Promoting H2O2 production via 2-electron oxygen reduction by coordinating partially oxidized Pd with defect carbon
Explore the source record for details and available documents.
99 GENERAL AND MISCELLANEOUS↗
SEARCH · Engineering Papers
Results for “functional containment”
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.
Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots
Abstract For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
Acharya, Shwetha M.↗
Renormalization and scale evolution of the soft-quark soft function
Soft functions defined in terms of matrix elements of soft fields dressed by Wilson lines are central components of factorization theorems for cross sections and decay rates in collider and heavy-quark physics. While in many cases the relevant soft functions are defined in terms of gluon operators, at subleading order in power counting soft functions containing quark fields appear. We present a detailed discussion of the properties of the soft-quark soft function consisting of a quark propagator dressed by two finite-length Wilson lines connecting at one point. This function enters in the factorization theorem for the Higgs-boson decay amplitude of the h → γγ process mediated by light-quark loops. We perform the renormalization of this soft function at one-loop order, present a conjecture for its two-loop anomalous dimension and discuss solutions to its renormalization-group evolution equation in momentum space, in Laplace space and in the “diagonal space”, where the evolution is strictly local in the momentum variable.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Experimental investigation into coal wettability changes caused by reactions with scCO 2 -H 2 O
Geological CO 2 sequestration (GCS) can help mitigate global warming and enhance methane recovery from coal beds. However, few studies have linked the effects of CO 2 to surface chemistry changes controlling wetting behavior in deep coal beds. Contact angles (CAs) of CO 2 /N 2 -high volatile bituminous coal-water systems were measured under different temperatures and pressures. The surface chemistry and physical structure of coals were characterized to investigate changes in physicochemical properties and their relations with wettability after reactions. For N 2 treatment, the time-dependence of static and dynamic CAs were insignificant, ranging within 4°. For gaseous CO 2 treatment, the static CAs and the average advancing angles increased slightly. With supercritical (sc) CO 2 , both the static and dynamic CAs increased significantly, and θ adv changed to intermediate-wet (92°). Reactions with minerals exposed to scCO 2 resulted in greater surface roughness and heterogeneity, greater contact angle hysteresis and more surface sites occupied by scCO 2 rather than H 2 O. Increases in hydrophobic functional groups and decreases in hydrophilicity were shown by FTIR spectra, reflecting the shedding of polar oxygen-containing functional groups, reduction of hydrogen bonds, and increasing percentage of hydrocarbons. XRD patterns obtained following scCO 2 -treatment showed that crystallite growth and molecular polymerization were higher toward graphite-like. The calculated structural parameters of functional groups and crystallites both showed elevated coal rank. Changes in crystallite structure, notably higher carbon content and decreased negative surface charge, are unfavorable for water-wetting. Finally, this study contributes to understanding surface chemistry changes responsible for decreased wettability during CO 2 -enhanced coal bed methane recovery and GCS in coal reservoirs.
01 COAL, LIGNITE, AND PEAT↗
Plug & play directed evolution of proteins with gradient-based discrete MCMC
Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.
59 BASIC BIOLOGICAL SCIENCES↗
Effect of Molecular Structure of Quinones and Carbon Electrode Surfaces on the Interfacial Electron Transfer Process
Quinones can undergo thermodynamically reversible proton-coupled electron transfer reactions and are being applied as electroactive compounds in aqueous organic batteries. However, the electrochemical reversibility of these compounds is affected not only by their molecular structure but also by the properties of a carbon-based electrode surface. This study combines experimental and theoretical approaches to understand this dependence. Specifically, we study the electron transfer kinetics of two synthesized quinone derivatives and two commercially available ones with a glassy carbon, a highly ordered pyrolytic graphite, and a high-edge-density graphite electrode (HEDGE). The electrochemical reversibility is notably improved on the HEDGE, which shows a higher density of defects and presents oxygenated functional groups at its surface. The electron transfer kinetics are controlled by adsorbed species onto the HEDGE. Molecular dynamics simulation and quantum mechanics calculations suggest defects with oxygen-containing functional groups, such as C-O and C$=$O, on HEDGE surfaces drive the interaction with the functional groups of the molecules, during physisorption from van der Waals forces. The presence of sulfonic acid side groups and a greater number of aromatic rings in the molecular structure may contribute to a higher stabilization of quinone derivatives on HEDGEs. We propose that high-performance carbon-based electrodes can be obtained without catalysts for organic batteries, by the engineering of carbon-based surfaces with edge-like defects and oxygenated functional groups.
