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At least 343 records · Page 19

Simplified Approximations of Direct Cumulus Entrainment and Detrainment

Abstract In recent years, direct calculations of simulated cumulus entrainment and detrainment have facilitated new physical insights into these highly elusive but critically important processes. However, these calculations require substantial computational resources that may limit their widespread usage. To facilitate such calculations, two simplified approximations of direct cumulus entrainment and detrainment are examined herein. The first approximation, termed the “semidirect” method, follows a standard bulk approach but makes more realistic assumptions about the sources of entrained and detrained air near the cloud edges. In contrast, the second approximation (the “projection” method) uses the governing equations of motion to project whether grid points near the cloud edge will entrain or detrain as the mean cloud ascends by one grid point. Verification exercises using large-eddy simulations reveal that both methods generally agree better with corresponding direct entrainment/detrainment estimates than the traditional bulk formulation, with the projection method outperforming the semidirect method. The two methods can be used in a synergistic fashion, with the semidirect method helping to optimize the projection method, to suit a wide range of applications. Because the latter incorporates the essential dynamics of entrainment and detrainment at the local scale, it can be used to gain physical insight into the causal mechanisms regulating these complex processes.

Meteorology & Atmospheric Sciences↗

Hydropower Infrastructure - LAkes, Reservoirs, and RIvers (HILARRI), v4

HILARRI is a database of links between major datasets of operational hydropower dams and powerplants, and inland water bodies. These connections are critical for conducting large-scale analysis of hydropower infrastructure and their associated natural and engineered water systems. Features include: – Dams from the National Inventory of Dams (2025) and the Global Reservoir and Dam Database (GRanD v1.3) – Hydropower plants from the Existing Hydropower Assets dataset (EHA 2025) – Power plants that are listed in the 2025 U.S. Hydropower Development Pipeline Data or were listed in previous versions of the dataset These hydropower infrastructure features are linked to several major datasets that provide hydrologic and hydraulic information relevant for analysis of hydropower systems that includes the integral water resources. That information comes from: – Products from the National Hydrography Dataset (NHD) – NHDPlusV2 Medium Resolution river network flowlines, – NHD waterbodies (limited to lakes and reservoirs), – NHD Watershed Boundary Dataset (HUC12-level for the Conterminous United States (CONUS)) – NHD High Resolution waterbodies – HydroLAKES water bodies (lakes and reservoirs) – LAGOS-US lakes and reservoirs – EPA National Lakes Assessment (2007, 2012, 2017, and 2022) – The Reservoir Sedimentation Database (RESSED) – EPA SuRGE sampling locations Unique identifiers are used to facilitate joining to the original full datasets. For example, characteristics of NHD flowlines such as estimated average flow rate can be joined from the NHDPlusV2 dataset to a dam or power plant listed in HILARRI based on the ID field, “COMID”, that is common to both datasets. HILARRI only includes basic information about identifiers, location, and data quality or usage notes. It does not contain the attributes or time series data associated with these sites. The HILARRI dataset incorporates information from several datasets to facilitate more effective and accurate analysis of hydropower infrastructure and their associated waterbodies. For example, dams were checked against the most recent American Rivers Dam Removal Database to identify and flag facilities that may no longer exist. Additionally, dams that are listed multiple times in the NID are identified and flagged to avoid double-counting when analyzing and summarizing information. Other quality flags include certainty of operational hydropower (i.e., if one or more datasets indicates hydropower at a particular location), whether an associated water body is accurate or composed of multiple polygons, or whether there is a known issue with reported characteristics in one of the underlying datasets. These additional data flags are designed to increase confidence in data usage for individual to large-scale analyses.

Hansen, Carly [ORNL] (ORCID:0000000193280838)↗

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando↗

Context matters: Natural tree mortality can lead to neighbor growth release or suppression

