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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

SPACE: 3D parallel solvers for Vlasov-Maxwell and Vlasov-Poisson equations for relativistic plasmas with atomic transformations

A parallel, relativistic, three-dimensional particle-in-cell code SPACE has been developed for the simulation of electromagnetic fields, relativistic particle beams, and plasmas. In addition to the standard second-order Particle-in-Cell (PIC) algorithm, SPACE includes efficient novel algorithms to resolve atomic physics processes such as multi-level ionization of plasma atoms, recombination, and electron attachment to dopants in dense neutral gases. SPACE also contains a highly adaptive particle-based method, called Adaptive Particle-in-Cloud (AP-Cloud), for solving the Vlasov-Poisson problems. It eliminates the traditional Cartesian mesh of PIC and replaces it with an adaptive octree data structure. The code's algorithms, structure, capabilities, parallelization strategy, and performance have been discussed. Additionally, typical examples of SPACE applications to accelerator science and engineering problems are described.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure

Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.

4K-TMA↗
DOE OSTI2025

A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta

The choanoflagellate Salpingoeca rosetta exemplifies the capacity of marine microeukaryotes to integrate environmental cues into their life histories. Some of the cues that S. rosetta detects are lipids from their bacterial prey that induce the development of multicellular colonies called rosettes. In the aquatic environments where S. rosetta would encounter bacterial cues, microbial communities gain refuge and food from algae. For example, microbes in coastal environments benefit from macroalgae that annually release ∼10 14 g of carbon, primarily in the form of polysaccharides that comprise ∼80% of dissolved organic carbon in surface waters. Despite the ecological impact of algae and historical descriptions of choanoflagellates attached to algae, the influence of algae on choanoflagellate life history transitions has remained unexplored. Here, we report that porphyran, a polysaccharide produced by the red macroalga Porphyra umbilicalis, induces multicellular development in S. rosetta. We first noticed this response when S. rosetta formed multicellular rosette colonies while growing in media prepared from P. umbilicalis, even though rosette-inducing bacteria were absent. By biochemically purifying extracts of P. umbilicalis, we identified porphyran as the rosette-inducing factor. This response provides a biochemical insight that indicates algal polysaccharides may serve as cues to mediate associations between choanoflagellates and algae. Moreover, this observation complements evidence from environmental and geochemical studies that show the impact that algae have exerted on the ecology and evolution of eukaryotes, including a rise in algal productivity during the origin of animals, the closest living relatives of choanoflagellates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Enhance the performance of organic solar cells by nonfused ring electron acceptors bearing a pendent perylenediimide group

A new nonfused ring electron acceptor PDI-DO-2F is designed and synthesized by attaching perylenediimide (PDI) unit as a pendent group to the central donor core. Compared with the control molecule DO-2F, the introduction of PDI lateral substituent can greatly enhance the solubility and decrease the crystallinity of the resulted acceptor. The PBDB-T:PDI-DO-2F blend film exhibits a much better morphology with higher and more balanced carrier mobility in contrast to PBDB-T:DO-2F one. PDI-DO-2F based organic solar cells (OSCs) give a power conversion efficiency (PCE) of 11.78%, higher than DO-2F based ones (9.82%). Furthermore, PDI-DO-2F based OSCs shows a ΔE non-rad value of 0.23 eV, which is significantly lower than the DO-2F based ones (0.28 eV). More importantly, the addition of PDI-DO-2F as the third component to the PBDB-T:DO-2F binary system can optimize the morphology of blend films and improve the shelf stability of devices. Finally, the PBDB-T:DO-2F:PDI-DO-2F based ternary OSCs achieve a higher PCE of 13.82%.

