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At least 253 records · Page 14

Debunking common myths in coastal circulation modeling

Despite tremendous progress in algorithm development, computational efficiency and transition into operations over the past two decades, coastal modeling still lacks scientific rigor due to proliferation of many ‘gray’ areas related to various modeling choices made by modelers. Here, in this paper, we propose some guiding principles for the modeling community to improve performance, and we also debunk commonly held myths that make the coastal modeling lack rigor. Using our own experience in developing seamless cross-scale unstructured-grid based models for the past two decades, we describe in unprecedented detail the end-to-end modeling process (i.e., from digital elevation models (DEMs) to mesh generation to post analysis), and demonstrate that defensible modeling is within reach for any end user by following three guiding principles: (1) Bathymetry is a first order forcing in coastal domains and thus should be respected in all aspects of modeling; (2) Oceanographic processes are driven across multiple spatial scales and so models should enable appropriate resolution as needed; and (3) Model assessment should focus on physical processes. Through qualitative and quantitative model assessments, we demonstrate the fundamental role played by bathymetry/topography as embedded in DEMs in making the results defensible, which is unfortunately glossed over in many modeling studies. Focusing on process-based assessment simplifies the calibration process. A major conclusion of this work is that model developers and operators should maximize the scientific rigor for in silico oceanography by avoiding some common pitfalls that rely on error compensation at the expense of representation of physical system processes. We present some best practice procedures for defensive and trustworthy numerical modeling.

54 ENVIRONMENTAL SCIENCES↗

Total Water Level Prediction at Continental Scale: Coastal Ocean

We demonstrate recent progress made in the simulation of total water level (TWL) at continental scale, using the coastal ocean of US East Coast/Gulf of Mexico coast as an example. A key difference between the continental-scale and small-scale modeling is that the former requires a more accurate vertical datum. Using a geoid-based datum (xGEOID20b), a satellite altimetry product, and a state-of-the-art 3D unstructured-grid model, we significantly improve the accuracy for TWL both near- and off-shore. The average root-mean-square error at all NOAA stations is 14 cm. The non-tidal signals are found to be sensitive to the representation of a large-scale current system near the boundary and extending the domain extent to accommodate this system improves these signals.

Cui, Linlin↗

A nonhydrostatic formulation for MPAS-Ocean

The Model for Prediction Across Scales-Ocean (MPAS-Ocean) is an open-source, global ocean model and is one component of a family of climate models within the MPAS framework, including atmosphere, sea-ice, and land-ice models. Here, in this work, a new formulation for the ocean model is presented that solves the nonhydrostatic, incompressible Boussinesq equations on an unstructured, staggered, z-level grid. The introduction of this nonhydrostatic capability is necessary for the resolution of internal wave dynamics and large eddy simulations. Compared to the standard, hydrostatic formulation, a nonhydrostatic pressure solver and a vertical momentum equation are added, where the PETSc (Portable Extensible Toolkit for Scientific Computation) library is used for the inversion of a large sparse system for the nonhydrostatic pressure. Numerical results on a stratified seiche, internal solitary wave, overflow and lock-exchange test cases are presented, and the parallel efficiency of the code is evaluated using up to 1024 processors.

3D Poisson equation↗

A nonhydrostatic formulation for MPAS-Ocean

The Model for Prediction Across Scales-Ocean (MPAS-Ocean) is an open-source, global ocean model and is one component of a family of climate models within the MPAS framework, including atmosphere, sea-ice, and land-ice models. Here, in this work, a new formulation for the ocean model is presented that solves the nonhydrostatic, incompressible Boussinesq equations on an unstructured, staggered, z-level grid. The introduction of this nonhydrostatic capability is necessary for the resolution of internal wave dynamics and large eddy simulations. Compared to the standard, hydrostatic formulation, a nonhydrostatic pressure solver and a vertical momentum equation are added, where the PETSc (Portable Extensible Toolkit for Scientific Computation) library is used for the inversion of a large sparse system for the nonhydrostatic pressure. Numerical results on a stratified seiche, internal solitary wave, overflow and lock-exchange test cases are presented, and the parallel efficiency of the code is evaluated using up to 1024 processors.

