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At least 145 records · Page 8

Evolution and engineering of pathways for aromatic O -demethylation in Pseudomonas putida KT2440

In this study, biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from lignin commonly contain methoxy groups, and O-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Several enzyme families catalyze aromatic O-demethylation, but they are rarely compared in vivo to determine an optimal biocatalytic strategy. Here, two pathways for aromatic O-demethylation were compared in Pseudomonas putida KT2440. The native Rieske non-heme iron monooxygenase (VanAB) and, separately, a heterologous tetrahydrofolate-dependent demethylase (LigM) were constitutively expressed in P. putida, and the strains were optimized via adaptive laboratory evolution (ALE) with vanillate as a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ~1.8x faster than those harboring the heterologous LigM pathway. Enzyme kinetics and transcriptomics studies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, the reductase for vanillate O-demethylase, PP_3494, a global regulator of vanillate catabolism, and fghA, involved in formaldehyde detoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms, yielding a platform strain for efficient O-demethylation of lignin-related aromatic compounds to value-added products.

09 BIOMASS FUELS↗

Toward Enhancing Wastewater Treatment with Resource Recovery in Integrated Assessment and Computable General Equilibrium Models

Sustainable water management is essential to increasing water availability and decreasing water pollution. The wastewater sector is expanding globally and beginning to incorporate technologies that recover nutrients from wastewater. Nutrient recovery increases energy consumption but may reduce the demand for nutrients from virgin sources. We estimate the increase in annual global energy consumption (1,100 million GJ) and greenhouse gas emissions (84 million t CO2e) for wastewater treatment in the year 2030 compared to today’s levels to meet sustainable development goals. To capture these trends, integrated assessment and computable general equilibrium models that address the energy-water nexus must evolve. We reviewed 16 of these models to assess how well they capture wastewater treatment plant energy consumption and GHG emissions. Only three models include biogas production from the wastewater organic content. Four explicitly represent energy demand for wastewater treatment, and eight include explicit representation of wastewater treatment plant greenhouse gas emissions. Of those eight models, six models quantify methane emissions from treatment, five include representation of emissions of nitrous oxide, and two include representation of emissions of carbon dioxide. Our review concludes with proposals to improve these models to better capture the energy-water nexus associated with the evolving wastewater treatment sector.

42 ENGINEERING↗

Modulating Mid-Gap Electronic States Through Site-Selective Modification in B-Pbx/B'-CuyV2O5/CdS Heterostructures for Photocatalytic Hydrogen Evolution

We interfaced ..beta..-Pbx/..beta..'-CuyV2O5 compounds, with varying stoichiometries of precisely positioned Pb-ions (x) and Cu-ions (y) in interstitial sites along a tunnel-structured ?-V2O5 framework, with cysteine-capped CdS (cysCdS) quantum dots (QDs) to yield heterostructured photocatalysts. ..beta..-Pbx/..beta..'-CuyV2O5 compounds exhibit midgap electronic states with orbital contributions from both Cu 3d and stereochemically active Pb 6s states that show distinctive light-initiated reactivity with photoexcited QDs. ..beta..-Pbx/..beta..'-CuyV2O5/CdS heterostructures were prepared by linker-assisted assembly (LAA). Scanning and transmission electron microscopy, energy-dispersive X-ray spectroscopy, and Raman spectroscopy revealed that cysCdS QDs were deposited onto surfaces of ..beta..-Pbx/..beta..'-CuyV2O5 via LAA. HAXPES revealed that the site-selective positioning of Pb-ions and Cu-ions promoted close energetic alignment of the midgap states of ..beta..-Pbx/..beta..'-CuyV2O5 compounds with the valence-band maximum of cysCdS QDs. Transient absorption spectroscopy revealed that photogenerated holes were transferred from CdS QDs to midgap states of ..beta..-Pbx/..beta..'-CuyV2O5 compounds on time scales <50 ps. Finally, photoelectrochemical and photochemical experiments revealed that ..beta..-Pbx/..beta..'-CuyV2O5/CdS heterostructures promoted the photocatalytic reduction of H+ to H2. In photoelectrochemical experiments, under oxidative conditions, for all ..beta..-Pbx/..beta..'-CuyV2O5/CdS heterostructures, H2 was evolved at a Pt counter electrode while a sacrificial donor was oxidized at the heterostructure-functionalized working electrode. In contrast, under reductive conditions, for ..beta..-Pb0.152V2O5/CdS and ..beta..-Pbx/..beta..'-CuyV2O5/CdS heterostructures, H2 was evolved at the working electrode. In photochemical experiments, dispersed ..beta..-Pbx/..beta..'-CuyV2O5/CdS heterostructures promoted the reduction of H+ to H2 under white-light illumination; ..beta..'-Cu0.55V2O5/CdS and ..beta..-Pbx/..beta..'-CuyV2O5/CdS heterostructures, for which midgap states have Cu 3d orbital character, generated 2-fold more H2 than ..beta..-Pb0.152V2O5/CdS heterostructures. Cu-ion insertion thus appends additional acceptor surface states that improve ligand-mediated hole transfer from photoexcited QDs, but such states are intrinsically limited in mediating hole transport to the substrate as a result of the low mobility of holes in narrow Cu 3d-states. Our results reveal that the density and orbital character of midgap states of ..beta..-Pbx/..beta..'-CuyV2O5 compounds, tunable through recently developed site-selective ion insertion strategies, determine efficiencies of charge-transfer and charge-transport mechanisms that underpin photocatalysis.