14 SOLAR ENERGY↗
DOE OSTI2025

Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mt), is one of the deadliest infectious diseases. The rise of multidrug-resistant strains represents a major public health threat, requiring new therapeutic options. Bacterial aminoacyl-tRNA synthetases (aaRS) have been shown to be highly promising drug targets, including for TB treatment. These enzymes play an essential role in translating the DNA gene code into protein sequence by attaching specific amino acid to their cognate tRNAs. They have multiple binding sites that can be targeted for inhibitor discovery: amino acid binding pocket, ATP binding pocket, tRNA binding site and an editing domain. Recently we reported several high-resolution structures of M. tuberculosis phenylalanyl-tRNA synthetase (MtPheRS) complexed with tRNA Phe and either L-Phe or a nonhydrolyzable phenylalanine adenylate analog. Here, in this study, using Nucleic Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) we identified fragments that bind to MtPheRS and we determined crystal structures of their complexes with MtPheRS/tRNA Phe . All the binders interact with the L-Phe amino acid binding site. The analysis of interactions of the new compounds combined with adenylate analog structure provides insights for the rational design of antituberculosis drugs. The 3 ' arm of the tRNA Phe in all the structures was disordered with exception of one complex with D-735 compound. In this structure the 3' CCA end of the acceptor stem is observed in the editing domain of MtPheRS providing insights regarding the post-transfer editing activity of class II aaRS.

Gade, Priyanka [Univ. of Chicago, IL (United State↗
DOE OSTI2022

Electronic interactions and stability issues at the copper-graphene interface in air and in alkaline solution under electrochemical control

A micro-electrochemical cell is sealed with a polymer-free single-layer graphene (SLG) membrane to monitor the stability of Cu nanoparticles (NPs) attached to SLG, as well as the interfacial electronic interactions between Cu NPs and SLG both in air and in a mildly alkaline aqueous solution under electrochemical control. A combination of techniques, including in-situ Kelvin probe force microscopy (KPFM) and ex-situ electron microscopy, are applied. When Cu NPs are metallic at cathodic potentials, there is a relatively bias-independent offset in the SLG work function due to charge transfer at the Cu-SLG contact. When Cu NPs are oxidized at anodic potentials, on the other hand, the work function of SLG also depends on the applied bias in a quasi-linear fashion due to electrochemical gating, in addition to charge transfer at the CuOx-SLG contact. Furthermore, Cu NPs were found to oxidize and detach from SLG when kept under anodic potentials for a few hours, whereas they remain adhered to SLG at cathodic potentials. This is attributed to water intercalation at the CuO-SLG interface associated with the enhanced hydrophilicity of positively polarized graphene, as supported by the absence of Cu detachment following oxidation by galvanic corrosion in air.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

An evaluation of the demand response potential of integrated dynamic window and HVAC systems

Demand response (DR) increases the flexibility and reliability of the electricity grid as use of intermittent renewable energy sources increases. HVAC and envelope DR measures present the largest aggregate energy and peak demand savings potential of all commercial building end uses because their net demand savings occur during critical peak demand periods. Controllable envelope measures include switchable electrochromic windows, operable window attachments such as outdoor louvers, roller shades, and awnings, as well as other innovative facade technologies that can modulate both solar heat gain and daylight admission over a broad solar-optical range. This study evaluated the technical potential of DR-enabled dynamic windows to reduce critical peak demand for a prototypical medium office building situated in all 16 U.S. climates. Model predictive control (MPC) algorithms were designed to minimize electricity cost in daylit perimeter office zones through control of an electrochromic window with and without HVAC thermostat setpoint control. Conventional and time-of-use rates were used to shape the degree of DR. Median annual peak demand savings with window and thermostat control across all climate zones were 24.3 kW (4.4 W/m 2 ) per building or 15.9 W/m 2 for non-north perimeter zones. Resource adequacy at the whole building level was estimated to be 13.1 to 43.4 $/kW per year over the 30-year life of the installation. Co-benefits were increased energy efficiency, and reduced electricity cost and emissions. Visual and thermal comfort requirements were met at all times. Dynamic facades controlled by MPC have substantial technical potential for DR across all U.S. climates and warrant serious consideration for inclusion in DR portfolios.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Winds of fortune? Understanding the geographic, sociodemographic, and temporal distribution of benefit mechanisms from land-based wind projects in the United States

