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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗
DOE OSTI2021

Benchmarking Coordination Number Prediction Algorithms on Inorganic Crystal Structures

Coordination numbers and geometries form a theoretical framework for understanding and predicting materials properties. Algorithms to determine coordination numbers automatically are increasingly used for machine learning and automatic structural analysis. In this work, we introduce MaterialsCoord, a benchmark suite containing 56 experimentally-derived crystal structures (spanning elements, binaries, and ternary compounds) and their corresponding coordination environments as described in the research literature. We also describe CrystalNN, a novel algorithm for determining near neighbors. We compare CrystalNN against 7 existing near-neighbor algorithms on the MaterialsCoord benchmark, finding CrystalNN to perform similarly to several well-established algorithms. For each algorithm, we also assess computational demand and sensitivity towards small perturbations that mimic thermal motion. Finally, we investigate the similarity between bonding algorithms when applied to the Materials Project database. Finally, we expect that this work will aid the development of coordination prediction algorithms as well as improve structural descriptors for machine learning and other applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Complexity-calibrated benchmarks for machine learning reveal when prediction algorithms succeed and mislead

Abstract Recurrent neural networks are used to forecast time series in finance, climate, language, and from many other domains. Reservoir computers are a particularly easily trainable form of recurrent neural network. Recently, a “next-generation” reservoir computer was introduced in which the memory trace involves only a finite number of previous symbols. We explore the inherent limitations of finite-past memory traces in this intriguing proposal. A lower bound from Fano’s inequality shows that, on highly non-Markovian processes generated by large probabilistic state machines, next-generation reservoir computers with reasonably long memory traces have an error probability that is at least $$\sim 60\%$$ ∼ 60 % higher than the minimal attainable error probability in predicting the next observation. More generally, it appears that popular recurrent neural networks fall far short of optimally predicting such complex processes. These results highlight the need for a new generation of optimized recurrent neural network architectures. Alongside this finding, we present concentration-of-measure results for randomly-generated but complex processes. One conclusion is that large probabilistic state machines—specifically, large $$\epsilon$$ ϵ -machines—are key to generating challenging and structurally-unbiased stimuli for ground-truthing recurrent neural network architectures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A New Evaluation Metric for Demand Response-Driven Real-Time Price Prediction Towards Sustainable Manufacturing

Abstract The increasing industry energy demand highlights the urgency of demand response management, while the emerging smart manufacturing technologies pave the way for the implementation of real-time price (RTP)-based demand response management towards sustainable manufacturing. The demand response management requires scheduling of manufacturing systems based on RTP predictions, and thus the prediction quality can directly alter the effectiveness of demand response. However, since the general price prediction algorithms and prediction evaluation metrics are not specifically designed for RTP in demand response problems, a good RTP prediction obtained and evaluated by these algorithms and metrics may not be suitable for demand response scheduling. Therefore, in this study, the relationships between the effectiveness of demand response for manufacturing systems and evaluation results from six commonly used metrics are investigated. Meanwhile, a new metric called k-peak distance (KPD), considering the characteristics of the demand response problem, is proposed and compared with the other six metrics. Furthermore, an encoder-decoder long short-term memory recurrent neural network with KPD is proposed to provide better RTP prediction for manufacturing demand response problems. The case studies indicate that the proposed KPD metric shows a 1.8–3.6 times higher correlation with the demand response effectiveness compared to the other metrics. In addition, the production schedule based on the RTP prediction obtained from the proposed algorithm can improve the effectiveness of demand response by 23.4% on average.

Engineering↗
DOE OSTI2025

An Advanced Machine Learning and Artificial Intelligence System for Demonstrating Radiation Regulatory Compliance in DOE Accelerator Facilities

In this Phase II proposal, Applied Research LLC (ARLLC), Thomas Jefferson National Accelerator Facility (Jefferson Lab), and Old Dominion University (ODU) propose the combination of domain knowledge (beam characteristics, fixed structural shielding, earthen burden (the soil and foliage added to the dome of the experimental halls as additional shielding), etc.), machine learning (ML) and/or artificial intelligence (AI) to correlate a variety of multi-modal onsite signals and the radiation fields seen in accessible areas of the accelerator site and the site boundary. The ML/AI will consider the complex influence of environmental parameters affecting the radon contribution of the measurements, focusing on actual data obtained from Jefferson Lab. In Phase I, the coded beam and location data were fed into a deep learning model to predict doses at several designated locations in Jefferson Lab’s facility. Moreover, a dense radiation map was generated using only a sparse collection of the samples in a facility. In Phase II, we will develop a software prototype containing a radiation prediction algorithm, dense radiation map algorithms, and background noise prediction algorithms, with actual data used to evaluate the prototype. This work will provide a framework for evaluation of radiation measurement results around the site based on learned responses. In addition, the proposed approach allows more granular mapping of radiation levels. Better understanding and communication of these levels is related to the overall approach in keeping doses to personnel ALARA.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Traffic Prediction for Merging Coordination Control in Mixed Traffic Scenarios

