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DOE OSTI2024

Automated AI-driven Molecular Design for Therapeutic Discovery

In recent years, artificial intelligence and machine learning (AI/ML) approaches have revolutionized the process of designing new therapeutics, enabling scientists to rapidly respond to emerging threats from various pathogens. A prime example is the SARS-CoV-2 main protease, a key target for the development of antiviral inhibitors. In this study, we employed a novel, integrated approach that combines AI-driven iterative design of inhibitor candidates, screening based on physio-chemical properties and toxicity, physics-based computational modeling of protein-inhibitor interactions, and AI-assisted analysis of Native MS biophysical assay and characterization of designed candidates. Our deep learning 3D-scaffold model, which uses an input scaffold as a starting point, generated tens of thousands of compounds while preserving the key scaffold. To optimize these candidates, we calculated a comprehensive set of 136 descriptors, including both 2D and 3D molecular features, for compounds targeting the SARS-CoV-2 Main protease (Mpro) and a neurodegenerative disease-associated protein, cyclophilin (Cyp). The generated compounds were initially filtered based on their properties and then ranked according to their predicted binding affinity using our automated modeling and ML methods. Experimental validation of the Mpro candidates showing inhibitory activity demonstrates that our workflow can expedite the therapeutic discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Best Practices for Body Temperature Measurement with Infrared Thermography: External Factors Affecting Accuracy

Infrared thermographs (IRTs) are commonly used during disease pandemics to screen individuals with elevated body temperature (EBT). To address the limited research on external factors affecting IRT accuracy, we conducted benchtop measurements and computer simulations with two IRTs, with or without an external temperature reference source (ETRS) for temperature compensation. The combination of an IRT and an ETRS forms a screening thermograph (ST). We investigated the effects of viewing angle (θ, 0–75°), ETRS set temperature (T ETRS , 30–40 °C), ambient temperature (T atm , 18–32 °C), relative humidity (RH, 15–80%), and working distance (d, 0.4–2.8 m). We discovered that STs exhibited higher accuracy compared to IRTs alone. Across the tested ranges of T atm and RH, both IRTs exhibited absolute measurement errors of less than 0.97 °C, while both STs maintained absolute measurement errors of less than 0.12 °C. The optimal T ETRS for EBT detection was 36–37 °C. When θ was below 30°, the two STs underestimated calibration source (CS) temperature (T CS ) of less than 0.05 °C. The computer simulations showed absolute temperature differences of up to 0.28 °C and 0.04 °C between estimated and theoretical temperatures for IRTs and STs, respectively, considering d of 0.2–3.0 m, T atm of 15–35 °C, and RH of 5–95%. The results highlight the importance of precise calibration and environmental control for reliable temperature readings and suggest proper ranges for these factors, aiming to enhance current standard documents and best practice guidelines. These insights enhance our understanding of IRT performance and their sensitivity to various factors, thereby facilitating the development of best practices for accurate EBT measurement.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Computational Advances in Ionic Liquid Applications for Green Chemistry: A Critical Review of Lignin Processing and Machine Learning Approaches

The valorization and dissolution of lignin using ionic liquids (ILs) is critical for developing sustainable biorefineries and a circular bioeconomy. This review aims to critically assess the current state of computational and machine learning methods for understanding and optimizing IL-based lignin dissolution and valorization processes reported since 2022. The paper examines various computational approaches, from quantum chemistry to machine learning, highlighting their strengths, limitations, and recent advances in predicting and optimizing lignin-IL interactions. Key themes include the challenges in accurately modeling lignin’s complex structure, the development of efficient screening methodologies for ionic liquids to enhance lignin dissolution and valorization processes, and the integration of machine learning with quantum calculations. These computational advances will drive progress in IL-based lignin valorization by providing deeper molecular-level insights and facilitating the rapid screening of novel IL-lignin systems.

09 BIOMASS FUELS↗

DOE OSTI2020

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Prediction of O and OH Adsorption on Transition Metal Oxide Surfaces from Bulk Descriptors

In the search for stable and active catalysts, density functional theory and machine learning (ML) based models can accelerate the screening of materials. While stability is conveniently addressed on the bulk level of computation, the modelling of catalytic activity requires expensive surface simulations. Here, in this work, we develop models for the surface adsorption energy of O and OH intermediates across a consistent and extensive dataset of pure transition metal oxide surfaces. We show that adsorption energies across metal oxidation states of +2 to +6 are well captured from the metal-oxygen bond strength extracted from the bulk level calculation. Specifically, we calculate the integrated crystal orbital Hamiltonian population (ICOHP) of the metal-oxygen bond in the bulk oxide and employ a simple normalization scheme to obtain a strong correlation with adsorption energetics. By combining our ICOHP descriptor with non DFT features in a Gaussian Process regression (GPR) model, we achieve high model accuracy with mean absolute errors of 0.166 and 0.219 eV for OH and O adsorption, respectively. By targeting the O-OH adsorption energy difference with our GPR model, we predict the the oxygen evolution reaction (OER) activity from bulk descriptors only. Furthermore, we utilize the strong correlation between the COHP and metal oxygen bond lengths to rapidly predict adsorption energetics and catalytic activity from the optimized bulk geometry. Our approach can enable an efficient search for active catalysts by eliminating the need for surface calculations in the initial screening phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Risk Importance Ranking of Fire Data Parameters to Enhance Fire PRA Model Realism

