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DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗

DOE OSTI2020

Radiation Mapping for an Unmanned Aerial Vehicle: Development and Simulated Testing of Algorithms for Source Mapping and Navigation Path Generation

Image reconstruction algorithms were developed for radiation source mapping and used for generating the search path of a moving radiation detector, such as one onboard an unmanned aerial vehicle. Simulations consisted of first assuming radioactive sources of varying complexity and estimating the radiation fields that would then be produced by that source distribution. Next, the "measurements" that would result from a pair of adjacent spatial locations were computed. A crude estimate of the source distribution likely to have produced such "measurements" was reconstructed based upon the limited measurements. Location of the next "measurement" was then determined as halfway between the location of the estimated source and the current "measurement." With each additional sample, improved source distribution reconstructions were made and used to inform the immediate direction of detector motion. Source reconstruction or mapping was formulated as an inverse problem solved with either maximum a posteriori or least squares (LS) regression deconvolution methods. Different amounts of noise were added to the simulated "measurements," allowing evaluation of the methods' performances as functions of signal-to-noise ratio of the measured map. As expected, methods that promote sparsity were better suited in reconstructing point sources. Reliable prior information of the source distribution also improved the reconstruction results, especially with distributed sources. With a non-negative least square algorithm and the suggested paths it generated, location of sources was successfully estimated to an accuracy of 0.014 m within nine iterations in a single-source scenario and 12 iterations in a two-source scenario, given a 10% error on the integrated counts and a Poisson distribution of the noise associated with the measured counts.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2025

Simulating Meson Scattering on Spin Quantum Simulators

Studying high-energy collisions of composite particles, such as hadrons and nuclei, is an outstanding goal for quantum simulators. However, preparation of hadronic wave packets has posed a significant challenge, due to the complexity of hadrons and the precise structure of wave packets. This has limited demonstrations of hadron scattering on quantum simulators to date. Observations of confinement and composite excitations in quantum spin systems have opened up the possibility to explore scattering dynamics in spin models. In this article, we develop two methods to create entangled spin states corresponding to wave packets of composite particles in analog quantum simulators of Ising spin Hamiltonians. One wave-packet preparation method uses the blockade effect enabled by beyond-nearest-neighbor Ising spin interactions. The other method utilizes a quantum-bus-mediated exchange, such as the native spin-phonon coupling in trapped-ion arrays. With a focus on trapped-ion simulators, we numerically benchmark both methods and show that high-fidelity wave packets can be achieved in near-term experiments. We numerically study scattering of wave packets for experimentally realizable parameters in the Ising model and find inelastic-scattering regimes, corresponding to particle production in the scattering event, with prominent and distinct experimental signals. Our proposal, therefore, demonstrates the potential of observing inelastic scattering in near-term quantum simulators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

3D modeling of deep borehole electromagnetic measurements with energized casing source for fracture mapping at the Utah Frontier Observatory for Research in Geothermal Energy

Here, we present a 3D numerical modelling analysis evaluating the deployment of a borehole electromagnetic measurement tool to detect and image a stimulated zone at the Utah Frontier Observatory for Research in Geothermal Energy geothermal site. As the depth to the geothermal reservoir is several kilometres and the size of the stimulated zone is limited to several 100 m, surface-based controlled-source electromagnetic measurements lack the sensitivity for detecting changes in electrical resistivity caused by the stimulation. To overcome the limitation, the study evaluates the feasibility of using a three-component borehole magnetic receiver system at the Frontier Observatory for Research in Geothermal Energy site. To provide sufficient currents inside and around the enhanced geothermal reservoir, we use an injection well as an energized casing source. To efficiently simulate energizing the injection well in a realistic 3D resistivity model, we introduce a novel modelling workflow that leverages the strengths of both 3D cylindrical-mesh-based electromagnetic modelling code and 3D tetrahedral-mesh-based electromagnetic modelling code. The former is particularly well-suited for modelling hollow cylindrical objects like casings, whereas the latter excels at representing more complex 3D geological structures. In this workflow, our initial step involves computing current densities along a vertical steel-cased well using a 3D cylindrical electromagnetic modelling code. Subsequently, we distribute a series of equivalent current sources along the well's trajectory within a complex 3D resistivity model. We then discretize this model using a tetrahedral mesh and simulate the borehole electromagnetic responses excited by the casing source using a 3D finite-element electromagnetic code. This multi-step approach enables us to simulate 3D casing source electromagnetic responses within a complex 3D resistivity model, without the need for explicit discretization of the well using an excessive number of fine cells. We discuss the applicability and limitations of this proposed workflow within an electromagnetic modelling scenario where an energized well is deviated, such as at the Frontier Observatory for Research in Geothermal Energy site. Using the workflow, we demonstrate that the combined use of the energized casing source and the borehole electromagnetic receiver system offer measurable magnetic field amplitudes and sensitivity to the deep localized stimulated zone. The measurements can also distinguish between parallel-fracture anisotropic reservoirs and isotropic cases, providing valuable insights into the fracture system of the stimulated zone. Besides the magnetic field measurements, vertical electric field measurements in the open well sections are also highly sensitive to the stimulated zone and can be used as additional data for detecting and imaging the target. We can also acquire additional multiple-source data by grounding the surface electrode at various locations and repeating borehole electromagnetic measurements. This approach can increase the number of monitoring data by several factors, providing a more comprehensive dataset for analysing the deep-localized stimulated zone. The numerical analysis indicates that it is feasible to use the combination of the energized casing and downhole electromagnetic measurements in monitoring localized stimulated zone at large depths.