25 ENERGY STORAGE↗
Organocatalysis in ring opening copolymerization as a means of tailoring molecular weight dispersity and the subsequent impact on physical properties in 4D printable photopolymers
Vat photopolymerization 3D printing has traditionally relied on free radical crosslinking between alkenes to produce non-degradable parts, which may have limited use in the biomedical and clinical spaces. Photopolymer resins containing functionalized degradable polymers, specifically polyesters, are greatly interesting for 3D printing tissue scaffolds and medical devices. Unfortunately, most polyesters produced for these applications have been made using metal-containing catalysts, which are not without risk for medical applications. Organocatalysis is a viable alternative route to achieving the same types of polyesters. Here, ring opening copolymerization (ROCOP) of allyl and cyclohexene-containing polyesters is examined using bipyridine and a guanidine-containing catalyst. The role of the catalysts, initiators, and cocatalysts are examined for bulk, open air ROCOP reactions. Unlike previous efforts with organocatalysis, the examined catalysts here could be used to tailor the dispersity of the polyesters, with ~10 kDa polyesters with dispersity ranging from 1.3 to 2.5 examined for the impact on rheological and thermomechanical properties related to resin/part behavior. The bipyridine catalysts and a thiourea cocatalyst further are shown, through the introduction of new fluorescence emissions of the purified polyesters. As a result, this work demonstrates that tuning the dispersity of polyester photopolymers provides a direct method of tailoring physical and optical properties in 3D/4D printable materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electrocatalytic Hydrotreatment of Bio-Oil: Exploring Interactions Between Functional Groups
Electrocatalytic hydrotreatment (ECH) is being explored as a sustainable route for upgrading bio-oil to renewable fuels and chemicals. Bio-oil, produced by the fast pyrolysis of lignocellulosic biomass, is a complex mixture of compounds with various oxygen-containing functional groups, such as anhydrosugars, carboxylic acids, ketones, aldehydes, furans, phenols and alcohols. The ECH of several bio-oil model compound binary mixtures was conducted to investigate the interactions between these functional groups. Notably, phenolic compound reduction was significantly inhibited in the presence of aldehydes, particularly furfural. A strategy involving the reagent-based reduction of the aldehyde to an alcohol prior to ECH was shown to partially mitigate this inhibitory effect. Additionally, qualitative studies on the ECH of catalytic fast pyrolysis (CFP) oil with low aldehyde content showed promising results. These studies achieved the conversion of cyclopentenones and phenolic compounds present in the CFP oil to cyclopentanols and cyclohexanols, respectively.
09 BIOMASS FUELS↗
Gas permeable fluoropolymers and ionomers
Novel copolymers that are fluoropolymers including a first repeat unit that is fluorinated and cyclic and a second repeat unit from a trifluorovinyl methylene ether monomer having sulfur or sulfone functionality in the pendant group are disclosed. The copolymers have relatively high gas permeability as a result of a cyclic repeat unit in the copolymer backbone and ionomers from oxidation of the sulfur containing functionality are particularity useful in the cathode structure of a proton exchange membrane fuel cell.
