SEARCH · Search NASA

Results for “sequencing experiments”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37

All sources NASA NTRS DOE OSTI

DOE OSTI2014

Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes

The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. Here in this paper, we describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of D-Ala-D-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗

DOE OSTI2016

Methodology for the structural design of single spoke accelerating cavities at Fermilab

Fermilab is planning to upgrade its accelerator complex to deliver a more powerful and intense proton-beam for neutrino experiments. In the framework of the so-called Proton Improvement Plan-II (PIP-II), we are designing and developing a cryomodule containing superconducting accelerating cavities, the Single Spoke Resonators of type 1 (SSR1). In this paper, we present the sequence of analysis and calculations performed for the structural de- sign of these cavities, using the rules of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code (BPVC). The lack of an accepted procedure for addressing the design, fabrication, and inspection of such unique pressure vessels makes the task demanding and challenging every time. Several factors such as exotic materials, unqualified brazing procedures, limited nondestructive examination, and the general R&D nature of these early generations of cavity design, conspire to make it impractical to obtain full compliance with all ASME BPVC requirements. However, the presented approach allowed us to validate the design of these new generation of single spoke cavities with values of maximum allowable working pressure that exceed the safety requirements. This set of rules could be used as a starting point for the structural design and development of similar objects.

42 ENGINEERING↗

DOE OSTI2019

Forfeiting the priority effect: turnover defines biofilm community succession

Microbial community succession is a fundamental process that affects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are often poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the ecological contribution of colonizers? We performed a succession experiment within a hypersaline ecosystem to investigate how different processes contributed to the turnover of founder species. Bacterial and eukaryotic colonizers were identified during primary succession and tracked through a defined, 79-day biofilm maturation period using 16S and 18S rRNA gene sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate successional patterns of primary producers and nitrogen fixers. The majority of the founder species did not maintain high abundance throughout succession. Species replacement (versus loss) was the dominant process shaping community succession. We also asked if different ecological processes acted on bacteria versus Eukaryotes during succession and found deterministic and stochastic forces corresponded more with microeukaryote and bacterial colonization, respectively. Our results show that taxa and functions belonging to different kingdoms, which share habitat in the tight spatial confines of a biofilm, were influenced by different ecological processes and time scales of succession.

Brislawn, Colin J.↗

DOE OSTI2025

Active learning path-dependent properties using a cloud-based materials acceleration platform

Solid state materials are central to many modern technologies in which a given material may be exposed to a variety of environments. The material properties often vary with the sequence of environments in an irreversible manner, resulting in a quintessential path-dependency in experimental observables. While sequential learning techniques have been effectively deployed for accelerating learning of state properties of materials, they often use a consistent environment path in all experiments. To elevate such techniques for making optimal decisions in experimental investigations of path-dependent properties, we introduce an iterated expected information gain acquisition function that optimizes over entire experimental trajectories. This approach is implemented within a cloud-based Materials Acceleration Platform architecture utilizing an event-driven stateful broker coupled with remote HELAO (Hierarchical Experimental Laboratory Automation and Orchestration) instances and an AI science manager. The platform's efficacy was demonstrated through a case study optimizing multi-step spectro-electrochemical experiments to identify optically stable potential windows in (Co–Ni–Sb)O z metal oxides. The system successfully integrated AI-driven experiment design, remote laboratory automation, and cloud-based data infrastructure, validating the platform's capability for managing complex, adaptive, path-dependent workflows in materials discovery.

Guevarra, Dan [California Institute of Technology ↗

DOE OSTI2015

Dynamics-based selective 2D {sup 1}H/{sup 1}H chemical shift correlation spectroscopy under ultrafast MAS conditions

Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of {sup 1}H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of {sup 1}H/{sup 1}H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Algorithm 1049: The Delaunay Density Diagnostic

