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A comprehensive and fair comparison of two neural operators (with practical extensions) based on $\mathrm{FAIR}$ data

Neural operators can learn nonlinear mappings between function spaces and offer a new simulation paradigm for real-time prediction of complex dynamics for realistic diverse applications as well as for system identification in science and engineering. Herein, we investigate the performance of two neural operators, which have shown promising results so far, and we develop new practical extensions that will make them more accurate and robust and importantly more suitable for industrial-complexity applications. The first neural operator, DeepONet, was published in 2019 (Lu et al., 2019), and its original architecture was based on the universal approximation theorem of Chen & Chen (1995). The second one, named Fourier Neural Operator or FNO, was published in 2020, and it is based on parameterizing the integral kernel in the Fourier space. DeepONet is represented by a summation of products of neural networks (NNs), corresponding to the branch NN for the input function and the trunk NN for the output function; both NNs are general architectures, e.g., the branch NN can be replaced with a CNN or a ResNet. According to Kovachki et al. (2021), FNO in its continuous form can be viewed conceptually as a DeepONet with a specific architecture of the branch NN and a trunk NN represented by a trigonometric basis. In order to compare FNO with DeepONet computationally for realistic setups, we develop several extensions of FNO that can deal with complex geometric domains as well as mappings where the input and output function spaces are of different dimensions. We also develop an extended DeepONet with special features that provide inductive bias and accelerate training, and we present a faster implementation of DeepONet with cost comparable to the computational cost of FNO, which is based on the Fast Fourier Transform. Here we consider 16 different benchmarks to demonstrate the relative performance of the two neural operators, including instability wave analysis in hypersonic boundary layers, prediction of the vorticity field of a flapping airfoil, porous media simulations in complex-geometry domains, etc. We follow the guiding principles of FAIR (Findability, Accessibility, Interoperability, and Reusability) for scientific data management and stewardship. The performance of DeepONet and FNO is comparable for relatively simple settings, but for complex geometries the performance of FNO deteriorates greatly. We also compare theoretically the two neural operators and obtain similar error estimates for DeepONet and FNO under the same regularity assumptions.

42 ENGINEERING↗

A gravo-aeroelastically scaled wind turbine rotor at field-prototype scale with strict structural requirements

A new sub-scale field-prototype design solution is developed to realize the dynamics, structural response, and distributed loads (gravitational, aerodynamic, centrifugal) that are characteristic of a full-scale large, modern wind turbine rotor. Prior work in sub-scale wind turbine testing has focused on matching aerodynamic/aero-elastic characteristics of full-scale rotors at wind tunnel scale. However, large-scale rotor designs must expand beyond this limited set of scaling parameters for cost-effective prototyping and meet strict requirements for structural safety for field testing. Here, the challenge lies in producing a structural design meeting two competing objectives: novel scaling objectives that prescribe the sub-scale blade to have low mass and stiffness; and traditional structural safety objectives that drive the design to have higher stiffness and mass. A 20% gravo-aeroelastically scaled wind turbine blade is developed successfully that satisfies these competing objectives. First, it achieved close agreement for non-dimensional tip deflection and flap-wise blade frequency (both within 2.1%) with a blade mass distribution constrained to produce target gravitational and centrifugal loads. Second, the entire blade structure was optimized to ensure a safe, manufacturable solution meeting strict strength requirements for a testing site that can experience up to 45 m/s wind gusts. The prototype-scale blade was fabricated and successfully proof-load tested.