Connected and autonomous vehicles (CAVs) have the potential to bring in safety, mobility, and energy benefits to transportation. The control decisions of CAVs are usually determined for a look-ahead horizon based on previewed traffic information. This requires an effective prediction of future traffic conditions and its integration with the CAV control framework. However, the short-term traffic prediction using information from connectivity is a challenging research topic, especially for mixed traffic scenarios. This work focuses on the development of a traffic prediction framework for a merging coordination controller. The previously developed merging controller coordinates the merging sequence and travel speed of CAVs to maximize the energy efficiency and overall mobility. In mixed traffic scenarios, the controller receives information regarding the position of all the vehicles traveling inside a control zone and controls the desired speed of all CAVs. The controller has no control on the human-driven vehicles. The merging controller does not have direct information or an explicit prediction on the behaviors of human-driven vehicles. Aiming to improve the performance of the merging controller in various mixed traffic conditions, a traffic prediction algorithm is developed and evaluated in this work. The performance of this traffic prediction algorithm is investigated for various penetration rates of connectivity for a single-lane secondary road merging to a single-lane primary road. The results show that compared to a constant speed assumption of human-driven vehicles, the proposed traffic prediction algorithm is able to reduce the prediction error of the arrival time of human-driven vehicles at the merging zone by more than 50%.

Shao, Yunli↗
DOE OSTI2024

Adaptive Online Model Update Algorithm for Predictive Control in Networked Systems

In this article, we introduce an adaptive on-line model update algorithm designed for predictive control applications in networked systems, particularly focusing on power distribution systems. Unlike traditional methods that depend on historical data for offline model identification, our approach utilizes real-time data for continuous model updates. This method integrates seamlessly with existing online control and optimization algorithms and provides timely updates in response to real-time changes. This methodology offers significant advantages, including a reduction in the communication network bandwidth requirements by minimizing the data exchanged at each iteration and enabling the model to adapt after disturbances. Furthermore, our algorithm is tailored for non-linear convex models, enhancing its applicability to practical scenarios. The efficacy of the proposed method is validated through a numerical study, demonstrating improved control performance using a synthetic IEEE test case.

data-driven model predictive control↗
DOE OSTI2022

A Hybrid Bulk Algorithm to Predict Turbulent Fluxes over Dry and Wet Bare Soils

Measurements made in the Columbia River basin (Oregon) in an area of irregular terrain during the second Wind Forecast Improvement Project (WFIP2) field campaign are used to develop an optimized hybrid bulk algorithm to predict the surface turbulent fluxes from readily measured or modeled quantities over dry and wet bare or lightly vegetated soil surfaces. The hybrid (synthetic) algorithm combines (i) an aerodynamic method for turbulent flow, which is based on the transfer coefficients (drag coefficient and Stanton number), roughness lengths, and Monin–Obukhov similarity; and (ii) a modified Priestley–Taylor (P-T) algorithm with physically based ecophysiological constraints, which is essentially based on the surface energy budget (SEB) equation. Soil heat flux in the latter case was estimated from measurements of soil temperature and soil moisture. In the framework of the hybrid algorithm, bulk estimates of the momentum flux and the sensible heat flux are derived from a traditional aerodynamic approach, whereas the latent heat flux (or moisture flux) is evaluated from a modified P-T model. Direct measurements of the surface fluxes (turbulent and radiative) and other ancillary atmospheric/soil parameters made during WFIP2 for different soil conditions (dry and wet) are used to optimize and tune the hybrid bulk algorithm. The bulk flux estimates are validated against the measured eddy-covariance fluxes. We also discuss the SEB closure over dry and wet surfaces at various time scales based on the modeled and measured fluxes. Although this bulk flux algorithm is optimized for the data collected during the WFIP2, a hybrid approach can be used for similar flux-tower sites and field campaigns.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Improved machine learning algorithm for predicting ground state properties

Finding the ground state of a quantum many-body system is a fundamental problem in quantum physics. In this work, we give a classical machine learning (ML) algorithm for predicting ground state properties with an inductive bias encoding geometric locality. The proposed ML model can efficiently predict ground state properties of an n-qubit gapped local Hamiltonian after learning from only $\mathcal{O}$(log(n)) data about other Hamiltonians in the same quantum phase of matter. This improves substantially upon previous results that require $\mathcal{O}$(n c ) data for a large constant c. Furthermore, the training and prediction time of the proposed ML model scale as $\mathcal{O}$(n log n) in the number of qubits n. Numerical experiments on physical systems with up to 45 qubits confirm the favorable scaling in predicting ground state properties using a small training dataset.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

