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At least 361 records · Page 20

Striving to translate shale physics across ten orders of magnitude: What have we learned?

Shales will play an important role in the successful transition of energy from fossil-based resources to renewables in the coming decades. Aside from being a significant source of low-carbon intensity fuels, like natural gas, they also serve as geologic seals of subsurface formations that may be used to isolate nuclear waste, sequester CO 2 , or store intermittent energy (e.g., solar hydrogen). Despite their importance, shales pose significant engineering and environmental challenges due to their nanoporous structure and extreme heterogeneity that spans at least ~10 orders of magnitude in spatial scale. Two challenges inhibit a system-level understanding: (1) the physics of fluid flow and phase behavior in shales are poorly understood due to the dominant molecular interactions between minerals and fluids under confinement, and (2) the apparent lack of scale separation that prevents a reliable (closed) description of the physics at any single scale of observation. In this review, we focus on the latter issue and discuss scale translation, which in its broadest sense is transforming data or simulations from one spatiotemporal scale to another. While effective scale translation is not exclusive to shales, but all geologic porous media, the need for it is especially acute in shales given their high degree of heterogeneity. Classical theories like homogenization, while indispensable, fail when scales are not separated. Other methods, like numerical upscaling, scale-translate in only one direction: small to large, but not the reverse, called downscaling. However, the confluence of advances in three areas are bringing challenging problems such as shales within reach: increased computational power and scalable algorithms; high-resolution imaging and multi-modal data acquisition; and machine learning to process massive amounts of data. While these advances equip geoscientists with a wide array of experimental and computational tools, no individual tool can probe the entire gamut of heterogeneity in shales. Their effective use, therefore, requires an ability to bridge between various data types obtained at different scales. The aim of this review is to present a coherent account of computational and experimental methods that may be used to achieve just that, i.e., to perform scale translation. We provide a broader definition of scale translation, one that transcends classical homogenization and upscaling methods, but is consistent with them and accommodates notions like downscaling and data translation. After a brief introduction to homogenization, we review hybrid methods, numerical upscaling and its recent extensions, multiscale computing, high-resolution imaging, and machine learning. We place particular emphasis on multiscale computing and propose an algorithmic framework to bridge between the pore (micro) and Darcy (macro) scales. Throughout the paper, we draw comparisons between the various methods and highlight their (often hidden) similarities, differences, benefits, and pitfalls. We finally conclude with two case studies on shales that exemplify some of the methods presented.

58 GEOSCIENCES↗

DNTTD (Distributed Non-Negative Tensor Train Decomposition)

The era of exascale computing opens new venues for innovations and discoveries in many scientific, engineering, and commercial fields. However, with the exa flops also come the extra-large high-dimensional data generated by high performance computing. High-dimensional data is presented as multidimensional arrays, aka tensors. The presence of latent (not directly observable) structures in the tensor allows a unique representation and compression of the data by classical tensor factorization techniques. However, the classical tensor methods are not always stable or they can be exponential in their memory requirements, which makes them not suitable for high-dimensional tensors. Tensor train (TT) is a state-of-the-art tensor network introduced for factorization of high-dimensional tensors. TT transforms the initial high-dimensional tensor in a network of three-dimensional tensors that requires only a linear storage. Many real-world data, such as, density, temperature, population, probability, etc., are non-negative and for an easy interpretation, the algorithms preserving non-negativity are preferred. Here, we introduce a distributed non-negative tensor-train and demonstrate its scalability and the compression on synthetic and real world big datasets.

Bhattarai, Manish↗

A Fundamentally New Coupled Approach to Contact Mechanics via the Dirichlet‐Neumann Schwarz Alternating Method

Contact phenomena are crucial for understanding the behavior of mechanical systems. However, existing computational approaches for simulating mechanical contact often face numerical challenges, such as inaccurate physical predictions, energy conservation errors, and unwanted oscillations. Here, we introduce an alternative technique for simulating dynamic contact based on the non‐overlapping Schwarz alternating method, originally developed for domain decomposition. In multibody contact scenarios, this method treats each body as a separate, non‐overlapping domain and prevents interpenetration using an alternating Dirichlet–Neumann iterative process. This approach has a strong theoretical foundation, eliminates the need for contact constraints, and offers flexibility, making it ideal for multiscale and multiphysics applications. We conducted a numerical comparison between the Schwarz method and traditional methods, such as the Lagrange multiplier and penalty methods, focusing on a benchmark impact problem. Our results indicate that the Schwarz alternating method outperforms traditional methods in several key areas: it provides more accurate predictions for various measurable quantities and demonstrates exceptional energy conservation capabilities. To address unwanted oscillations in contact velocities and forces, we explored various algorithms and stabilization techniques, ultimately opting for the naïve‐stabilized Newmark scheme for its simplicity and effectiveness. Additionally, we validated the efficiency of the Schwarz method in a three‐dimensional impact problem, highlighting its inherent capacity to accommodate different mesh topologies, time‐integration schemes, and time steps for each interacting body.