Accurate approximation of a real-valued function depends on two aspects of the available data: the density of inputs within the domain of interest and the variation of the outputs over that domain. There are few methods for assessing whether the density of inputs is sufficient to identify the relevant variations in outputs—i.e., the “geometric scale” of the function—despite the fact that sampling density is closely tied to the success or failure of an approximation method. In this article, we introduce a general purpose, computational approach to detecting the geometric scale of real-valued functions over a fixed domain using a deterministic interpolation technique from computational geometry. The algorithm is intended to work on scalar data in moderate dimensions (2–10). Our algorithm is based on the observation that a sequence of piecewise linear interpolants will converge to a continuous function at a quadratic rate (in L 2 norm) if and only if the data are sampled densely enough to distinguish the feature from noise (assuming sufficiently regular sampling). We present numerical experiments demonstrating how our method can identify feature scale, estimate uncertainty in feature scale, and assess the sampling density for fixed (i.e., static) datasets of input–output pairs. Finally, we include analytical results in support of our numerical findings and have released lightweight code that can be adapted for use in a variety of data science settings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Design and validation of a nanosecond short-wave infrared streak camera using gaseous detonation experiments

A custom short-wave infrared (SWIR) galvanometric streak camera was developed to provide nanosecond- scale, time-resolved optical diagnostics. The system was designed as a compact, mechanically driven alternative to traditional tube-based streak cameras, using a galvanometer mirror and multiple-reflection optical path to achieve high temporal resolution while maintaining electronic synchronization for trigger sequencing. Temporal resolution achieved 139.5 ns/px, allowing direct conversion of image-slope gradients to physical wave velocities. The instrument was validated using hydrogen-oxygen-argon detonations within a modular detonation tube, capturing transient emission structures and post-detonation decay behavior with microsecond precision. Although signal levels in filtered configurations were limited by lens transmission and detector sensitivity, the system successfully resolved intensity rise and decay characteristics across 10-60 % argon mixtures. The observed trends demonstrate the feasibility of compact galvanometer-based streak systems for high-speed SWIR imaging in reactive environments!

42 ENGINEERING↗

DOE OSTI2017

Kinetic characterization of Vibrio cholerae ApbE: Substrate specificity and regulatory mechanisms

ApbE is a member of a novel family of flavin transferases that incorporates flavin mononucleotide (FMN) to subunits of diverse respiratory complexes, which fulfill important homeostatic functions. In this work a detailed characterization of Vibrio cholerae ApbE physiologic activity, substrate specificity and pH dependency was carried out. The data obtained show novel characteristics of the regulation and function of this family. For instance, our experiments indicate that divalent cations are essential for ApbE function, and that the selectivity depends largely on size and the coordination sphere of the cation. Our data also show that ApbE regulation by pH, ADP and potassium is an important mechanism that enhances the adaptation, survival and colonization of V. cholerae in the small intestine. Moreover, studies of the pH-dependency of the activity show that the reaction is favored under alkaline conditions, with a pKa of 8.4. These studies, together with sequence and structure analysis allowed us to identify His257, which is absolutely conserved in the family, as a candidate for the residue whose deprotonation controls the activity. Remarkably, the mutant H257G abolished the flavin transfer activity, strongly indicating that this residue plays an important role in the catalytic mechanism of ApbE.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Initiating Event Rates at U.S. Nuclear Power Plants 1988–2013

Analyzing initiating event rates is important because it indicates performance among plants and also provides inputs to several U.S. Nuclear Regulatory Commission (NRC) risk-informed regulatory activities. This report presents an analysis of initiating event frequencies at U.S. commercial nuclear power plants since each plant’s low-power license date. The evaluation is based on the operating experience from fiscal year 1988 through 2013 as reported in licensee event reports. Engineers with nuclear power plant experience staff reviewed each event report since the last update to this report for the presence of valid scrams or reactor trips at power. To be included in the study, an event had to meet all of the following criteria: includes an unplanned reactor trip (not a scheduled reactor trip on the daily operations schedule), sequence of events starts when reactor is critical and at or above the point of adding heat, occurs at a U.S. commercial nuclear power plant (excluding Fort St. Vrain and LaCrosse), and is reported by a licensee event report. This report displays occurrence rates (baseline frequencies) for the categories of initiating events that contribute to the NRC’s Industry Trends Program. Sixteen initiating event groupings are trended and displayed. Initiators are plotted separately for initiating events with different occurrence rates for boiling water reactors and pressurized water reactors. p-values are given for the possible presence of a trend over the most recent 10 years.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Disruption thermal load mitigation with shattered pellet injection on the Joint European Torus (JET)

