Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “solution species”

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.

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

At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗
DOE OSTI2025

The Role of Cu 3+ in the Oxygen Evolution Activity of Copper Oxides

Cu-based oxides and hydroxides represent an important class of materials from a catalytic and corrosion perspective. In this study, we investigate the formation of bulk and surface Cu 3+ species that are stable under water oxidation catalysis in alkaline media. So far, no direct evidence existed for the presence of hydroxides (CuOOH) or oxides, which were primarily proposed by theory. Here, this work directly places CuOOH in the oxygen evolution reaction (OER) Pourbaix stability region with a calculated free energy of −208.68 kJ/mol, necessitating a revision of known Cu–H 2 O phase diagrams. We also predict that the active sites of CuOOH for the OER are consistent with a bridge O* site between the two Cu 3+ atoms with onset at ≥1.6 V vs the reversible hydrogen electrode (RHE), aligning with experimentally observed Cu 2+/3+ oxidation waves in cyclic voltammetry of Fe-free and Fe-spiked copper in alkaline media. Trace amounts of Fe (2 μg/mL (ppm) to 5 μg/mL) in the solution measurably enhance the catalytic activity of the OER, likely due to the adsorption of Fe species that serve as the active sites . Importantly, modulation excitation X-ray absorption spectroscopy (ME-XAS) of a Cu thin-film electrode shows a distinct Cu 3+ fingerprint under OER conditions at 1.8 V vs RHE. Additionally, in situ Raman spectroscopy of polycrystalline Cu in 0.1 mol/L (M) KOH revealed features consistent with those calculated for CuOOH in addition to CuO. Overall, this work provides direct evidence of bulk electrochemical Cu 3+ species under OER conditions and expands our longstanding understanding of the oxidation mechanism and catalytic activity of copper.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Developing A Space-Based Solution to Increase Accessibility, Quality, and Utility of Animal Tracking Data for Research and Management: the Internet of Animals Project

Animal tracking technology has advanced dramatically over the last several decades, but researchers and wildlife managers still encounter technological roadblocks in the study of animal movement and acquisition of animal movement data. For example, we still lack technology that provides automated high-resolution data for small animals that travel long distances, which limits our ability to answer both theoretical and applied questions about these species. In response to these needs, NASA has initiated a five-year study of potential space-based solutions that could provide global low-latency tracking of small migratory animals. This study, named Internet of Animals (IOA), aims to 1) systematically assess the needs of animal movement researchers and ecological managers, 2) design a next-generation space-based animal tracking system, i.e. an ‘Internet of Animals’ or IoA, to meet those needs, and 3) developing science and technology needed to link animal tracking data to the many other dimensions of biodiversity that can now be mapped from space using remote sensing. Here, we present results from the first IOA workshop, which highlighted the diverse needs of researchers and managers working across systems and realms. We also provide opportunities for the community to engage in the future.

remote sensing↗
NASA NTRS1986

Sulfur isotope effects associated with protonation of HS- and volatilization of H2S

The isotope effects associated with: (1) formation of H2S from HS- by protonation in aqueous solution; and (2) volatilization of H2S have been experimentally determined. Both isotopic distributions in closed systems at equilibrium and differential rates of volatilization of isotopic species in open systems were measured at 22 +/- 1 degrees C. It was found that, at equilibrium aqueous H2S is enriched in 34S by 2.0 - 2.7% relative to HS- and that H2S volatilized from solution is depleted in 34S by 0.5% relative to dissolved H2S. A small kinetic isotope effect accompanying volatilization of H2S was observed in the open-system experiments.