58 GEOSCIENCES↗

DOE OSTI2021

Meshfree simulation and experimental validation of extreme thermomechanical conditions in friction stir extrusion

Abstract Friction stir extrusion (FSE) is a novel solid-phase processing technique that consolidates and extrudes metal powders, flakes, chips, or billets into high-performance parts by plastic deformation, which has the potential to save substantial processing time and energy. Currently, most studies on FSE are experimental and only a few numerical models have been developed to explain and predict the complex physics of the process. In this work, a meshfree simulation framework based on smoothed particle hydrodynamics (SPH) was developed for FSE. Unlike traditional grid-based methods, SPH is a Lagrangian particle-based method that can handle severe material deformations, capture moving interfaces and surfaces, and monitor the field variable histories explicitly without complicated tracking schemes. These aspects of SPH make it attractive for the FSE process, where in situ evolution of field variables is difficult to observe experimentally. To this end, a 3-D, fully thermomechanically coupled SPH model was developed to simulate the FSE of aluminum wires. The developed model was thoroughly validated by comparing the numerically predicted material flow, strain, temperature history, and extrusion force with experimental results for a certain set of process parameters. The validated SPH model can serve as an effective tool to predict and better understand the extreme thermomechanical conditions during the FSE process.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Global variability in atmospheric new particle formation mechanisms

A key challenge in aerosol pollution studies and climate change assessment is to understand how atmospheric aerosol particles are initially formed. Although new particle formation (NPF) mechanisms have been described at specific sites, in most regions, such mechanisms remain uncertain to a large extent because of the limited ability of atmospheric models to simulate critical NPF processes. Here we synthesize molecular-level experiments to develop comprehensive representations of 11 NPF mechanisms and the complex chemical transformation of precursor gases in a fully coupled global climate model. Combined simulations and observations show that the dominant NPF mechanisms are distinct worldwide and vary with region and altitude. Previously neglected or underrepresented mechanisms involving organics, amines, iodine oxoacids and HNO 3 probably dominate NPF in most regions with high concentrations of aerosols or large aerosol radiative forcing; such regions include oceanic and human-polluted continental boundary layers, as well as the upper troposphere over rainforests and Asian monsoon regions. These underrepresented mechanisms also play notable roles in other areas, such as the upper troposphere of the Pacific and Atlantic oceans. Accordingly, NPF accounts for different fractions (10–80%) of the nuclei on which cloud forms at 0.5% supersaturation over various regions in the lower troposphere. The comprehensive simulation of global NPF mechanisms can help improve estimation and source attribution of the climate effects of aerosols.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Impact of bar resonances in the velocity–space distribution of the solar neighbourhood stars in a self-consistent N -body Galactic disc simulation

ABSTRACT The velocity–space distribution of the solar neighbourhood stars shows complex substructures. Most of the previous studies use static potentials to investigate their origins. Instead we use a self-consistent N-body model of the Milky Way, whose potential is asymmetric and evolves with time. In this paper, we quantitatively evaluate the similarities of the velocity–space distributions in the N-body model and that of the solar neighbourhood, using Kullback–Leibler divergence (KLD). The KLD analysis shows the time evolution and spatial variation of the velocity–space distribution. The KLD fluctuates with time, which indicates the velocity–space distribution at a fixed position is not always similar to that of the solar neighbourhood. Some positions show velocity–space distributions with small KLDs (high similarities) more frequently than others. One of them locates at $(R,\phi)=(8.2\,\,\rm{\mathrm{kpc}}, 30^\circ)$, where R and ϕ are the distance from the galactic centre and the angle with respect to the bar’s major axis, respectively. The detection frequency is higher in the inter-arm regions than in the arm regions. In the velocity maps with small KLDs, we identify the velocity–space substructures, which consist of particles trapped in bar resonances. The bar resonances have significant impact on the stellar velocity–space distribution even though the galactic potential is not static.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Doppler-Lidar Evaluation of HRRR-Model Skill at Simulating Summertime Wind Regimes in the Columbia River Basin during WFIP2

