding of uranium chemistry during and after energy production. This review covers contemporary research on the coordination chemistry and behavior of uranium with the coolant and pyroprocessing salts as proposed for use in future reactor designs. Discussed topics include the nature of U redox reactions involving the reduction of U(III) to U metal and oxidation of U(III) to U(IV). These systems have been interrogated using cyclic voltammetry, chronopotentiometry, and optical and X-ray absorption spectroscopies. Insights obtained into the electrode potentials, the uranium species, and their diffusion coefficients in alkali halide melts from decades of research are summarized selectively. Further, perspectives are provided on the importance of unifying studies for comparison across multiple institutions. The application of synchrotron radiation research and multimodal approaches involving two (or more) probes, such as the widespread combination of UV–visible spectroscopy and electroanalysis known as spectroelectrochemistry, can provide new knowledge about the main process of uranium electrorefining—diffusion, as will be demonstrated in this review through the lack of comparable results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Deposition of tungsten metal by an immersion process

A new multi-step, solution-phase method for the spontaneous deposition of tungsten from a room temperature ethereal solution is reported. This immersion process relies on the deposition of a sacrificial zinc coating which is galvanically displaced by the ether-mediated reduction of oxophilic WCl 6 . Subsequent thermal treatment renders a crystalline, metallic tungsten film. The chemical evolution of the surface and formation of a complex intermediate tungsten species is characterized by X-ray diffraction, infrared spectroscopy, and X-ray photoelectron spectroscopy. Efficient metallic tungsten deposition is first characterized on a graphite substrate and then demonstrated on a functional carbon foam electrode. The resulting electrochemical performance of the modified electrode is interrogated with the canonical aqueous ferricyanide system. A tungsten-coated carbon foam electrode showed that both electrode resistance and overall electrochemical cell resistance were reduced by 50%, resulting in a concomitant decrease in redox peak separation from 1.902 V to 0.783 V. Furthermore, this process promises voltage efficiency gains in electrodes for energy storage technologies and demonstrates the viability of a new route to tungsten coating for technologies and industries where high conductivity and chemical stability are paramount.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Statistical Design of Experiments Enables Rapid Exploration of Perfluorobutane Sulfonate Degradation

The phase-out of long-chain PFAS has led to the proliferation of highly recalcitrant short-chain analogs, and mineralization technologies for these short-chain PFAS are needed to mitigate their deleterious effects on environmental and human health. In this study, we utilize a statistical design of experiments, specifically, response surface methodology, to rapidly evaluate the electrochemical degradation of the short-chain PFAS, perfluorobutane sulfonate (PFBS). We evaluate the impacts of the three primary electrochemical parameters (concentration of PFBS, concentration of supporting electrolyte, and applied current) over multiple orders of magnitude on the three primary reaction outcomes of electrochemical PFBS degradation (incomplete PFBS decomposition, complete PFBS mineralization as fluorine, and anodic energy consumption). Our results correspond with literature and clearly identify the well-known tradeoff between energy consumption and complete mineralization. Intriguingly, partial PFBS decomposition and energy consumption demonstrate nonlinear dependencies in the current/supporting electrolyte concentration space and the current/PFBS concentration space, respectively. These findings highlight the utility of the response surface methodology model to efficiently interrogate a large parameter space, identifying both common results and less-obvious interactions between electrochemical parameters and their influences on reaction outcomes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Meta-analysis of global metabolomics and proteomics data to link alterations with phenotype

Global metabolomics has emerged as a powerful tool to interrogate cellular biochemistry at the systems level by tracking alterations in the levels of small molecules. One approach to define cellular dynamics with respect to this dysregulation of small molecules has been to consider metabolic flux as a function of time. While flux measurements have proven effective for model organisms, acquiring multiple time points at appropriate temporal intervals for many sample types (e.g., clinical specimens) is challenging. As an alternative, meta-analysis provides another strategy for delineating metabolic cause and effect perturbations. That is, the combination of untargeted metabolomic data from multiple pairwise comparisons enables the association of specific changes in small molecules with unique phenotypic alterations. We recently developed metabolomic software called metaXCMS to automate these types of higher order comparisons. Here we discuss the potential of metaXCMS for analyzing proteomic datasets and highlight the biological value of combining meta-results from both metabolomic and proteomic analyses. The combined meta-analysis has the potential to facilitate efforts in functional genomics and the identification of metabolic disruptions related to disease pathogenesis.

Patti, Gary J.↗