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DOE OSTI2024

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↗

DOE OSTI2023

De novo design of protein structure and function with RFdiffusion

Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

Science & Technology - Other Topics↗

DOE OSTI2021

Denoising Convolutional Networks to Accelerate Detector Simulation [Poster]

The high accuracy of detector simulation is crucial for modern particle physics experiments. However, this accuracy comes with a high computational cost, which will be exacerbated by the large datasets and complex detector upgrades associated with next-generation facilities such as the High Luminosity LHC. We explore the viability of regression-based machine learning (ML) approaches using convolutional neural networks (CNN) to ``denoise'' faster, lower-quality detector simulations, augmenting them to produce a higher-quality final result with a reduced computational burden. The denoising CNN works in concert with classical detector simulation software rather than replacing it entirely, increasing its reliability compared to other ML approaches to simulation. We obtain promising results from a prototype based on photon showers in the CMS electromagnetic calorimeter. Future directions are also discussed.

43 PARTICLE ACCELERATORS↗

NASA NTRS1994

Neural networks: Alternatives to conventional techniques for automatic docking

Automatic docking of orbiting spacecraft is a crucial operation involving the identification of vehicle orientation as well as complex approach dynamics. The chaser spacecraft must be able to recognize the target spacecraft within a scene and achieve accurate closing maneuvers. In a video-based system, a target scene must be captured and transformed into a pattern of pixels. Successful recognition lies in the interpretation of this pattern. Due to their powerful pattern recognition capabilities, artificial neural networks offer a potential role in interpretation and automatic docking processes. Neural networks can reduce the computational time required by existing image processing and control software. In addition, neural networks are capable of recognizing and adapting to changes in their dynamic environment, enabling enhanced performance, redundancy, and fault tolerance. Most neural networks are robust to failure, capable of continued operation with a slight degradation in performance after minor failures. This paper discusses the particular automatic docking tasks neural networks can perform as viable alternatives to conventional techniques.

Vinz, Bradley L.↗

NASA NTRSDate not supplied

Assumption Generation for the Verification of Learning-Enabled Autonomous Systems

Providing safety guarantees for autonomous systems is difficultas these systems operate in complex environments that require the use of learning-enabled components, such as deep neural networks (DNNs) for visual perception. DNNs are hard to analyze due to their size (they can have thousands or millions of parameters), lack of formal specifications (DNNs are typically learnt from labeled data, in the absence of any formal or informal requirements), and sensitivity to small changes in the environment. We present an assume-guarantee style compositional approach for the formal verification of system-level safety properties of such autonomous systems. Our insight is that we can analyze the system in the absence of the DNN perception components by automatically synthesizing assumptions on the DNN behaviour that guarantee the satisfaction of the required safety properties. The synthesized assumptions are the weakest in the sense that they characterize the output sequences of all the possible DNNs that, plugged into the autonomous system, guarantee the required safety properties. The assumptions can be leveraged as run-time monitors over a deployed DNN to guarantee the safety of the overall system; they can also be mined to extract local specifications for use during training and testing of DNNs. We illustrate our approach on a case study taken from the autonomous airplanes domain that uses a complex DNN for perception

Autonomous systems↗

NASA NTRS2017

Vascular Patterning Analysis by VESGEN 2D/3D with Bioinformatics: Updates for Rodent Tissues

Fractally branching vascular systems are a complex physiological requirement shared by humans with all higher terrestrial life forms, including other vertebrates, insects, and higher land plants. Vascular trees, networks, and tree-network composites are therefore mapped and quantified by the VESsel GENeration Analysis (VESGEN) software according to weighted physiological vascular rules that include vessel connectivity, tapering and bifurcational branching. According to fluid dynamics, successful vascular transport depends upon a complex distributed system of highly regulated laminar flow. VESGEN has elucidated changes in vascular patterning resulting from inflammatory, developmental and other signaling pathways within numerous tissues of major model organisms important for Space Biology, especially for rodents. Important early stage regenerative opportunities have been identified by VESGEN vascular analysis for visual impairments in the human retina, and is currently being used for research into astronaut visual and ocular disorders associated with long duration missions. The VESGEN 2D software is a mature, automated, widely published capability for which beta testing and public release by NASA is planned for the upcoming year. Early-stage capabilities for VESGEN 3D analysis are under development for the rodent retina and intestine as prototype tissues. A prototype VESGEN 2D Bioinformatics software capability has also been developed to associate phenotypic changes in molecular expression with vascular structure and function. By new VESGEN bioinformatic innovations, expression patterns of the genetic, transcriptional, protein and other markers for regulatory molecules such as vascular endothelial growth factor (VEGF) and their receptors, often indicators of tissue oxygenation status, are co-localized with alterations in vascular pattern. Biomarkers are therefore mapped and quantified as information dimensions directly correlated with the spatial dimensions of a vascular pattern. Further important technology innovations by NASA include substantial image segmentation advances for more automated binary extraction of the grayscale vascular patterns, together with informative associated image quality assessments. Vascular mapping and quantification capabilities for the rodent retina and intestine are illustrated for VESGEN 2D, along with technology status reports on VESGEN 3D and Bioinformatic capabilities. Research partially supported by Ames Center Innovation Awards.