Complex-terrain locations often have repeatable near-surface wind patterns, such as synoptic gap flows and local thermally forced flows. An example is the Columbia River Valley in east-central Oregon-Washington, a significant wind-energy-generation region and the site of the Second Wind-Forecast Improvement Project (WFIP2). Data from three Doppler lidars deployed during WFIP2 define and characterize summertime wind regimes and their large-scale contexts, and provide insight into NWP model errors by examining differences in the ability of a model [NOAA’s High-Resolution Rapid-Refresh (HRRR-version1)] to forecast wind-speed profiles for different regimes. Seven regimes were identified based on daily time series of the lidar-measured rotor-layer winds, which then suggested two broad categories. First, in three regimes the primary dynamic forcing was the large-scale pressure gradient. Second, in two regimes the dominant forcing was the diurnal heating-cooling cycle (regional sea-breeze-type dynamics), including the marine intrusion previously described, which generates strong nocturnal winds over the region. The other two included a hybrid regime and a non-conforming regime. For the large-scale pressure-gradient regimes, HRRR had wind-speed biases of ~1 m s -1 and RMSEs of 2-3 m s -1 . Errors were much larger for the thermally forced regimes, owing to the premature demise of the strong nocturnal flow in HRRR. Thus, the more dominant the role of surface heating in generating the flow, the larger the errors. Major errors could result from surface heating of the atmosphere, boundary-layer responses to that heating, and associated terrain interactions. Finally, measurement/modeling research programs should be aimed at determining which modeled processes produce the largest errors, so those processes can be improved and errors reduced.

17 WIND ENERGY↗

DOE OSTI2021

Empirical Model of Puncture Energy for Metals

The purpose of this work is to fit a previously developed empirical equation for puncture energy to simulation data. The conservative puncture energy equation could be used to expedite the process of performing calculations in the development of safety measures, avoiding the need to create complex finite element models for specific puncture scenarios. A total of 108 simulations are developed by varying coupon thickness, coupon material, probe shape, and probe diameter. The simulations are comprised of a low-velocity probe puncturing the coupons, from which the probe kinetic energy change is calculated. The empirical equation is fit to the dimensions, material properties, and energy results using a non-linear least-squares regression method within Python, which determines the two constant parameters for each fit. More statistically significant fit results are achieved by separating the data by probe shape and coupon material.

42 ENGINEERING↗

DOE OSTI2021

ForSE: A GAN-based Algorithm for Extending CMB Foreground Models to Subdegree Angular Scales

We present ForSE (Foreground Scale Extender), a novel Python package that aims to overcome the current limitations in the simulation of diffuse Galactic radiation, in the context of cosmic microwave background (CMB) experiments. ForSE exploits the ability of generative adversarial neural networks (GANs) to learn and reproduce complex features present in a set of images, with the goal of simulating realistic and non-Gaussian foreground radiation at subdegree angular scales. This is of great importance in order to estimate the foreground contamination to lensing reconstruction, delensing, and primordial B-modes for future CMB experiments. We applied this algorithm to Galactic thermal dust emission in both total intensity and polarization. Our results show how ForSE is able to generate small-scale features (at 12') having as input the large-scale ones (80'). The injected structures have statistical properties, evaluated by means of the Minkowski functionals, in good agreement with those of the real sky and which show the correct amplitude scaling as a function of the angular dimension. Furthermore, the obtained thermal dust Stokes Q and U full-sky maps as well as the ForSE package are publicly available for download.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin

The lanmodulin (LanM) protein has emerged as an effective means for rare earth element (REE) extraction and separation from complex feedstocks without the use of organic solvents. Whereas the binding of LanM to individual REEs has been well characterized, little is known about the thermodynamics of mixed metal binding complexes (i.e., heterogeneous ion complexes), which limits the ability to accurately predict separation performance for a given metal ion mixture. In this paper, we employ the law of mass action to establish a theory of perfect cooperativity for LanM-REE complexation at the two highest-affinity binding sites. The theory is then used to derive an equation that explains the nonintuitive REE binding behavior of LanM, where separation factors for binary pairs of ions vary widely based on the ratio of ions in the aqueous phase, a phenomenon that is distinct from single-ion-binding chemical chelators. We then experimentally validate this theory and perform the first quantitative characterization of LanM complexation with heterogeneous ion pairs using resin-immobilized LanM. Importantly, the resulting homogeneous and heterogeneous constants enable accurate prediction of the equilibrium state of LanM in the presence of mixtures of up to 10 REEs, confirming that the perfect cooperativity model is an accurate mechanistic description of REE complexation by LanM. We further employ the model to simulate separation performance over a range of homogeneous and heterogeneous binding constants, revealing important insights into how mixed binding differentially impacts REE separations based on the relative positioning of the ion pairs within the lanthanide series. In addition to informing REE separation process optimization, these results provide mathematical and experimental insight into competition dynamics in other ubiquitous and medically relevant, cooperative binding proteins, such as calmodulin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Aquaplanets as a Framework for Examination of Aerosol Effects

Although fundamental to the planetary radiative balance, aerosol impacts are highly uncertain in climate simulations because of the uneven distribution of aerosol sources and the complex interactions with radiation and clouds that are difficult to represent in climate models. This study proposes that aquaplanet configurations represent an idealized framework to investigate aerosol effects. As a simple demonstration, a series of aquaplanet simulations with the Community Atmosphere Model version 6 shows that the spatial distribution of aerosol emissions changes the aerosol effective radiative forcing even with unchanged total emissions. Some statistical properties of the simulations are presented to show that relatively short model integrations yield robust results. Much of the aerosol effect is shown to arise from aerosol–cloud interactions, especially through rapid adjustments associated with the aerosol lifetime effect that alter the cloud optical thickness.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

NED_Asteroid_Energy_Deposition

In the event of a potentially catastrophic asteroid impact, with sufficient warning time, deploying a nuclear device remains a powerful option for planetary defense if a kinetic impactor proves insufficient. Predicting the effectiveness of a potential nuclear deflection or disruption mission depends on accurate multiphysics simulations of the device's x-ray energy deposition into the asteroid and the resulting material ablation. These simulations span many orders of magnitude, require a variety of different complex physics packages, and are computationally expensive. Having an efficient and accurate way of modeling this system is necessary for exploring a mission's sensitivity to the asteroid's range of physical properties. To expedite future simulations, we present a completed x-ray energy deposition model developed using the radiation-hydrodynamics code Kull which can be used to initiate a nuclear mitigation mission hydrocode. The model spans a wide variety of possible mission initial conditions: four different asteroid-like materials (Silicon Dioxide, Forsterite, Iron, and Ice), two different source spectra (1 and 2 keV blackbodies), and then a broad range of radiation fluences (0.0001 to 1 kt per square meter), source durations (10 to 100 ns), and asteroid porosities (0 to 80 percent). Using blowoff momentum as the primary metric, the modelinitiated simulation results match the full radiation-hydrodynamics results to within 10 percent. Please reference the journal article: Burkey et al., X-Ray Energy Deposition Model for Simulating Asteroid Response to a Nuclear Planetary Defense Mitigation Mission, Planetary Science Journal, (2023) for more information.

Managan, RobertA↗

DOE OSTI2023

X-Ray Energy Deposition Model for Simulating Asteroid Response to a Nuclear Planetary Defense Mitigation Mission

Abstract In the event of a potentially catastrophic asteroid impact, with sufficient warning time, deploying a nuclear device remains a powerful option for planetary defense if a kinetic impactor or other means of deflection proves insufficient. Predicting the effectiveness of a potential nuclear deflection or disruption mission depends on accurate multiphysics simulations of the device's X-ray energy deposition into the asteroid and the resulting material ablation. The relevant physics in these simulations span many orders of magnitude, require a variety of different complex physics packages, and are computationally expensive. Having an efficient and accurate way of modeling this system is necessary for exploring a mission's sensitivity to the asteroid's range of physical properties. To expedite future simulations, we present a completed X-ray energy deposition model developed using the radiation-hydrodynamics code Kull that can be used to initiate a nuclear mitigation mission calculation. The model spans a wide variety of possible mission initial conditions: four different asteroid-like materials at a range of porosities, two different source spectra, and a broad range of radiation fluences, source durations, and angles of incidence. Using blowoff momentum as the primary metric, the model-initiated simulation results match the full radiation-hydrodynamics results to within 10%.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