NASA Discipline Exobiology↗
DOE OSTI2024

Synthesis and Characterization of Isostructural Th(IV) and U(IV) Pyridine Dipyrrolide Complexes

A series of pyridine dipyrrolide actinide(IV) complexes, ( Mes PDP Ph )AnCl 2 (THF) and An( Mes PDP Ph ) 2 (An = U, Th, where ( Mes PDP Ph ) is the doubly deprotonated form of 2,6-bis(5-(2,4,6-trimethylphenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine), have been prepared. Characterization of all four complexes has been performed through a combination of solid- and solution-state methods, including elemental analysis, single crystal X-ray diffraction, and electronic absorption and nuclear magnetic resonance spectroscopies. Collectively, these data confirm the formation of the mono- and bis-ligated species. Time-dependent density functional theory has been performed on all four An(IV) complexes, providing insight into the nature of electronic transitions that are observed in the electronic absorption spectra of these compounds. Room temperature, solution-state luminescence of the actinide complexes is presented. Both Th(IV) derivatives exhibit strong photoluminescence; in contrast, the U(IV) species are nonemissive.

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

Modeling and Optimization of Zeolites for Contaminant Removal from Coal Combustion Impoundment Leachates

Coal Combustion Residual (CCR) landfills in the U.S. can lead to elevated contaminant concentrations in groundwater and runoff, particularly of arsenic, boron, and selenium. Zeolites can be readily synthesized from materials contained within the coal combustion ash impoundments and can be cation-exchanged to enhance adsorption capacity, selectivity, and reactivity. However, the optimization of zeolites becomes a daunting task when accounting for the variety of Si:Al ratios, the species of extra-framework cations present, and the zeolite pore structure. Molecular simulations provide methods to study and guide the design of zeolites for the sorption of contaminants from aqueous solution. In this work, models that predict the sorption of arsenic, boron, and selenium from water using cation-exchanged zeolites. Because of the lack of experimental adsorption data for these species of contaminants, models were parametrized to reproduce the results of first-principles calculations and then used to predict sorption for zeolites for a dataset containing 6000 combinations of zeolites and sorption conditions. Machine learning was used to train a model to predict sorption for materials in this database based on the results of the molecular simulations. Next, a genetic algorithm was used to optimize zeolites for the removal of each contaminant from aqueous solution for individual impoundment sites based on contaminant concentrations reported by the Electric Power Research Institute.

Findley, John↗
NASA NTRS1989

Nonaqueous chemical depth profiling of YBa2Cu3O(7-x)

A nonaqueous solution of Br in absolute ethanol (EtOH) has recently been reported to be effective at removing nonsuperconducting surface species from YBa2Cu3O(7-x) films, leaving the surface close to the ideal stoichiometry. This same etchant is shown here to be an effective bulk etchant in chemical depth profiling through 1-micron-thick films. The Cu remains in the 2 + oxidation state and the stoichiometry, as determined by X-ray photoelectron spectroscopy, is close to ideal and nearly constant throughout the profile, indicating the absence of any large preferential etching effects. The reaction of YBa2Cu3O(7-x) films with HF/EtOH, HCl/EtOH, and I/EtOH solutions is also reported.

Vasquez, R. P.↗
DOE OSTI2023

Concentration‐dependent Cycling of Phenothiazine‐based Electrolytes in Nonaqueous Redox Flow Cells

Increasing redox-active species concentrations can improve viability for organic redox flow batteries by enabling higher energy densities, but the required concentrated solutions can become viscous and less conductive, leading to inefficient electrochemical cycling and low material utilization at higher current densities. To better understand these tradeoffs in a model system, we study a highly soluble and stable redox-active couple, N-(2-(2-methoxyethoxy)ethyl)phenothiazine (MEEPT), and its bis(trifluoromethanesulfonyl)imide radical cation salt (MEEPT-TFSI). We measure the physicochemical properties of electrolytes containing 0.2–1 M active species and connect these to symmetric cell cycling behavior, achieving robust cycling performance. Specifically, for a 1 M electrolyte concentration, we demonstrate 94% materials utilization, 89% capacity retention, and 99.8% average coulombic efficiency over 435 h (100 full cycles). This demonstration helps to establish potential for high-performing, concentrated nonaqueous electrolytes and highlights possible failure modes in such systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2020

