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At least 649 records · Page 36

Graph neural networks for CO 2 solubility predictions in Deep Eutectic Solvents

Deep Eutectic Solvents (DESs) are a promising class of solvents for CO 2 capture. DESs are complex mixtures that can be designed to optimize CO solubility and overall capture process efficiency. However, the vast design landscape of DES mixtures makes experimental investigation prohibitive; as such, there is a need for computational models that can quickly and efficiently navigate the design space and inform data collection efforts. In this work, we propose Graph Neural Network (GNN) models for predicting CO 2 solubility for DESs; the GNN leverages a mixture graph representation that captures the molecular structure of the DES components as well as their intermolecular interactions. Here, we compare the GNN framework against alternative architectures (neural networks, graph convolution networks, and random forests) and data representations (molecular fingerprints, sigma profiles, and graphs). We show that the proposed approach offers superior predictive performance; specifically, we show that solubility can be predicted reliably directly from molecular structure (without the need of using sigma profiles as proposed in previous studies). This result is important, as obtaining sigma profiles requires expensive density functional theory computations. We also explored the ability of GNNs to predict solubility for new DES mixtures and operating conditions. We found that the model extrapolates across temperature reliably. However, we also found deficiencies in the ability of the model to predict solubility for DES mixtures, pressures, and molar ratio not included in the training sets; we show that this is due to an inherent lack of chemical diversity in datasets available in the literature. The proposed computational capabilities can thus help navigate the design space of DES and inform data collection efforts. Our models, data, and benchmarks are shared as Python code implemented in Jupyter notebooks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Continuum-Level Modeling of Li-Ion Battery SEI by Upscaling Atomistically Informed Reaction Mechanisms

Understanding and controlling solid-electrolyte interphase (SEI) formation to stabilize cell performance is a significant challenge for next-generation Li-ion battery technologies. In recent years, computational modeling has become an essential tool in providing fundamental insights into SEI properties and dynamics. However, neither atomistic nor continuum-level approaches alone can capture the complexities of SEI chemistry across all relevant length and time scales. In this work, a continuum-level model is developed that is informed by reaction mechanisms obtained from first-principle calculations. The atomistically informed continuum-level model is used to understand electrolyte degradation, including the decomposition of ethylene carbonate (EC), ethyl methyl carbonate (EMC), and fluoroethylene carbonate (FEC). The model presented here is the most chemically complex continuum-level SEI model in the literature to date. The SEI model is calibrated against experimental irreversible leakage currents and shows qualitative agreement with expected SEI growth trends. The model framework is expected to accelerate fundamental understanding of SEI formation, facilitate mechanism development feedback, and dynamically interact with experimental insights.

continuum-level model↗

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

MOTIVATION: High-throughput sequencing (HTS) is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragments from the microorganisms within a given sample. This technology presents a unique opportunity for artificial intelligence to comprehend the underlying functional relationships of microbial communities. However, due to the unstructured nature of HTS data, nearly all computational models are limited to processing DNA sequences individually. This limitation causes them to miss out on key interactions between microorganisms, significantly hindering our understanding of how these interactions influence the microbial communities as a whole. Furthermore, most computational methods rely on post-processing of samples which could inadvertently introduce unintentional protocol-specific bias. RESULTS: Addressing these concerns, we present SetBERT, a robust pre-training methodology for creating generalized deep learning models for processing HTS data to produce contextualized embeddings and be fine-tuned for downstream tasks with explainable predictions. By leveraging sequence interactions, we show that SetBERT significantly outperforms other models in taxonomic classification with genus-level classification accuracy of 95%. Furthermore, we demonstrate that SetBERT is able to accurately explain its predictions autonomously by confirming the biological-relevance of taxa identified by the model. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/DLii-Research/setbert. SetBERT may be used through the q2-deepdna QIIME 2 plugin whose source code is available at https://github.com/DLii-Research/q2-deepdna.

