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At least 469 records · Page 26

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Abstract Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript’s impacts on plant metabolism has employed data from controlled environments. Here, we generated and analyzed data on the variation in the abundance of 26 metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies (GWAS)) and transcripts (using both transcriptome-wide association studies (TWAS) and an explainable artificial intelligence (AI) approach based on random forest (RF)) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

Mathivanan, Ramesh Kanna↗

MCNP6 Modification for the Calculation of Rossi and Feynman Distributions

The Rossi distribution is given by the number of captured neutron pairs as a function of the time interval between the two capture events. This distribution contains a random part, which is given by neutron captures caused by neutrons of different fission chains, and a correlated part, which is given by neutron captures caused by neutrons from the same fission chain. The correlated part exponentially vanishes with the {Delta}t time interval following the decay of prompt neutrons. The Rossi distribution peaks when the time interval between two capture events is small since this condition is satisfied for neutrons generated from the same fission chain. In the Poisson probability distribution, the variance is equal to the mean and the next event probability is independent of the elapsed time since the previous event. Neutron captures events do not follow the Poisson probability distribution because they are correlated events via fission chains. Consequently, the Feynman distribution Y is defined as the variance to mean ratio minus one, of the neutron counts array as a function of a fixed time interval. The MCNP6 source code has been modified to allow the calculation of the Rossi and Feynman distributions. The source code modification takes into account the time when a neutron is emitted by the external neutron source and gives a precision in the timestamp lower than a fraction of nanosecond. The modified MCNP6 version has been used to model KUKA facility driven by a californium neutron source. The prompt neutron decay constants obtained by the Rossi and Feynman methods are in agreement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Prediction on Underestimation of Statistical Uncertainty in Monte Carlo Eigenvalue Calculation for Two-dimensional Heterogeneous Color Set Geometry

In a Monte Carlo calculation, statistical uncertainty is inevitably included in the result. The statistical uncertainty is commonly estimated by the central limit theorem without considering correlation among generations. The statistical uncertainty is usually expected to decrease at the inverse square root of the number of neutron histories. However, in a Monte Carlo eigenvalue calculation in a large geometry whose dominance ratio is close to unity, the central limit theorem would not be valid and thus the statistical uncertainty of fission source distribution can be significantly underestimated when inter-cycle correlation is not appropriately taken into account. The true statistical uncertainty can be calculated by statistical processing of the results obtained by multiple Monte Carlo runs using different initial random seeds, but this approach has a drawback of large calculation cost. Therefore, prediction of true statistical uncertainty by alternate approach is desirable. One of the solutions for this issue is an evaluation method of statistical uncertainty based on the eigenfunction expansion and the Autoregressive model (AR model). In this method, the true statistical uncertainty is theoretically derived by applying the AR model to behavior of expansion coefficients of eigenfunction in fission source distribution during cycles. Underestimation ratio of statistical uncertainty of fission source distribution can be predicted by this method. Note that the underestimation ratio of statistical uncertainty is defined by the ratio of estimated error by a Monte Carlo calculation to the true statistical error. In the previous study, the proposed method was verified in a simple condition such as one energy group, one dimensional homogeneous slab geometry. Contributions of this summary are as follows. Firstly, expression of the noise term that is appeared in the AR model is theoretically derived. Secondly, prediction on underestimation ratio of statistical uncertainty is carried out in a more general case, i.e., flux of each fuel cell in 2 x 2 heterogeneous assembly geometry taken from the C5G7 benchmark problem. Through the present study, applicability of the theoretical prediction for underestimation of statistical uncertainty in practical problems will be verified. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Computing the QRPA level density with the finite amplitude method

Here, we describe a new algorithm to calculate the vibrational nuclear level density of an atomic nucleus. Fictitious perturbation operators that probe the response of the system are generated by drawing their matrix elements from some probability distribution function. We use the Finite Amplitude Method to explicitly compute the response for each such sample. With the help of the Kernel Polynomial Method, we build an estimator of the vibrational level density and provide the upper bound of the relative error in the limit of infinitely many random samples. The new algorithm can give accurate estimates of the vibrational level density. Since it is based on drawing multiple samples of perturbation operators, its computational implementation is naturally parallel and scales like the number of available processing units.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nuclear data uncertainty propagation and modeling uncertainty impact evaluation in neutronics core simulation

