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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Characterization of the biofilm landscape of Bacillus subtilis by spatial microproteomics

Bulk proteomics has been demonstrated to differentiate subpopulations within bacterial colonies, yet advanced analyses by mass spectrometry imaging (MSI) hold even greater promise for the future. This technology can enable high-throughput spatial phenotyping that can reshape biological discovery by providing visualization of components of various biomolecular mechanisms. With high mass resolving power and high spatial resolution analyses being routine, we can confidently enable intact protein imaging directly from samples with minimal preparation. Pairing those analyses with bulk experimental libraries can provide high confidence in annotations of post-translational modifications (PTMs) and truncations. Revealing PTM localization within the samples unlocks a direct window into unknown biology at the microscale. However, top-down proteomics (TDP) is not commonplace for microbial species, largely due to challenges in identifying detected peptides and proteins; considering the theoretical proteome of even the well-studied model bacterium Bacillus subtilis was only partially mapped recently. With little still known about the form and function of many of these proteins – let alone proteoforms, where PTMs and truncations of the same protein may possess unique physiological roles – there is a wealth of work to be done. Here we jointly apply TDP and MSI to describe the microscale spatial proteomic landscape within B. subtilis and further demonstrate the feasibility of detecting differentiated subpopulations through proteoforms across the biofilm landscape.

bacterial biofilms↗
DOE OSTI2022

Extrapolating Contaminant Effects from Individuals to Populations: A Case Study on Nanoparticle Toxicity to Daphnia Fed Environmentally Relevant Food Levels

Ecological risk assessment (ERA) is charged with assessing the likelihood a chemical will have adverse environmental or ecological effects. When assessing the risk of a potential contaminant to biological organisms, ecologists are most concerned with the sustainability of populations of organisms, rather than protecting every individual. However, ERA most commonly relies on data on the effect of a potential contaminant on individuals because these experiments are more feasible than costly population-level exposures. In this work, we address the challenge of extrapolating these individual-level results to predict population-level effects. Previous per-capita population growth rate estimates calculated from individual-level exposures of Daphnia pulicaria to silver nanoparticles (AgNPs) at different food rations predict a critical daily food requirement for daphnid populations exposed to 200 μg/L AgNPs to avoid extinction. To test this, we exposed daphnid populations to the same AgNP concentration at three different food inputs, with the lowest ration close to the extinction threshold predicted from data on individuals. The two populations with the higher food inputs persisted, and the population with the lowest food input went extinct after 50 days but did persist through two generations. Further, we demonstrate that we can extrapolate between these levels of biological organization by parameterizing an individual-level biomass model with data on individuals’ response to AgNPs and using these parameters to predict the outcome for control and AgNP-exposed populations. Key to successful extrapolation is careful modeling of temporal changes in resource density, driven by both the experimental protocols and feedback from the consumer. The implication for ecotoxicology is that estimates of extinction thresholds based on studies of individuals may be reliable predictors of population outcomes, but only with careful treatment of resource dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Thermophilic biocatalysts for one-step conversion of citrus waste into lactic acid

Agri-food residues offer significant potential as a raw material for the production of L-lactic acid through microbial fermentation. Weizmannia coagulans, previously known as Bacillus coagulans, is a spore-forming, lactic acid-producing, gram-positive, with known probiotic and prebiotic properties. This study aimed to evaluate the feasibility of utilizing untreated citrus waste as a sustainable feedstock for the production of L-lactic acid in a one-step process, by using the strain W. coagulans MA-13. By employing a thermophilic enzymatic cocktail (Cellic CTec2) in conjunction with the hydrolytic capabilities of MA-13, biomass degradation was enhanced by up to 62%. Moreover, batch and fed-batch fermentation experiments demonstrated the complete fermentation of glucose into L-lactic acid, achieving a concentration of up to 44.8 g/L. These results point to MA-13 as a microbial cell factory for one-step production of L-lactic acid, by combining cost-effective saccharification with MA-13 fermentative performance, on agri-food wastes. Moreover, the potential of this approach for sustainable valorization of agricultural waste streams is successfully proven.