Parsons-Wingerter, P.↗

DOE OSTI2023

Quantifying uncertainty for deep learning based forecasting and flow-reconstruction using neural architecture search ensembles

Classical problems in computational physics such as data-driven forecasting and signal reconstruction from sparse sensors have recently seen an explosion in deep neural network (DNN) based algorithmic approaches. However, most DNN models do not provide uncertainty estimates, which are crucial for establishing the trustworthiness of these techniques in downstream decision making tasks and scenarios. In recent years, ensemble-based methods have achieved significant success for the uncertainty quantification in DNNs on a number of benchmark problems. However, their performance on real-world applications remains under-explored. In this work, we present an automated approach to DNN discovery and demonstrate how this may also be utilized for ensemble-based uncertainty quantification. Specifically, we propose the use of a scalable neural and hyperparameter architecture search for discovering an ensemble of DNN models for complex dynamical systems. We highlight how the proposed method not only discovers high-performing neural network ensembles for our tasks, but also quantifies uncertainty seamlessly. This is achieved by using genetic algorithms and Bayesian optimization for sampling the search space of neural network architectures and hyperparameters. Subsequently, a model selection approach is used to identify candidate models for an ensemble set construction. Afterwards, a variance decomposition approach is used to estimate the uncertainty of the predictions from the ensemble. We demonstrate the feasibility of this framework for two tasks — forecasting from historical data and flow reconstruction from sparse sensors for the sea-surface temperature. In conclusion, we demonstrate superior performance from the ensemble in contrast with individual high-performing models and other benchmarks.

Deep ensembles↗

DOE OSTI2025

Storage-Induced Collapse of Lignin Macromolecular Structure and Its Impacts on the Biorefinery

Lignin plays a vital role in the economics of biorefineries, serving as a source of process energy and a feedstock for sustainable fuels and chemical production. While understanding lignin’s chemical composition is crucial, emerging evidence suggests that a more comprehensive understanding of its macromolecular structure is critical to explaining its complex behavior in the biorefinery. This study investigated the partial collapse of the lignin network in corn stover feedstock after harvest and storage as a result of the microbial digestion of hemicellulose. Fluorescence microscopy was used to detect the collapse of lignin in terms of lignin’s inter-molecular interaction and the re-orientation of lignin’s chromophores, by the changes in lignin’s fluorescence lifetime, anisotropy, and the number of effective emitters. With minimal sample perturbation, our in-situ microscopic results revealed lignin's coil-globule transition phenomena, which was only previously predicted by molecular dynamics modeling extracted lignin in solvent. This collapse of lignin macromolecular structure was confirmed by results from NMR, IR, Raman, and powder X-ray diffraction. We also investigated the impact of this storage-induced collapse on the downstream biorefinery processes. Our study revealed that the two major approaches for lignin valorization in the lignin-first biorefinery model, namely monomer extraction and milled wood lignin extraction, were negatively impacted by the lignin collapse. As changes during storage are a source of feedstock variability, our study highlights the importance of understanding the effect of feedstock handling on biorefinery operations and economics.

09 BIOMASS FUELS↗

DOE OSTI2024

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Machine-learning-based spectral methods for partial differential equations

Spectral methods are an important part of scientific computing’s arsenal for solving partial differential equations (PDEs). However, their applicability and effectiveness depend crucially on the choice of basis functions used to expand the solution of a PDE. The last decade has seen the emergence of deep learning as a strong contender in providing efficient representations of complex functions. In the current work, we present an approach for combining deep neural networks with spectral methods to solve PDEs. In particular, we use a deep learning technique known as the Deep Operator Network (DeepONet) to identify candidate functions on which to expand the solution of PDEs. We have devised an approach that uses the candidate functions provided by the DeepONet as a starting point to construct a set of functions that have the following properties: (1) they constitute a basis, (2) they are orthonormal, and (3) they are hierarchical, i.e., akin to Fourier series or orthogonal polynomials. We have exploited the favorable properties of our custom-made basis functions to both study their approximation capability and use them to expand the solution of linear and nonlinear time-dependent PDEs. The proposed approach advances the state of the art and versatility of spectral methods and, more generally, promotes the synergy between traditional scientific computing and machine learning.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Data-Driven Day-Ahead PV Estimation Using Autoencoder-LSTM and Persistence Model