Schwarz alternating method↗

PMU-Based Decoupled State Estimation for Unsymmetrical Power Systems

Modal decomposition of measurement equations has already been shown to simplify the formulation and resulting computational complexity of three-phase state estimation of systems where all the transmission lines are three-phase and fully transposed. When there are non-transposed and/or mixed-phase lines, modal decomposition can no longer fully decouple the threephase measurement equations. Here, this paper addresses the above shortcoming by proposing a simple yet practical solution based on the commonly used numerical compensation techniques. Thus, it enables application of the powerful decoupling approach to any type of three-phase networks which may contain non-transposed or mixed-phase lines and are fully observable by PMUs. The proposed procedure modifies the measurement set by deriving additive terms that compensate for the neglected unsymmetrical effects. It will be shown that unbalanced systems including nontransposed and mixed-phase elements, can still be transformed into three decoupled subsystems and solved in parallel by the proposed approach. Performance of the proposed algorithm is validated against several IEEE test cases.

42 ENGINEERING↗

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

Pele: An Exascale-Ready Suite of Combustion Codes

High fidelity simulations of realistic combustion devices are extremely demanding computationally because of the requirements to capture complex fuel chemical decomposition, its intricate interactions with turbulent, often multiphase, flows, and the wide separation of space and time scales between the thin flame and the device boundaries. Software required to carry out such computations tends to be extremely complex, particularly when designed to exploit hardware accelerators, and can be difficult to port and maintain. We present Pele, a performance portable suite of tools for the simulation of combustion systems, including codes to evolve reactive multiphase configurations in the low Mach number and compressible flow regimes, along with a set of inter-compatible post processing and in situ analysis tools. The Pele suite of tools is built on top of the AMReX framework for block-structured adaptive mesh refinement, which provides efficient data structures and algorithms that enable the development of a wide variety of efficient mesh and particle based PDE integration schemes. A hierarchical MPI+X parallelism scheme supports CPU-only and accelerated architectures, where X can be OpenMP, CUDA, and HIP based approaches for intra-node computational work distribution. The algorithms and data structures underlying the Pele simulation and analysis tools are highly scalable and performant across a wide variety of high-performance computing platforms, including DOEs newest exascale-class machines, Frontier and Aurora. The simulation and analysis tools are fully documented and freely distributed as open source via GitHub. We present key algorithmic and software challenges, solution strategies, performance and resulting set of capabilities.

AMReX↗

Machine learning-based bias-corrected future projections of ozone concentrations from a chemistry-climate model

Reliable projection of future near-surface ozone is crucial for air quality management and health risk assessment. However, potential biases in spatial distribution, magnitude and trends in ozone concentrations simulated by global chemistry-climate models limit their applicability in regional-scale evaluations. In this study, LightGBM, a machine learning (ML) algorithm is applied to correct biases in CESM2-simulated ozone concentrations over China, the United States and Europe and calibrate future ozone projections under two diverse Shared Socioeconomic Pathways (SSP1-2.6 and SSP5-8.5) scenarios from 2020 to 2060. The ML-based correction significantly improves the spatial distribution and reduces the model bias by 40%–60%. It also reverses the potentially incorrect trend of ozone change under SSP1-2.6 in eastern China. When applying ML-based bias correction to CESM2 future projections, warm season mean ozone concentrations decrease across China, the United States, and Europe by –13.5, –17.9, and –13.7 µg/m³, respectively, between 2020 and 2060 in SSP1-2.6, while they increase by 9.4, 2.0, and 5.2 µg/m³ in SSP5-8.5. Decomposition analysis show that changes in anthropogenic emissions dominate future ozone changes in both scenarios, while strong climate penalty from ozone changes occurs in polluted eastern China and climate benefit is found in western China, the United States and Europe under SSP5-8.5. These findings demonstrate the value of combining ML with chemistry-climate models to produce more accurate air quality projections, thereby informing more effective and region-specific environmental protection strategies.