Where competition suppresses tree growth, mortality of adjacent trees can release the surviving individuals, leading to a growth increase. However, primary forests are complicated systems, where trees interact in both competitive and facilitative ways mediated by their size, species, and the broad ecological context in which they grow. Thus, the magnitude and even direction of growth responses to the mortality of nearby trees may vary, which has implications for our understanding of community- and ecosystem-level dynamics following mortality events. Unfortunately, although many studies focus on the impacts of light availability and general crowding on tree growth, we know relatively little about the effects of naturally occurring mortality events on the growth of neighboring trees. To address this issue, we used 40 years of data from 15 permanent forest-monitoring plots in Mt Rainier old-growth forests, comparing observed to expected radial growth of individual trees following the death of their nearest neighbor. Although we found evidence of a general growth-release response, this was not universal among all trees, with small trees in particular exhibiting growth suppression (rather than release) following neighboring tree mortality. In addition to small size, growth-suppression was more likely if the dead neighbor was the same species, consistent with facilitative effects as mediated through belowground networks. At the stand level, the average growth release after nearest neighbor mortality was greatest in low-density stands with large trees, with elevation and community composition also playing a role. Decades more monitoring could reveal how long growth release (or suppression) is sustained by individual trees following neighboring mortality events, as well as potential response lags and the role of species identity in determining whether interactions with neighbors are competitive or facilitative. Nonetheless, our results suggest that although mature trees have competitive effects on their larger neighbors, they also have an important role in supporting the ingrowth of small trees. More broadly, we demonstrate that the nature of interactions between individual neighboring trees is highly context dependent.

54 ENVIRONMENTAL SCIENCES↗

Structures and Mechanisms of a Novel Bacterial Transport System for Fatty Acids

Abstract Bacterial acquisition of metabolites is largely facilitated by transporters with unique substrate scopes. The tripartite ATP‐independent periplasmic (TRAP) transporters comprise a large family of bacterial proteins that facilitate the uptake of a variety of small molecules. It has been reported that some TRAP systems encode a fourth protein, the T component. The T‐component, or TatT, is predicted to be a periplasmic‐facing lipoprotein that enables the uptake of metabolites from the outer membrane. However, no substrates were revealed for any TatT and their functional role(s) remained enigmatic. We recently identified a homolog in Methylococcus capsulatus that binds to sterols, and herein, we report two additional homologs that demonstrate a preference for long‐chain fatty acids. Our bioinformatics, quantitative analyses of protein‐ligand interactions, and high‐resolution crystal structures suggest that TatTs might facilitate the trafficking of hydrophobic or lipophilic substrates and represent a new class of bacterial lipid and fatty acid transporters.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing occupant behavior representation for interoperability between building information modeling and building energy modeling

Building Performance Simulation (BPS) has been adopted as an essential tool for designing, operating, and retrofitting buildings to optimize energy efficiency throughout the building life cycle. The Green Building XML (gbXML) schema facilitates seamless data exchange between Building Information Modeling (BIM) and Building Energy Modeling (BEM) software tools. However, limited occupant behavior (OB) representation in BIM often leads to inconsistent and inaccurate energy simulation in BEM software. This paper presents 154 systematic enhancements to the existing occupant behavior XML (obXML) schema v1.3.4, initially developed for standardizing OB representation for BEM, to address existing limitations and improve interoperability with BIM models. The enhancements encompass improved integration with BIM models through extended building representations and system operations, expanded support for advanced OB models with additional environmental parameters and mathematical capabilities, and implementation of a standardized model documentation framework. To facilitate seamless data transformation between gbXML and obXML schemas, we developed a publicly available gb-obXML Schema Converter. Three case studies demonstrate the enhanced schema’s capabilities: representation of building information using a two-story office building model, documentation of a window operation behavior model, and validation of the schema converter’s functionality. The enhanced obXML schema v1.4 enables sophisticated modeling of occupant-building interactions while maintaining consistency with industry-standard BIM schemas. The standardized documentation framework facilitates reproducibility and knowledge sharing in the OB research community, while the schema converter automates the integration of building information into OB simulation workflows. These enhancements establish a foundation for more accurate building performance simulation by supporting sophisticated representation of occupant behavior within the BIM-to-BEM simulation workflows.