Robotic Specialization in Autonomous Robotic Structural Assembly

Robotic in-space assembly of large space structures is a long-term NASA goal to reduce launch costs and enable larger scale missions. Recently, researchers have proposed using discrete lattice building blocks and co-designed robots to build high-performance, scalable primary structure for various on-orbit and surface applications. These robots would locomote on the lattice and work in teams to build and reconfigure building-blocks into functional structure. However, the most reliable and efficient robotic system architecture, characterized by the number of different robotic 'species' and the allocation of functionality between species, is an open question. To address this problem, we decompose the robotic building-block assembly task into functional primitives and, in simulation, study the performance of the the variety of possible resulting architectures. For a set consisting of five process types (move self, move block, move friend, align bock, fasten block), we describe a method of feature space exploration and ranking based on energy and reliability cost functions. The solution space is enumerated, filtered for unique solutions, and evaluated against energy and reliability cost functions for various simulated build sizes. We find that a 2 species system, dividing the five mentioned process types between one unit cell transport robot and one fastening robot, results in the lowest energy cost system, at some cost to reliability. This system enables fastening functionality to occupy the build front while reducing the need for that functional mass to travel back and forth from a feed station. Because the details of a robot design affect the weighting and final allocation of functionality, a sensitivity analysis was conducted to evaluate the effect of changing mass allocations on architecture performance. Future systems with additional functionalities such as repair, inspection, and others may use this process to analyze and determine alternative robot architectures.

Bernus, Borbala↗
DOE OSTI2020

Self-Assembled Solute Networks in Crowded Electrolyte Solutions and Nanoconfinement of Charged Redoxmer Molecules

Redoxmers are electrochemically active organic molecules storing charge and energy in electrolyte fluids circulating through redox flow batteries (RFBs). Such molecules typically have solvent-repelling cores and solvent-attracting pendant groups introduced to increase solubility in liquid electrolytes. These two features can facilitate nanoscale aggregation of the redoxmer molecules in crowded solutions. In some cases, this aggregation leads to the emergence of continuous networks of solute molecules in contact, and the solution becomes microscopically heterogeneous. In this study, we used small-angle X-ray scattering (SAXS) and molecular dynamics modeling to demonstrate formation of such networks and examine structural factors controlling this self-assembly. We also show that salt ions become excluded from these solute aggregates into small pockets of electrolytes, where these ions strongly associate. This confinement by exclusion is also likely to occur to charged redoxmer molecules in a “sea” of neutral precursors coexisting in the same solution. Here, we demonstrate that the decay lifetime of the confined charged molecules in such solutions can increase several fold compared to dilute solutions. We attribute this behavior to a “microreactor effect” on reverse reactions of the confined species during their decomposition.

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

Predicting initial dissolution rates using structural features from molecular dynamics simulations

Predicting chemical durability of glass materials is important for various applications from daily life such as drink glass and kitchen ware to advanced technologies such as nuclear waste disposal and biomedicine. In this work, we explored prediction of initial dissolution rate through structural features from molecular dynamics (MD) simulations for a wide range of glass compositions (total 28) including borosilicate and aluminosilicate glasses, ZrO 2 -containing and V 2 O 5 -containing boroaluminosilicate glasses. The initial dissolution rates (r 0 ) measured experimentally at 90 °C with varying solution conditions were correlated with structural features (e.g., polyhedral linkages and non-bridging oxygen species) obtained from MD simulations, either from this study or from literature. Since hydrolysis of the glass network through breaking of the network former linkages (e.g., Si-O-Si, Si-O-Al, etc.) is a critical step of network glass dissolution, the statistics of these linkages obtained from MD were correlated to r0 through linear regression, where the coefficient of determination (R 2 ) and root mean square error are found to be 0.949 and 0.681, respectively. This model was compared and discussed with existing models developed by various approaches including machine learning, the kinetic rate equation, topological constraint theory, and other descriptors from MD simulations. The discussion provides insights on future model improvements to predict glass dissolution. In addition, the impact of V 2 O 5 on the glass dissolution was examined in detail, implicating that the impact is not the same across all glass compositions and test conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