Ludwig, David W↗

Communication Lower Bounds and Optimal Algorithms for Symmetric Matrix Computations

In this article, we focus on the communication costs of three symmetric matrix computations: (i) multiplying a matrix with its transpose, known as a symmetric rank-k update (SYRK) (ii) adding the result of the multiplication of a matrix with the transpose of another matrix and the transpose of that result, known as a symmetric rank-2k update (SYR2K) (iii) performing matrix multiplication with a symmetric input matrix (SYMM). All three computations appear in the Level 3 Basic Linear Algebra Subroutines (BLAS) and have wide use in applications involving symmetric matrices. We establish communication lower bounds for these kernels using sequential and distributed-memory parallel computational models, and we show that our bounds are tight by presenting communication-optimal algorithms for each setting. Our lower bound proofs rely on applying a geometric inequality for symmetric computations and analytically solving constrained nonlinear optimization problems. As a result, the symmetric matrix and its corresponding computations are accessed and performed according to a triangular block partitioning scheme in the optimal algorithms.

Al Daas, Hussam [Rutherford Appleton Laboratory, D↗

A Computational-experimental Study to Simulate Mixing and Thermal Stratification in SFRs

This NEUP project 16-10579 entitled “A Computational-Experimental Study to Simulate Mixing and Thermal Stratification in SFRs”, has investigated important phenomena of thermal stratification and mixing in Sodium-cooled Faster reactors (SFRs). A liquid metal experimental set-up was built at Kansas State University to generate high fidelity experimental data and validate computational models. The scope of the work involved - scaled down design of experimental facility, construction and commissioning of the new facility, conducting thermal-hydraulics experiments relevant to the physics of thermal stratification and mixing in the plena, developing 3D CFD models of the experiments, developing SAS4A/SASSYS-1 system model of the liquid metal experimental facility , survey of previous data in literature on stratification experiments and recommendations for improved models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

MatCal Users Guide: Release 1.3.0

Any continuum mechanics model will require three components: (1) a discretized geometry of the boundary value problem being studied, (2) the partial differential equations to be solved, and (3) the initial conditions and boundary conditions for the problem. To describe material behavior in these computational models, material models contribute to (2) the underlying equations and, occasionally, to (3) the initial conditions for the simulation. These material models can exhibit a mathematical form that is empirically based, based on first principles, or developed from both empirical observations and known physics. In general, these models are meant to represent a class of materials with well understood behavior. As a result, material models have parameters that must be tuned or calibrated so that the model response matches characterization data available for the specific material it is intended to represent when used to simulate a specific system. For simple models, such as isotropic, linear elastic materials in solid mechanics, this calibration process can be a simple analytical calculation directly extracting the parameters from experimental measurements. For complex models that have many inputs and require many characterization datasets to adequately identify the material behavior, the model calibration process can require an inverse problem approach where an optimization is performed to tune the model parameters to the available data.

36 MATERIALS SCIENCE↗

DIRAC current, upcoming and planned capabilities and technologies

DIRAC is the interware for building and operating large scale distributed computing systems. It is adopted by multiple collaborations from various scientific domains for implementing their computing models. DIRAC provides a framework and a rich set of ready-to-use services for Workload, Data and Production Management tasks of small, medium and large scientific communities having different computing requirements. The base functionality can be easily extended by custom components supporting community specific workflows. DIRAC is at the same time an aging project, and a new DiracX project is taking shape for replacing DIRAC in the long term. This contribution will highlight DIRAC’s current, upcoming and planned capabilities and technologies, and how the transition to DiracX will take place. Examples include, but are not limited to, adoption of security tokens and interactions with Identity Provider services, integration of Clouds and High Performance Computers, interface with Rucio, improved monitoring and deployment procedures.