Uncertainty analysis is a critical requirement in reactor simulation as it is used to quantify the reliability of best-estimate calculation. A comprehensive uncertainty analysis should characterize all sources of uncertainties in a computationally-feasible and scientifically-defendable manner. Here we employ a well-established reduced order modeling (ROM) based uncertainty quantification methodology to propagate uncertainties throughout neutronic calculations. ROM relies on recent advances in randomized data mining techniques applied to large data streams. In our proposed implementation, the nuclear data uncertainties are first propagated from multi-group level through lattice physics calculation to generate few-group parameter uncertainties, described using a vector of mean values and a covariance matrix. Employing an ROM-based compression of the covariance matrix, the few-group uncertainties are then propagated through downstream core simulation in a computationally efficient manner. This straightforward approach, albeit efficient as compared to brute force forward and/or adjoint-based methods, often employs a number of assumptions that have been unquestioned in the literature of neutronic uncertainty analysis. This manuscript argues that these assumptions could introduce another source of uncertainty referred to as modeling uncertainties, whose magnitude needs to be quantified in tandem with nuclear data uncertainties. Thus, our primary goal is to explore the interactions between these two uncertainty sources in order to assess whether modeling uncertainties have an impact on parameter uncertainties. To explore this endeavor, the impact of a number of modeling assumptions on core attributes uncertainties is quantified. The study employs a CANDU reactor model, with Serpent and NEWT as lattice physics solvers and NESTLE-C as core simulator. The modeling assumptions investigated include those related with the uncertainty propagation method employed, e.g., deterministic vs. stochastic, the few-group energy structure employed to represent the cross-sections, the resonance treatment in lattice physics calculation, the reference values for the cross-section, and the number of samples employed to render ROM compression. Results indicate that some of the modeling assumptions could have a non-negligible impact on the core responses propagated uncertainties, highlighting the need for a more comprehensive approach to combine parameter and modeling uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A graph embedding‐based approach for automatic cyber‐physical power system risk assessment to prevent and mitigate threats at scale

Abstract Power systems are facing an increasing number of cyber incidents, potentially leading to damaging consequences to both physical and cyber aspects. However, the development of analytical methods for the study of large‐scale power infrastructures as cyber‐physical systems is still in its early stages. Drawing inspiration from machine‐learning techniques, the authors introduce a method inspired by the principles of graph embedding that is tailored for quantitative risk assessment and the exploration of possible mitigation strategies of large‐scale cyber‐physical power systems. The primary advantage of the graph embedding approach lies in its ability to generate numerous random walks on a graph, simulating potential access paths. Meanwhile, it enables capturing high‐dimensional structures in low‐dimensional spaces, facilitating advanced machine‐learning applications, and ensuring scalability and adaptability for comprehensive network analysis. By employing this graph embedding‐based approach, the authors present a structured and methodical framework for risk assessment in cyber‐physical systems. The proposed graph embedding‐based risk analysis framework aims to provide a more insightful perspective on cyber‐physical risk assessment and situation awareness for power systems. To validate and demonstrate its applicability, the method has been tested on two cyber‐physical power system models: the Western System Coordinating Council (WSCC) 9‐Bus System and the Illinois 200‐Bus System , thereby showing its advantages in enhancing the accuracy of risk analysis and comprehensiveness of situational awareness.

Sun, Shining↗

Large scale Brownian dynamics of confined suspensions of rigid particles

We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217–296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its “square” root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.

97 MATHEMATICS AND COMPUTING↗

Fast optimization algorithms and the cosmological constant

Denef and Douglas have observed that in certain landscape models the problem of finding small values of the cosmological constant is a large instance of a problem that is hard for the complexity class NP (Nondeterministic Polynomial-time). The number of elementary operations (quantum gates) needed to solve this problem by brute force search exceeds the estimated computational capacity of the observable Universe. Here in this paper, we describe a way out of this puzzling circumstance: despite being NP-hard, the problem of finding a small cosmological constant can be attacked by more sophisticated algorithms whose performance vastly exceeds brute force search. In fact, in some parameter regimes the average-case complexity is polynomial. We demonstrate this by explicitly finding a cosmological constant of order 10 -120 in a randomly generated 10 9 -dimensional Arkani-Hamed–Dimopoulos–Kachru landscape.