Lousenberg, Robert Daniel↗
Determination of Phenolic Groups in Bio-Oils Using Revised Folin-Ciocalteu Methods: Single Cuvette and Plate Reader. Laboratory Analytical Procedure (LAP), Issue Date: May 12, 2022
Phenol components are ubiquitous in wood-derived bio-oils and biocrudes. Their reaction with other functional groups (e.g., aldehydes) may contribute to the formation of carbonaceous species and the expected thermal instability of pyrolysis oils. During hydrotreating, phenols can be recalcitrant species, requiring higher reaction temperatures than other oxygen-containing functional groups. Phenols are also present in upgraded products and have been shown to lead to catalyst deactivation during hydrotreating. They also are the first oxygenated functional group to re-appear in the upgraded product, signaling catalyst deactivation. This procedure covers the determination of phenolic compounds in fast pyrolysis oils. This Laboratory Analytical Procedure (LAP) includes two methods, the first allowing for shorter analysis time at increased reaction temperature, while the second employs a longer analysis time but at room temperature. Additionally, the use of both a single cuvette and of a plate reader are also presented.
09 BIOMASS FUELS↗
Logistic function as a characteristic of multipactor development
Simulations of multipacting with or without space charge effect bring out a different behavior of particle number growth, namely, the exponential growth of particle number in the simulations without space charge effect and the saturation of particle number (or collision and emission currents) when space charge is considered. That creates a certain confusion in evaluation and comparison of overall danger of multipactor between the approaches. On the other hand, both growth rate and total multipactor current loading at saturation are important for multipactor barriers evaluation. It was noticed and then verified that the logistic function, widely used in chemistry, biology, and ecosystem study, reproduces the particle number growth curves remarkably well. The function contains the parameters, which can be interpreted as particle number growth rate and multipactor current saturation level, so both become correlated and obtained simultaneously in one run. In this work it is shown how the logistic function can be used for characterization of the multipactor barriers and how it can be used for possible reduction of simulation time in the simulations with space charge effect.
Romanov, Gennady↗
cabbi-bio/ESM-R-script
This script is intended to provide a starting point for users to implement the equivalent soil mass (ESM) approach for calculating soil organic carbon (SOC) stocks and SOC mass percentages (commonly called “SOC concentration”). The user should read this readme file and understand how the script works before using it. The script contains some basic error checking algorithms, but it cannot catch all data entry mistakes. It is possible to misuse the script and produce invalid results. The script was designed to work on individual soil cores that have been divided into three or more contiguous segments, as the cubic spline function contains four coefficients. The script has not been tested on soil cores containing fewer than three contiguous segments. If only one segment is present, interpolation will necessarily be linear rather than cubic, which is expected to result in higher predictive error (Wendt & Hauser, 2013). Considering the wide range of potential applications, the script should not be expected to function correctly in all situations. The user is encouraged to modify or rewrite the script to meet their specific needs.
von Haden, Adam↗
Fundamental Studies of Bifunctional Catalysts for Tandem Reactions
During the past few years of our funding from DOE Basic Energy Sciences, we have focused on the catalytic conversion of biomass-derived 5-hydroxymethyl furfural (HMF) as a platform molecule for sustainable synthesis of value-added chemicals. The combination of the diene and aldehyde functionalities in HMF enables catalytic production of acetalized HMF derivatives with diol or epoxy reactants to allow reversible synthesis of norcantharimide derivatives upon Diels-Alder reaction with maleimides. Whereas the electron-withdrawing nature of aldehyde group inhibits the reactivity of diene group in HMF to undergo Diels-Alder reactions with dienophiles, by converting the aldehyde group in HMF to an electron-donating hydroxyl group, HMF can append maleimide-based chemicals through Diels-Alder coupling. Acetalization of HMF not only