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At least 487 records · Page 27

Mechanism and dynamics of fatty acid photodecarboxylase

Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geophysical survey associated with NEON AOP survey, East River, CO 2018

The package contains data layers developed and used in Falco et al. 2024: “EcoImaging: Advanced Sensing to Investigate Plant and Abiotic Hierarchical Spatial Patterns in Mountainous Watersheds". The package is part of the DOE Watershed Function Science Focus Area (SFA) project and includes geophysical measurements collected at the East River, Colorado, in conjunction with the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) survey conducted in June 2018. This dataset provide soil geophysical information and were used to investigate soil-plant relationships. The dataset consists of: - NEON_2018_EMI_survey.zip: the electromagnetic induction (EMI) survey as shape-file; - NEON_plot_TDR.csv: plot‑level data from Time‑Domain Reflectometry (TDR) measurements, providing: * volumetric water content (VWC) in percent (%); * soil temperature in degrees Celsius (°C); - file level metadata (flmd.csv) - data dictionary (dd.csv) file This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

Early animal evolution: emerging views from comparative biology and geology

The Cambrian appearance of fossils representing diverse phyla has long inspired hypotheses about possible genetic or environmental catalysts of early animal evolution. Only recently, however, have data begun to emerge that can resolve the sequence of genetic and morphological innovations, environmental events, and ecological interactions that collectively shaped Cambrian evolution. Assembly of the modern genetic tool kit for development and the initial divergence of major animal clades occurred during the Proterozoic Eon. Crown group morphologies diversified in the Cambrian through changes in the genetic regulatory networks that organize animal ontogeny. Cambrian radiation may have been triggered by environmental perturbation near the Proterozoic-Cambrian boundary and subsequently amplified by ecological interactions within reorganized ecosystems.

Non-NASA Center↗

A unifying framework for systems modeling, control systems design, and system operation

Current engineering practice in the analysis and design of large-scale multi-disciplinary control systems is typified by some form of decomposition- whether functional or physical or discipline-based-that enables multiple teams to work in parallel and in relative isolation. Too often, the resulting system after integration is an awkward marriage of different control and data mechanisms with poor end-to-end accountability. System of systems engineering, which faces this problem on a large scale, cries out for a unifying framework to guide analysis, design, and operation. This paper describes such a framework based on a state-, model-, and goal-based architecture for semi-autonomous control systems that guides analysis and modeling, shapes control system software design, and directly specifies operational intent. This paper illustrates the key concepts in the context of a large-scale, concurrent, globally distributed system of systems: NASA's proposed Array-based Deep Space Network.

systems modeling↗

Utilizing a Dynamic Segmentation Convolutional Neural Network for Microstructure Analysis of Additively Manufactured Superalloy 718

Additive manufacturing (AM) is revolutionizing almost all industries through the production of intricate geometries previously prohibited by cost or machinability. Ni-based superalloys form a primary alloy class for high temperature applications in the petrochemical, aerospace, and nuclear industries because of their intrinsic resistance to creep and the ability to heat treat the superalloy for high strength. Despite these attractive properties, the extreme work hardening of Ni-based superalloys makes traditional manufacturing of complex shapes difficult and thus, these alloys are an attractive target for AM. Superalloy 718 was chosen as an example superalloy because of the wide variety of precipitates that can form within its composition space from the repetitive heating and cooling cycles of the AM process. The precipitates and other microstructure features, such as grain boundaries and dislocations, will dictate the mechanical properties and thus, there is an extensive challenge to characterize the size, number density, composition, and volume fraction of each microstructural feature from AM fabrication using analytical electron microscopy. This work focused on the application of a pixel-wise classification machine learning (ML) model called a dynamic segmentation convolutional neural network (DSCNN) to identify the microstructural features of an as-fabricated additively manufactured superalloy 718.