TChem-atm v1.0

SAND2024-11300O TChem-atm is a software library that was developed to solve complex kinetic models for atmospheric chemistry applications. TChem-atm interface employs a hierarchical parallelism design to exploit the massive parallelism available from modern computing platforms. It also supports gas atmospheric chemistry applications, e.g., the energy exascale earth system model. TChem can be used as a box model or coupled with a climate model to compute the time evolution of gas tracer species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Safta, Cosmin↗
DOE OSTI2024

Poplar

SAND2025-00683O Poplar is a software tool that generates a phylogenetic tree from input gene and genome sequences. It integrates established tools to identify genes within genomes, group sequences, construct gene trees, and infer a species tree. Poplar processes nucleotide sequences, identifies similar sequences using Nucleotide BLAST, groups them with DBSCAN, aligns sequences with MAFFT, constructs gene trees with RAxML-NG, and infers a species tree using ASTRAL-Pro3. This pipeline provides a structured approach to phylogenetic analysis, facilitating the study of evolutionary relationships among species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Krishnakumar, Raga↗
DOE OSTI2021

Effects of Carbonate Minerals on Shale-Hydraulic Fracturing Fluid Interactions in the Marcellus Shale

Natural gas extracted from tight shale formations, such as the Marcellus Shale, represents a significant and developing front in energy exploration. By fracturing these formations using pressurized fracturing fluid, previously unobtainable hydrocarbon reserves may be tapped. While pursuing this resource, hydraulic fracturing operations leave chemically complex fluids in the shale formation for at least two weeks. This provides a substantial opportunity for the hydraulic fracturing fluid (HFF) to react with the shale formation at reservoir temperature and pressure. In this study, we investigated the effects of the carbonates on shale-HFF reactions with a focus on the Marcellus Shale. We performed autoclave experiments at high temperature and pressure reservoir conditions using a carbonate-rich and a decarbonated or carbonate-free version of the same shale sample. We observed that carbonate minerals buffer the pH of the solution, which in turn prevents clay dissolution. Carbonate and bicarbonate ions also scavenge reactive oxidizing species (ROS), which prevents oxidation of shale organic matter and volatile organic compounds (VOCs). Carbonate-free samples also show higher pyrite dissolution compared to the carbonate-rich sample due to chelation reactions. This study demonstrates how carbonate minerals (keeping all other variables constant) affect shale-HFF reactions that can potentially impact porosity, microfracture integrity, and the release of heavy metals and volatile organic contaminants in the produced water.

58 GEOSCIENCES↗
NASA NTRS1973

Evaluation of proposed Skylab and SSP soap products

Three personal hygiene cleansing agents and one laundry detergent (sodium dodecyl benzene sulfonate), which are all candidates for use on long-duration space missions, were evaluated in terms of dermatological effects on human subjects and effects on microbiological species. None of the four materials exhibited adverse dermatological effects from either skin patch tests of two weeks duration or a simulated Skylab personal hygiene regimen of up to four weeks duration. No significant alterations in skin microflora during the use regimen were found. None of the four materials were found to serve as microbiological support media for the species tested, but a species of air-borne mold was observed to grow rapidly in a neutralized aqueous solution. None of the candidate agents was found to be strongly biocidal.

Whitmore, F. C.↗
NASA NTRS1978

Prediction of hydrodynamics and chemistry of confined turbulent methane-air frames in a two concentric tube combustor

A formulation of the governing partial differential equations for fluid flow and reacting chemical species in a two-concentric-tube combustor is presented. A numerical procedure for the solution of the governing differential equations is described and models for chemical-equilibrium and chemical-kinetics calculations are presented. The chemical-equilibrium model is used to characterize the hydrocarbon reactions. The chemical-kinetics model is used to predict the concentrations of the oxides of nitrogen. The combustor considered consists of two coaxial ducts. Concentric streams of gaseous fuel and air enter the inlet duct at one end; the flow then reverses and flows out through the outer duct. Two sample cases with specified inlet and boundary conditions are considered and the results are discussed.

Markatos, N. C.↗