Inherent variability in photovoltaic (PV) and associated impacts on power systems is a challenging problem for both the PV owners and the grid operators. Existing statistical and machine learning algorithms typically work well for weather conditions similar to historical data. Furthermore, uncertain weather conditions pose a great challenge to the estimation accuracy of the estimation models. With the enhanced integration of intelligent electronic devices and the realization of associated automation in the power grid, renewable energy data is becoming more accessible, which can be utilized by deep learning models and improve the PV power generation estimation accuracy. In this paper, a hybrid deep learning model driven by external weather data is proposed to do day-ahead PV output forecasting at 15-minute-interval. The proposed model is motivated by the recent advancement of Long-Short-Term-Memory (LSTM) networks and AutoEncoder (AE), which estimates uncertainties in sequence while making the prediction for complex weather conditions. Meanwhile, the persistence model (PM) is used to predict continuous sunny weather conditions. The forecasting result is validated with data from multiple locations

42 ENGINEERING↗

DOE OSTI2023

Modeling and Rapid Prototyping of Integrated Transmission-Distribution OPF Formulations with PowerModelsITD.jl

Conventional electric power systems are composed of different unidirectional power flow stages of generation, transmission, and distribution, managed independently by transmission system and distribution system operators. However, as distribution systems increase in complexity due to the integration of distributed energy resources, coordination between transmission and distribution networks will be imperative for the optimal operation of the power grid. However, coupling models and formulations between transmission and distribution is non-trivial, in particular due to the common practice of modeling transmission systems as single-phase, and distribution systems as multi-conductor phase-unbalanced. To enable the rapid prototyping of power flow formulations, in particular in the modeling of the boundary conditions between these two seemingly incompatible data models, we introduce PowerModelsITD.jl, a free, open-source toolkit written in Julia for integrated transmission-distribution (ITD) optimization that leverages mature optimization libraries from the InfrastructureModels.jl-ecosystem. The primary objective of the proposed framework is to provide baseline implementations of steady-state ITD optimization problems, while providing a common platform for the evaluation of emerging formulations and optimization problems. In this work, we introduce the nonlinear formulations currently supported in PowerModelsITD.jl, which include AC-polar, AC-rectangular, current-voltage, and a linear network transportation model. Results are validated using combinations of IEEE transmission and distribution networks.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Guest Editorial: Special Section on Sustainable Energy for Enhancing Grid Resiliency

Extreme weather threatens lives, disables communities, and devastates energy generation, transmission, and distribution systems. These extreme events are likely to become more frequent or more intense due to climate change. Energy networks have shown significant vulnerability during record hurricanes, deadly heat waves, destructive wildfires, and winter storms in the past few years. Because of the energy transition process, modern power grids will feature a high penetration level of the use of renewable resources. The adoption of renewable energy and the rise of omnidirectional power delivery mean that our energy network is more decentralized than ever. In this new environment, grid operation becomes more complex, and achieving resiliency is more difficult than in the past. Many utilities are seeking the latest technologies to improve energy security and responsiveness to severe events. On the one hand, sustainable energy resources can provide emergency power and assist grid restoration in disastrous events. On the other hand, their volatility, susceptibility, interdependency, and other unique features must be carefully considered when being used for grid resilience enhancement. This special section brings together 22 papers that range from innovative research advances tackling fundamental challenges of achieving more resilient grids to real-world demonstrations of leveraging sustainable energy resources to enhance grid resiliency. These papers can be categorized into three groups.

climate change↗

DOE OSTI2021

Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolor

Abstract Background The development of bioenergy crops with reduced recalcitrance to enzymatic degradation represents an important challenge to enable the sustainable production of advanced biofuels and bioproducts. Biomass recalcitrance is partly attributed to the complex structure of plant cell walls inside which cellulose microfibrils are protected by a network of hemicellulosic xylan chains that crosslink with each other or with lignin via ferulate (FA) bridges. Overexpression of the rice acyltransferase OsAT10 is an effective bioengineering strategy to lower the amount of FA involved in the formation of cell wall crosslinks and thereby reduce cell wall recalcitrance. The annual crop sorghum represents an attractive feedstock for bioenergy purposes considering its high biomass yields and low input requirements. Although we previously validated the OsAT10 engineering approach in the perennial bioenergy crop switchgrass, the effect of OsAT10 expression on biomass composition and digestibility in sorghum remains to be explored. Results We obtained eight independent sorghum ( Sorghum bicolor (L.) Moench) transgenic lines with a single copy of a construct designed for OsAT10 expression. Consistent with the proposed role of OsAT10 in acylating arabinosyl residues on xylan with p -coumarate ( p CA), a higher amount of p -coumaroyl-arabinose was released from the cell walls of these lines upon hydrolysis with trifluoroacetic acid. However, no major changes were observed regarding the total amount of p CA or FA esters released from cell walls upon mild alkaline hydrolysis. Certain diferulate (diFA) isomers identified in alkaline hydrolysates were increased in some transgenic lines. The amount of the main cell wall monosaccharides glucose, xylose, and arabinose was unaffected. The transgenic lines showed reduced lignin content and their biomass released higher yields of sugars after ionic liquid pretreatment followed by enzymatic saccharification. Conclusions Expression of OsAT10 in sorghum leads to an increase of xylan-bound p CA without reducing the overall content of cell wall FA esters. Nevertheless, the amount of total cell wall p CA remains unchanged indicating that most p CA is ester-linked to lignin. Unlike other engineered plants overexpressing OsAT10 or a phylogenetically related acyltransferase with similar putative function, the improvements of biomass saccharification efficiency in sorghum OsAT10 lines are likely the result of lignin reductions rather than reductions of cell wall-bound FA. These results also suggest a relationship between xylan-bound p CA and lignification in cell walls.