Despite decades of research on factors shaping local responses to wind development, there is relatively little known about benefit mechanisms (e.g., agreements, funds, donations) used by developers in the U.S. land-based wind sector. To address this gap, we collected benefit mechanism data across all current utility-scale land-based wind projects installed between 1982 and 2024 (n = 1047), finding that just under one-third of projects had a benefit mechanism attached to them. We find the use of benefit mechanisms has become more common over time, is associated with larger projects, and varies by region. In terms of host community characteristics, the use of benefit mechanisms is associated with characteristics like higher education level, higher percent white, higher percent Republican, higher decision-making capacity, lower unemployment rate, and higher poverty rate. Building on a theoretical framework of purposes, we discuss what these findings could suggest about the motivations driving developers' use of these mechanisms, such as increasing local acceptance of a wind project or supporting distributive fairness. This first-of-its-kind study builds a comprehensive understanding of how benefit mechanisms have been used in the U.S. wind industry throughout its history, which can inform future approaches to benefit-sharing across sectors.

17 WIND ENERGY↗
DOE OSTI2023

Enhanced thermal reliability and performance of calcium chloride hexahydrate phase change material using cellulose nanofibril and graphene nanoplatelet

In recent years, thermal energy storage (TES) has gained attention for its role in enhancing renewable energy solutions and sustainable energy consumption. The usage of strontium chloride hexahydrate (SCH), graphene nanoplatelet (GNP), and cellulose nanofibril (CNF) additives were investigated to enhance the performance of calcium chloride hexahydrate (CCH) based on the melting/solidification behavior for TES applications. In this work, we develop a promising phase-change-material (PCM) formulation by introducing these additives that reduce supercooling, improve the thermal conductivity and stabilizing the energy storage capacity of CCH. Rheological characterizations demonstrated that the addition of 1 wt% of CNF into CCH produced the required improvement in viscosity and boosted solid-like rheological behavior. Structural characterizations show a physical mixing of the materials within the PCM composites. Our observations show that the amphiphilicity of CNF enables the surface attachment to GNP via hydrophobic interactions providing effective dispersion of GNP throughout the PCM composite. The addition of a nucleating agent, SCH decreased the degree of supercooling of ~20 g of CCH from >20 °C to 3 °C at a cooling rate of 5 °C/min. Thermal characterization showed the resulting PCM composite has a latent heat of melting of 186 Jg -1 , phase change temperature of 32 °C, and stable thermal properties after being subjected to 70 melt-freeze cycles. Adding CNF and GNP to pure CCH increased its thermal conductivity by 76 %. The high thermal conductivity of GNP and its effective dispersion by CNF is responsible for this enhancement. The study highlights the use of biodegradable nanocellulose for the preparation of sustainable PCM composites with improved performance. In conclusion, these PCM composites are scalable, they have potential to increase energy efficiency and revolutionalize the heating/cooling applications in buildings and other TES systems.

25 ENERGY STORAGE↗
DOE OSTI2021

Facet-specific oxidation of Mn(II) and heterogeneous growth of manganese (oxyhydr)oxides on hematite nanoparticles

It is recognized that different facets of minerals vary distinctively in their chemical reactivity with aqueous solutions. However, detailed molecular and atomistic understandings of these phenomena are relatively limited. This study investigated the interaction of aqueous Mn2+ and dissolved oxygen on various facets of two morphology-types of iron oxide (hematite) nanocrystals. These interactions result in the oxidation of manganese and the heterogeneous nucleation and growth of Mn(II)/Mn(III), and Mn(III) oxides. The nanoscale morphology and atomic structure of the manganese oxide products were characterized in detail. Our results, for the first time, directly demonstrate the facet-dependent oxidation of Mn 2+ and nucleation of Mn(II/III) oxides, followed by their epitaxial growth on hematite. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and electron diffraction measurements reveal the growth of MnOx nanowires on {012} facets of both hematite nanoplates (HNP) and hematite nanocubes (HNC), while the basal {001} facets on the HNP particles do not produce precipitates. The average oxidation state of the MnO x on HNP and HNC determined using electron energy-loss spectroscopy (EELS) show that both Mn(II) and Mn(III) are present. The facet-dependent oxidation of Mn 2+ may be attributed to adsorption-induced electron transfer (ET), and hematite {001} facets generally exhibiting weaker ability in the uptake of ions relative to {012} facets, and the bulk ET from {012} to {001} facets through the conduction band of hematite. Nevertheless, the mineral composition and growth mechanisms of MnOx catalyzed by HNP and HNC are similar. High-resolution TEM analysis reveals the presence of both hausmannite and manganite on HNP and HNC. The nanoscale observations and thermodynamic considerations indicate that the growth mechanisms/processes of MnO x include heterogeneous nucleation of hausmannite nanoparticles, crystallization by particle attachment, transformation from hausmannite to manganite, and self-catalyzed MnO x growth. It is possible that all of these processes are concurrent. The crystallographic relationship between the heterogeneously formed manganite with hematite, which has not been reported before, proves that hematite provides reaction sites and functions as an atomic template for the formation of MnO x nanowires. These findings advance our understanding of the redox chemistry and heterogeneous growth of minerals as controlled by the surficial structure of the substrate mineral. This has important geochemical implications as the catalytic growth of less common, highly reactive phases like MnO x are known to be consequential in complex natural and anthropogenic environments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Functional variability in specific root respiration translates to autotrophic differences in soil respiration in a temperate deciduous forest