Taller, Stephen↗

Using dorsal surface for individual identification of dairy calves through 3D deep learning algorithms

Advances in machine learning techniques have allowed the development of computer vision systems (CVS) that can accurately predict several phenotypes of interest for livestock operations. In this context, 3D images taken from a top-down view are particularly useful for estimating body condition score, growth development, and body biometrics in cattle. Frequently, such CVS rely on identification (ID) systems, such as electronic tags, as a way to match animal ID and the predicted phenotype. However, the same 3D images used to predict body weight and other animal biometrics could be adopted for animal recognition as well. Such alternative would optimize CVS to recognize animal ID and monitor growth development simultaneously while leveraging the same hardware infrastructure. Furthermore, this strategy could be used to recognize animals with similar color patterns. Nonetheless, growing animals are continuously changing body shape, which could limit its use as an invariant feature for pattern recognition. Thus, the objectives of this study were: (1) to compare algorithms for different 3D object representations to identify individual animals; and (2) to evaluate how short-term changes in body shape due to animal growth affect the predictive performance of these algorithms. For objective 1, the algorithms were trained (n = 4,558) and tested (n = 1,139) using images from 38 Holstein calves. For objective 2, we designed three different experiments using images (n = 2,347) from five Holstein calves taken over six weeks during their growing period, always training and testing on different weeks. Each experiment evaluated how changing a different parameter of the image capturing procedure affected the predictive ability of the trained algorithms. In the first experiment, we varied the total number of images per animal in the training set; in the second experiment, we varied the number of weeks while keeping a fixed number of images in the training set; and in the third experiment, we skipped weeks between images in the training and test sets. The F 1 score for objective (1) was up to 0.804 when testing with the last frames of each video, and up to 0.959 when using random frames for testing. For objective (2), the F 1 score was up to 0.947 for the first experiment when using 130 images per animal; up to 0.979 for the second experiment when using all five weeks; and up to 0.917 when not skipping weeks between training and testing. In conclusion, these results show that deep learning algorithms can be used to identify individual animals through their dorsal area 3D surfaces, and, from our experiments using calves in their growing period, that they are robust enough to account for changes in body shape and size, making them a promising tool for animal recognition during growth.

3D neural networks↗

How to see hidden patterns in metamaterials with interpretable machine learning

Machine learning models can assist with metamaterials design by approximating computationally expensive simulators or solving inverse design problems. However, past work has usually relied on black box deep neural networks, whose reasoning processes are opaque and require enormous datasets that are expensive to obtain. Here, in this work, we develop two novel machine learning approaches to metamaterials discovery that have neither of these disadvantages. These approaches, called shape-frequency features and unit-cell templates, can discover 2D metamaterials with user-specified frequency band gaps. Our approaches provide logical rule-based conditions on metamaterial unit-cells that allow for interpretable reasoning processes, and generalize well across design spaces of different resolutions. The templates also provide design flexibility where users can almost freely design the fine resolution features of a unit-cell without affecting the user’s desired band gap.

36 MATERIALS SCIENCE↗

Diabatic Valence-Hole Concept

A global diabatization scheme, based on the “valence-hole” concept, has been previously applied to model webs of avoided crossings that exist in four electronic-state symmetry manifolds of C 2 ( 1 Π g , 3 Π g , 1 Σ u + , and 3 Σ u + ). Here, this model is extended to the electronically excited states of four more molecules: CN ( 2 Σ + ), N 2 ( 3 Π u ), SiC ( 3 Π), and Si 2 ( 3 Π g ). Many strangenesses in the spectroscopic observations (e.g., energy level structure, predissociation linewidths, and radiative lifetimes) for all four electronic state systems discussed here are accounted for by this unified model. The key concept of the model is valence-hole electron configurations: 3σ 2 4σ 1 1π 4 5σ 2 in CN ( 2 Σ + ), 2σ g 2 2σ u 1 1π u 4 3σ g 2 1π g 1 in N 2 ( 3 Π u ), 5σ 2 6σ 1 7σ 2 2π 3 in SiC ( 3 Π), and 4σ g 2 4σ u 1 5σ g 2 2π u 3 in Si 2 ( 3 Π g ), all of which have a triply occupied “valence-core” (i.e., 2σ g 2 2σ u 1 or the equivalent). These valence-hole configurations have a nominal bond order of three or higher and correlate with high-energy separated-atom limits with an np ← ns (n = 2, 3) promotion in one of the atomic constituents. On its way to dissociation, the strongly bound diabatic valence-hole state crosses multiple weakly bound or repulsive states, which belong to electron configurations with a completely filled valence-core. These curve crossings between diabatic potentials result in a network of many avoided crossings among multiple electronic states, analogous to the well-studied electronic structure landscape of ionic-covalent crossings in strongly ionic molecules. In conclusion, considering the unique role of valence-hole states in shaping the global electronic structure, the valence-hole concept should be added to our intuitive framework of chemical bonding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microfluidic, One-Batch Synthesis of Pd Nanocrystals on N-Doped Carbon in Surfactant-Free Deep Eutectic Solvents for Formic Acid Electrochemical Oxidation