97 MATHEMATICS AND COMPUTING↗

Directional response of several geometries for reactor-neutrino detectors

Here we have modeled six abstracted detector designs, with the goal of determining their ability to resolve the direction to an antineutrino source, including two for which we have operational data for validating our computer modeling and analytical processes. We have found that the most promising options, regardless of scale and range, have angular resolutions on the order of a few degrees, which is better than any yet achieved in practice by a factor of at least two. We examine and compare several approaches to detector geometry for their ability not only to detect the inverse beta decay (IBD) reaction, but also to determine the source direction of incident antineutrinos. The information from these detectors provides insight into reactor power and burning profile, which is especially useful in constraining the clandestine production of weapons material. In a live deployment, a nonproliferation detector must be able to isolate the subject reactor, possibly from a field of much-larger power reactors; directional sensitivity can help greatly with this task. We also discuss implications for using such detectors in longer-distance observation of reactors, from a few kilometers to hundreds of kilometers.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quantifying the Impact of Vertical Resolution on the Representation of Marine Boundary Layer Physics for Global-Scale Models

Abstract While GCM horizontal resolution has received the majority of scale improvements in recent years, ample evidence suggests that a model’s vertical resolution exerts a strong control on its ability to accurately simulate the physics of the marine boundary layer. Here we show that, regardless of parameter tuning, the ability of a single-column model (SCM) to simulate the subtropical marine boundary layer improves when its vertical resolution is improved. We introduce a novel objective tuning technique to optimize the parameters of an SCM against profiles of temperature and moisture and their turbulent fluxes, horizontal winds, cloud water, and rainwater from large-eddy simulations (LES). We use this method to identify optimal parameters for simulating marine stratocumulus and shallow cumulus. The novel tuning method utilizes an objective performance metric that accounts for the uncertainty in the LES output, including the covariability between model variables. Optimization is performed independently for different vertical grid spacings and value of time step, ranging from coarse scales often used in current global models (120 m, 180 s) to fine scales often used in parameterization development and large-eddy simulations (10 m, 15 s). Uncertainty-weighted disagreement between the SCM and LES decreases by a factor of ∼5 when vertical grid spacing is improved from 120 to 10 m, with time step reductions being of secondary importance. Model performance is shown to converge at a vertical grid spacing of 20 m, with further refinements to 10 m leading to little further improvement. Significance Statement In successive generations of computer models that simulate Earth’s atmosphere, improvements have been mainly accomplished by reducing the horizontal sizes of discretized grid boxes, while the vertical grid spacing has seen comparatively lesser refinements. Here we advocate for additional attention to be paid to the number of vertical layers in these models, especially in the model layers closest to Earth’s surface where climatologically important marine stratocumulus and shallow cumulus clouds reside. Our experiments show that the ability of a one-dimensional model to represent physical processes important to these clouds is strongly dependent on the model’s vertical grid spacing.

Meteorology & Atmospheric Sciences↗

Computational Theory Applied to Nanostructures (Final Report)

Within the nanoscale, phenomena occur that are characteristic of neither the atomic limit, nor the macroscopic limit. In particular, properties that are intensive at the macroscopic scale become size dependent at the nanoscale. These phenomena can have direct consequence for understanding and characterizing materials used in electronic, optical, and micro-mechanical applications related to energy science and technologies. To capitalize properly on predicting and understanding such phenomena in this nano regime, a deeper understanding of the quantum properties of materials will be required. The objective of our research program was to advance the field in computational modeling, analysis and understanding of materials at the nano scale, both in terms of dimensionality and quantum confinement. We employed a multidisciplinary approach, drawing from physics, materials science, chemical engineering and computer science. This research will provide new knowledge, computational techniques, and provide high-potential links across all these disciplines. Over sixty papers were published during the period in question. Ten of the papers were published in high impact journals such as Nano Letters, Nature Communications and Physical Review Letters.