3D Poisson equation↗

Sequentially coupled flow and geomechanical simulation with a discrete fracture model for analyzing fracturing fluid recovery and distribution in fractured ultra-low permeability gas reservoirs

More accurate characterization and prediction of the in-situ distribution of fracturing fluid in fractured reservoirs are needed for enhancing well productivity. In this study, an implicit-sequentially coupled flow/geomechanics simulator incorporating an efficient discrete fracture model is developed to model fluid distribution and recovery performance of ultra-low permeability gas reservoirs. The finite-volume and finite-element methods are used for space discretization of the flow and geomechanics equations, respectively, while the backward Euler method is employed for time discretization. The flow and geomechanics equations are solved sequentially based on fixed-stress splitting. An efficient discrete-fracture model is used to explicitly model the fractured system. Flexible unstructured gridding is employed to model arbitrarily-oriented fractures. The interrelations among pore volume, permeability and geomechanical conditions are considered dynamically using two-way coupled flow and geomechanics computations. The geometry of fracture (networks) due to hydraulic fracturing has significant impacts on the fracturing fluid recovery efficiency and ensuing fluid distribution. Under the same injection volume, the fracturing fluid recovery is higher when the fracture geometry is planar. Fluid recovery is relatively lower whenever natural fractures are activated during fracturing treatments; flowback time is also shortened when complex fracture network with enlarged fracture interface is present. Fracturing fluid in hydraulic fractures may leak off into the natural fractures and subsequently imbibes into the surrounding matrix due to capillarity effects. The fracturing fluid recovery and in-situ fluid distribution are sensitive to the shut-in duration and fracture closure behavior. This study analyzes the coupled flow-geomechanical responses of fractured gas reservoirs during the post-fracturing periods. Understanding the fate of the fracturing fluid can provide insights on, to some extent, the stimulated fracture volume, size of the water invasion zone, and efficiency of the fracturing design. The simulation predictions can also provide more accurate initial reservoir conditions (e.g. distributions of different phases and pressure) for long-term well performance estimation.

42 ENGINEERING↗

Wave resource characterization at regional and nearshore scales for the U.S. Alaska coast based on a 32-year high-resolution hindcast

A wave resource characterization was performed for the southern coast of Alaska based on a 32-year hindcast covering the period from 1979 to 2010. The characterization closely followed International Electrotechnical Commission (IEC) Technical Specifications. An unstructured-grid Simulating WAves Nearshore (SWAN) model, which had an approximate spatial resolution of 300 m within 30 km from the nearest shoreline, was developed. Additionally, extensive model validation and error characterization was performed. The model was found to perform well with an average absolute percent error of 8.6% in significant wave height, averaged over 18 buoys. Statistics for the six IEC wave resource parameters were calculated and aggregated at 20 km from shore to quantify the incident wave power and its variability at a regional scale. The southern coast of the Aleutian Archipelago was found to have the most available wave energy in the region. A nearshore resource assessment was performed by evaluating resource hotspots located 1 km from shore. More than 900 nearshore stations had an Optimum Hotspot Identifier value of 5 (kW/m) at diverse water depths, thereby positioning Alaska as a promising location for wave energy development.