CO 2 release from forest soils (R s ) is a prominent flux in the global carbon cycle. Rs is derived from roots (autotrophic respiration, R a ) and microbial (heterotrophic) respiration and is highly dynamic, as it depends on edaphic and environmental conditions as well as root functional traits and microbial community composition. It is unclear how root functional traits affect root and microbial respiration rates; however, their consideration may help parse out the relative contributions of root and microbial respiration to R s . At a temperate forest site, root systems of 3–4 functional root orders and their surrounding surface soil were carefully excavated and placed into custom trays designed to repeatedly measure R s in situ on eight temperate tree species that varied in their root functional strategies and mycorrhizal affinity. R s was measured bi-weekly to monthly for nearly one year using a custom chamber attached to a gas exchange system. R s varied over time, ranging from 0.3 to 12 µmol m -2 s -1 . Comparable root systems of the same species were excised from the soil and specific root respiration rates (R r ) were measured. Rr ranged from 2.5 to 9.0 nmol g -1 s -1 and was negatively correlated with root tissue density and positively related to root tissue nitrogen concentration. Using R r to estimate R a , we estimate that R a accounts for <10%, on average 2–3%, of R s for individual root systems (averaging 1.2 g dry biomass) housed in surrounding soil (average 1.3 kg dry mass) in situ; thus, Ra was roughly 20 times greater than Rh per unit mass. The contribution of R a peaked in the fall and coincided with leaf senescence of the forest canopy. A soil-sterilizing experimental treatment designed to help isolate R a in situ reduced bacterial biomass and shifted fungal community composition, but there was no reduction in Rs of the in-situ root-soil tray systems. The relative R a to R s ratio increased with root functional strategies characterized by greater specific root length and tip abundance, but also to greater root tissue density. The ratio of R a to R s also increased with warmer soil temperatures and decreased slightly with increasing soil moisture. We discuss how incorporating root functional traits as modulators of the autotrophic contribution to R s could be considered when modeling total soil CO 2 efflux from forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

An engineered lactate oxidase based electrochemical sensor for continuous detection of biomarker lactic acid in human sweat and serum

Lactate levels in humans reveal intensity and duration of exertion and provide a critical readout for the severity of life-threatening illnesses such as pediatric sepsis. Using the lactate oxidase enzyme (Lox) from Aerococcus viridians, we demonstrated its functionality for lactate electrochemical sensing in physiological fluids in a lab setting. The structure and dynamics of LOx were validated by crystallography, X-ray scattering, and hydroxyl radical protein footprinting. This provided a validated protein template for understanding and designing an enzyme-based electrochemical sensing elements. Using this template, LOx enzyme variants were generated and compared. Comparison of the variants demonstrates that one exhibits effective lactate sensing at significantly reduced operating voltages. Additionally, we demonstrate that the four hexahistidine-tags on each enzyme tetramer are sufficient for immobilization to create a durable, functional sensor, with no need for a covalent attachment, enabling self-immobilization and eliminating the need for additional immobilization steps. The functionality of the LOx enzyme variants was verified at physiological lactate concentrations in both human serum (0–4 mM) and artificial sweat (0–100 mM) using 3-electrode setups for analysis of the three variants in parallel. Accuracy of measurement in both artificial sweat and human serum were high. Employing a microfluidic flow cell, we successfully monitored varying lactate levels in physiological fluids continuously over a 2h period. Overall, this optimized LOx enzyme, which self-immobilizes onto gold sensing electrodes, facilitates efficient and reliable lactate detection and continuous monitoring at reduced operating voltages suitable for further development towards commercial use.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Data-driven enhancement of coherent structure-based models for predicting instantaneous wall turbulence