79 ASTRONOMY AND ASTROPHYSICS↗

Linear Estimation of Particle Bulk Parameters from Multi-Wavelength Lidar Measurements

An algorithm for linear estimation of aerosol bulk properties such as particle volume, effective radius and complex refractive index from multiwavelength lidar measurements is presented. The approach uses the fact that the total aerosol concentration can well be approximated as a linear combination of aerosol characteristics measured by multiwavelength lidar. Therefore, the aerosol concentration can be estimated from lidar measurements without the need to derive the size distribution, which entails more sophisticated procedures. The definition of the coefficients required for the linear estimates is based on an expansion of the particle size distribution in terms of the measurement kernels. Once the coefficients are established, the approach permits fast retrieval of aerosol bulk properties when compared with the full regularization technique. In addition, the straightforward estimation of bulk properties stabilizes the inversion making it more resistant to noise in the optical data. Numerical tests demonstrate that for data sets containing three aerosol backscattering and two extinction coefficients (so called 3 + 2 ) the uncertainties in the retrieval of particle volume and surface area are below 45% when input data random uncertainties are below 20 %. Moreover, using linear estimates allows reliable retrievals even when the number of input data is reduced. To evaluate the approach, the results obtained using this technique are compared with those based on the previously developed full inversion scheme that relies on the regularization procedure. Both techniques were applied to the data measured by multiwavelength lidar at NASA/GSFC. The results obtained with both methods using the same observations are in good agreement. At the same time, the high speed of the retrieval using linear estimates makes the method preferable for generating aerosol information from extended lidar observations. To demonstrate the efficiency of the method, an extended time series of observations acquired in Turkey in May 2010 was processed using the linear estimates technique permitting, for what we believe to be the first time, temporal-height distributions of particle parameters.

linear estimation↗

Molecular-dynamics study of amorphous SiO{sub 2} relaxation

Using Molecular-Dynamics simulation we observed the generation of amorphous SiO{sub 2} target from a randomly distributed Si and O atoms. We applied a sequence of annealing of the target with various temperature and quenching to room temperature. The relaxation time required by the system to form SiO{sub 4} tetrahedral mesh after a relatively long simulation time, is studied. The final amorphous target was analyzed using the radial distribution function method, which can be compared with the available theoretical and experimental data. We found that up to 70% of the target atoms form the tetrahedral SiO{sub 4} molecules. The number of formed tetrahedral increases following the growth function and the rate of SiO{sub 4} formation follows Arrhenius law, depends on the annealing temperature. The local structure of amorphous SiO{sub 2} after this treatment agrees well with those reported in some literatures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Transient cycling of nitrogen, organic carbon and oxygen within the free-flowing Columbia River corridor: Linking exposure time dependent biogeochemical reactions to river stage fluctuations (Final project report)

The objective of this project was to develop next-generation techniques for representing the transformations of complex reaction networks like those impacting transient river-corridors, then apply them to develop upscaling tools. The project contributed significantly to the development of Lagrangian “mass transfer particle tracking” (MTPT) tools that are the first numerical framework that explicitly separates mixing and spreading processes; a crucial distinction for accurate representations of reaction rates across scales. The MTPT approach uses an operator splitting scheme where physical transport processes are simulated using classical random walk methods and each particle is treated as a “container” that carries with it any number of chemical species. Mixing between particles is simulated using a colocation-probability based mass transfer kernel and reactions are evaluated on each particle after mixing. The method is stable, accurate, and also allows the explicit modeling of residence time distributions of the individual containers of mass. The MTPT scheme allowed us to explore several research questions related to reactive transport in river corridors and complex reaction networks. We found that it is possible to quantify the exposure time distributions (ETDs) of reactants and that this does suggest some pathways to upscaling. However, comparable approximations can be obtained using simplified (reduced dimensionality) MTPT simulations in less time with similar uncertainty, so development of extensive ETD-based methods was not productive. The major findings are that i) the MTPT schemes are robust and highly accurate across a range of arbitrarily complex reactions, ii) the methods can be efficiently parallelized and the parallel performance characteristics of MTPT are predictable, and iii) the MTPT tools allow simultaneous tracking of residence time. The development of these research tools into efficient software packages continues. The methods are already available to the community because open-source, working examples have been included with all publications.

54 ENVIRONMENTAL SCIENCES↗

Atmospheric Propagation Effects Relevant to Optical Communications

A number of atmospheric phenomena affect the propagation of light. This article reviews the effects of clear-air turbulence as well as atmospheric turbidity on optical communications. Among the phenomena considered are astronomical and random refraction, scintillation, beam broadening, spatial coherence, angle of arrival, aperture averaging, absorption and scattering, and the effect of opaque clouds. An extensive reference list is also provided for further study, Useful information on the atmospheric propagation of light in resolution to optical deep-space communications to an earth-based receiving station is available, however, further data must be generated before such a link can be designed with committed performance.