17 WIND ENERGY↗

Servo-aero-gravo-elastic (SAGE) scaling and its application to a 13-MW downwind turbine

Reduced scale wind turbines can be extremely cost-effective to test new rotor concepts since prototype costs are heavily dependent on the rotor diameter. Ideally, the scaled model would have the same non-dimensional deflections, dynamics, and control behavior as the full-scale model. This would provide a high-fidelity demonstration of the full-scale performance, which is ideal if the full-scale turbine has significant aeroelastic interactions. To this end, servo-aero-gravo-elastic (SAGE) scaling is developed and applied to a 13-MW turbine that is scaled to a 20% scale model. The scaling preserves the tip-speed ratio, the rotor speed normalized by the flapping frequency, and the tip deflections normalized by the blade length. In addition, the controller employs the same control structure (gain-scheduled pitch control and variable speed torque control) and is scaled dynamically (e.g., matching non-dimensional time constant of the pitch angle, etc.). Furthermore, the thrust, gravity, and centrifugal moments are scaled such that the load angles are preserved as a function of a non-dimensional wind speed. However, the environmental scaling must consider differences in Reynolds number (since this parameter cannot be held constant) and subsequent changes in the axial induction factor. While the presented results showcase these differences during operational conditions, the non-dimensional tip deflections remain comparable through all wind speed ranges, indicating the viability of the SAGE scaling method in matching full-scale aeroelastic responses.

Kaminski, Meghan (ORCID:0000000322334784)↗

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗

Probabilistic neural networks for fluid flow surrogate modeling and data recovery

We consider the use of probabilistic neural networks for fluid flow surrogate modeling and data recovery. This framework is constructed by assuming that the target variables are sampled from a Gaussian distribution conditioned on the inputs. Consequently, the overall formulation sets up a procedure to predict the hyperparameters of this distribution which are then used to compute an objective function given training data. We demonstrate that this framework has the ability to provide for prediction confidence intervals based on the assumption of a probabilistic posterior, given an appropriate model architecture and adequate training data. The applicability of the present framework to cases with noisy measurements and limited observations is also assessed. To demonstrate the capabilities of this framework, we consider canonical regression problems of fluid dynamics from the viewpoint of reduced-order modeling and spatial data recovery for four canonical data sets. The examples considered in this study arise from (i) the shallow-water equations, (ii) a two-dimensional cylinder flow, (iii) the wake of a NACA0012 airfoil with a Gurney flap, and (iv) the NOAA sea surface temperature data set. Furthermore, the present results indicate that the probabilistic neural network not only produces a machine-learning-based fluid flow surrogate model but also systematically quantifies the uncertainty therein to assist with model interpretability.

42 ENGINEERING↗

Sweeping Jet Film Cooling at High Blowing Ratio on a Turbine Vane

Abstract Experimental and numerical investigations were performed to study the effects of high blowing ratios and high freestream turbulence on sweeping jet film cooling. Experiments were conducted on a nozzle guide vane suction surface in a low-speed linear cascade at a range of blowing ratios of 0.5–3.5 and freestream turbulence of 0.6% and 14.3%. Infrared thermography was used to estimate the adiabatic cooling effectiveness. Thermal field and boundary layer measurements were conducted at a cross-plane at x/D = 12 downstream of the hole exit. Results were compared with a baseline 777-shaped hole and showed that the sweeping jet hole has improved cooling effectiveness at high blowing ratios (M > 1). The thermal field data revealed that the coolant separates from the surface at high blowing ratios for the 777-shaped hole while the coolant remains attached for the sweeping jet hole. Boundary layer measurements further confirmed that due to the sweeping motion of the jet, the effective jet momentum of the sweeping jet hole remains much lower than that of a 777-shaped hole. Thus, the coolant remains closer to the wall even at high blowing ratios. Large Eddy simulations (LES) were performed for both the sweeping jet and 777-shaped hole to evaluate the interaction between the coolant jet and the freestream in the near hole regions. Results showed that 777-shaped hole has a strong jetting at high blowing ratio that originates inside the hole breakout edges thus causing the jet to blow-off from the surface. In contrast, the sweeping jet does not show this behavior due to its internal geometry and flapping motion of the jet.