Chung, Jihoon↗

Reduction of uranyl and uranyl-organic complexes mediated by magnetite and ilmenite: A combined electrochemical AFM and DFT study

Reduction of mobile aqueous uranyl complexes can be hindered by the strength of the uranyl-ligand complex and the resistivity of the complexes to electron transfer. Semiconducting solids, such as magnetite (Fe 3 O 4 ) and ilmenite (FeTiO 3 ), can facilitate otherwise-slow electron transfer between the reductant and oxidant, especially if these species are adsorbed on their surfaces as inner-sphere complexes. Electrons can then be shuttled through the surface or the structure. This process can be facilitated by either finding a new electron transfer path or by weakening or destroying the ligand-uranyl complex. Using in situ electrochemical atomic force microscopy (EC-AFM), we imaged reduction products of uranyl as mediated by magnetite and ilmenite in the absence or presence of the organic ligands, ethylenediaminetetraacetate (EDTA) and oxalate. In situ images of uranyl reduction show gradual nucleation and growth of reduced uranium on the mineral surfaces with decreasing reduction potentials. X-ray photoelectron spectroscopy (XPS) measurements indicate pentavalent uranium as the dominant uranium species resulting from uranyl reduction mediated by magnetite and ilmenite. The reduction potentials of uranyl-organic species relevant to our reaction system, (U VI O 2 ∙oxalate) 0 and (U VI O 2 ∙HEDTA) - , are derived using quantum–mechanical modeling and compared with the midpoint potentials obtained from cyclic voltammetry measurements. The spectroscopic, electrochemical, and computational data suggest that the catalysis of Fe-bearing minerals facilitates the reduction of uranyl-organic complexes. U(VI)-oxalate complexes are redox-active and participate directly in the reduction mediated by magnetite. In the presence of EDTA, reduction of uranyl may proceed in concert with ligand exchange between metals (i.e., U and Fe) on the mineral surface. Finally, the proposed mechanism is the breaking of uranyl-organic bonds upon interaction with the mineral surface followed by the formation of Fe-organic bonds, thereby allowing the reduction of hexavalent uranyl to pentavalent one.

58 GEOSCIENCES↗

Volatility Basis Set Distributions and Viscosity of Organic Aerosol Mixtures: Insights from Chemical Characterization Using Temperature-Programmed Desorption–Direct Analysis in Real-Time High-Resolution Mass Spectrometry

Quantitative assessment of gas-particle partitioning of individual components within complex atmospheric organic aerosols (OA) mixtures is critical for predicting and comprehending the formation and evolution of OA particles in the atmosphere. This investigation leverages previously documented data obtained through a temperature programmed desorption - direct analysis in real time – high resolution mass spectrometry (TPD-DART-HRMS) platform. This methodology facilitates the bottom-up construction of volatility basis set (VBS) distributions for constituents found in three biogenic secondary organic aerosol (SOA) mixtures produced through the ozonolysis of a-pinene, limonene, and ocimene. The apparent enthalpies (ΔH*, kJ mol -1 ) and saturated vapor mass concentrations (C T *, µg∙m -3 ) of individual SOA components, determined as a function of temperature (T, K), facilitated an assessment of changes in VBS distributions and gas-particle partitioning with respect to T and atmospheric total organic mass loadings (tOM, µg∙m -3 ). Further, the VBS distributions reveal distinct differences in volatilities among monomers, dimers, and trimers, enabling their categorization into separate volatility bins. At the ambient temperature of T = 298 K, only monomers efficiently partition between gas and particle phases across a broad range of atmospherically relevant total organic mass loadings (tOM) values of 1–100 µg∙m -3 . Partitioning of dimers and trimers becomes notable only at T > 360 K and T > 420 K, respectively. The viscosity of SOA mixtures is assessed using a bottom-up calculation approach, incorporating the input of elemental formulas, ΔH*, C T *, and particle-phase mass fractions of the SOA components. Through this approach, we are able to accurately estimate the variations in SOA viscosity that result from the evaporation of its components. These variations are, in turn, influenced by atmospherically relevant changes in tOM and T. Comparison of the calculated SOA viscosity and diffusivity values with literature reported experimental results shows close agreement, thereby validating the employed calculation approach. These findings underscore the significant potential for TPD-DART-HRMS measurements in enabling the untargeted analysis of organic molecules within OA mixtures. This approach facilitates quantitative assessment of their gas-particle partitioning and allows for the estimation of their viscosity and condensed-phase diffusion, thereby contributing valuable insights to atmospheric models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synergistic Coupling of CO2 and H2O during Expansion of Clays in Supercritical CO2-CH4 Fluid Mixtures