54 ENVIRONMENTAL SCIENCES↗

Wave energy resources assessment for the multi-modal sea state of Hawaii

This paper describes development and validation of a 32-year wave hindcast for Hawaii as part of the wave energy resources assessment for the Exclusive Economic Zones of the US and affiliated territories. The nested model system comprises structured WAVEWATCH III models for the entire globe and the Central North Pacific as well as an unstructured SWAN model around the Hawaiian Islands with wind forcing from the Global Forecast System Reanalysis and its regional downscaling. The development effort follows the standards introduced by the International Electrotechnical Commission (IEC). The hindcast dataset was firstly validated with buoy measurements in terms of the six IEC wave energy resources parameters including the omnidirectional wave power ????, significant wave height ????????0, energy period ????????, spectral width ????0, direction of maximum directionally resolved wave power ?????????? ????????, and directionality coefficient ????. The comparison shows good overall agreement but with greater uncertainties for the spectral parameters ????0, ???????????????????? , and ???? formulated for narrow band spectra. The multimodal sea state in Hawaii always includes a mix of short-period wind seas, long-period swells from the North and South Pacific as well as waves with moderate periods from multiple sources. We partition the hindcast spectra based on the respective period ranges and directions and validate the partitioned spectral energy and parameters with measured values for implementation in wave energy resources assessment. The partitioned wave parameters from the hindcast allow separate seasonal descriptions of wind seas, north and south swells, and moderate-period waves for in-depth understanding of the wave climate and resources in Hawaii.

Li, Ning↗

Wave climate and energy resources in American Samoa from a 42-year high-resolution hindcast

Here, this paper presents an analysis of the wave climate and a characterization of the wave energy resources in American Samoa, a U.S. territory covering seven south central Pacific islands and atolls. A numerical wave model based on WAVEWATCH III® and unstructured SWAN was developed, validated, and executed for 1979–2020 to generate a hindcast dataset suitable for resource characterization. Model-data comparisons were performed with measurements collected in situ and from satellite-based altimeters. The model was found to perform well with a bias in significant wave height of -0.14 m and -0.06 m against buoy and altimeters, respectively. The multimodal sea state of American Samoa is investigated by identifying the sources of energy reaching the islands and partitioning the wave spectrum accordingly. The wave resources characterization follows the International Electrotechnical Commission Technical Specifications to be compatible with studies performed for other U.S. regions. The average omnidirectional wave power at 2 km from shore around Tutuila, the main island of American Samoa, is 14 kW/m. Locations east and west of the islands have a more consistent resource throughout the year because the northwest and southwest swells that are dominant during different seasons complement each other.

16 TIDAL AND WAVE POWER↗

Wave climate and energy resources in the Mariana Islands from a 42-year high-resolution hindcast

We report a high-resolution wave hindcast from 1979 to 2020 was developed for Guam and the Commonwealth of the Northern Mariana Islands, which are influenced by mesoscale and synoptic weather systems from the western Pacific Rim to the Central Pacific. The spectral wave modeling utilized structured global and unstructured regional grids with improved resolution in nearshore waters, where wave resources development is most feasible. The hindcast demonstrates its capability in capturing multi-modal seas through reproduction of bulk and partitioned wave parameters derived from altimetry and buoy measurements. The local wave climate is influenced by the year-round trade winds and tropical cyclones as well as seasonal monsoons, frontal systems, and mid-latitude high- and low-pressure systems. The strong intra-annual variation of the significant wave height and power flux reflects transitions between local and distant weather systems, which account for the diverse wave conditions comprised of short-period wind waves, intermediate-period seas, and long-period swells around the islands. Among the Pacific island regions, spectral partitioning is particularly important for describing the dominant wave components by period and direction with pertinent information conducive to energy resources characterization and coastal zone management in the Mariana Islands.

16 TIDAL AND WAVE POWER↗

Characterization of Gulf Stream energy resources: A 30-year high-resolution simulation study

The strength and proximity of the Gulf Stream (GS) along the U.S. coast offers opportunities for marine energy extraction. Leveraging high-resolution (up to 400 m) long-term (30-year) hindcasts based on an unstructured grid model, this study characterizes the energy potential of the GS in two viable locations: the Florida Straits (FS) and Cape Hatteras (CH). Results reveal distinct characteristics in the kinetic energy flux (KEF) and kinetic energy density (KED) for the two regions. The 30-year mean KEF at CH is 27.50 GW, surpassing the 19.74 GW estimated for the FS, which is attributed to the wider cross-section of the GS in CH. Additionally, CH exhibits higher KEF variability due to GS’s larger path shifts and meanders. Estimated KEDs at ADCP site locations reach up to 2,908 W/m 2 in the FS and 1,512 W/m 2 in the CH at a depth of 20 m. High-energy zones are closer to shore in the FS, whereas energy-rich areas at CH are located further offshore. A depth-based KED analysis shows significant decreases across typical energy extraction depths (20 to 100 m), with reductions up to 44%. Finally, this study provides high-resolution resource characterization, forming a foundation for optimized site selection and marine hydrokinetic system design.