Engineering↗

A three-dimensional model of terrain-induced updrafts for movement ecology studies

Abstract Background Spatially explicit simulation models of animal movements through the atmosphere necessarily require a representation of the spatial and temporal variation of atmospheric conditions. In particular, for movements of soaring birds that rely extensively on vertical updrafts to avoid flapping flight, accurate and reliable estimation of the vertical component of wind is critical. The interaction between wind and complex terrain shapes both the horizontal and vertical wind fields, highlighting the need to model the coupling between local terrain features and atmospheric conditions at scales relevant to animal movement. Methods In this work, we propose a new empirical model for estimating the orographic updraft field. The model is developed using computational fluid dynamics simulations of canonical atmospheric conditions over moderately complex terrain. To isolate buoyancy and thermal effects, and focus on terrain-induced effects, we use only simulations of a neutrally stratified atmosphere to develop the model. The model, which we name Engineering Vertical Velocity Estimator (EVVE), is simple to implement and is a function of the underlying terrain elevation map, the desired height above ground level (AGL), and wind conditions at a reference height (80 m). We validate the model with data from the Alaiz mountain (Spain) field campaign. Results Compared to observations, the proposed improved model estimates the updrafts at 120 m AGL with a mean error of 0.11 m/s ( $$\sigma =0.28$$ σ = 0.28 m/s), compared to 0.85 m/s ( $$\sigma =0.58$$ σ = 0.58 m/s) for its baseline. For typical land-based wind turbine hub heights of 80 m AGL, the proposed model has a mean error of 0.04 m/s ( $$\sigma =0.25$$ σ = 0.25 m/s), compared to baseline 0.54 m/s ( $$\sigma =0.45$$ σ = 0.45 m/s) estimations. We illustrate an application of the model in movement ecology by comparing simulated tracks and presence maps of golden eagles ( Aquila chrysaetos ) moving across two distinct landscapes. The tracks and presence maps are obtained using a simple heuristic-based movement model, with the updraft field given by the proposed model and a wind vector-based estimation approach that is currently in wide use in movement ecology studies of raptors and other soaring birds. Conclusions We highlight that movement model results can be sensitive to the underlying orographic updraft model, especially in studies of fine-scale movements in regions of complex topography. We suggest adopting the proposed model rather than the wind vector estimation method for studies of soaring bird movements.

17 WIND ENERGY↗

Techno-Economic Optimization of the SurgeWEC Device

This is the post-access report for a Teamer-funded effort to optimize the SurgeWEC device, a near-shore pivoting flap wave energy conversion device used to desalinate water. Parametrically driven cost and performance models enabled an integrated optimization approach at the farm scale. The metric used for this study was the levelized cost of water (LCOW). The data-set includes: 1. A public-domain post access report 2. An excel file with the data and plots generated under this study

16 TIDAL AND WAVE POWER↗

Morphological and molecular characterization of Paratylenchus beltsvillensis n. sp. (Tylenchida: Paratylenchidae) from the rhizosphere of pine tree ( Pinus virginiana Mill) in Maryland, USA

The pin nematode, Paratylechus beltsvillensis sp. collected from rhizosphere soil of a Virginia pine tree (Pinus virginiana Mill) growing in Little Paint Branch Park, Beltsville, Prince George’s County, Maryland, USA, is described and illustrated along with light and scanning electron photomicrographs. Females, males, and juveniles of this new species were recovered from soil samples using the sugar centrifugal flotation and Baermann funnel extraction methods. Morphologically, females are short, body length ranging from 245 to 267 μm, stylet from 70 to 75 μm long with anchor shaped knobs, vulva located at 70–73% and small vulval flap, spermatheca large, and ovoid filled with sperms. Lateral field with three incisures, of which the outer two are prominent. Tail slender, having a rounded tail terminus. Males without stylet and have a degenerated pharynx, spicules = 17–20 µm and gubernaculum = 5.0–5.5 µm. Both morphological observations and molecular analysis of ITS and partial 28S ribosomal RNA gene sequences indicated that the specimens collected from the soil at Beltsville Park from rhizosphere soil samples from Virginia pine represents a new pin nematode species.