Chemistry Model↗

Spinor representations for fields with any spin: Lorentz tensor basis for operators and covariant multipole decomposition

This paper discusses a framework to parametrize and decompose operator matrix elements for particles with higher spin (j > 1/2) using chiral representations of the Lorentz group, i.e. the (j, 0) and (0, j) representations and their parity-invariant direct sum. Unlike traditional approaches that require imposing constraints to eliminate spurious degrees of freedom, these chiral representations contain exactly the 2j + 1 components needed to describe a spin-j particle. The central objects in the construction are the t-tensors, which are generalizations of the Pauli four-vector σ μ for higher spin. For the generalized spinors of these representations, we demonstrate how the algebra of the t-tensors allows to formulate a generalization of the Dirac matrix basis for any spin. For on-shell bilinears, we show that a set consisting exclusively of covariant multipoles of order 0 ≤ m ≤ 2j forms a complete basis. We provide explicit expressions for all bilinears of the generalized Dirac matrix basis, which are valid for any spin value. As a byproduct of our derivations we present an efficient algorithm to compute the t-tensor matrix elements. The formalism presented here paves the way to use a more unified approach to analyze the non-perturbative QCD structure of hadrons and nuclei across different spin values, with clear physical interpretation of the resulting distributions as covariant multipoles.

Angular momentum of light↗

GenMod: A generative modeling approach for spectral representation of PDEs with random inputs

Here, we propose a method for quantifying uncertainty in high-dimensional PDE systems with random parameters, where the number of solution evaluations is small. Parametric PDE solutions are often approximated using a spectral decomposition based on polynomial chaos expansions. For the class of systems we consider (i.e., high dimensional with limited solution evaluations) the coefficients are given by an underdetermined linear system in a regression formulation. This implies additional assumptions, such as sparsity of the coefficient vector, are needed to approximate the solution. Here, we present an approach where we assume the coefficients are close to the range of a generative model that maps from a low to a high dimensional space of coefficients. Our approach is inspired be recent work examining how generative models can be used for compressed sensing in systems with random Gaussian measurement matrices. Using results from PDE theory on coefficient decay rates, we construct an explicit generative model that predicts the polynomial chaos coefficient magnitudes. The algorithm we developed to find the coefficients, which we call GenMod, is composed of two main steps. First, we predict the coefficient signs using Orthogonal Matching Pursuit. Then, we assume the coefficients are within a sparse deviation from the range of a sign-adjusted generative model. This allows us to find the coefficients by solving a nonconvex optimization problem, over the input space of the generative model and the space of sparse vectors. We obtain theoretical recovery results for a Lipschitz continuous generative model and for a more specific generative model, based on coefficient decay rate bounds. We examine three high-dimensional problems and show that, for all three examples, the generative model approach outperforms sparsity promoting methods at small sample sizes.

97 MATHEMATICS AND COMPUTING↗

Computational Framework for Machine-Learning-Enabled 13 C Fluxomics

13 C metabolic flux analysis (MFA) has emerged as a powerful tool for synthetic biology. This optimization-based approach suffers long computation time and unstable solutions depending on the initial guess. Here, we develop a machine-learning-based framework for 13 C fluxomics. Specifically, training and test data sets are generated by metabolic network decomposition and flux sampling, in which flux ratios at metabolic nodes and simulated labeling patterns of metabolites are used as training targets and features, respectively. To improve prediction accuracy and simplify the model, automated processes are developed for flux ratio selection based on solvability and feature screening based on importance. We found that predictive performance can be significantly improved using both amino acids and central carbon metabolites in comparison with amino acids alone. Together with measured external fluxes, the predicted flux ratios determine the mass balance system, yielding global flux distributions. This approach is validated by flux estimation using both simulated and experimental data in comparison with canonical 13 C MFA. The approach represents a reliable fluxomics method readily applicable to high-throughput metabolic phenotyping, which highlights the advances of intelligent learning algorithms in synthetic biology, specifically in the Test and Learn stage of the Design-Build-Test-Learn cycle.