produces an electron-rich diene for Diels-Alder reaction, but it also alters the reversibility of acetal formation and thereby allows for the controlled release of chemicals by hydrolysis. Therefore, we synthesized various norcantharimide derivatives from biomass-derived HMF by acetalization over an acid catalyst, Amberlyst-15, followed by Diels-Alder reaction with maleimide. The norcantharimides release the starting materials by retro Diels-Alder reaction that is triggered by acetal hydrolysis under acidic (≤pH 3) conditions. In subsequent work, we explored the synthesis and properties of functional polyurethanes and polyesters with tunable properties from biomass-derived (HMF)-Acetone-HMF (HAH) monomers. HAH can be selectively hydrogenated over Cu and Ru catalysts to produce partially-hydrogenated HAH (PHAH) and fully-hydrogenated HAH (FHAH). HAH contains functional groups, including hydroxyl, furan, enone, and ketone functionalities, that can be exploited to further tune the polymer properties. The π-electron conjugation between the enone and furan groups in HAH monomer stabilizes the furan group to prevent the uncontrolled degradation of furans during reactions, such as etherification. Therefore, HAH is a renewable monomer that can be used to synthesize polymers, having high molecular weight, symmetric functionalities, an inexpensive production price, and being derived from renewable resources without competition with food resources. We demonstrated the synthesis of functional polyurethanes and a renewable polyester from HAH-derived monomers, and 4,4’-methylenebis(phenyl isocyanate) (MDI). We showed that it is essential to be able to selective hydrogenate C=C double bonds in HAH to be able to achieve effective Diels Alder reactions of the furan ring. Therefore, we studied the hydrogenation at temperatures from 313 – 393 K of HAH over Pd, Ru, and Cu based catalysts. HAH was selectively hydrogenated to produce partially-hydrogenated monomers (PHAH) over Cu and Ru catalysts and to fully-hydrogenated HAH monomers (FHAH) over the Ru catalyst. Pd based catalysts yielded a mixture of partially and fully hydrogenated monomers. Reaction kinetics models were employed to quantify the kinetic behavior for hydrogenation over Ru, Cu, and Pd catalysts. A 5-step pathway exhibited over Pd and Ru catalysts consists of both series and parallel reaction steps, where HAH is both converted to fully hydrogenated products sequentially via series reactions of partially hydrogenated intermediates, as well as converted directly in parallel reactions to form the fully hydrogenated products. In contrast, a 3-step pathway over the Cu catalyst consists only of the consecutive reaction steps, where the final product was formed via series reactions of intermediate products. Additionally, reaction over the Cu catalyst did not hydrogenate the furan rings of the HAH molecule and yielded a different final product than those hydrogenation over Pd and Ru catalysts. Using the results from our detailed reaction kinetics studies, we developed universal conditions for the maximum production of the various hydrogenated products for both batch and plug flow systems. In subsequent work, we employed reaction schemes to optimize the yields of products from selective hydrogenations of HAH in isopropanol solvent and in the presence of liquid water. Reaction schemes consisting of 7, 9, and 11 steps were examined to describe the rates of formation of the observed products and reaction intermediates for hydrogenation of HAH over Ru and Pd catalysts, and a 3-step scheme was studied over Cu catalysts. Rate constants and activation energies were calculated using these reaction schemes, and we then apply these reaction schemes to explore the effects of water addition on the hydrogenation pathways. The effects of water addition to isopropanol (IPA) solvents on the hydrogenation of HAH were markedly different over Pd, Ru, and Cu catalysts. Over the Pd catalyst, the addition of water to IPA increased hydrogenation rates and promoted hydrogenation of furan rings. The addition of water to IPA yielded significant carbon losses over the Ru catalyst, and slowed hydrogenation steps over Cu, while significantly inhibiting hydrogenation of the ketone group. This behavior opened routes toward increased production rates of PHAH=O (a partially hydrogenated form of HAH containing a C=O bond), a product in which the diene groups of the furan rings were not hydrogenated. Addition of water also allowed increased feed concentrations of HAH that were previously not possible in pure IPA solvents.