Fire is historically and analytically a significant contributor to nuclear power plant risk. The level of fire risk and the methods, tools and data for modeling this risk is highly debated by experts. One area of debate is the input data used in fire modeling and how to deal with this data’s high uncertainty. This report outlines initial work performed for determining the key parameters causing this uncertainty and how it propagates into nuclear power plant models. This research paves the way for the development of methods to reduce fire data uncertainty used in modeling. The Nuclear Regulatory Commission has mandated that nuclear power plants perform fire risk modeling. However, there are several issues with the current risk modeling implementation that affect the results. Approved modeling methods can be overly conservative and often do not match plant experience. Also, the data used in the modeling can have high uncertainties and is influenced by expert judgement. To evaluate input data uncertainty, researchers performed an initial review of several fire experiments done at Sandia National Laboratories. Uncertainties for fire data can come from many sources, such as experiment design constraints, environmental conditions, or other plant-specific aspects. There are many different significant and insignificant parameters driving the uncertainty. Additionally, the uncertainty of the different input data used in the fire modeling could have a significant or insignificant effect on the entire plant risk. A four-step methodology was developed to perform Integrated Probabilistic Risk Assessment Importance Ranking. A demonstration case using these steps was set up and three of the four steps were completed in fiscal year (FY) 2019 and the fourth step done FY 2020. These steps are: 1. The qualitative analysis of potential sources was conducted with the following items identified for the demonstration. • Maximum heat release rate • Time to maximum heat release rate • Duration of max heat release rate • Time to decay • Thermal conductivity of concrete • Specific heat of concrete • Density of concrete • Cable jacket thickness 2. A quantitative characterization of dominant sources of uncertainty was performed. A list of distributions and determined values of the dominant sources is shown in Appendix A. 3. A quantitative screening of the potential sources of uncertainty using Morris Elementary Effects Analysis was completed. An experimental model using the physics-based fire modeling tool Fire Dynamics Simulator was developed and coupled with the Risk Analysis Virtual Environment. The Morris analysis identified at least two parameters that can be eliminated as significant contributors (specific heat of concrete and cable jacket thickness). 4. Global importance measure (Global IM) analysis to generate a comprehensive ranking based on their influence on the plant risk. In this research, a moment-independent Global IM is used since it can address (a) uncertainty in the input parameters of the fire model, (b) uncertainty in the risk outputs, and (c) non-linearity and interactions among input parameters in the fire model, more accurately than the correlation-based and variance-based global methods. The observations from the research showed that, depending on the initial and boundary conditions of the fire scenarios, fire-induced damage could have a very small probability and could be dominated by the tail of the uncertainty distribution; hence, the accuracy of the correlation-based and variance-based methods is questionable. The moment-independent Global IM analysis in this research provides a better understanding of how experimental uncertainty data affects industry’s plant models and where improvements in that data will have the largest benefit for improving fire modeling accuracy in causing core damage. Among the five unscreened parameters obtained from the Morris EE analysis, the Global IM analysis results for the case study indicated that max heat release rate and fire location are the most important parameters. The report also outlines benefits of using a unified computational platform that integrates the underlying simulations (e.g., a fire progression model), quantitative screening (using the Morris EE method), and the Global IM analysis. A unified platform can (i) facilitate the ranking of input parameters considering multiple key fire scenarios simultaneously, rather than considering one scenario at a time, (ii) contribute to more explicit and accurate treatment of dependencies at multiple levels of Fire PRA, (iii) facilitate the sampling-based uncertainty quantification for Fire PRA, and (iv) help generating both “industry-wide” and "plant-specific" ranking of uncertainty sources in Fire PRA. Future research should be done to include additional parameters such as detection/suppression or cable fire spread. Adding a PRA software such as SAPHIRE to the RAVEN platform would help with plant model integration and improve treatment of fire-induced dependency. The I-PRA risk importance ranking methodology offered in this report can provide valuable information for efficiently (a) enhancing the realism of Fire PRA for existing plants and (b) supporting the development of Dynamic Fire PRA for advanced reactors and new plants.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Machine learning dielectric screening for the simulation of excited state properties of molecules and materials