One of the grand challenges that impedes practical applications of nanomaterials is the lack of robust manufacturing methods that are scalable, cheap, and environmentally friendly. In this work, we address this challenge by developing a microfluidic approach that produces surfactant-free Pd nanocrystals (NCs) uniformly loaded on N-doped porous carbon in a one-batch process. The deep eutectic solvent (DES) prepared from choline chloride and ethylene glycol was employed as a novel synthesis solvent, and its extended hydrogen networks and abundant ionic species effectively stabilize Pd facets and confine nanocrystal sizes without using surfactants. The microreactors provide faster heat exchange and more uniform mass transport, which in combination with DES produced Pd NCs with better-defined shape and predominately exposed Pd (100) facet. Furthermore, we describe that the N-doped functional groups in porous carbon direct dense and uniform heterogeneous growth of Pd NCs in a one-batch process, thereby eliminating a separate catalyst deposition step that is often involved in conventional synthesis. The Pd NCs in the one-batch-produced Pd/C catalysts exhibited a size distribution of similar to ~13 ± 3.5 nm and a high ESCA of 46.0 m 2 /g and delivered 362 mA/mg for formic acid electrochemical oxidation with improved stability, demonstrating the unique potentials of microfluidic reactors and DES for the controllable and scalable synthesis of electrocatalyst materials for practical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic reaction-induced phase separation in tunable, adaptive covalent networks

A series of catalyst-free, room temperature dynamic bonds derived from a reversible thia-Michael reaction are utilized to access mechanically robust dynamic covalent network films. The equilibrium of the thiol addition to benzalcyanoacetate-based Michael-acceptors can be directly tuned by controlling the electron-donating/withdrawing nature of the Michael-acceptor. By modulating the composition of different Michael-acceptors in a dynamic covalent network, a wide range of mechanical properties and thermal responses can be realized. Additionally, the reported systems phase-separate in a process, coined dynamic reaction-induced phase separation (DRIPS), that yields reconfigurable phase morphologies and reprogrammable shape-memory behaviour as highlighted by the heat-induced folding of a predetermined structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Breeding of microbiomes conferring salt tolerance to plants

Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes’ effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns. Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetically-Switched, Long-Pulse XeCl Laser

Careful shaping of input pulses helps XeCl excimer laser produce lowdivergence, narrow-band light beam. Long-pulse laser achieves narrow-band output by multiple passes of beam through precisely adjusted Fabry-Perot etalons. Pulse-forming network and saturable-inductor switch enable fast pulse rise to peak voltage, followed by long residence at peak.

Pacala, T. J.↗

RIACS

Topics considered include: high-performance computing; cognitive and perceptual prostheses (computational aids designed to leverage human abilities); autonomous systems. Also included: development of a 3D unstructured grid code based on a finite volume formulation and applied to the Navier-stokes equations; Cartesian grid methods for complex geometry; multigrid methods for solving elliptic problems on unstructured grids; algebraic non-overlapping domain decomposition methods for compressible fluid flow problems on unstructured meshes; numerical methods for the compressible navier-stokes equations with application to aerodynamic flows; research in aerodynamic shape optimization; S-HARP: a parallel dynamic spectral partitioner; numerical schemes for the Hamilton-Jacobi and level set equations on triangulated domains; application of high-order shock capturing schemes to direct simulation of turbulence; multicast technology; network testbeds; supercomputer consolidation project.

Oliger, Joseph↗

Tensegrity II. How structural networks influence cellular information processing networks