09 BIOMASS FUELS↗

DOE OSTI2021

Comparison of Tempered and Truncated Fractional Models

Tempered fractional operators are able to model effects that classical partial differential equations cannot quite capture. For example, this includes the super- and subdiffusion effects that are present in hydrology and geophysics models. However, tempered fractional operators are computationally intensive. We analyze a truncated variation of the fractional operators, which are less computationally intensive, in an effort to use them in place of the more complex tempered variation. In particular, we train parameters of the truncated operator using neural networks in order to optimize the difference of the actions of the two operators.

58 GEOSCIENCES↗

DOE OSTI2021

A Nuclear Security Enterprise Study of High-Reliability Systems, Collaboration, and Data

It may seem simple and trivial, but defining the difference between data and information is contested and has implications that may affect the security of United States interests and even cost lives. For security, data are raw facts or figures without context, while information is the compilation or articulation of data that forms context. Security depends on clarity in the differences between data and information and controlling them. Control is necessary to ensure that data and information are not inadvertently released to foreign governments, the public, or those without Need-to-Know. A primary concern in the practice of security is the control of data to avoid the inadvertent conversion to sensitive information. The complexity of this concern is further augmented when institutions are part of tightly coupled networks that informally share data and information. Additionally, those that share data as a function of legislative action—and/or formally integrate data and information system infrastructures—may be a higher security risk. This paper will present a case study that utilizes elements of literature from Knowledge Management and networks to tell a story of an issue in security—specifically, controlling the conversion of data to information.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

High-Reliability Systems and the Control of National Security Data and Information

High-reliability systems are characterized by catastrophic implications in the event of failure. These implications can include substantive damage to the environment, social order, and loss of life. Examples of high-reliability systems include nuclear submarines, nuclear reactors, the electric grid, and nuclear weapons. Due to the catastrophic implications of failure, there are heightened awareness and control mechanisms surrounding related data and information. However, defining the difference between data and information is often ambiguous across scholarly disciplines and in United States policy and legislation. For high-reliability systems, the implications of ambiguity between data and information may affect the security of United States interests and even cost lives. For security, data are raw facts or figures without context, while information is the compilation or articulation of data that forms context. Security depends on clarity in the differences between data and information and how to control them. Control is necessary to ensure that data and information are not unintentionally released to foreign governments, the public, or those without need-to-know. A primary concern in the practice of security is the control of data to avoid the unintended conversion to information. Intra-institutionally, this control is highly complex given the amalgam of legacy data systems and the numerous and constantly evolving nature of modern data systems that were not necessarily designed to be integrated. The complexity of this concern is augmented when institutions are part of interinstitutional collaborations or networks of public-private partnerships that share data and information. Additionally, institutions that share data as a function of policy and legislative action— particularly formally integrated data and information system infrastructures—may be at higher security risk. This paper will present an intra-institutional paradigm that utilizes and integrates concepts from numerous disciplines to frame a critical and underspecified practical issue in security—controlling for the unintended conversion of data to information.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2025

Real-Time Sea State Estimation for Wave Energy Converter Control via Machine Learning

Wave energy converters (WECs) harness the untapped power of ocean waves to generate renewable energy, offering a promising solution to sustainable energy. An optimal WEC control strategy is essential to maximize power capture that dynamically adjusts system parameters in response to rapidly changing sea states. This study presents a novel control approach that leverages neural networks to estimate sea states from onboard WEC measurements such as position, velocity, and force. Using a point absorber WEC device as a test platform, our proposed approach estimates sea states in real-time and subsequently adjusts PID controller gains to maximize energy extraction. Simulation results across diverse sea conditions demonstrate that our strategy eliminates the need for external wave monitoring equipment while maintaining power capture efficiency. The results show that our neural network-based control technique can improve power capture by 25.6% while significantly reducing system complexity. This approach offers a practical alternative for WEC deployments where direct wave measurements are either infeasible or cost prohibitive.

PIDcontrol↗