13C metabolic flux analysis↗

Flow and heat transfer in the wake of a triangular arrangement of spheres

This research work seeks to investigate the influence of spacing and heat transfer on the wake behavior of a triangular arrangement of spheres. Four experimental configurations have been investigated at three Reynolds numbers, Re 1 = 350, Re 2 = 700, and Re 3 = 1050. Two isothermal cases were investigated with spacing between the spheres of zero and one sphere diameter, and two cases were investigated with an applied heat flux at the same spacing conditions. The time resolved particle image velocimetry results revealed various flow phenomena including flow separations, von Karman vortex shedding, and Kelvin–Helmholtz instabilities. The turbulent statistics reveal the effect of proximity and heat transfer on the time averaged values of the wake size, turbulent strengths, and Reynolds shear stress in the wake of each sphere, namely, the laminarization effects from the addition of heat and the suppression of the lead sphere wake from the proximity of the trailing spheres. These results are complemented by the application of proper orthogonal decomposition (POD) to the flow fields, which extracts the coherent structures from the flow. Here the modes that describe the coherent structures are extracted and described in detail, which provide further insight into effects of the experimental conditions on the temporal behavior of the flow. Many of the low order modes are found to be associated in pairs, corresponding to asymmetric structures or advection of a given structure downstream. The capability of POD to produce reduced order models of the flow is then utilized to facilitate vortex identification analysis. A turbulent kinetic energy based mode truncation criteria, which has been found to enhance vortex identification capability, is applied to select the POD modes and temporal coefficients to be used in the reduced order modeling. The reconstructed velocity fields are then analyzed with vortex identification algorithms to extract the vortex cores and boundaries. The combination of these approaches allows the study of the effect of proximity and heat transfer on the vortex characteristics, such as size, strength, and distribution.

42 ENGINEERING↗

Identification of Solid-Electrolyte Interphase Species by Joint Characterization of Li-Ion Battery Chemistry by Mass Spectrometry and Electrochemical Reaction Networks

The formation and stability of the solid-electrolyte interphase (SEI) play central roles in determining the long-term performance and safety of modern electrochemical energy storage systems. Despite decades of research, the SEI’s heterogeneous, dynamic, and multiphase nature has defied comprehensive molecular-level characterization, creating a critical knowledge gap that limits rational battery design. In this work, we introduce a computational−experimental framework that integrates high-throughput quantum chemistry calculations, data-driven electrochemical reaction networks (eCRNs), stochastic algorithms, and laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (LDI-FTICR-MS) to unravel SEI formation in carbonatebased electrolytes without imposing predefined mechanisms. We constructed the most comprehensive eCRN to date, spanning over 10,000 species and 209 million reactions. Through stochastic network analysis, we successfully recovered 27 species that were previously reported in the literature and predicted 28 novel SEI species nearly doubling our scientific knowledge in this area. Each new species was rigorously confirmed through advanced mass spectral analysis of its distinct molecular and isotopic signatures. We kinetically refined the formation pathways for a select set of both previously reported and novel SEI products, revealing kinetically feasible elementary reaction mechanisms with activation barriers below 1 eV. This computational−experimental approach deepens our molecular-level understanding of SEI chemistry by resolving which species form and through which decomposition mechanisms they emerge. Such knowledge provides the foundation necessary to connect electrolyte composition to the resulting SEI components, a critical step toward a more informed electrolyte development in next-generation lithium-based batteries.

25 ENERGY STORAGE↗

Decentralized Schemes with Overlap for Solving Graph-Structured Optimization Problems

We present a new algorithmic paradigm for the decentralized solution of graph-structured optimization problems that arise in the estimation and control of network systems. A key and novel design concept of the proposed approach is that it uses overlapping subdomains to promote and accelerate convergence. We show that the algorithm converges if the size of the overlap is sufficiently large and that the convergence rate improves exponentially with the size of the overlap. The proposed approach provides a bridge between fully decentralized and centralized architectures and is flexible in that it enables the implementation of asynchronous schemes, handling of constraints, and balancing of computing, communication, and data privacy needs. The proposed scheme is tested in an estimation problem for a 9241-node power network and we show that it outperforms the alternating direction method of multipliers.

asynchronous↗

Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of LBNL (Lawrence Berkeley National Laboratory) TES (Terrestrial Ecosystem Science) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization.Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from soil depth profiles collected from 2014 to 2021 from three paired control and warming plots. We collected soil samples across a range of depth profiles (spanning surface to 90 cm deep) from three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. 101 soil metagenomes were sequenced at JGI (Joint Genome Institute) and UCSF (University of California San Francisco) Center for Advanced Technology and can be found under the JGI (Joint Genome Institute) GOLD (Genomes Online Database) Sequencing project Gs0151586 and NCBI (National Center for Biotechnology Information) Projects PRJNA1225762 and PRJEB39497. Metagenomes were assembled using JGI (Joint Genome Institute) Metagenome Workflow (10.1128/mSystems.00804-20). For each metagenome, the assembled contigs were binned into genomes using 3 binning algorithms (cocacola, metabat, and maxbin) and the resulting bins were consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>50%) and contamination (<25%), and dereplicated at 99% ANI (average nucleotide identity) using dRep (https://github.com/MrOlm/drep).The dataset includes a zip file of 2321 MAG (Metagenome Assembled Genome) fasta files, the accession numbers for the underlying metagenomes, and a csv file with MAG (Metagenome Assembled Genome) quality metrics and taxonomic classification (GTDB -Genome Taxonomy Database-RS220). This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. A sample metadata file (samples.csv) that contains site information has also been included.