36 MATERIALS SCIENCE↗

Cooperative Education

Los Alamos National Laboratory (LANL) is a multidisciplinary national laboratory that conducts research and development in national security, engineering, materials science, computational modeling, and advanced manufacturing. The laboratory develops innovative technologies to address complex scientific and engineering challenges. This project focuses on the development and evaluation of high-performance absorbing structures through computational design, simulation, and engineering analysis. Absorbing structures are used in applications where damage mitigation, structural protection, and material efficiency are critical performance requirements. The increasing demand for lightweight, high-strength, and highly efficient structural systems has created a need for improved design methodologies capable of maximizing absorption while minimizing weight and material usage. The project utilizes advanced engineering software, including 3D CAD software and FEA, to generate and optimize structural concepts. Computational simulations are performed to evaluate structural behavior under loading conditions, while mathematical analyses are conducted using Python-based tools as well as established analytical equations from material and structural mechanics. The project benefits LANL by supporting the development of advanced design methodologies and improving the understanding of material and structural performance. During the internship term, a significant portion of the design development, simulation, and data analysis activities will be completed. Success of the project depends on collaboration among engineering mentors and technical staff members. Work will be conducted at Los Alamos National Laboratory using laboratory computing resources and engineering software.

42 ENGINEERING↗

LigninGraphs: lignin structure determination with multiscale graph modeling

Lignin is an aromatic biopolymer found in ubiquitous sources of woody biomass. Designing and optimizing lignin valorization processes requires a fundamental understanding of lignin structures. Experimental characterization techniques, such as 2D-heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra, could elucidate the global properties of the polymer molecules. Computer models could extend the resolution of experiments by representing structures at the molecular and atomistic scales. We introduce a graph-based multiscale modeling framework for lignin structure generation and visualization. The framework employs accelerated rejection-free polymerization and hierarchical Metropolis Monte Carlo optimization algorithms. We obtain structure libraries for various lignin feedstocks based on literature and new experimental NMR data for poplar wood, pinewood, and herbaceous lignin. The framework could guide researchers towards feasible lignin structures, efficient space exploration, and future kinetics modeling. Its software implementation in Python, LigninGraphs, is open-source and available on GitHub.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Peridynamic Model for Microballistic Perforation of Multilayer Graphene

The peridynamic theory of solid mechanics is applied to the continuum modeling of the impact of small, high-velocity silica spheres on multilayer graphene targets. The model treats the laminate as a brittle elastic membrane. The material model includes separate failure criteria for the initial rupture of the membrane and for propagating cracks. Material variability is incorporated by assigning random variations in elastic properties within Voronoi cells. Here, the computational model is shown to reproduce the primary aspects of the response observed in experiments, including the growth of a family of radial cracks from the point of impact.

42 ENGINEERING↗

Santa Barbara Desalination Digital Twin Technical Report

A digital twin is a computer model that has sufficient breadth and fidelity to enable diagnostic and predictive analyses for outputs of interest. We have constructed a digital twin of the SB desal plant using the ProteusLib software developed for NAWI under task 4.2.2, and specifically the ProteusLib models of pumps, filters, mixers, splitters, and reverse osmosis units and a seawater property model. The steps needed to configure this digital twin with the real conditions of the SB desal plant are: (1) Data reconciliation, which is gathering the data and plant connectivity and ensure that all relevant values are present and in the correct units and validating the data using material and energy balances, and correct for errors, gaps, or deviations; (2) Parameter estimation, which is matching model parameters with data from previous step, filling missing parameters with initial estimates, then iteratively refining estimated values. Once we completed the digital twin, we used the optimization capabilities of ProteusLib to compute outputs of interest over a chosen range of inputs. The primary output of interest to the owners of the plant is its specific energy consumption (kWh/acre-foot). The remainder of this report will provide more detail on the data reconciliation, parameter estimation, and analyses we performed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Macroalgal Cultivation Modeling System (MACMODS): Evaluating the Role of Physical-Biological Coupling on Nutrients and Farm Yield