36 MATERIALS SCIENCE↗

Extreme Thermal Stabilization of Carborane–Cyanate Composites via B–N Dative-Bonded Boroxine Barriers

Enhancing the thermal stability of cyanate ester (CE) resins is crucial for high-temperature aerospace applications. This study elucidates the degradation mechanisms of CE composites reinforced with carborane additives, focusing on the formation of boron–nitrogen (B–N) dative bonds and their role in improving thermal resistance. Using thermogravimetric analysis, we examined char formation and evolved gases at multiple degradation stages. Reaction sequences and char products were characterized via Fourier transform infrared spectroscopy (FTIR), solid-state 13C and 11B NMR, and evolved gas analysis using mass spectrometry and FTIR. The solid-state 11B NMR was instrumental in detecting various boron oxidation states and the formation of B–N dative bonds during decomposition. These bonds facilitate cross-linking in the char phase, enhancing material integrity at elevated temperatures. However, in inert environments, the volatility of boron additives like carborane limits their effectiveness. These findings advance the understanding of CE composite degradation mechanisms and offer critical insights for developing high-temperature-resistant materials for aerospace applications.

Fourier transform infrared spectroscopy↗

Unraveling the Surface Termination and Evolution of Surface States for Electrocatalyst PtSn 4 in Alkaline HER

Semimetal PtSn 4 has been experimentally demonstrated as a promising topological electrocatalyst for the hydrogen evolution reaction (HER) under both acidic and alkaline conditions. While two possible mechanisms have been proposed to explain its activity, the role of its surface states in HER remains unclear. It is indeed in question how the surface states of this alloy evolve as HER proceeds. In this study, we investigate the surface termination that sustains conducting surface states on PtSn 4 , and we track their evolution during HER catalysis. We show that a reconstructed surface with a Sn-poor termination reproduces the scanning tunneling microscopy pattern observed in experiments and sustains a conducting surface. Through phase diagram and geometric structure analysis, we outline the HER profile following the Volmer–Heyrovsky mechanism. As hydrogen atoms adsorb onto the surface, the structure undergoes further reconstruction to an equilibrium phase with a coverage of two hydrides per unit cell. Meanwhile, the surface electronic bands evolve in response to interactions with the adsorbed hydrogen atoms. A hybridization diagram is further proposed for understanding the surface state evolution based on wave function and chemical bonding analyses. While the Pt atoms serve as conventional sites for hydrogen binding, the surface states of PtSn 4 are essential for stabilizing the hydrogen antibonding states via in-phase electronic interactions with the Sn components. This stabilization results in frontier surface bands that are responsible for driving the HER catalysis. Here, our findings provide a detailed description for the direct involvement of surface states on PtSn4 when employed as a catalyst for HER.