Accurate and efficient calculations of absorption spectra of molecules and materials are essential for the understanding and rational design of broad classes of systems. Solving the Bethe–Salpeter equation (BSE) for electron–hole pairs usually yields accurate predictions of absorption spectra, but it is computationally expensive, especially if thermal averages of spectra computed for multiple configurations are required. We present a method based on machine learning to evaluate a key quantity entering the definition of absorption spectra: the dielectric screening. We show that our approach yields a model for the screening that is transferable between multiple configurations sampled during first principles molecular dynamics simulations; hence it leads to a substantial improvement in the efficiency of calculations of finite temperature spectra. We obtained computational gains of one to two orders of magnitude for systems with 50 to 500 atoms, including liquids, solids, nanostructures, and solid/liquid interfaces. Importantly, the models of dielectric screening derived here may be used not only in the solution of the BSE but also in developing functionals for time-dependent density functional theory (TDDFT) calculations of homogeneous and heterogeneous systems. Overall, our work provides a strategy to combine machine learning with electronic structure calculations to accelerate first principles simulations of excited-state properties.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Mechanochemical Solid Form Screening of Zeolitic Imidazolate Frameworks Using Structure-Directing Liquid Additives

We demonstrate a systematic application of the mechanochemical liquid-assisted grinding (LAG) methodology to screen for forms of zinc imidazolate (ZnIm 2 ), of fundamental importance as the simplest member of the zeolitic imidazolate framework materials family. The exploration of 45 different liquid additives, selected based on their molecular structure and physicochemical properties has resulted in eight different ZnIm 2 topological forms, appearing in 13 crystallographically distinct solid forms (including two previously unknown forms of the crb (BCT) topology), amorphous phases, and the interrupted moc-Zn 4 Im 8 HIm. All prepared topological forms were also explored computationally, using dispersion-corrected periodic density functional theory (DFT) calculations, enabling the rationalization of screening outcomes, and setting the stage for future prediction of additive-directed metal–organic framework (MOF) synthesis. This first systematic exploration of LAG in screening for three-dimensional MOFs demonstrates the potential of the liquid additive to not only accelerate materials synthesis, but also to direct it toward topologically different MOFs. The discovery of novel forms of a material that already exhibits at least 21 crystallographically and functionally different forms provides a strong testimony on the power of mechanochemistry in metal–organic materials discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

BEAST DB: Grand-Canonical Database of Electrocatalyst Properties

We present BEAST DB, an open-source database comprised of ab initio electrochemical data computed using grand-canonical density functional theory in implicit solvent at consistent calculation parameters. The database contains over 20,000 surface calculations and covers a broad set of heterogeneous catalyst materials and electrochemical reactions. Calculations were performed at self-consistent fixed potential as well as constant charge to facilitate comparisons to the computational hydrogen electrode. This article presents common use cases of the database to rationalize trends in catalyst activity, screen catalyst material spaces, understand elementary mechanistic steps, analyze the electronic structure, and train machine learning models to predict higher fidelity properties. Users can interact graphically with the database by querying for individual calculations to gain a granular understanding of reaction steps or by querying for an entire reaction pathway on a given material using an interactive reaction pathway tool. BEAST DB will be periodically updated, with planned future updates to include advanced electronic structure data, surface speciation studies, and greater reaction coverage.

database↗

DOE OSTI2022

Dielectric screening and vacancy formation for large neutral and charged Si n H m ( n > 1500 ) nanocrystals using real-space pseudopotentials

A commonly used procedure for computing the properties of defects in crystalline materials is to consider a large supercell that includes the defect of interest. This is a straightforward technique as standard energy band codes can be used for such computations. For neutral defects, the only impediment of such an approach is to avoid defect-defect interactions between adjoining cells. However, this procedure can be complex if the defect of interest is charged as the system at large contains Coulombic divergences. Moreover, some have recently argued that the conventional definition of formation energies for charged defects cannot be reconciled with statistical mechanics. Here, we focus on an alternative approach. We consider large nanocrystals wherein a charged defect can be placed. Since the system is confined, a charged defect within the nanocrystal does not result in a Coulombic divergence. The chief impediment is computational, i.e., while no defect-defect or Coulombic divergences are present, the nanocrystal must be sufficiently large to allow the system to properly replicate a bulklike configuration. With the development of new algorithms and hardware advances, computations for systems of sufficient size to address this issue are feasible. In particular, we solve the Kohn-Sham equation in real space using pseudopotential-density-functional theory for large silicon nanocrystals, which contain thousands of atoms. Further, we focus on (i) the screening of a point charge and (ii) the formation of a charged vacancy in hydrogen-terminated silicon nanocrystals. This approach allows us to examine the role of quantum confinement in addition to exploring the bulk limit. Comparisons to other methods confirm the viability of this approach.