Predictions of the spatial representation of instantaneous wall-bounded flows, via coherent structure-based models, are highly sensitive to the geometry of the representative structures employed by them. In this study, we propose a methodology to extract the three-dimensional (3-D) geometry of the statistically significant eddies from multi-point wall-turbulence datasets, for direct implementation into these models to improve their predictions. The methodology is employed here for reconstructing a 3-D statistical picture of the inertial wall coherent turbulence for all canonical wall-bounded flows, across a decade of friction Reynolds number (Re T ). These structures are responsible for the Re T -dependence of the skin-friction drag and also facilitate the inner-outer interactions, making them key targets of structure-based models. The empirical analysis brings out the geometric self-similarity of the large-scale wall-coherent motions and also suggests the hairpin packet as the representative flow structure for all wall-bounded flows, thereby aligning with the framework on which the attached eddy model (AEM) is based. The same framework is extended here to also model the very-large-scaled motions, with a consideration of their differences in internal versus external flows. Implementation of the empirically-obtained geometric scalings for these large structures into the AEM is shown to enhance the instantaneous flow predictions for all three velocity components. Finally, an active flow control system driven by the same geometric scalings is conceptualized, towards favourably altering the influence of the wall coherent motions on the skin-friction drag.

42 ENGINEERING↗
DOE OSTI2021

Microscopic ejecta measurements from hypervelocity impacts on aluminum and powdered regolith targets

Meteoroids and space debris pose a two-fold threat to spacecraft due to the risk of both mechanical damage from the impact and electrical damage from the impact-generated plasma, which produces electromagnetic emissions. Analysis of impact products, however, has the potential to provide useful information about planetary rings and small solar system bodies, such as asteroids and comets. Understanding the plasma dynamics and radiation mechanism is essential to addressing the impact threat and extracting science data from impacts. Charge attachment to condensed-phase debris may lead to a dusty plasma under certain conditions, so interpreting hypervelocity impacts requires knowledge of both the nature of the plasma and of the ejecta. We address the latter with measurements of the microscopic ejecta distribution produced by light gas gun impacts on solid aluminum and powdered regolith simulant targets. We examine both the size and shape of the ejecta using thin-film witness plates and find that the size distributions of microscopic ejecta follow power laws. Observations from the powdered regolith simulant match well with disruption experiments of solid basalt, while measurements from the aluminum impacts diverge from extrapolations based on studies of macroscopic debris. Analysis of the ejecta shape shows a transition from smooth to irregularly shaped ejecta at the material grain size, and the shape of debris may provide insight on the phase of the ejected material. Finally, based on our results, we predict a significant number of secondary impacts on plasma sensors due to ejecta, even at considerable distance from the target, supporting the hypothesis that charged dust affects plasma measurements in the ejecta curtain.

42 ENGINEERING↗
DOE OSTI2022

Automated bubble analysis of high-speed subcooled flow boiling images using U-net transfer learning and global optical flow