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

FLEET velocimetry measurements in the ONR-UTA arc-jet wind tunnel

This manuscript presents and discusses the very first successful application of the Femtosecond Laser Electronic Excitation Tagging (FLEET) velocimetry technique in an arc-jet flow. Specifically, one-dimensional, quantitative, FLEET velocimetry data were obtained in the effort to characterize the 1.6 MW ONR-UTA arc-jet plasma wind tunnel, Leste, housed at the Aerodynamics Research Center of the University of Texas at Arlington. While the FLEET technique has been used in other types of high-speed wind tunnel facilities, application to flows with high background radiation, such as arc-jets, has never been demonstrated before this work. The high background emissions posed concerns on the feasibility of performing FLEET velocimetry measurements. However, this work demonstrates how these concerns were addressed and presents the first successful application of the FLEET technique in arc-jet flows. The FLEET emissions in the arc-jet plume were successfully imaged, and a significant spatio-temporal variation in the tag’s displacement was observed. For the selected operational condition in this study, the average measured gas velocity in the arc-jet plume was 1.78 km/s.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Tomographic X-ray particle tracking velocimetry

We investigate the feasibility of in-laboratory tomographic X-ray particle tracking velocimetry (TXPTV) and consider creeping flows with nearly density matched flow tracers. Specifically, in these proof-of-concept experiments we examined a Poiseuille flow, flow through porous media and a multiphase flow with a Taylor bubble. For a full 360° computed tomography (CT) scan we show that the specially selected 60 micron tracer particles could be imaged in less than 3 seconds with a signal-to-noise ratio between the tracers and the fluid of 2.5, sufficient to achieve proper volumetric segmentation at each time step. In the pipe flow, continuous Lagrangian particle trajectories were obtained, after which all the standard techniques used for PTV or PIV (taken at visible wave lengths) could also be employed for TXPTV data. And, with TXPTV we can examine flows inaccessible with visible wave lengths due to opaque media or numerous refractive interfaces. In the case of opaque porous media we were able to observe material accumulation and pore clogging, and for flow with Taylor bubble we can trace the particles and hence obtain velocities in the liquid film between the wall and bubble, with thickness of liquid film itself also simultaneously obtained from the volumetric reconstruction after segmentation. While improvements in scan speed are anticipated due to continuing improvements in CT system components, we show that for the flows examined even the presently available CT systems could yield quantitative flow data with the primary limitation being the quality of available flow tracers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Volcano infrasound: progress and future directions

Over the past two decades (2000–2020), volcano infrasound (acoustic waves with frequencies less than 20 Hz propagating in the atmosphere) has evolved from an area of academic research to a useful monitoring tool. As a result, infrasound is routinely used by volcano observatories around the world to detect, locate, and characterize volcanic activity. It is particularly useful in confirming subaerial activity and monitoring remote eruptions, and it has shown promise in forecasting paroxysmal activity at open-vent systems. Fundamental research on volcano infrasound is providing substantial new insights on eruption dynamics and volcanic processes and will continue to do so over the next decade. The increased availability of infrasound sensors will expand observations of varied eruption styles, and the associated increase in data volume will make machine learning workflows more feasible. More sophisticated modeling will be applied to examine infrasound source and propagation effects from local to global distances, leading to improved infrasound-derived estimates of eruption properties. Future work will use infrasound to detect, locate, and characterize moving flows, such as pyroclastic density currents, lahars, rockfalls, lava flows, and avalanches. Infrasound observations will be further integrated with other data streams, such as seismic, ground- and satellite-based thermal and visual imagery, geodetic, lightning, and gas data. The volcano infrasound community should continue efforts to make data and codes accessible and to improve diversity, equity, and inclusion in the field. In summary, the next decade of volcano infrasound research will continue to advance our understanding of complex volcano processes through increased data availability, sensor technologies, enhanced modeling capabilities, and novel data analysis methods that will improve hazard detection and mitigation.