59 BASIC BIOLOGICAL SCIENCES↗

Development of Multi-Filament Textured-Powder Bi-2212/Ag Wire with Enhanced Local Area Ratio (Final Technical Report)

ATC has successfully developed a new method for making high-performance Bi-2212/Ag su-perconducting wire with a favorable local area ratio (LAR)=Ag:Bi-2212. The method begins by texturing a fine powder of Bi-2212: the powder is loaded uniformly into an open-sided silver foil channel, the flaps of foil are folded over the powder filling, and the package is hydraulically com-pressed in a die set to form a textured-powder (TP) bar. XRD analysis of the interior powder in a compressed bar shows a texture of 80% after 200 MPa compression.

36 MATERIALS SCIENCE↗

Investigation of an Intermittent Binary Control Strategy for Distributed Aerodynamic Control Devices for Load Alleviation in Wind Turbine Blades

A study was conducted of an intermittent binary control strategy for trailing edge flaps and leading edge spoilers installed on wind turbine blades for the purpose of load alleviation. Cost estimation models were developed for the systems to predict overall impact on levelized cost of energy over the lifecycle of the turbine system. Aeroelastic simulations of turbines with the control strategy implemented showed improved levelized cost for some, but not all cases.

17 WIND ENERGY↗

Comparison of Numerical Methods for Modeling the Wave Field Effects Generated by Individual Wave Energy Converters and Multiple Converter Wave Farms

This numerical study compares the wave field generated by the spectral wave action balance code, SNL-SWAN, to the linear-wave boundary-element method (BEM) code, WAMIT. The objective of this study is to assess the performance of SNL-SWAN for modeling wave field effects produced by individual wave energy converters (WECs) and wave farms comprising multiple WECs by comparing results from SNL-SWAN with those produced by the BEM code WAMIT. BEM codes better model the physics of wave-body interactions and thus simulate a more accurate near-field wave field than spectral codes. In SNL-SWAN, the wave field’s energy extraction is modeled parametrically based on the WEC’s power curve. The comparison between SNL-SWAN and WAMIT is made over a range of incident wave conditions, including short-, medium-, and long-wavelength waves with various amounts of directional spreading, and for three WEC archetypes: a point absorber (PA), a pitching flap (PF) terminator, and a hinged raft (HR) attenuator. Individual WECs and wave farms of five WECs in various configuration were studied with qualitative comparisons made of wave height and spectra at specific locations, and quantitative comparisons of the wave fields over circular arcs around the WECs as a function of radial distance. Results from this numerical study demonstrate that in the near-field, the difference between SNL-SWAN and WAMIT is relatively large (between 20% and 50%), but in the far-field from the array the differences are minimal (between 1% and 5%). The resultant wave field generated by the two different numerical approaches is highly dependent on parameters such as: directional wave spreading, wave reflection or scattering, and the WEC’s power curve.