Capturing and analyzing the bubble dynamics is crucial to improving the understanding of boiling heat transfer mechanisms and predicting boiling heat transfer coefficient and boiling crisis. High speed video (HSV) imaging has been used for decades towards this end. Still, there is no universal approach to quantitatively analyze bubble dynamics from HSV images. In this study, we propose a data-driven post-processing approach to segment, track, and identify wall-attached vapor bubbles from HSV images of the boiling process in subcooled flow conditions. Firstly, we employ a transfer learning framework with a U-Net-based convolution neural network (CNN) architecture to detect and segment bubbles in HSV images of diverse contrast and surface texture using very little data (e.g., 10 images) for training. Then, we evaluate the trained CNN model with 100 ground-truth images, and the validation results show that the model accuracy and precision in detecting the optical footprint of bubbles are higher than 90%. Finally, we suggest a criterion to identify a condensing bubble based on the divergence of the bubble displacement, which is calculated from sequential segmented bubble images using a global optical flow code. Using this combination of machine learning and optical flow, we can identify nucleation sites and track the growth of bubbles nucleating at each site to quantify nucleation site density, nucleation frequency, and other fundamental boiling parameters. The proposed system is validated using results obtained on a special heater, which enables both infrared (IR) thermometry and HSV imaging on a metallic surface. We compare the fundamental boiling parameters obtained by the two different diagnostics. The results show good agreement. In conclusion, the difference between the measurements of nucleation site density, averaged nucleation frequency, and averaged growth time performed with the two techniques is always within ± 20% and mostly ± 10% of the values measured with IR thermometry.

42 ENGINEERING↗
DOE OSTI2020

Conversion of Loblolly pine biomass residues to bio-oil in a two-step process: Fast pyrolysis in the presence of zeolite and catalytic hydrogenation

In this work, Loblolly pine biomass residue was converted to bio-oil in a two-step process, consisting of 1) fast pyrolysis in the presence of zeolite ZSM-5 as a catalyst to produce pyrolysis oil, 2) hydrogenation of pyrolysis oil using formic acid as the hydrogen source in presence of Ru/activated carbon catalyst. Pyrolysis oils were analyzed by 13 C, 31 P and HSQC-NMR and the results revealed that the zeolite-induced catalytic fast pyrolysis process led to effective demethoxylation, producing more catechol and p-hydroxy-phenyl hydroxyl groups in the bio-oils, resulting in a decrease in the methoxyl group content by about 85 % and rich aromatic structures in the pyrolysis oils. The properties of pyrolysis oil with and without zeolite were in the bio-oil range. Hydrogenated pyrolysis oil showed that 79 % of the aromatic protons are eliminated and 87 % of protons are aliphatic in nature, with no oxygen attached to the α-carbon.

09 BIOMASS FUELS↗
DOE OSTI2021

Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, including a catalytic domain and carbohydrate binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our ML results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.

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

Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects

Acetylcholinesterase (EC 3.1.1.7), a key acetylcholine-hydrolyzing enzyme in cholinergic neurotransmission, is present in a variety of states in situ, including monomers, C-terminally disulfide-linked homodimers, homotetramers, and up to three tetramers covalently attached to structural subunits. Could oligomerization that ensures high local concentrations of catalytic sites necessary for efficient neurotransmission be affected by environmental factors? Using small-angle X-ray scattering (SAXS) and cryo-EM, we demonstrate that homodimerization of recombinant monomeric human acetylcholinesterase (hAChE) in solution occurs through a C-terminal four-helix bundle at micromolar concentrations. We show that diethylphosphorylation of the active serine in the catalytic gorge or isopropylmethylphosphonylation by the R P enantiomer of sarin promotes a 10-fold increase in homodimer dissociation. We also demonstrate the dissociation of organophosphate (OP)-conjugated dimers is reversed by structurally diverse oximes 2PAM, HI6, or RS194B, as demonstrated by SAXS of diethylphosphoryl-hAChE. However, binding of oximes to the native ligand-free hAChE, binding of high-affinity reversible ligands, or formation of an S P -sarin-hAChE conjugate had no effect on homodimerization. Dissociation monitored by time-resolved SAXS occurs in milliseconds, consistent with rates of hAChE covalent inhibition. OP-induced dissociation was not observed in the SAXS profiles of the double-mutant Y337A/F338A, where the active center gorge volume is larger than in wildtype hAChE. These observations suggest a key role of the tightly packed acyl pocket in allosterically triggered OP-induced dimer dissociation, with the potential for local reduction of acetylcholine-hydrolytic power in situ. Computational models predict allosteric correlated motions extending from the acyl pocket toward the four-helix bundle dimerization interface 25 Å away.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