58 GEOSCIENCES↗
DOE OSTI2022

Consolidation of composite cathodes with NCM and sulfide solid-state electrolytes by hot pressing for all-solid-state Li metal batteries

In this study, hot pressing was evaluated as a method of cell fabrication to increase the energy density of next-generation all-solid-state batteries with NCM active material and sulfide solid-state electrolyte. Hot pressing involves consolidating glassy sulfide electrolyte by the application of pressure at a temperature above the electrolyte’s glass transition temperature. Typically, cell stacks are formed at room temperature and retain 15–30% porosity that limits cell energy density. On the other hand, the porosity of hot-pressed cell stacks is reduced to less than 10%. The electrochemical function of hot-pressed cathode composites was assessed as a function of active material and solid-state electrolyte compositions. Specifically, LiNi 0.85 Co 0.10 Mn 0.05 O 2 and LiNi 0.6 Co 0.2 Mn 0.2 O 2 were studied in combination with either glassy Li 7 P 3 S 11 , glassy Li 3 PS 4 , or β-Li 3 PS 4 solid-state electrolytes. Cathode composites composed of LiNi 0.6 Co 0.2 Mn 0.2 O 2 and Li 3 PS 4 maintained the best function after hot pressing at 200 °C and 370 MPa for 10 min. It was found that LiNi 0.6 Co 0.2 Mn 0.2 O 2 ’s resistance to microcracking and the inherent stability of Li 3 PS 4 ’s fully de-networked local structure are critical to maintain good electrochemical function after hot pressing. Furthermore, the results of this study show that hot pressing reduces porosity in the cathode composite and confirms the feasibility of cathode support of consolidated, reinforced glass separators.

25 ENERGY STORAGE↗
DOE OSTI2021

Considerations for testing full-scale wind turbine nacelles with hardware-in-the-loop

In this paper, pole placement control techniques are utilized to compensate for variations in the torsional dynamics resulting from the different boundary conditions experienced by a wind turbine nacelle when mounted on a test bench. Simulation case studies are used to understand the baseline torsional characteristics of the nacelle coupled to the test bench versus that coupled to the rotor. It was found that the frequency shifts by up to 200% and 400% for the first and second torsional modes, respectively. The feasibility of utilizing pole placement technique to match the torsional characteristics of the turbine on the test bench is investigated using PI and PID controllers. Here, the performance of the tuned controller is then verified under two test scenarios: Low Voltage Ride Through (LVRT), and a highly dynamic turbulent wind input. It is demonstrated that tuning the test bench speed controller can effectively shift the poles of the closed-loop system to match the desired first and second modes of the full turbine and replicate transient field events on the test bench.

17 WIND ENERGY↗
DOE OSTI2025

On the Sampling-Based Computation of Nash Equilibria Under Uncertainty via the Nikaido–Isoda Function

We consider the computation of an equilibrium of a stochastic Nash equilibrium problem, where the player objectives are assumed to be L 0 -Lipschitz continuous and convex, given rival decisions with convex and closed player-specific feasibility sets. To address this problem, we consider minimizing a suitably defined value function defined using the Nikaido–Isoda function. Such an avenue does not necessitate either monotonicity properties of the concatenated gradient map or potentiality requirements on the game but does require a suitable regularity requirement under which a stationary point is a Nash equilibrium. We design and analyze a sampling-enabled projected-gradient-response method, reliant on inexact resolution of a player-level best-response subproblem. Here, by deriving suitable Lipschitzian guarantees on the value function, we derive both asymptotic guarantees for the sequence of generated iterates as well as rate and complexity guarantees for computing a stationary point by appropriate choices of the sampling rate and inexactness sequence.