Disruption mitigation remains a critical, unresolved challenge for ITER. To aid in addressing this challenge, a shattered pellet injection (SPI) system was installed on JET and experiments conducted at a range of thermal energy fractions and stored energies in excess of 7 MJ. The primary goals of these experiments were to investigate the efficacy of the SPI on JET and the ability of the plasma to assimilate multiple pellets. Single pellet injections produced a saturation in total radiated energy (Wrad) with increasing injected neon content, suggesting total radiation of stored thermal energy. Further increases in injected neon quantities resulted in reduced cooling times and current quench (CQ) durations, indicating higher impurity assimilation. No significant variation in CQ duration or W rad was observed when varying the deuterium content at fixed neon quantities. Additionally, higher assimilation, inferred by shorter CQ durations, was measured when a mechanical punch was used to launch the pellets and this was attributed to a lower pellet velocity leading to higher solid content in the pellet plume and larger fragments penetrating deeper into the plasma. Radiation asymmetries averaged over the cooling time were inferred from Emis3D and ranged from 1.6 to 1.9. Asymmetries averaged over the entire disruption sequence were found to increase at higher thermal energy fractions. The radiated energy fractions decreased with increasing thermal energy fractions but this trend was eliminated when toroidal asymmetries were accounted for with Emis3D. Pure deuterium pellets were able to produce cooling times of up to 75 ms with a gradual loss in thermal stored energy of up to 80%. Experiments with multiple pellet injection indicated W rad can be increased through pellet superposition and density can be increased with an additional D2 injection without a reduction in W rad . KPRAD modelling accurately reproduced the cooling times and the CQ duration at high thermal energies. Assimilation estimates from KPRAD indicated CQ rates scale strongly whilst W rad scales weakly and saturates with assimilated neon content. Comparable W rad can be achieved with lower assimilated neon quantities as longer cooling times are attained. Thus reduced neon content can be preferential in a thermal load mitigation scheme as it may reduce radiation asymmetries and prevent flash melting.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2014

Initiating Event Rates at U.S. Nuclear Power Plants. 1988 - 2013

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2017

Sediment gravity flows triggered by remotely generated earthquake waves

Recent great earthquakes and tsunamis around the world have heightened awareness of the inevitability of similar events occurring within the Cascadia Subduction Zone of the Pacific Northwest. We analyzed seafloor temperature, pressure, and seismic signals, and video stills of sediment–enveloped instruments recorded during the 2011–2015 Cascadia Initiative experiment, and seafloor morphology. Our results led us to suggest that thick accretionary prism sediments amplified and extended seismic wave durations from the 11 April 2012 M w 8.6 Indian Ocean earthquake, located more than 13,500 km away. These waves triggered a sequence of small slope failures on the Cascadia margin that led to sediment gravity flows culminating in turbidity currents. Previous studies have related the triggering of sediment–laden gravity flows and turbidite deposition to local earthquakes, but this is the first study in which the originating seismic event is extremely distant (> 10,000 km). The possibility of remotely triggered slope failures that generate sediment–laden gravity flows should be considered in inferences of recurrence intervals of past great Cascadia earthquakes from turbidite sequences. In conclusion, future similar studies may provide new understanding of submarine slope failures and turbidity currents and the hazards they pose to seafloor infrastructure and tsunami generation in regions both with and without local earthquakes.

58 GEOSCIENCES↗

DOE OSTI2018

Post-ischemic administration of 5-methoxyindole-2-carboxylic acid at the onset of reperfusion affords neuroprotection against stroke injury by preserving mitochondrial function and attenuating oxidative stress

Highlights: • MICA administered at the onset of reperfusion triggers a postconditioning effect. • MICA postconditioning preserves mitochondrial function. • MICA-triggered neuroprotection involves NQO1 upregulation by the Nrf2 signaling. • Oxidative damage is attenuated by MICA postconditioning. We previously reported that 5-methoxyindole-2-carboxylic acid (MICA) could induce preconditioning effect in the ischemic brain of rat. In the present study, we addressed the question of whether MICA could also trigger a postconditioning effect in ischemic stroke. To this end, MICA (100 mg/kg body weight) was injected intraperitoneally at the onset of 24 h reperfusion following 1 h ischemia in rat brain. Results indicate that stroked animals treated with MICA showed less brain infarction volume than that of vehicle-treated animals. Further experiments revealed that brain mitochondrial complexes I and IV showed elevated enzymatic activities in MICA treated group and the elevation in complex I activity was likely contributed by seemingly enhanced expression of many complex I subunits, which was determined by mass spectral peptide sequencing. When compared with vehicle-treated rats, the preservation of complexes I and IV activities was shown to be accompanied by enhanced mitochondrial membrane potential, increased ATP production, and decreased caspase-3 activity. Additional studies also indicate the involvement of NQO1 upregulation by the Nrf2 signaling pathway in this MICA postconditioning paradigm. Consequently, attenuated oxidative stress in the MICA treated group reflected by decrease in H{sub 2}O{sub 2} production and protein carbonylation and lipid peroxidation was detected. Taken together, the present study demonstrates that MICA can also induce a postconditioning effect in the ischemic brain of rat and the underlying mechanism likely involves preservation of mitochondrial function, upregulation of cellular antioxidative capacity, and attenuation of oxidative stress.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