54 ENVIRONMENTAL SCIENCES↗

Enhancing SRF cavity stability and minimizing detuning with data-driven resonance control based on dynamic mode decomposition

Effective resonance control of superconducting radio frequency (SRF) cavities is critical for large machines like LCLS-II, as failure to achieve proper control can result in increased RF power consumption, higher cryogenic heat loads, and increased costs. To address this challenge, we have developed a machine learning (ML) model based on the dynamic mode decomposition method to represent the forced cavity dynamics. Using this model, we designed a model predictive controller (MPC) and demonstrated through simulation that the MPC can effectively stabilize the amplitude and phase of SRF cavities using only a frequency actuator, even in the presence of multiple mechanical modes. The lightweight and explicit ML model makes the controller suitable for direct implementation on field-programmable gate arrays, unlocking the full potential of SRF linacs like LCLS-II, enabling higher beam power and energy, and also serving as an advanced motion controller for various applications, such as photon beamlines and storage rings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Disjunctive optimization model and algorithm for long-term capacity expansion planning of reliable power generation systems

This paper proposes a new optimization model and algorithm for long-term capacity expansion planning of reliable power generation systems. The model optimizes both investment decisions (e.g., size, location, and time to install, retire and decommission facilities) and operation decisions (e.g., on/off status, operating capacity, and expected power output). It is also able to optimize reserve systems (or backup systems), as well as the main systems, to improve power systems reliability. An impact of operational strategies of generators (i.e., participating in electricity production vs. remaining as idle units during operation) on power systems reliability is considered. Probability of equipment failures and capacity failure states are used to rigorously estimate the power systems reliability depending on design and operation strategies. The optimization model is formulated with Generalized Disjunctive Programming (GDP), which is reformulated as a mixed-integer linear programming (MILP) model using the Hull relaxation. Two reliability-related penalties, such as downtime penalty and unmet demand penalty, are included in the objective function to maximize reliability while minimizing the total net present cost. Furthermore, a bilevel decomposition with tailored cuts is developed to reduce computational times of the multi-scale optimization model. The effectiveness of the proposed model is shown by comparing the results with the results obtained from the expansion planning models that do not explicitly consider reliability. In conclusion, we also show that the proposed bilevel decomposition is computationally efficient for solving large scale problems through 5-years and 10-years planning case studies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

An Algorithmic and Software Pipeline for Very Large Scale Scientific Data Compression with Error Guarantees

Efficient data compression is becoming increasingly critical for storing scientific data because many scientific applications produce vast amounts of data. This paper presents an end-to-end algorithmic and software pipeline for data compression that guarantees both error bounds on primary data (PD) and derived data, known as Quantities of Interest (QoI).We demonstrate the effectiveness of the pipeline by compressing fusion data generated by a large-scale fusion code, XGC, which produces tens of petabytes of data in a single day. We demonstrate that the compression is conducted by setting aside computational resources known as staging nodes, and does not impact the simulation performance. For efficient parallel I/O, the pipeline uses ADIOS2, which many codes such as XGC already use for their parallel I/O. We show that our approach can compress the data by two orders of magnitude while guaranteeing high accuracy on both the PD and the QoIs. Further, the amount of resources required by compression is a few percent of the resources required by simulation while ensuring that the compression time for each stage is less than the corresponding simulation time.This pipeline consists of three main steps. The first step decomposes the data using domain decomposition into small subdomains. Each subdomain is then compressed independently to achieve a high level of parallelism. The second step uses existing techniques that guarantee error bounds on the primary data for each subdomain. The third step uses a post-processing optimization technique based on Lagrange multipliers to reduce the QoI errors for data corresponding to each subdomain. The Lagrange multipliers generated can be further quantized or truncated to increase the compression level. All of the above characteristics of our approach make it highly practical to apply on-the-fly compression while guaranteeing errors on QoIs that are critical to the scientists.

Banerjee, Tania↗