Nikaido-Isoda function↗
DOE OSTI2020

Groundwater characterization and monitoring at a complex industrial waste site using electrical resistivity imaging

A contaminated industrial waste site in Washington State (USA) containing buried, metallic-waste storage tanks, pipes, and wells, was evaluated to determine the feasibility of monitoring groundwater remediation activities associated with an underlying perched aquifer system using electrical resistivity tomography. The perched aquifer, located ~65 m below ground surface and ~10 m above the regional water table, contains high concentrations of nitrate, uranium, and other contaminants of concern from past tank leaks and intentional releases of wastes to surface disposal sites. The extent of the perched water aquifer is not well known, and the effectiveness of groundwater extraction for contaminant removal is uncertain, so supplemental characterization and monitoring technologies are being evaluated. Numerical simulations of subsurface flow and contaminant transport were performed with a highly resolved model of the hydrogeologic system and waste site infrastructure, and these simulations were used as the physical basis for electrical resistivity tomography modeling. The modeling explicitly accounted for metallic infrastructure at the site. The effectiveness of using surface electrodes versus surface and horizontal subsurface electrodes, for imaging groundwater extraction from the perched water aquifer, was investigated. Although directional drilling is a mature technology, its use for electrode emplacement in the deep subsurface under a complex industrial waste site via horizontal wells has not yet been demonstrated. Results from this study indicate that using horizontal subsurface electrode arrays could significantly improve the ability of electrical resistivity tomography to image deep subsurface features and monitor remediation activities under complex industrial waste sites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The contribution of bioenergy to the decarbonization of transport: a multi-model assessment

The expected growth in the demand for passenger and freight services exacerbates the challenges of reducing transport GHG emissions, especially as commercial low-carbon alternatives to petroleum fuels are limited for shipping, air and long-distance road travel. Biofuels can offer a pathway to significantly reduce emissions from these sectors, as they can easily substitute for conventional liquid fuels in internal combustion engines. In this paper, we assess the potential of bioenergy to reduce transport GHG emissions through an analysis leveraging various integrated assessment models and scenarios, as part of the 33rd Energy Modeling Forum study (EMF-33). Furthermore, we find that bioenergy can contribute a significant, albeit not dominant, proportion of energy supply to the future transport sector: in scenarios aiming to keep the temperature increase below 2 °C by the end of the twenty-first century, models project that in 2100 bioenergy can provide on average 42 EJ/yr (ranging from 5 to 85 EJ/yr) for transport (compared to 3.7 EJ in 2018), mainly through lignocellulosic fuels. This makes up 9–62% of final transport energy use. Only a small amount of bioenergy is projected to be used in transport through electricity and hydrogen pathways, with a larger role for biofuels in road passenger transport than in freight. The association of carbon capture and storage (CCS) with bioenergy technologies (BECCS) is a key determinant in the role of biofuels in transport, because of the competition for biomass feedstock to provide other final energy carriers along with carbon removal. Among models that consider CCS in the biofuel conversion process the average market share of biofuels is 21% in 2100 (ranging from 2 to 44%), compared to 10% (0–30%) for models that do not. Cumulative direct emissions from the transport sector account for half of the emission budget (from 306 to 776 out of 1,000 GtCO 2 ). However, the carbon intensity of transport decreases as much as other energy sectors in 2100 when accounting for process emissions, including carbon removal from BECCS. Lignocellulosic fuels become more attractive for transport decarbonization if BECCS is not feasible for any energy sectors. Since global transport service demand increases and biomass supply is limited, its allocation to and within the transport sector is uncertain and sensitive to assumptions about political as well as technological and socioeconomic factors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Explaining and predicting human behavior and social dynamics in simulated virtual worlds: reproducibility, generalizability, and robustness of causal discovery methods