The Role of Mineral Composition on the Frictional and Stability Properties of Powdered Reservoir Rocks

The growing hazard of induced seismicity driven by the boom in unconventional resources exploitation is strongly linked to fault activation. We perform laboratory measurements on simulated fault gouges comprising powdered reservoir rocks from major oil and gas production sites in China, to probe the control of mineral composition on fault friction and stability responses during reservoir stimulation. Double direct shear experiments were conducted on gouges with phyllosilicate content ranging from 0 to 30 wt.% and grain sizes <150 μm, at constant normal stresses of 10–40 MPa and conditions of room temperature and water saturation. The velocity step and slide-hold-slide sequences were employed to evaluate frictional stability and static healing, respectively. Results indicate that the mineralogy of the gouges exhibit a strong control on the frictional strength, stability, and healing. Phyllosilicate-rich samples show lower frictional strength μ and higher values of (a – b ), promoting stable sliding. For the gouges studied, the frictional strength decreases monotonically with increasing phyllosilicate content, and a transition from velocity weakening to velocity strengthening behavior is evident at 15 wt.% phyllosilicates. Intermediate healing rates are common in gouges with higher content of phyllosilicates, with high healing rates predominantly in phyllosilicate-poor gouges. As an indispensable component in reservoir rocks, the carbonates are shown to affect both the frictional stability and healing response. These findings can have important implications for understanding the effects of mineralogy on fault behavior and induced seismic potential in geoengineering activities, particularly in reservoirs in China.

58 GEOSCIENCES↗

DOE OSTI2013

Vortices catapult droplets in atomization

A droplet ejection mechanism in planar two-phase mixing layers is examined. Any disturbance on the gas-liquid interface grows into a Kelvin-Helmholtz wave, and the wave crest forms a thin liquid film that flaps as the wave grows downstream. Increasing the gas speed, it is observed that the film breaks up into droplets which are eventually thrown into the gas stream at large angles. In a flow where most of the momentum is in the horizontal direction, it is surprising to observe these large ejection angles. Our experiments and simulations show that a recirculation region grows downstream of the wave and leads to vortex shedding similar to the wake of a backward-facing step. The ejection mechanism results from the interaction between the liquid film and the vortex shedding sequence: a recirculation zone appears in the wake of the wave and a liquid film emerges from the wave crest; the recirculation region detaches into a vortex and the gas flow over the wave momentarily reattaches due to the departure of the vortex; this reattached flow pushes the liquid film down; by now, a new recirculation vortex is being created in the wake of the wave—just where the liquid film is now located; the liquid film is blown up from below by the newly formed recirculation vortex in a manner similar to a bag-breakup event; the resulting droplets are catapulted by the recirculation vortex.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

A Privacy-Preserving Distributed Control of Optimal Power Flow

Here, we consider a distributed optimal power flow formulated as an optimization problem that maximizes a nondifferentiable concave function. Solving such a problem by the existing distributed algorithms can lead to data privacy issues because the solution information exchanged within the algorithms can be utilized by an adversary to infer the data. To preserve data privacy, in this paper we propose a differentially private projected subgradient (DP-PS) algorithm that includes a solution encryption step. We show that a sequence generated by DP-PS converges in expectation, in probability, and with probability 1. Moreover, we show that the rate of convergence in expectation is affected by a target privacy level of DP-PS chosen by the user. We conduct numerical experiments that demonstrate the convergence and data privacy preservation of DP-PS.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly

Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO 3 – , Ca 2+ , PO 4 3– , and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.

plant biomass↗