16 TIDAL AND WAVE POWER↗

Street-level temperature estimation using graph neural networks: Performance, feature embedding and interpretability

Estimating street-level air temperature is a challenging task due to the highly heterogeneous urban surfaces, canyon-like street morphology, and the diverse physical processes in the built environment. Though pioneering studies have embarked on investigations via data-driven approaches, many questions remain to be answered. Here, in this study, we leveraged an innovative framework and redefined the street-level temperature estimation problem using Graph Neural Networks (GNN) with spatial embedding techniques. The results showed that GNN models are more capable and consistent of estimating street-level temperature among tested locations, benefiting from its unique strength in handling extensive data over unstructured graph topology. In addition, we conducted in-depth analysis of feature importance to enhance the model interpretability. Among the urban features analyzed in this study, the time-variant canopy density and meter-level land use data emerge as crucial factors. Our findings highlight GNN 's high potential in capturing the complex dynamics between urban elements and their impacts on microclimate, thus offering valuable insights for comprehensive urban data collection and urban climate modeling in general. Collectively, this study also contributes to urban planning and policy by providing avenues to enhance city resilience against climate change, thereby advancing the agenda for environmental stewardship and urban sustainability.

54 ENVIRONMENTAL SCIENCES↗

Assembly of JAZ–JAZ and JAZ–NINJA complexes in jasmonate signaling

Jasmonates (JAs) are plant hormones with crucial roles in development and stress resilience. They activate MYC transcription factors by mediating the proteolysis of MYC inhibitors called JAZ proteins. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC–JAZ–Novel Interactor of JAZ (NINJA)–TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which has precluded their experimental structure determination. Through a combination of biochemical, mutational, and biophysical analyses and AlphaFold-derived ColabFold modeling, we characterized JAZ–JAZ and JAZ–NINJA interactions and generated models with detailed, high-confidence domain interfaces. We demonstrate that JAZ, NINJA, and MYC interface domains are dynamic in isolation and become stabilized in a stepwise order upon complex assembly. By contrast, most JAZ and NINJA regions outside of the interfaces remain highly dynamic and cannot be modeled in a single conformation. Our data indicate that the small JAZ Zinc finger expressed in Inflorescence Meristem (ZIM) motif mediates JAZ–JAZ and JAZ–NINJA interactions through separate surfaces, and our data further suggest that NINJA modulates JAZ dimerization. This study advances our understanding of JA signaling by providing insights into the dynamics, interactions, and structure of the JAZ–NINJA core of the JA repressor complex.

59 BASIC BIOLOGICAL SCIENCES↗

Scalable algorithms for physics-informed neural and graph networks

Physics-informed machine learning (PIML) has emerged as a promising new approach for simulating complex physical and biological systems that are governed by complex multiscale processes for which some data are also available. In some instances, the objective is to discover part of the hidden physics from the available data, and PIML has been shown to be particularly effective for such problems for which conventional methods may fail. Unlike commercial machine learning where training of deep neural networks requires big data, in PIML big data are not available. Instead, we can train such networks from additional information obtained by employing the physical laws and evaluating them at random points in the space–time domain. Such PIML integrates multimodality and multifidelity data with mathematical models, and implements them using neural networks or graph networks. Here, we review some of the prevailing trends in embedding physics into machine learning, using physics-informed neural networks (PINNs) based primarily on feed-forward neural networks and automatic differentiation. For more complex systems or systems of systems and unstructured data, graph neural networks (GNNs) present some distinct advantages, and here we review how physics-informed learning can be accomplished with GNNs based on graph exterior calculus to construct differential operators; we refer to these architectures as physics-informed graph networks (PIGNs). We present representative examples for both forward and inverse problems and discuss what advances are needed to scale up PINNs, PIGNs and more broadly GNNs for large-scale engineering problems.