16 TIDAL AND WAVE POWER↗

Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module

Proteins containing a FIC domain catalyze AMPylation and other post-translational modifications (PTMs). In bacteria, they are typically part of FicTA toxin-antitoxin modules that control conserved biochemical processes such as topoisomerase activity, but they have also repeatedly diversified into host-targeted virulence factors. Among these, Bartonella effector proteins (Beps) comprise a particularly diverse ensemble of FIC domains that subvert various host cellular functions. However, no comprehensive comparative analysis has been performed to infer molecular mechanisms underlying the biochemical and functional diversification of FIC domains in the vast Bep family. Here, we used X-ray crystallography, structural modelling, and phylogenetic analyses to unravel the expansion and diversification of Bep repertoires that evolved in parallel in three Bartonella lineages from a single ancestral FicTA toxin-antitoxin module. Our analysis is based on 99 non-redundant Bep sequences and nine crystal structures. Inferred from the conservation of the FIC signature motif that comprises the catalytic histidine and residues involved in substrate binding, about half of them represent AMP transferases. A quarter of Beps show a glutamate in a strategic position in the putative substrate binding pocket that would interfere with triphosphate-nucleotide binding but may allow binding of an AMPylated target for deAMPylation or another substrate to catalyze a distinct PTM. The β-hairpin flap that registers the modifiable target segment to the active site exhibits remarkable structural variability. The corresponding sequences form few well-defined groups that may recognize distinct target proteins. The binding of Beps to promiscuous FicA antitoxins is well conserved, indicating a role of the antitoxin to inhibit enzymatic activity or to serve as a chaperone for the FIC domain before translocation of the Bep into host cells. Taken together, our analysis indicates a remarkable functional plasticity of Beps that is mostly brought about by structural changes in the substrate pocket and the target dock. These findings may guide future structure–function analyses of the highly versatile FIC domains.

59 BASIC BIOLOGICAL SCIENCES↗

Multibody for Everybody (M4E) - A Linearization Approach to Enable Frequency Domain Analysis, Time Integration and Control Co-Design

1.1 Background/Objectives: Marine energy represents a promising yet underexploited source of power. To increase the harvested power, significant efforts have been made to improve wave energy converter (WEC) modeling capabilities and optimize power take-off (PTO) performance; however, these efforts have often treated WEC dynamics, PTO design, and controller development sequentially. In contrast, control co-design (CCD) is emerging as a promising strategy to address these issues directly, creating a growing need for fast analysis tools suitable for repeated simulation and parametric studies [1]. To support this need, this work presents the Multibody for Everybody (M4E) [2] linearization module, which employs a symbolic toolbox to provide deeper insight of WEC design parameters. The objective is to demonstrate that a minimal-coordinate linearization of articulated WEC dynamics can provide accurate wave response predictions and substantial computational savings relative to nonlinear time-domain simulation, while preserving compatibility with broader wave-energy analysis workflows, enabling CCD. 1.2 Approach/Activities: The proposed approach linearizes the equations of motion, generated by M4E, in minimal coordinates about a selected operating point and combines the resulting system with frequencydomain hydrodynamic terms to incorporate the reduced mass, damping, stiffness, and forcing operators. The linearized model is used for both impedance-based response amplitude operator (RAO) prediction and rapid regular-wave time integration. The methodology is demonstrated on a single-flap device and a FOSWEC configuration, with linearized M4E responses compared against the corresponding nonlinear M4E simulations and WEC-Sim results. Regular-wave time histories, RAO trends, and runtime differences are assessed. The framework is also compatible with broader wave-energy workflows, including coupling to WecOptTool, although that capability is not the focus of this work [3]. 1.3 Results/Lessons: The linearized M4E model reproduces key regularwave response characteristics such as integration and Response Amplitude over multiple frequencies. This module matches nonlinear M4E and WEC-Sim results while substantially reducing integration cost. Thus, the proposed framework can serve as a rapid analysis layer for articulated WEC design, parameter studies, and controls-oriented workflows. The analysis is most appropriate in the near-equilibrium regime, about the linearization point.

16 TIDAL AND WAVE POWER↗

Optimizing Power Generation of a Bottom-Raised Oscillating Surge Wave Energy Converter Using a Theoretical Model: Preprint