A combination of in operando IR and XRD methods were used to investigate the interaction of variably hydrated supercritical CO2-CH4 fluids with Na/NH4/Cs substituted montmorillonites. Comparing the behavior of Na-clay exposed to CH4 versus CO2 dominant fluid phases demonstrated that CO2 disrupts the H-bond network of intercalated H2O. At relatively low potentials of H2O, CO2 facilitates H2O intercalation and expansion of the interlayer region of the Na-clay. In contrast, CO2 inhibited H2O intercalation but promoted expansion of the Cs-clay. The NH4-clay displayed intermediated behavior. Methane likely intercalated the clays but opportunistically, filling unoccupied space after CO2 and H2O actively expanded the interlayer region. By comparing and contrasting the behavior of the Cs and NH4 clays to the Na Clay we conclude that, whereas H2O is required for initial Na-clay expansion, CO2 synergistically facilitated expansion and hydration of Na-clay by mixing with H2O (the entropic contribution) and participating in the outer solvation sphere of Na (the enthalpic contribution). In contrast, CO2 can directly solvate interlayer Cs and NH4 and cause expansion in the absence of H2O; nonetheless, H2O and CO2 also act synergistically to facilitate expansion of the Cs and NH4 clays at low H2O concentrations.

Loring, John S.↗

Impact of Confinement and Zwitterionic Ligand Chemistry on Ion–Ion Selectivity of Functionalized Nanopores

Membranes incorporating zwitterionic chemistries have recently emerged as promising candidates for facilitating challenging ion–ion separations. Transport of ions in such membranes predominantly occurs in hydrated nanopores lined with zwitterionic monomers. Here, to shed light on the physics of ion–ion selectivity underlying such materials, we conducted molecular dynamics simulations of sodium halide transport in model nanopores grafted with sulfobetaine methacrylate molecules. Our results reveal that in both functionalized and unfunctionalized nanopores smaller ions prefer to reside near the pore center, while the larger ions tend to reside near the pore walls. An enhancement in the selective transport of larger anions is observed within the unfunctionalized nanopores relative to that in salt-in-water solutions. Upon functionalization of the nanopores with zwitterions (ZIs), the disparities in the anionic distribution profiles within the pores coupled with differences in the anion-ZI interactions result in a slowdown of larger anions relative to smaller anions. Increasing the ZI grafting density exacerbates these effects, further promoting the selective transport of smaller anions. Our results suggest that selectivity toward large anions can be realized by using nanoporous membranes with ZI content that is high enough to facilitate ion/water partitioning into the pores while preserving the characteristic tendency of the unfunctionalized pores to facilitate faster transport of the larger anions. On the other hand, selectivity toward smaller anions can be achieved by targeting ZI content within the pores that is high enough to significantly slow down the transport of large anions but not high enough to hinder the partitioning of ions/water molecules into the pore due to steric effects.

anions↗

Programmable Anisotropy and Percolation in Supramolecular Patchy Particle Gels

Patchy particle interactions are predicted to facilitate the controlled self-assembly and arrest of particles into phase-stable and morphologically tunable "equilibrium" gels, which avoids the arrested phase separation and subsequent aging that is typically observed in traditional particle gels with isotropic interactions. Despite these promising traits of patchy particle interactions, such tunable equilibrium gels have yet to be realized in the laboratory due to experimental limitations associated with synthesizing patchy particles in high yield. Here, we introduce a supramolecular metal-coordination platform consisting of metallic nanoparticles linked by telechelic polymer chains, which validates the predictions associated with patchy particle interactions and facilitates the design of equilibrium particle hydrogels through limited valency interactions. We demonstrate that the interaction valency and self-assembly of the particles can be effectively controlled by adjusting the relative concentration of polymeric linkers to nanoparticles, which enables the gelation of patchy particle hydrogels with programmable local anisotropy, morphology, and low mechanical percolation thresholds. Moreover, by crowding the local environment around the patchy particles with competing interactions, we introduce an independent method to control the self-assembly of the nanoparticles, thereby enabling the design of highly anisotropic particle hydrogels with substantially reduced percolation thresholds. We thus establish a canonical platform that facilitates multifaceted control of the self-assembly of the patchy nanoparticles en route to the design of patchy particle gels with tunable valencies, morphologies, and percolation thresholds. These advances lay important foundations for further fundamental studies of patchy particle systems and for designing tunable gel materials that address a wide range of engineering applications.