Offshore aquaculture has the potential to expand the macroalgal industry. However, moving into deeper waters requires suspended structures that will present novel farm-environment interactions. Here, we present a computational modeling framework, the Macroalgal Cultivation Modeling System (MACMODS), to explore within-farm modifications to light, seawater flow, and nutrient fields across time and space scales relevant to macroalgae. A regional ocean model informs the site-specific setting, the Santa Barbara Channel in the Southern California Bight. A fine-scale hydrodynamic model predicts modified flows and turbulent mixing within the farm. A spatially resolved macroalgal growth model, parameterized for giant kelp, Macrocystis pyrifera , predicts kelp biomass. Key findings from model integration are that regional ocean conditions set overall farm performance, while fine-scale within-farm circulation and nutrient delivery are important to resolve variation in within-farm macroalgal performance. Therefore, we conclude that models resolving within-farm dynamics can provide benefit to farmers with insight on how farm design and regional ocean conditions interact to influence overall yield. Here, the presence of repeating longlines aligned with the mean current generate flow diversions around the farm as well as attached Langmuir circulations and increased turbulence intensity. These flow-induced phenomena lead to less biomass in the interior portion of the farm relative to the edges. We also find that there is an effluent “footprint” that extends as much as 20 km beyond the farm. In this regard, MACMODS can be used to not only evaluate farm design and cultivation practices that maximize yield but also explore interactions between the farm and ecosystem in order to minimize impacts.

54 ENVIRONMENTAL SCIENCES↗

A Scoping Study to Develop a Computational Fluid Dynamics Based Model to Predict Radiological Materials Packaging Temperatures within a Generic Staging Building

The objective of this work is to perform computational fluid dynamics simulations of a ventilated radiological-material-package staging building to determine the effect of including or excluding a variety of physical effects and computational methods on both the predicted package temperatures and required computational resources. The generic building contains 640 drum-packages containing heat-generating, radiological material supported on four racks that are eight levels tall. Additionally, there is a forced ventilation system, lighting, and insulated walls. Computational models were constructed that included or excluded (a) shelving, (b) effects of unsteadiness, and (c) radiation heat transfer. Simulations with each drum modeled separately were compared to simpler simulations with sets of four drums represented by an equivalent box-package. These models employed between 106 to 107 elements. Steady state simulations predicted package temperatures that were within 0.1°C of simulations that included transient effects and required only one-eighth the computational resources. Calculations that excluded shelving predicted temperatures within 0.6°C of simulations that included shelving and required one-fourth the computational resources. Excluding radiation heat transfer systematically increased temperatures by around 1.5°C but reduced computational resources by a factor of four. The box-package model reduced the computational resources by a factor of 3, but systematically predicted higher temperatures by around 1.1°C. These results will be used to develop an efficient computational fluid dynamics model to assess the ability of different staging building designs to prevent the temperature of package components from exceeding specified limits.

42 ENGINEERING↗

Microstructure-Sensitive modeling of surface roughness and notch effects on extreme value fatigue response

Fatigue life knockdown due to surface roughness induces local stress concentrations. Physical fatigue experiments are crucial to qualify materials for use but are limited in their capability to examine the mechanisms underlying the fatigue crack formation driving force due to these stress concentrations. Microstructure-sensitive computational models can aid in this regard and are employed in this work to examine the effects of surface roughness in Al 7075-T6. Digital microstructure models are subjected to crystal plasticity finite element method (CPFEM) simulations to examine the combined effects of microstructure and grain scale asperities on the driving force for fatigue crack formation. Following elastic–plastic shakedown, mesoscale volume-averaged fatigue indicator parameters (FIPs) are computed within fatigue damage process zones of grains. An increase in the intensity of realistic surface roughness profiles corresponds accordingly to larger FIPs but it is difficult to precisely interpret the mechanisms and effects of this intensification. We thus parametrically investigate surface asperities that couple with microstructure and lack of constraint on slip at the free surface to describe microstructure-sensitive surface roughness knockdown effects on fatigue resistance. The depth of a single valley (i.e., notch) due to surface roughness is found to be more detrimental to fatigue resistance than the radius (i.e., notch width, not to be confused with notch acuity). Finally, we also find that different crystallographic textures, grain morphologies, and number of sampled grains have a limited effect on the depth of influence of these notches.

36 MATERIALS SCIENCE↗

Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease

Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.

60 APPLIED LIFE SCIENCES↗