36 MATERIALS SCIENCE↗

DOE OSTI2021

EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Computation-guided discovery of coating materials to stabilize the interface between lithium garnet solid electrolyte and high-energy cathodes for all-solid-state lithium batteries

All-solid-state batteries with a lithium metal anode, enabled by lithium garnet solid electrolytes such as Li 7 La 3 Zr 2 O 12 (LLZO), are a promising next-generation energy-storage technology. The further development of all-solid-state battery requires the integration of high-energy cathodes such as LiNi 1-x-y Mn x Co y O 2 (NMC) with the garnet solid electrolyte with stable and low-resistance interfaces, which requires a coating layer to stabilize the interface during high-temperature sintering and electrochemical cycling. In order to guide the future development of interfacial coatings, we perform high-throughput thermodynamic analyses based on first-principles computation to investigate the stability of LLZO garnet and high-energy NMC cathodes with a wide range of materials chemistries. Here our study reveals the factors governing the materials stability with LLZO garnet and NMC cathodes, and identifies the mechanisms of good coating layers stable with LLZO and NMC. In addition to classifying known coating layers, our study provides detailed guiding charts and multiple new materials systems as promising coatings for stabilizing LLZO—NMC interfaces to enable high-energy-density garnet-based all-solid-state batteries. Our demonstrated computation scheme and high-throughput analyses are generally applicable to investigate and screen coating materials for stabilizing interfaces in energy-related applications.

25 ENERGY STORAGE↗

DOE OSTI2025

In silico λ-dynamics predicts protein binding specificities to modified RNAs

Abstract RNA modifications shape gene expression through a variety of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.

Biochemistry & Molecular Biology↗

DOE OSTI2026

SynthEsizing Novel H2 Sensors for Operational Resilience in Pipeline Infrastructure (SENSOR)

A flexible and extensible computational framework acts as a black-box materials discovery engine, capable of screening, predicting, and designing advanced materials with minimal manual intervention was developed. While developed for hydrogen sensing, the approach can be readily adapted to other materials challenges, offering a powerful tool for data-driven materials innovation.

08 HYDROGEN↗

DOE OSTI2021

deeprob/ThioesteraseEnzymeSpecificity: EnZymClass-first-release

Banerjee, Deepro↗

DOE OSTI2020

Ensemble transfer learning for the prediction of anti-cancer drug response

Abstract Transfer learning, which transfers patterns learned on a source dataset to a related target dataset for constructing prediction models, has been shown effective in many applications. In this paper, we investigate whether transfer learning can be used to improve the performance of anti-cancer drug response prediction models. Previous transfer learning studies for drug response prediction focused on building models to predict the response of tumor cells to a specific drug treatment. We target the more challenging task of building general prediction models that can make predictions for both new tumor cells and new drugs. Uniquely, we investigate the power of transfer learning for three drug response prediction applications including drug repurposing, precision oncology, and new drug development, through different data partition schemes in cross-validation. We extend the classic transfer learning framework through ensemble and demonstrate its general utility with three representative prediction algorithms including a gradient boosting model and two deep neural networks. The ensemble transfer learning framework is tested on benchmark in vitro drug screening datasets. The results demonstrate that our framework broadly improves the prediction performance in all three drug response prediction applications with all three prediction algorithms.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Defect Diffusion Graph Neural Networks for Materials Discovery in High-Temperature Energy Applications

Here, the migration of crystallographic defects dictates material properties and performance for a plethora of technological applications. Density functional theory (DFT)-based nudged elastic band (NEB) calculations are a powerful computational technique for predicting defect migration activation energy barriers, yet they become prohibitively expensive for high-throughput screening of defect diffusivities. Without introducing hand-crafted (i.e., chemistry- or structure-specific) descriptors, we propose a generalized deep learning approach to train surrogate models for NEB energies of vacancy migration by hybridizing graph neural networks with transformer encoders and simply using pristine host structures as input. With sufficient training data, computationally efficient and simultaneous inference of vacancy defect thermodynamics and migration activation energies can be obtained to compute temperature-dependent vacancy diffusivities and to down-select candidates for more thorough DFT analysis or experiments. Thus, as we specifically demonstrate for potential water-splitting materials, candidates with desired defect thermodynamics, kinetics, and host stability properties can be more rapidly targeted from open-source databases of experimentally validated or hypothetical materials.

14 SOLAR ENERGY↗

DOE OSTI2021

Preliminary Assessment of Qiskit Quantum Simulator Capabilities for Development of Quantum Hopfield Neural Network for Anomaly Detection Applications (Q4 Report)

Quantum information processing offers potentially faster performance compared to the classical counterpart. The goal of this work is to investigate performance of Quantum Hopfield Neural Network for applications to anomaly detection. Preliminary study consist of assessment of computational capabilities of Qiskit quantum simulator. Eventual objective is to implement Quantum Hopfield Network algorithm for detection of weak nuisance and anomaly signal in the presence of strong and highly varying background in gamma radiation data measured during environmental screening.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