36 MATERIALS SCIENCE↗

Cesium-Induced Active Sites for C–C Coupling and Ethanol Synthesis from CO 2 Hydrogenation on Cu/ZnO(000$\bar{1}$) Surfaces

The efficient conversion of carbon dioxide, a major air pollutant, into ethanol or higher alcohols is a big challenge in heterogeneous catalysis, generating great interest in both basic scientific research and commercial applications. Here, we report the facilitated methanol synthesis and the enabled ethanol synthesis from carbon dioxide hydrogenation on a catalyst generated by codepositing Cs and Cu on a ZnO(000$\bar{1}$) substrate. A combination of catalytic testing, X-ray photoelectron spectroscopy (XPS) measurements, and calculations based on density functional theory (DFT) and kinetic Monte Carlo (KMC) simulation was used. The results of XPS showed a clear change in the reaction mechanism when going from Cs/Cu(111) to a Cs/Cu/ZnO(000$\bar{1}$) catalyst. The Cs-promoting effect on C–C coupling is a result of a synergy among Cs, Cu, and ZnO components that leads to the presence of CH x and CH y O species on the surface. Furthermore, according to the DFT-based KMC simulations, the deposition of Cs introduces multifunctional sites with a unique structure at the Cu–Cs–ZnO interface, particularly being able to promote the interaction with CO 2 and thus the methanol synthesis predominantly via the formate pathway. More importantly, it tunes the CHO binding strongly enough to facilitate the HCOOH decomposition to CHO via the formate pathway, but weakly enough to allow further hydrogenation to methanol. The fine-tuning of CHO binding also enables a close alignment of a CHO pair to facilitate the C–C coupling and eventually ethanol synthesis. Our study opens new possibilities to allow the highly active and selective conversion of carbon dioxide to higher alcohols on widely used and low-cost Cu-based catalysts.

36 MATERIALS SCIENCE↗

Framework-Topology-Controlled Singlet Fission in Metal–Organic Frameworks

Singlet fission (SF) has been explored as a viable route to improve photovoltaic performance by producing more excitons. Efficient SF is achieved through a high degree of interchromophoric coupling that facilitates electron super exchange to generate triplet pairs. However, strongly coupled chromophores often form excimers that can serve as an SF intermediate or a low-energy trap site. The succeeding decoherence process, however, requires an optimum electronic coupling to facilitate the isolation of triplet production from the initially prepared correlated triplet pair. Conformational flexibility and dielectric modulation can provide a means to tune the SF mechanism and efficiency by modulating the interchromophoric electronic interaction. Such a strategy cannot be easily adopted in densely stacked traditional organic solids. Here, we show that the assembly of the SF-active chromophores around well-defined pores of solution-stable metal-organic frameworks (MOFs) can be a great platform for a modular SF process. A series of three new MOFs, built out from 9,10-bis(ethynylenephenyl)anthracene-derived struts, show a topology-defined packing density and conformational flexibility of the anthracene core to dictate the SF mechanism. Various steady-state and transient spectroscopic data suggest that the initially prepared singlet population can prefer either an excimer-mediated SF or a direct SF (both through a virtual charge-transfer (CT) state). Finally, these solution-stable frameworks offer the tunability of the dielectric environment to facilitate the SF process by stabilizing the CT state. Given that MOFs are a great platform for various photophysical and photochemical developments, generating a large population of long-lived triplets can expand their utilities in various photon energy conversion schemes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Preparation of Neptunyl and Plutonyl Acetates To Access Nonaqueous Transuranium Coordination Chemistry

Uranyl diacetate dihydrate is a useful reagent for the preparation of uranyl (UO 2 2+ ) coordination complexes, as it is a well-defined stoichiometric compound featuring moderately basic acetates that can facilitate protonolysis reactivity, unlike other anions commonly used in synthetic actinide chemistry such as halides or nitrate. Despite these attractive features, analogous neptunium (Np) and plutonium (Pu) compounds are unknown to date. Here, in this study, a modular synthetic route is reported for accessing stoichiometric neptunyl(VI) and plutonyl(VI) diacetate compounds that can serve as starting materials for transuranic coordination chemistry. The new NpO 2 2+ and PuO 2 2+ complexes, as well as a corresponding molecular UO 2 2+ complex, are isomorphous in the solid state, and in solution show similar solubility properties that facilitate their use in synthesis. In both solid and solution state, the +VI oxidation state (O.S.) is maintained, as demonstrated by vibrational and optical spectroscopy, confirming that acetate anions stabilize the oxidizing, high-valent +VI states of Np and Pu as they do for the more stable U(VI). All three acetate salts readily react with a model diprotic ligand, affording incorporation of U(VI), Np(VI), and Pu(VI) cores into molecular coordination compounds that occurs concomitantly with elimination of acetic acid; the new complexes are high-valent, yet overall charge neutral, facilitating entry into nonaqueous chemistry by rational synthesis. Computational studies reveal that the dianionic ligand framework assists in stabilizing the +VI O.S. via donation to the 5f shells of the actinides, highlighting the potential usefulness of protonolysis reactivity toward preparation of stabilized high-valent transuranic species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomically synergistic Zn-Cr catalyst for iso-stoichiometric co-conversion of ethane and CO2 to ethylene and CO