09 BIOMASS FUELS↗
Graphene U-Net v1
Graphene U-Net is a library that provides a simplified platform for training deep neural networks for the task of microscopy image segmentation. It contains functions and classes that make the process of training a neural network simple such that non-ML experts can train and evaluate models on their own datasets. It uses Pytorch as a backend and can run on both CUDA-enable GPUs and CPUs. It contains the main library file Microscopy_Unet.py as well as unet.py which contains the UNET model used for this software. This can be replaced with any other fully convolutional deep learning architecture with relative ease.
Sadre, Robbie↗
Regression models using shapes of functions as predictors
Functional variables are often used as predictors in regression problems. A commonly used parametric approach, called scalar-on-function regression, uses the $\mathbb L^2$ inner product to map functional predictors into scalar responses. This method can perform poorly when predictor functions contain undesired phase variability, causing phases to have disproportionately large influence on the response variable. One past solution has been to perform phase–amplitude separation (as a pre-processing step) and then use only the amplitudes in the regression model. In this paper, we propose a more integrated approach, termed elastic functional regression model (EFRM), where phase-separation is performed inside the regression model, rather than as a pre-processing step. This approach generalizes the notion of phase in functional data, and is based on the norm-preserving time warping of predictors. Due to its invariance properties, this representation provides robustness to predictor phase variability and results in improved predictions of the response variable over traditional models. We demonstrate this framework using a number of datasets involving gait signals, NMR data, and stock market prices.
97 MATHEMATICS AND COMPUTING↗
Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain
Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Elastomeric Nanocomposite with Solvent‐Free, One Step, In Situ Shear Exfoliation of Graphite to Graphene
A graphene nanoflake (GNF)‐enhanced elastomeric nanocomposite (G‐EMC) is fabricated following an innovative, cost‐effective, single‐step, in situ shear exfoliation (ISE) method from low‐cost bulk material, graphite, where uniform mixing happens simultaneously within the elastomer matrix. Electron microscopy, atomic force microscopy, and photo‐induced force microscopy results show good dispersion of GNFs with exfoliation to a few layers and uniform distribution in the elastomer matrix. X‐ray photoelectron spectroscopy analysis shows less than 1% oxygen‐containing functional groups/impurity, enhanced bonding through the formation of edge sites as fracture occurs across the GNF basal plane, and pi‐pi interactions with newly exfoliated planar basal plane surfaces of the GNFs. Raman spectroscopy results confirm the formation of GNFs with only a few layers of graphene formed by the ISE process. Fabricated 10 wt.% G‐EMC nanocomposites show a 400%–500% increase in strength and fracture toughness. And 35 wt.% G‐EMCs provide an electrical conductivity of 25.64 S m −1 and a sensor gauge factor of 45. The resulting intrinsic piezo resistivity of the fabricated nanocomposite has been exploited to fabricate a multi‐functional wired and wireless sensor for detecting different body movements, speech, human vital functions, solvents, and biomolecules.
36 MATERIALS SCIENCE↗
Influence of Oxygen Uptake on Pitch Carbon Fiber
Carbon fiber precursor materials, such as polyacrylonitrile, pitch, and cellulose/rayon, require thermal stabilization to maintain structural integrity during conversion into carbon fiber. Thermal stabilization mitigates undesirable decomposition and liquification of the fibers during the carbonization process. Generally, the thermal stabilization of mesophase pitch consists of the attachment of oxygen-containing functional groups onto the polymeric structure. In this study, the oxidation of mesophase pitch precursor fibers at various weight percentage increases (1, 3.5, 5, 7.5 wt%) and temperatures (260, 280, 290 °C) using in situ differential scanning calorimetry and thermogravimetric analysis is investigated. The results are analyzed to determine the effect of temperature and weight percentage increase on the stabilization process of the fibers, and the fibers are subsequently carbonized and tested for tensile mechanical performance. Finally, the findings provide insight into the relationship between stabilization conditions, fiber microstructure, and mechanical properties of the resulting carbon fibers.
36 MATERIALS SCIENCE↗