Preliminary sizing of an oscillating surge wave energy converter (OSWEC) is an iterative process that relies on knowledge of the relevant hydrodynamic coefficients for a given geometry. Often, the complex definition of the device geometry requires coefficients to be obtained through experiments or numerical boundary element solvers such as WAMIT. These techniques demand significant user and computational effort, therefore inhibiting the fine scale parametrization of object dimensions. In this study, a theoretical model, originally presented in Michele et al. (2016), is developed and demonstrated to efficiently optimize the power production for an OSWEC device (subjected to certain environmental conditions) with variations in device widths, heights, and distances from the seabed. Assuming negligible device thickness, the OSWEC motions are modelled as a bottom-raised two-dimensional flap in regular waves using potential flow theory formulated in elliptical coordinates. The solutions to this diffraction-radiation problem are obtained using Mathieu functions with appropriate boundary conditions. The resulting potentials are then used to derive frequency-dependent expressions for the added mass and radiation damping coefficients, along with wave excitation magnitude in surge, pitch, and coupled surge-pitch motions. Good agreement in hydrodynamic coefficient curves is shown between the theoretical model and the numerical results obtained from the boundary element-based program WAMIT. The theoretical model is then employed to maximize the time-averaged output power while maintaining or reducing the hinge reaction force, with variations in device dimensions, wave frequency and amplitude.

ACE↗

Optimizing Power Generation of a Bottomraised Oscillating Surge Wave Energy Converter Using a Theoretical Model

Preliminary sizing of an oscillating surge wave energy converter (OSWEC) is an iterative process that relies on knowledge of the relevant hydrodynamic coefficients for a given geometry. Often, the complex definition of the device geometry requires coefficients to be obtained through experiments or numerical boundary element solvers such as WAMIT. These techniques demand significant user and computational effort, therefore inhibiting the fine scale parametrization of object dimensions. In this study, a theoretical model, originally presented in Michele et al. (2016), is developed and demonstrated to efficiently optimize the power production for an OSWEC device (subjected to certain environmental conditions) with variations in device widths, heights, and distances from the seabed. Assuming negligible device thickness, the OSWEC motions are modelled as a bottom-raised two-dimensional flap in regular waves using potential flow theory formulated in elliptical coordinates. The solutions to this diffraction-radiation problem are obtained using Mathieu functions with appropriate boundary conditions. The resulting potentials are then used to derive frequency-dependent expressions for the added mass and radiation damping coefficients, along with wave excitation magnitude in surge, pitch, and coupled surge-pitch motions. Good agreement in hydrodynamic coefficient curves is shown between the theoretical model and the numerical results obtained from the boundary element-based program WAMIT. The theoretical model is then employed to maximize the time-averaged output power while maintaining or reducing the hinge reaction force, with variations in device dimensions, wave frequency and amplitude.

ACE↗

Systems and methods for post-treatment of dry adhesive microstructures

Provided are systems and methods for the post-treatment of dry adhesive microstructures. The microstructures may be post-treated to comprise mushroom-like flaps at their tips to interface with the contact surface. In some aspects, a change in material composition of the microstructures in a dry adhesive may affect mechanical properties to enhance or diminish overall adhesive performance. For example, conductive additives can be added to the material to improve adhesive performance. In other aspects, microstructures comprising conductive material may allow for preload engagement sensing systems to be integrated into the microstructures.

Dadkhah Tehrani, Mohammad↗

Parameter-Varying Hydrodynamic Model of a Single Vane in a Variable-Geometry Oscillating Surge Wave Energy Converter: Preprint

This paper presents a study on the time-varying hydrodynamic modeling of an individual flap of a variable geometry oscillating surge wave energy converter (VGOSWEC). The WEC design incorporates controlled surfaces that can modify their orientation relative to the wave motion, reducing hydrodynamic pressure and related loads. This research focuses on characterizing the behavior of the oscillating WEC using a simplified model and three methods for achieving a continuous time-variant model: discrete hydrodynamic parameters, interpolation of hydrodynamic parameters, and a fitting function. The results of this study contribute to the understanding of time-varying hydrodynamic effects in variable geometry oscillating WECs. The findings provide insights into the potential for reducing structural loads and improving the overall performance of such devices. Further research and development in this area could lead to advancements in WEC technologies, enabling their integration into the competitive energy market.

HYDRO ENERGY,TIDAL AND WAVE POWER↗