Ground Truth program was designed to evaluate social science modeling approaches using simulation test beds with ground truth intentionally and systematically embedded to understand and model complex Human Domain systems and their dynamics Lazer et al. (Science 369:1060–1062, 2020). Our multidisciplinary team of data scientists, statisticians, experts in Artificial Intelligence (AI) and visual analytics had a unique role on the program to investigate accuracy, reproducibility, generalizability, and robustness of the state-of-the-art (SOTA) causal structure learning approaches applied to fully observed and sampled simulated data across virtual worlds. In addition, we analyzed the feasibility of using machine learning models to predict future social behavior with and without causal knowledge explicitly embedded. In this paper, we first present our causal modeling approach to discover the causal structure of four virtual worlds produced by the simulation teams—Urban Life, Financial Governance, Disaster and Geopolitical Conflict. Our approach adapts the state-of-the-art causal discovery (including ensemble models), machine learning, data analytics, and visualization techniques to allow a human-machine team to reverse-engineer the true causal relations from sampled and fully observed data. We next present our reproducibility analysis of two research methods team’s performance using a range of causal discovery models applied to both sampled and fully observed data, and analyze their effectiveness and limitations. We further investigate the generalizability and robustness to sampling of the SOTA causal discovery approaches on additional simulated datasets with known ground truth. Our results reveal the limitations of existing causal modeling approaches when applied to large-scale, noisy, high-dimensional data with unobserved variables and unknown relationships between them. We show that the SOTA causal models explored in our experiments are not designed to take advantage from vasts amounts of data and have difficulty recovering ground truth when latent confounders are present; they do not generalize well across simulation scenarios and are not robust to sampling; they are vulnerable to data and modeling assumptions, and therefore, the results are hard to reproduce. Finally, when we outline lessons learned and provide recommendations to improve models for causal discovery and prediction of human social behavior from observational data, we highlight the importance of learning data to knowledge representations or transformations to improve causal discovery and describe the benefit of causal feature selection for predictive and prescriptive modeling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Modeling design and control problems involving neural network surrogates

Here, we consider nonlinear optimization problems that involve surrogate models represented by neural networks. We demonstrate first how to directly embed neural network evaluation into optimization models, highlight a difficulty with this approach that can prevent convergence, and then characterize stationarity of such models. We then present two alternative formulations of these problems in the specific case of feedforward neural networks with ReLU activation: as a mixed-integer optimization problem and as a mathematical program with complementarity constraints. For the latter formulation we prove that stationarity at a point for this problem corresponds to stationarity of the embedded formulation. Each of these formulations may be solved with state-of-the-art optimization methods, and we show how to obtain good initial feasible solutions for these methods. We compare our formulations on three practical applications arising in the design and control of combustion engines, in the generation of adversarial attacks on classifier networks, and in the determination of optimal flows in an oil well network.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A mixed-integer PDE-constrained optimization formulation for constructing electromagnetic cloaks with multiple materials

We study the design of an electromagnetic cloak from multiple materials with an additional constraint on the mass of the cloak. Our problem is an example of a topology optimization problem, and we formulate this problem as a mixed-integer partial-differential equation constrained optimization (MIPDECO) problem, where Maxwell’s equation models the propagation of the wave through the cloak and surrounding medium. We use binary variables to model the assignment of the different materials, and their relevant properties (permittivity and density). The mass constraint adds a nontrivial constraint to this problem. We propose a two-phase strategy to solve this problem. In the first phase, we solve a continuous relaxation, and then propose a new variant of the feasibility pump that exploits the structure of the PDE to obtain an initial integral solution candidate. In the second phase, we use a trust-region approach to improve this incumbent. We also consider a continuation or mesh-sequencing approach to find better solutions faster on consecutively finer meshes. We present detailed numerical results to illustrate the effectiveness of our approaches for constructing multi-material cloaks with a mass constraint.