catalysts↗

Theoretical Insights into Reaction-Induced Transformation and Tuning of Catalytic Behavior in Heterogenous Catalysis

Reaction-induced transformations in heterogenous catalysis represent diverse phenomena that challenge traditional views of static catalyst surfaces. From surface adsorbate dynamics, atomic rearrangements, to composition and phase transitions, these processes reveal the profound differences between idealized model systems under ultrahigh vacuum and the complex, evolving interfaces that govern real catalytic behaviors under reaction conditions. Here, this perspective reviews recent theoretical efforts to provide atomic-level mechanistic insights into significant reaction-induced transformations and their impact on catalytic activity and selectivity. It underscores the need for an integrated framework that combines predictive simulations with operando characterization to uncover active sites and mechanisms under realistic operating conditions. Achieving this requires accelerating existing simulations to fully capture diverse reaction-induced surface dynamics, enabling scalable and accurate modeling of catalysts as condition-dependent, dynamically evolving systems. Such approaches are critical to bridge the gap between theory and practice, offering a pathway to more impactful and predictive catalyst design.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Impact of Interposer Microstructure on Ionic Transport in Liquid-Phase Bicarbonate Electrolysis

The electrochemical reduction of CO 2 (CO 2 RR) is a potentially scalable approach for converting captured carbon dioxide into value-added products. Conventional gas-phase electrolysis systems can suffer from carbonate crossover, which limits the efficiency of the system. Liquid-phase (bi)carbonate electrolysis using bipolar membrane electrode assemblies (BPMMEA) has emerged as a promising alternative. The interposer layer, a porous mass-transport material between the BPM and the catalyst, is an essential component of the MEA, as it allows evolved CO 2 to reach the catalyst surface for reaction. In the absence of this layer, evolved CO 2 generated by the pH swing process at the BPM can be converted back into (bi)carbonate (CO 2 recapture) due to the high bulk pH. Thus, clear design guidelines are needed to maximize CO 2 conversion, minimize CO 2 recapture in the catholyte, and improve energy efficiency. Here, the transport properties of the interposer are systematically characterized by X-ray tomography and symmetric-cell impedance spectroscopy to quantify porosity, tortuosity, and the resulting MacMullin number. We then examine the correlation between these material properties and the electrolyzer performance. We focus on characterizing two commercial porous membrane filters, mixed cellulose ester (MCE) and poly(ether sulfone) (PES).

CO2 electrolysis↗

Organosilica Nanoparticles

The dynamic field of nanotechnology is continually evolving, with organosilica nanoparticles (OSNPs) standing out as a significant and versatile class of materials. Combining the advantageous properties of organic and inorganic components, OSNPs offer unique capabilities that drive innovation across multiple scientific disciplines. Here, this primer is designed to be an accessible and informative guide for researchers embarking on their journey into the world of organosilica nanoparticles. Whether you want to incorporate OSNPs into your research or seek to understand the latest developments, this primer will provide the foundational knowledge and context needed to navigate this exciting and rapidly evolving field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Lens into the Cu Nanograin by In Situ Vibrational Spectroscopy

Cu-based catalysts are uniquely capable of C-C coupling during electrochemical CO 2 reduction (CO 2 R), yet further mechanistic understanding remains hampered by the lack of spectroscopically resolved descriptors that demonstrate how surface adsorbates emerge and evolve within their catalytic environment. Here, in this study, we correlate in situ surface-enhanced Raman spectroscopy (SERS) and surface-enhanced infrared absorption spectroscopy (SEIRAS) to resolve the potential-dependent dynamics during CO 2 R on Cu nanograin catalysts. By building on previous benchmarking of low overpotential performance and nanograin structural evolution, we offer a diagnostic framework linking vibrational signatures to catalytic function, unveiling which species appear, persist, and turnover as the electrified surface and interfacial environment evolve under bias. The onset of linear CO is marked below -0.45 V, coincident with persistent adsorbed *OH/*O domains beyond the CO 2 R onset. In this context, Cu nanograins serve as a platform to dissect contributions of adsorbate coverage. By carefully dissecting the potential dependence of emergent twin-defect/step CO stretch bands (P1-P2), alongside the prototypical terrace-site CO stretch band (P3), we provide important context for interpreting coupled spectroscopic trends driven by coverage effects and resolve this for the evidently complex nanograin morphology. Together, these observations highlight the intertwined roles of surface stabilization and interfacial flux in steering multicarbon product formation. By directly linking vibrational signatures to catalytic behavior, this work aims to bridge the gap between observation and control and help guide toward a predictive framework of fine-tuned selectivity for CO 2 R.