Shaik, K. S.↗

Multi-field inflation with random potentials: field dimension, feature scale and non-Gaussianity

We explore the super-horizon evolution of the two-point and three-point correlation functions of the primordial density perturbation in randomly-generated multi-field potentials. We use the Transport method to evolve perturbations and give full evolutionary histories for observables. Identifying the separate universe assumption as being analogous to a geometrical description of light rays, we give an expression for the width of the bundle, thereby allowing us to monitor evolution towards the adiabatic limit, as well as providing a useful means of understanding the behaviour in f{sub NL}. Finally, viewing our random potential as a toy model of inflation in the string landscape, we build distributions for observables by evolving trajectories for a large number of realisations of the potential and comment on the prospects for testing such models. We find the distributions for observables to be insensitive to the number of fields over the range 2 to 6, but that these distributions are highly sensitive to the scale of features in the potential. Most sensitive to the scale of features is the spectral index, with more than an order of magnitude increase in the dispersion of predictions over the range of feature scales investigated. Least sensitive was the non-Gaussianity parameter f{sub NL}, which was consistently small; we found no examples of realisations whose non-Gaussianity is capable of being observed by any planned experiment.

79 ASTRONOMY AND ASTROPHYSICS↗

A novel framework for hosting capacity analysis with spatio-temporal probabilistic voltage sensitivity analysis

Smart grids are envisioned to accommodate high penetration of distributed photovoltaic (PV) generation, which may cause adverse grid impacts in terms of voltage violations. Therefore, PV Hosting capacity is being used as a planning tool to determine the maximum PV installation capacity that causes the first voltage violation and above which would require infrastructure upgrades. Additionally, traditional methods of Hosting capacity analysis are scenario based and computationally complex as they rely on iterative load flow algorithms that require investigating a large number of scenarios for accurate assessment of PV impacts. Therefore, this paper presents a computationally efficient analytical approach to compute the probability distribution of voltage change due to random behavior of randomly located multiple distributed PVs. The proposed approach is based on Spatio-temporal probabilistic voltage sensitivity analysis that exploits both spatial and temporal uncertainties associated with PV injections. Thereafter, the derived distribution is used to quantify voltage violations for various PV penetration levels and subsequently determine the hosting capacity of the system without the need to examine large number of scenarios. Results of the proposed framework are validated via conventional load flow based simulation approach on the IEEE 37 and IEEE 123 node test systems.

42 ENGINEERING↗

A mixture of grass–legume cover crop species may ameliorate water stress in a changing climate

Climate change models predict increasing precipitation variability in the mid-latitude regions of Earth, generating a need to reduce the negative impacts of these changes on crop production. Despite considerable research on how cover crops support agriculture in a changing climate, understanding is limited of how climate change influences the growth of cover crops. We investigated the early development of two common cover crop species—crimson clover (Trifolium incarnatum) and rye (Secale cereale)—and hypothesized that growing them in the mixture would ameliorate stress from drought or waterlogging. This hypothesis was tested in a 25-day greenhouse experiment, where the two factors (species number and water stress) were fully crossed in randomized blocks, and plant responses were quantified through survival, growth rate, biomass production and root morphology. Water stress negatively influenced the early growth of these two species in contrasting ways: crimson clover was susceptible to drought while rye performed poorly under waterlogging. Per-plant biomass in rye was always greater in mixture than in monoculture, while per-plant biomass of crimson clover was greater in mixture under drought. Both species grew longer roots in mixture than in monoculture under drought, and total biomass of mixtures did not differ significantly from the more-productive monoculture (rye) in any water condition. In the face of increasingly variable precipitation, growing crimson clover and rye together has potential to ameliorate water stress, a possibility that should be further investigated in field experiments.