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Review↗

Tailored Silicone Network Architecture for Ultimate Mechanical Reinforcement

Hydrosilylation cured silicone elastomers are subject to reaction inefficiency, leading to incomplete and non-uniform crosslink networks, restricting the potential of mechanical reinforcement. This work investigates pre-synthesized, functional PDMS architectures as additives to improve ultimate mechanical performance relative to conventional single-step curing. Three custom, functional structures were prepared: a partially crosslinked PDMS scaffold (Structure A), a bottle-brush PDMS (Structure B), and a star-shaped PDMS derived from an MQ resin (Structure C). Rheological characterization was used to identify the ultimate design space and proper stoichiometric ratio for Structure A, and confirm successful formation of all structures for suitable incorporation into a base silicone formulation at 30wt%. Mechanical tests indicated that all three structures increased in ultimate tensile strength relative to their single-step counterparts, with Structure A providing additional improvements to toughness (432 vs. 258 kJ/m3) and ultimate elongation (158 vs. 115%). Furthermore, Structure B remained very soft in the unfilled state, while Structure C provided hardness (23 vs. 18 Shore A) and stiffness (780 vs. 420 kPa Young’s modulus) increases. In silica filled systems, Structure A retained increased strength but reduced elongation, while Structure B indicated strong reinforcement in terms of strength, toughness, and stiffness. Thermal analysis on the cure profiles of these materials suggested that pre-formation of network architectures enable a more complete reaction than a single-step process (15.9 vs. 15.1 J/g). Ultimately, these results indicate that tailoring PDMS architecture before the final cure can improve ultimate mechanical properties via improved network development in silicone elastomers. Furthermore, this work offers a promising strategy for designing higher-performance, more tunable silicone formulations.

36 MATERIALS SCIENCE↗

Adversarial sampling of unknown and high-dimensional conditional distributions

Many engineering problems require the prediction of realization-to-realization variability or a refined description of modeled quantities. In that case, it is necessary to sample elements from unknown high-dimensional spaces with possibly millions of degrees of freedom. While there exist methods able to sample elements from probability density functions (PDF) with known shapes, several approximations need to be made when the distribution is unknown. In this paper the sampling method, as well as the inference of the underlying distribution, are both handled with a data-driven method known as generative adversarial networks (GAN), which trains two competing neural networks to produce a network that can effectively generate samples from the training set distribution. In practice, it is often necessary to draw samples from conditional distributions. When the conditional variables are continuous, only one (if any) data point corresponding to a particular value of a conditioning variable may be available, which is not sufficient to estimate the conditional distribution. This work handles this problem using an a priori estimation of the conditional moments of a PDF. Herein, two approaches, stochastic estimation, and an external neural network are compared for computing these moments; however, any preferred method can be used. The algorithm is demonstrated in the case of the deconvolution of a filtered turbulent flow field. It is shown that all the versions of the proposed algorithm effectively sample the target conditional distribution with minimal impact on the quality of the samples compared to state-of-the-art methods. Additionally, the procedure can be used as a metric for the diversity of samples generated by a conditional GAN (cGAN) conditioned with continuous variables.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Localized Magnetopause Erosion at Geosynchronous Orbit by Reconnection

This study presents observations of magnetopause reconnection and erosion at geosynchronous orbit, utilizing in situ satellite measurements and remote sensing ground‐based instruments. During the main phase of a geomagnetic storm, Geostationary Operational Environmental Satellites (GOES) 15 was on the dawnside of the dayside magnetopause (10.6 MLT) and observed significant magnetopause erosion, while GOES 13, observing duskside (14.6 MLT), remained within the magnetosphere. Combined observations from the THEMIS satellites and Super Dual Auroral Radar Network radars verified that magnetopause erosion was primarily caused by reconnection. While various factors may contribute to asymmetric erosion, the observations suggest that the weak reconnection rate on the duskside can play a role in the formation of asymmetric magnetopause shape. This discrepancy in reconnection rate is associated with the presence of cold dense plasma on the duskside of the magnetosphere, which limits the reconnection rate by mass loading, resulting in more efficient magnetopause erosion on the dawnside.

Hyangpyo Kim↗

Solar thermal power systems point-focusing distributed receiver technology project. Volume 2: Detailed report

The accomplishments of the Point-Focusing Distributed Receiver Technology Project during fiscal year 1979 are detailed. Present studies involve designs of modular units that collect and concentrate solar energy via highly reflective, parabolic-shaped dishes. The concentrated energy is then converted to heat in a working fluid, such as hot gas. In modules designed to produce heat for industrial applications, a flexible line conveys the heated fluid from the module to a heat transfer network. In modules designed to produce electricity the fluid carries the heat directly to an engine in a power conversion unit located at the focus of the concentrator. The engine is mechanically linked to an electric generator. A Brayton-cycle engine is currently being developed as the most promising electrical energy converter to meet near-future needs.

Source record↗