Fonseca Guzman, Maria V. [University of California↗

Microcanonical Kinetics of Water-Mediated Proton Transfer in 4ABAH + ·(H 2 O) n = 4–6 Clusters (ABA = Aminobenzoic Acid): A Model System for Size-Dependent Relaxation to Ergodic Behavior

Here, we leverage the unique properties of the 4ABAH + · (H 2 O) n clusters (ABA = 4-aminobenzoic acid, n = 4−6) to quantitatively address how a finite, isolated system evolves into an ergodic condition starting from localized arrangements in configuration space. This system adopts two distinct structural isomers in which water molecules cluster around the cationic centers of its two protomers with widely separated positive charge centers. These isomers arise from excess proton attachment to either the acid (O) or amino (N) group on opposite sides of the benzene ring. Both forms are captured and kinetically trapped using cryogenic ion methods and then selectively vibrationally excited through their mutually exclusive IR bands involving NH and OH stretching fundamentals. Because the IR excitation lies below the water binding energy, the system can evolve to explore slow, rare events that lead to the interconversion between the two isomers. The rates of these intracluster reactions are determined by using a pump−probe scheme involving ∼5 ns IR pump and UV probe lasers. The rates occur on the microsecond time scale, leading to steady state populations of the isomers, thus revealing the cluster size-dependent fractionation between the two species at microcanonical equilibrium. The steady state distributions are correlated with the expected trend in the cluster size-dependent reaction energetics, which are in turn consistent with changes in the relative densities of states of the two species. These results thus provide an unusually clear example in which complex, protic-solvent-mediated chemical transformations are captured within a finite system at a precisely determined internal energy.

Rana, Abhijit [Yale Univ., New Haven, CT (United S↗

Ion-Electron Coupling-Driven Redox Behavior in Metal–Organic Frameworks

Redox-active metal–organic frameworks (MOFs) have long been proposed as electronic transport platforms, yet the microscopic origin of their conductivity remains debated. A theoretical demonstration reveals charge transport in a Zn(pyrazole–naphthalene diimide (NDI)) MOF arising not from delocalized band-like states but from redox hopping between discrete linker sites. Using ab initio molecular dynamics simulations combined with electronic structure analysis, we established a direct link among electron injection, structural reorganization, and transport. Electron accumulation proceeds sequentially and site-selectively from imide and carbonyl groups of the NDI core progressively involving pyrazole N atoms at higher reduction states, through a hierarchy of redox-active sites. In contrast, Zn nodes remain essentially redox-inactive, which confirms their structural role. Density-of-states analysis corroborates a transport regime dominated by linker-centered states with evolving p-character upon reduction, resulting in dynamically reconfigured conduction networks. Real-time trajectories reveal anisotropic linker-to-linker electron transfer modulated by counterion coordination. This cooperative ion–electron regime emerges from potential energy surface collapse into a single low-barrier transition (ΔG ‡ ≈ 45 meV), where ionic and electronic motions evolve adiabatically on the same free-energy landscape. Elucidating redox conductivity in Zn(pyrazole–NDI) MOFs provides a theoretical framework for use in neuromorphic computing and related technologies.