54 ENVIRONMENTAL SCIENCES↗

Effect of the Inhomogeneity of Ice Crystals on Retrieving Ice Cloud Optical Thickness and Effective Particle Size

Spherical or spheroidal air bubbles are generally trapped in the formation of rapidly growing ice crystals. In this study the single-scattering properties of inhomogeneous ice crystals containing air bubbles are investigated. Specifically, a computational model based on an improved geometric-optics method (IGOM) has been developed to simulate the scattering of light by randomly oriented hexagonal ice crystals containing spherical or spheroidal air bubbles. A combination of the ray-tracing technique and the Monte Carlo method is used. The effect of the air bubbles within ice crystals is to smooth the phase functions, diminish the 22deg and 46deg halo peaks, and substantially reduce the backscatter relative to bubble-free particles. These features vary with the number, sizes, locations and shapes of the air bubbles within ice crystals. Moreover, the asymmetry factors of inhomogeneous ice crystals decrease as the volume of air bubbles increases. Cloud reflectance lookup tables were generated at wavelengths 0.65 m and 2.13 m with different air-bubble conditions to examine the impact of the bubbles on retrieving ice cloud optical thickness and effective particle size. The reflectances simulated for inhomogeneous ice crystals are slightly larger than those computed for homogenous ice crystals at a wavelength of 0.65 microns. Thus, the retrieved cloud optical thicknesses are reduced by employing inhomogeneous ice cloud models. At a wavelength of 2.13 microns, including air bubbles in ice cloud models may also increase the reflectance. This effect implies that the retrieved effective particle sizes for inhomogeneous ice crystals are larger than those retrieved for homogeneous ice crystals, particularly, in the case of large air bubbles.

Xie, Yu↗

Tool for Generation of MAC/GMC Representative Unit Cell for CMC/PMC Analysis

This document describes a recently developed analysis tool that enhances the resident capabilities of the Micromechanics Analysis Code with the Generalized Method of Cells (MAC/GMC) 4.0. This tool is especially useful in analyzing ceramic matrix composites (CMCs), where higher fidelity with improved accuracy of local response is needed. The tool, however, can be used for analyzing polymer matrix composites (PMCs) as well. MAC/GMC 4.0 is a composite material and laminate analysis software developed at NASA Glenn Research Center. The software package has been built around the concept of the generalized method of cells (GMC). The computer code is developed with a user friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermomechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The primary focus of the current effort is to provide a graphical user interface (GUI) capability that generates a number of different user-defined repeating unit cells (RUCs). In addition, the code has provisions for generation of a MAC/GMC-compatible input text file that can be merged with any MAC/GMC input file tailored to analyze composite materials. Although the primary intention was to address the three different constituents and phases that are usually present in CMCs-namely, fibers, matrix, and interphase-it can be easily modified to address two-phase polymer matrix composite (PMC) materials where an interphase is absent. Currently, the tool capability includes generation of RUCs for square packing, hexagonal packing, and random fiber packing as well as RUCs based on actual composite micrographs. All these options have the fibers modeled as having a circular cross-sectional area. In addition, a simplified version of RUC is provided where the fibers are treated as having a square cross section and are distributed randomly. This RUC facilitates a speedy analysis using the higher fidelity version of GMC known as HFGMC. The first four mentioned options above support uniform subcell discretization. The last one has variable subcell sizes due to the primary intention of keeping the RUC size to a minimum to gain the speed ups using the higher fidelity version of MAC. The code is implemented within the MATLAB (The Mathworks, Inc., Natick, MA) developmental framework; however, a standalone application that does not need a priori MATLAB installation is also created with the aid of the MATLAB compiler.

Materials Engineering↗

Optimal calibration of gates in trapped-ion quantum computers

Abstract To harness the power of quantum computing, it is essential that a quantum computer provide maximal possible fidelity for a quantum circuit. To this end, much work has been done in the context of qubit routing or embedding, i.e., mapping circuit qubits to physical qubits based on gate performance metrics to optimize the fidelity of execution. Here, we take an alternative approach that leverages a unique capability of a trapped-ion quantum computer, i.e., the all-to-all qubit connectivity. We develop a method to determine a fixed number (budget) of quantum gates that, when calibrated, will maximize the fidelity of a batch of input quantum programs. This dynamic allocation of calibration resources on randomly accessible gates, determined using our heuristics, increases, for a wide range of calibration budget, the average fidelity from 70% or lower to 90% or higher for a typical batch of jobs on an 11-qubit device, in which the fidelity of calibrated and uncalibrated gates are taken to be 99% and 90%, respectively. Our heuristics are scalable, more than 2.5 orders of magnitude faster than a randomized method for synthetic benchmark circuits generated based on real-world use cases.

Maksymov, Andrii (ORCID:0000000282442851)↗