CompF2: Theoretical Calculations and Simulation Topical Group Report

This report summarizes the work of the Computational Frontier topical group on theoretical calculations and simulation for Snowmass 2021. We discuss the challenges, potential solutions, and needs facing six diverse but related topical areas that span the subject of theoretical calculations and simulation in high energy physics (HEP): cosmic calculations, particle accelerator modeling, detector simulation, event generators, perturbative calculations, and lattice QCD (quantum chromodynamics). The challenges arise from the next generations of HEP experiments, which will include more complex instruments, provide larger data volumes, and perform more precise measurements. Calculations and simulations will need to keep up with these increased requirements. The other aspect of the challenge is the evolution of computing landscape away from general-purpose computing on CPUs and toward special-purpose accelerators and coprocessors such as GPUs and FPGAs. These newer devices can provide substantial improvements for certain categories of algorithms, at the expense of more specialized programming and memory and data access patterns.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Overview of Geant4 Physics

Geant4 is a powerful toolkit for simulating particle interactions across a wide energy range (0 to ~TeV). It offers comprehensive physics processes for various particle types, allowing users to define custom processes using the G4VProcess interface. Major categories include electromagnetic, hadronic, decay, parameterized processes, and transportation. A critical feature is the PhysicsList, which specifies particles and processes for simulations. Users can choose between G4VUserPhysicsList for simpler environments or G4VModularPhysicsList for more complex scenarios, leveraging pre-defined or custom G4VPhysicsConstructors. Additionally, Geant4 provides reference physics lists and the G4PhysicsListFactory for well-established applications, facilitating simulation development in diverse domains.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Hybridized Methods for Quantum Simulation in the Interaction Picture

Conventional methods of quantum simulation involve trade-offs that limit their applicability to specific contexts where their use is optimal. In particular, the interaction picture simulation has been found to provide substantial asymptotic advantages for some Hamiltonians, but incurs prohibitive constant factors and is incompatible with methods like qubitization. We provide a framework that allows different simulation methods to be hybridized and thereby improve performance for interaction picture simulations over known algorithms. These approaches show asymptotic improvements over the individual methods that comprise them and further make interaction picture simulation methods practical in the near term. Physical applications of these hybridized methods yield a gate complexity scaling as log 2 ⁡ Λ in the electric cutoff Λ for the Schwinger Model and independent of the electron density for collective neutrino oscillations, outperforming the scaling for all current algorithms with these parameters. For the general problem of Hamiltonian simulation subject to dynamical constraints, these methods yield a query complexity independent of the penalty parameter λ used to impose an energy cost on time-evolution into an unphysical subspace.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation

This Final Scientific and Technical Report summarizes work performed under the Phase IIA SBIR project “Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation” (DE-SC0020906) from August 2023 through August 2025. The objective of the Phase IIA effort was to mature and harden capabilities developed during Phase II, with the goal of enabling practical interoperability between Coreform’s isogeometric analysis (IGA) technologies and the Multiphysics Object-Oriented Simulation Environment (MOOSE), while improving robustness, performance, and scalability for complex, nuclear-relevant geometries. Over the course of Phase IIA, the project established and validated an extraction-based interoperability pathway between Coreform tools and MOOSE. A combined mesh and matrix format was defined collaboratively with MOOSE developers and integrated into the solver, enabling standard MOOSE workflows to operate on data exported from Coreform’s IGA and Flex Representation Method (FRM) pipelines. Early demonstrations validated architectural compatibility using linear solid mechanics problems, while later efforts focused on benchmark testing and external use. By the end of the project period, engineers at BWXT were able to independently set up and execute a simulation using the Coreform–MOOSE workflow and provide direct feedback that informed further refinement. In parallel, substantial effort was devoted to improving the robustness of trimmed U-spline construction for complex CAD geometries. A growing test suite of nuclear-relevant models was compiled through collaboration with multiple stakeholders and used to drive extensive bug fixing and reliability improvements. These efforts resulted in improved robustness and performance, including the addition of fallback capabilities that enhance reliability when the underlying commercial CAD kernel fails. Performance-oriented work progressed later in the project, with the development and demonstration of methods to decompose complex geometries into structured subregions and updated data representations to support more efficient solver processing. Additionally, extensive enhancements to threadsafe parallel data structures and trimming operations established a foundation for scalable processing of large assemblies. Collaboration with Sandia National Laboratories on the SGM geometric modeling kernel advanced to a functioning interface test case, positioning the workflow for future kernel integration. Overall, the Phase IIA effort successfully transitioned the project from architectural proof-of-concept to externally exercised, solver-integrated capability, while clarifying remaining technical challenges related to standardization, performance optimization, and kernel integration.

42 ENGINEERING↗