Charge transfer↗

Intermittent Criticality Multi‐Scale Processes Leading to Large Slip Events on Rough Laboratory Faults

Abstract We discuss data of three laboratory stick‐slip experiments on Westerly Granite samples performed at elevated confining pressure and constant displacement rate on rough fracture surfaces. The experiments produced complex slip patterns including fast and slow ruptures with large and small fault slips, as well as failure events on the fault surface producing acoustic emission bursts without externally‐detectable stress drop. Preparatory processes leading to large slips were tracked with an ensemble of ten seismo‐mechanical and statistical parameters characterizing local and global damage and stress evolution, localization and clustering processes, as well as event interactions. We decompose complex spatio‐temporal trends in the lab‐quake characteristics and identify persistent effects of evolving fault roughness and damage at different length scales, and local stress evolution approaching large events. The observed trends highlight labquake localization processes on different spatial and temporal scales. The preparatory process of large slip events includes smaller events marked by confined bursts of acoustic emission activity that collectively prepare the fault surface for a system‐wide failure by conditioning the large‐scale stress field. Our results are consistent overall with an evolving process of intermittent criticality leading to large failure events, and may contribute to improved forecasting of large natural earthquakes.

Geochemistry & Geophysics↗

Earth Sciences Are the Model Sciences of the Anthropocene

After 4.5 billion years as a dynamic and evolving planet, Earth today continues to evolve but with new dynamics. Earth scientists writ large have special opportunities and responsibilities to accelerate our understanding of the changes that are transforming our most remarkable home.

Richter, Daniel↗

Monitoring Fracture Hydromechanical Evolution in the Lab and Field Using Unsupervised Metric Learning

Fractures evolve in time through thermal‐hydraulic‐mechanical‐chemical (THMC) processes that alter their long‐range hydraulic transport properties and modify subsurface behavior and activities. The location of subsurface fractures makes it necessary to use remote sensing techniques such as passive or active seismic monitoring for fracture characterization. In this paper, we develop a machine learning approach to monitor the evolution of fracture properties using passive seismic sources in a laboratory setting and using active seismic monitoring from the Sanford Underground Research Facility in Lead, South Dakota, at a depth of 1.25 km in amphibolite rock during stimulation of natural fractures as well as during induced fracturing. The unsupervised metric learning technique applies tandem neural networks (twin (Siamese) or triplet) with contrastive loss and adaptive margins to track slowly varying systems for which class or similarity labels are not available. The approach adopts locality‐sensitive hashing to divide time‐ordered contiguous data into an arbitrary number of pseudo‐classes. Contrastive‐loss training with many hash bins generates an evolving latent‐space trajectory. This approach enables unsupervised metric learning for seismic data stacks under the condition of contiguous state sampling and slowly varying fracture properties. The displacement discontinuity theory provides a mechanistic foundation for the fracture‐dependent trajectories that are related to relaxation of fractures with time‐dependent specific stiffness responding to changes in stress or fluid saturation.

02 PETROLEUM↗

Mineralogical evidence for hydrothermal alteration of Bennu samples

Samples of asteroid (101955) Bennu delivered by the OSIRIS-REx mission offer the opportunity to study pristine planetary materials unchanged by exposure to the terrestrial environment. Here we use a combination of X-ray diffraction and various electron microscopy techniques to explore the detailed mineralogy of Bennu samples and determine the alteration history of the planetesimal protolith from which they originated. The samples consist largely of hydrated sheet-silicate minerals, namely nanoscale serpentine and saponite of varied grain size, which are decorated with micro- to nanoscale Fe-sulfides, magnetite and carbonates. We observe sheet silicates parallel and normal to sulfide surfaces and as inclusions in sulfides; sulfur-rich veins transecting the sheet-silicate matrix; zoned carbonates and phosphates and sulfide and magnetite grains exhibiting embayment. The mineralogical evidence indicates alteration of accreted minerals by a fluid that evolved with time, leading to etching, dissolution and reprecipitation. Sulfide compositions indicate alteration at ~25 °C, similar to conditions inferred for asteroid (162173) Ryugu and Ivuna-type (CI) chondrite meteorites. The fluid probably evolved from neutral to alkaline, culminating with the precipitation of highly soluble salts. We conclude that Bennu’s protolith comprised mainly nanometre to micrometre silicates, with fewer chondrules and calcium–aluminium-rich inclusions than those of most chondrite groups.