Calculus of Variations and Optimization↗
DOE OSTI2021

An empirical investigation of organic software product lines

Abstract Software product line engineering is a best practice for managing reuse in families of software systems that is increasingly being applied to novel and emerging domains. In this work we investigate the use of software product line engineering in one of these new domains, synthetic biology. In synthetic biology living organisms are programmed to perform new functions or improve existing functions. These programs are designed and constructed using small building blocks made out of DNA. We conjecture that there are families of products that consist of common and variable DNA parts, and we can leverage product line engineering to help synthetic biologists build, evolve, and reuse DNA parts. In this paper we perform an investigation of domain engineering that leverages an open-source repository of more than 45,000 reusable DNA parts. We show the feasibility of these new types of product line models by identifying features and related artifacts in up to 93.5% of products, and that there is indeed both commonality and variability. We then construct feature models for four commonly engineered functions leading to product lines ranging from 10 to 7.5 × 10 20 products. In a case study we demonstrate how we can use the feature models to help guide new experimentation in aspects of application engineering. Finally, in an empirical study we demonstrate the effectiveness and efficiency of automated reverse engineering on both complete and incomplete sets of products. In the process of these studies, we highlight key challenges and uncovered limitations of existing SPL techniques and tools which provide a roadmap for making SPL engineering applicable to new and emerging domains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Global interfertility and heterosis in sugar kelp populations: a next step in sugar kelp breeding

Abstract The potential of seaweed aquaculture is restricted by high labor, production and processing costs, leading to low economic viability. Selective breeding can improve yields and cultivation efficiency, thereby decreasing production costs. Until now, genetic resources as input for Saccharina latissimabreeding trials have been sourced strictly locally, due to concerns regarding outplanting genetically exogenous material in local waters. Here we study, for the first time, worldwide interregional fertility of the seaweedS. latissima,in order to assess the potential of including globalS. latissimagenetic resources for selective breeding with regard to heterosis. We quantified the yield (as an indicative aquacultural performance) and morphological traits of intra- and interregionalS. latissimahybrids originating from a broad range of locations in a common garden experiment. Our results show that the practical application of worldwideS. latissimagenetic resources in breeding programs is feasible based on global interfertility. We found a wide morphological diversity of hybrids and observed significant heterosis in interregional hybrids. The degree of heterosis could not be linked to geographic distance. These findings reveal that worldwide genetic resources can considerably contribute toS. latissimabreeding programs and could offer a major next step in improving yields and quality traits.

Biotechnology & Applied Microbiology↗
DOE OSTI2020

In situ X-ray measurements over large Q-space to study the evolution of oxide thin films prepared by RF sputter deposition

Sputter deposition is a versatile and industrially important deposition technique for thin films, with increasing demand for matching the characteristics of thin film materials to specific requirements. Additionally, the actual film properties are largely determined by sputtering parameters such as pressure conditions, temperature and power settings. By means of various X-ray diffraction and scattering techniques, it is shown that the characterization of film formation and growth is feasible in real time at synchrotron sources, thus adding an important dimension to the fundamental understanding of the evolution of thin film microstructure. In particular, grazing incidence small-angle X-ray scattering, grazing incidence X-ray powder diffraction and X-ray reflectometry are used in a complementary manner to study the influence of deposition temperature and substrate choice on the crystallization kinetics and growth of polycrystalline BaTiO 3 films.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Approaching air buoyancy in aero/cryogel vacuum vessels

Air impermeability has been observed in low-density aerogel and cryogel materials, which has led to a series of experiments to investigate the feasibility of an air buoyant vacuum vessel, as well as the fabrication and testing of sub-buoyant prototypes. Here, bulk samples of silica aerogel were shown to isolate vacuum from ambient air for several hours with optimal vacuum isolation occurring at a density of approximately 85 mg cm –3 . It was demonstrated using polyimide aerogel and cryogel materials that the ability of these foam materials to provide an air impermeable layer between vacuum and atmosphere, in spite of being comprised of mostly void space, is related to material stiffness. It is hypothesized that this behavior is due to local deformation of the random nanostructure of the material. Spherical shell vacuum vessels were produced using the polyimide cryogel, and less than 133 Pa vacuum containment was demonstrated under active pumping. In order to approach the non-buoyant to buoyant transition for these vacuum vessels, a polyimide composite was produced using helical fibers for which preliminary mechanical testing was performed.

36 MATERIALS SCIENCE↗