42 ENGINEERING↗

ATCUN-like Copper Site in βB2-Crystallin Plays a Protective Role in Cataract-Associated Aggregation

Cataract is the leading cause of blindness worldwide, and it is caused by crystallin damage and aggregation. Senile cataractous lenses have relatively high levels of metals, while some metal ions can directly induce the aggregation of human γ-crystallins. Here, for this work, we evaluated the impact of divalent metal ions in the aggregation of human βB2-crystallin, one of the most abundant crystallins in the lens. Turbidity assays showed that Pb 2+ , Hg 2+ , Cu 2+ , and Zn 2+ ions induce the aggregation of βB2-crystallin. Metal-induced aggregation is partially reverted by a chelating agent, indicating the formation of metal-bridged species. Our study focused on the mechanism of copper-induced aggregation of βB2-crystallin, finding that it involves metal-bridging, disulfide-bridging, and loss of protein stability. Circular dichroism and electron paramagnetic resonance (EPR) revealed the presence of at least three Cu 2+ binding sites in βB2-crystallin, one of them with spectroscopic features typical for Cu 2+ bound to an amino-terminal copper and nickel (ATCUN) binding motif, which is found in Cu transport proteins. The ATCUN-like Cu binding site is located at the unstructured N-terminus of βB2-crystallin, and it could be modeled by a peptide with the first six residues in the protein sequence (NH 2 -ASDHQF-). Isothermal titration calorimetry indicates a nanomolar Cu 2+ binding affinity for the ATCUN-like site. An N-truncated form of βB2-crystallin is more susceptible to Cu-induced aggregation and is less thermally stable, indicating a protective role for the ATCUN-like site. EPR and X-ray absorption spectroscopy studies reveal the presence of a copper redox active site in βB2-crystallin that is associated with metal-induced aggregation and formation of disulfide-bridged oligomers. Our study demonstrates metal-induced aggregation of βB2-crystallin and the presence of putative copper binding sites in the protein. Whether the copper-transport ATCUN-like site in βB2-crystallin plays a functional/protective role or constitutes a vestige from its evolution as a lens structural protein remains to be elucidated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MechBERT: Language Models for Extracting Chemical and Property Relationships about Mechanical Stress and Strain

Language models are transforming materials-aware naturallanguage processing by enabling the extraction of dynamic, context-rich information from unstructured text, thus, moving beyond the limitations of traditional information-extraction methods. Moreover, small language models are on the rise because some of them can perform better than large language models (LLMs) when given domain-specific questionanswer tasks, especially about an application area that relies on a highly specialized vernacular, such as materials science. We therefore present a new class of MechBERT language models for understanding mechanical stress and strain in materials. These employ Bidirectional Encoder Representations for transformer (BERT) architectures. We showcase four MechBERT models, all of which were pretrained on a corpus of documents that are textually rich in chemicals and their stress–strain properties and were fine-tuned on question-answering tasks. We evaluated the level of performance of our models on domain-specific as well as general English-language question-answer tasks and also explored the influence of the size and type of BERT architectures on model performance. We find that our MechBERT models outperform BERT-based models of the same size and maintain relevancy better than much larger BERT-based models when tasked with domain-specific question-answering tasks within the stress–strain engineering sector. These small language models also enable much faster processing and require a much smaller fraction of data to pretrain them, affording them greater operational efficiency and energy sustainability than LLMs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Substituent Effects on the Electronic Spectroscopy of Four-Carbon Criegee Intermediates