Zega, T J↗

Ancient co-option of LTR retrotransposons as yeast centromeres

Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes leaving the origins of new centromere architectures unclear. The brewer’s yeast Saccharomyces cerevisiae exemplifies this long-standing puzzle. Its centromeres shifted ancestrally from large, repeat-rich, epigenetically specified forms to the compact, genetically defined ‘point’ centromeres. How this transition occurred has remained unresolved6. Here we identify evolutionarily related ‘proto-point’ centromeres that provide a resolution to the evolutionary origins of point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, accompanied by relaxed organization and sequence variability of flanking cis-elements. In two species, these proto-point centromeres lie within retrotransposon-derived repeat clusters, linking ancestral repeat-rich centromeres to genetically encoded ones. Comparative and phylogenetic analyses indicate that proto-point and point centromeres evolved in an ancestor with retrotransposon-rich centromeres. These results identify long-terminal-repeat retrotransposons, specifically Ty5 sequences, as the genetic substrate for point-centromere evolution and provide a mechanistic route by which an epigenetic centromere can become genetically specified. More broadly, they show how selfish elements can be co-opted to perform essential chromosomal functions.

Haase, Max A. B. [Max Planck Institute of Molecula↗

A non-canonical fungal peroxisome PTS-1 signal, SYM, and its evolutionary aspects

Abstract Proteins localized to peroxisomes, particularly those expressed under specific conditions or in low abundance, are often undetected by routine proteomics methods due to detection sensitivity limits. In silico identification and experimental validation of peroxisomal targeting signals (PTSs) offer a reliable alternative. We demonstrate that SYM, a non-canonical plant PTS-1 signal, functions similarly inAspergillus nidulans, as GFP tagged with a SYM C-terminal tripeptide localizes to peroxisomes. One of two nativeA. nidulansproteins with C-terminal SYM tripeptide shows weak peroxisomal localization alongside cytoplasmic presence, indicating that only a subset of proteins with non-canonical signals access peroxisomes.In silicoanalysis of 1,010 fungal genomes identified diverse SYM-proteins with variable functions, suggesting that non-canonical PTS-1 signals may evolve spontaneously. Two-thirds of SYM-proteins are predicted to localize to specific intracellular compartments other than the peroxisome. We propose that despite their predicted localization, these proteins possessing SYM as a non-canonical peroxisomal signal might also have peroxisomal presence. Among SYM-proteins, pectinesterases, known plant pathogen virulence factors, were frequent. Notably, 25% of fungal pectinesterases harbor non-canonical PTS-1 signals, suggesting that partial peroxisomal localization of pectinesterases has evolved convergently. This suggests that partial peroxisomal localization may enhance protein functional flexibility, contributing to the organism’s adaptability.

Science & Technology - Other Topics↗

Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes

As the tree of life becomes increasingly accessible to molecular investigations, describing mechanisms underlying evolutionary convergence and constraint will be crucial to understanding diversification. The lineage including the model yeast Saccharomyces cerevisiae evolved aerobic fermentation in part through an ancient whole genome duplication and retention of glycolytic genes. To evaluate glycolytic rates across diverse yeasts, we developed and deployed an extracellular acidification rates (ECAR) assay on 299 species that span more than 400 million years of evolution and identified a clade in the genus Saturnispora that convergently evolved aerobic fermentation. Through comparative genomics and transcriptomics, we found that several glycolytic genes had higher expression and novel cis-regulatory elements in aerobically fermenting Saturnispora species. When the transcription factor required for their activation was deleted in Saturnispora dispora, the mutants had reduced glycolytic rates and increased respiration. Intriguingly, many of the upregulated genes are orthologous to duplicated glycolytic genes in S. cerevisiae. These divergent genetic mechanisms affecting the same set of genes suggest that there are strong evolutionary constraints on how aerobic fermentation can arise.

Horianopoulos, Linda C. [Great Lakes Bioenergy Res↗