Abstract Developing atomically synergistic bifunctional catalysts relies on the creation of colocalized active atoms to facilitate distinct elementary steps in catalytic cycles. Herein, we show that the atomically-synergistic binuclear-site catalyst (ABC) consisting of $${{{{{\rm{Zn}}}}}}^{\delta+}$$ Zn δ + -O-Cr 6+ on zeolite SSZ-13 displays unique catalytic properties for iso-stoichiometric co-conversion of ethane and CO 2 . Ethylene selectivity and utilization of converted CO 2 can reach 100 % and 99.0% under 500 °C at ethane conversion of 9.6%, respectively. In-situ/ex-situ spectroscopic studies and DFT calculations reveal atomic synergies between acidic Zn and redox Cr sites. $${{{{{\rm{Zn}}}}}}^{\delta+}$$ Zn δ + ( $$0 \, < \, \delta \, < \, 2$$ 0 < δ < 2 ) sites facilitate β-C-H bond cleavage in ethane and the formation of Zn-H δ - hydride, thereby the enhanced basicity promotes CO 2 adsorption/activation and prevents ethane C-C bond scission. The redox Cr site accelerates CO 2 dissociation by replenishing lattice oxygen and facilitates H 2 O formation/desorption. This study presents the advantages of the ABC concept, paving the way for the rational design of novel advanced catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.

Draisma, Arjan [Wageningen University & Research (↗

The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein

Abstract Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based ‘organelles’ found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~ 25–50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure–function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model Thermotoga maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryo-EM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the Thermotoga maritima encapsulin, the decameric cargo protein with fivefold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier—it also plays a significant role in the structure and function of the cargo enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Scenario Generation for Built Environment Decision Support under Uncertainty: Case Studies of Airflow Modeling and Climate-Resilient Infrastructure System Design

When confronted with unforeseen challenges, practicing informed decision making is crucial for enhancing resilience in the built environment. While scan-to-building information modeling (BIM) is a well-established approach for creating detailed digital representations of physical assets, its application in assessing and improving infrastructure resilience remains underexplored. This study addresses this gap by proposing a novel application of scan-to-BIM, namely, scan-to-BIM-to-digital twin (S-BIM-DT) workflow. By integrating reality capture and digital twin technologies, this workflow creates continuously updated and accurate digital representations of physical assets, enabling the generation of various scenarios. Unlike traditional methods, the S BIM-DT workflow facilitates continuous model refinement, supporting informed resilience strategies. By combining these technologies into a cohesive process, the workflow facilitates decision making under uncertainty, enabling stakeholders to evaluate and respond to various scenarios effectively. We demonstrate the implementation of the S-BIM-DT workflow through two use cases that highlight its capability to enhance resilience at different scales. The first use case involves the Combined Transportation, Emergency, and Communications Center (CTECC) in Austin, Texas. BIM-enriched computational fluid dynamics (CFD) modeling simulates airflow and develops alternative scenarios for optimizing the heating, ventilation, and air conditioning (HVAC) systems. This approach enhances resilience against airborne health threats in a postCOVID context. The second use case focuses on designated areas within Beaumont, Texas, as part of the Southeast Texas Urban Integrated Field Laboratory (SETx-UIFL) research. By developing inundation maps to assess extreme weather events, this modeling aids in preparedness efforts and informs the development of climate-resilient infrastructure in vulnerable neighborhoods. Results indicate that the S-BIM-DT workflow effectively generates scenarios that enhance resilience in the built environment by facilitating informed decision making. Furthermore, this study serves as a bridge between advanced scan-to-BIM methodologies and the practical strategies needed to improve built infrastructure resilience.

Built environment↗