Atmospheric ozonolysis of biogenic and anthropogenic alkenes generates zwitterionic carbonyl oxide intermediates (R 1 R 2 C=O + O – ), known as Criegee intermediates, with different structural motifs and conformations. This study reports a systematic laboratory study of substituent effects on the electronic spectroscopy of four-carbon Criegee intermediates (CIs) with methyl–ethyl (MECI) and isopropyl (IPCI) groups, which are isomers produced in ozonolysis of asymmetric branched alkenes. The four-carbon CIs are separately generated by an alternative synthetic route, and spectroscopically characterized on the strong π* ← π transition associated with the carbonyl oxide group in a pulsed supersonic expansion with VUV photoionization at 118 nm and UV-induced depletion of the m/z 88 signal. The resultant broad and unstructured UV spectral features for MECI and IPCI are peaked at ca. 320 and 330 nm, respectively, with large absorption cross-sections of ca. 10 –17 cm 2 . Comparisons are made with the four-carbon CIs formed in isoprene ozonolysis, methyl vinyl ketone oxide (MVK-oxide) and methacrolein oxide (MACR-oxide), which have the same backbone connectivity as MECI and IPCI but have extended conjugation across the vinyl and carbonyl groups. A remarkable 50 nm shift of the peak absorption to longer wavelength is observed for MVK-oxide and MACR-oxide compared to MECI and IPCI, respectively. Furthermore, vertical excitation energies computed theoretically agree well with the experimental findings, confirming that the spectral shifts are caused by the extended π conjugation in the isoprene-derived Criegee intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic Spectroscopy and Dissociation Dynamics of Vinyl-Substituted Criegee Intermediates: 2-Butenal Oxide and Comparison with Methyl Vinyl Ketone Oxide and Methacrolein Oxide Isomers

The 2-butenal oxide Criegee intermediate [(CH 3 CH=CH)CHOO], an isomer of the four-carbon unsaturated Criegee intermediates derived from isoprene ozonolysis, is characterized on its first π * ←π electronic transition and by the resultant dissociation dynamics to O ( 1 D) + 2-butenal [(CH 3 CH=CH)CHO] products. The electronic spectrum of 2-butenal oxide under jet-cooled conditions is observed to be broad and unstructured with peak absorption at 373 nm, spanning to half maxima at 320 and 420 nm, and in good accord with the computed vertical excitation energies and absorption spectra obtained for its lowest energy conformers. The distribution of total kinetic energy released to products is ascertained through velocity map imaging of the O ( 1 D) products. About half of the available energy, deduced from the theoretically computed asymptotic energy, is accommodated as internal excitation of the 2-butenal fragment. A reduced impulsive model is introduced to interpret the photodissociation dynamics, which accounts for the geometric changes between 2-butenal oxide and the 2-butenal fragment, and vibrational activation of associated modes in the 2-butenal product. Application of the reduced impulsive model to the photodissociation of isomeric methyl vinyl ketone oxide reveals greater internal activation of the methyl vinyl ketone product arising from methyl internal rotation and rock, which is distinctly different than the dissociation dynamics of 2-butenal oxide or methacrolein oxide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scalable and Resilient Etched Metallic Micro- and Nanostructured Surfaces for Enhanced Flow Boiling

Flow boiling and evaporation in tubes and channels occur in a wide variety of energy systems, such as refrigeration, air conditioning, power generation, electronics cooling, distillation, and purification. In this work, we demonstrate remarkably increased heat transfer coefficients of 270% during refrigerant flow boiling in scalable microstructured (~40 µm), industrial-scale (~1 m long) aluminum (Al) tubes, when compared to smooth unstructured Al tubes. To achieve scalable nanomanufacturing, we create highly conformal and durable structured surfaces by relying on hydrochloric acid Al etching. Flow boiling tests were conducted in 6.35 mm diameter Al tubes using R134a refrigerant as the working fluid. To benchmark our approach and to elucidate the effect of the structure length scale, we also fabricated ultrascalable boehmite (AlO(OH)) nanostructured (~300 nm) Al tubes, showing that etched microscale features are necessary and key to enhancement. Durability tests conducted using a 28 day long continual flow boiling experiment demonstrated negligible degradation of the etched surfaces. The scalable and cost-effective techniques used to create these durable, etched-Al microstructures may significantly reduce manufacturing cost when contrasted with current enhancement approaches such as extrusion, drawing, and welding.

36 MATERIALS SCIENCE↗