A New Proposal Generalized Predictive Control Algorithm With Polynomial Reference Tracking Applied for Sodium Fast Reactors

This paper proposes a generalized predictive control (GPC) with constraints and orthonormal Laguerre functions using the simplified model of the primary system (reactor core and intermediate heat exchanger (IHX)) of a prototypical sodium fast reactor (SFR). This paper develops a multiple-input multiple-output (MIMO) GPC with input constraints able to track polynomial references of any degree applied in coolant temperature difference across the core and fractional power. The manipulated variables of the GPC-SFR are the reactivity and the sodium flow rate of the primary and secondary pipes. Moreover, orthonormal Laguerre functions and step down condition number techniques were also applied to avoid the numerical ill-conditioning issue in quadratic programming of large systems. Thus, a GPC type-2 was designed to control fractional power, coolant temperature difference across the core and sodium tank temperature of the SFR primary system when temperature references change according to a linear ramp after reaching their steady-state operation, sustaining 100% power operation on the reactor. In order to analyze the load tracking capability of the GPC-SFR type-2, the load following from 100% fractional power (FP) to 60% FP at 0.8% FP/min rate is simulated. Constraints on the rate of coolant temperature difference across the core and reactivity were applied for the design safety. For comparison criteria, this paper compares the GPC-SFR type-2 with the GPC-SFR type-1, i.e., standard model predictive control (MPC), to verify the viability and superior performance of the proposal regarding: (a) ramp-tracking capability of temperature and load; (b) the rejections of a reactivity disturbance of -1 cent and a secondary sodium inlet temperature disturbance of +10°F; and (c) a simulation with uncertainty in reactor design. The simulations show that the GPC-SFR type-2 overcome the GPC-SFR type-1 robustness and performance.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Utilizing computer vision and artificial intelligence algorithms to predict and design the mechanical compression response of direct ink write 3D printed foam replacement structures

Additive Manufacturing (AM) of porous polymeric materials, such as foams, recently became a topic of intensive research due their unique combination of low density, impressive mechanical properties, and stress dissipation capabilities. Conventional methods for fabricating foams rely on complex and stochastic processes, making it challenging to achieve precise architectural control of structured porosity. In contrast, AM provides access to a wide range of printable materials, where precise spatial control over structured porosity can be modulated during the fabrication process enabling the production of foam replacement structures (FRS). Current approaches for designing FRS are based on intuitive understanding of their properties or an extensive number of finite element method (FEM) simulations. These approaches, however, are computationally expensive and time consuming. As such, in this work, we present a novel methodology for determining the mechanical compression response of direct ink write (DIW) 3D printed FRS using a simple cross-sectional image. By obtaining measurement data for a relatively small number of samples, an artificial neural network (ANN) was trained, and a computer vision algorithm was used to make inferences about foam compression characteristics from a single cross-sectional image. Finally, a genetic algorithm (GA) was used to solve the inverse design problem, generating the AM printing parameters that an engineer should use to achieve a desired compression response from a DIW printed FRS. The methods developed herein present an avenue for entirely autonomous design and analysis of additively manufactured structures using artificial intelligence.

36 MATERIALS SCIENCE↗
DOE OSTI2024

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Philympics 2021: Prophage Predictions Perplex Programs

Most bacterial genomes contain integrated bacteriophages—prophages—in various states of decay. Many are active and able to excise from the genome and replicate, while others are cryptic prophages, remnants of their former selves. Over the last two decades, many computational tools have been developed to identify the prophage components of bacterial genomes, and it is a particularly active area for the application of machine learning approaches. However, progress is hindered and comparisons thwarted because there are no manually curated bacterial genomes that can be used to test new prophage prediction algorithms. Here, we present a library of gold-standard bacterial genome annotations that include manually curated prophage annotations, and a computational framework to compare the predictions from different algorithms. We use this suite to compare all extant stand-alone prophage prediction algorithms to identify their strengths and weaknesses. We provide a FAIR dataset for prophage identification, and demonstrate the accuracy, precision, recall, and f 1 score from the analysis of seven different algorithms for the prediction of prophages. We discuss caveats and concerns in this analysis and how those concerns may be mitigated.

Roach, Michael J.↗
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 OSTI2023

Privacy-preserving federated learning: Application to behind-the-meter solar photovoltaic generation forecasting

Here, the growing usage of decentralized renewable energy sources has made accurate estimation of their aggregated generation crucial for maintaining grid flexibility and reliability. However, the majority of distributed photovoltaic (PV) systems are behind-the-meter (BTM) and invisible to utilities, leading to three challenges in obtaining an accurate forecast of their aggregated output. Firstly, traditional centralized prediction algorithms used in previous studies may not be appropriate due to privacy concerns. There is therefore a need for decentralized forecasting methods, such as federated learning (FL), to protect privacy. Secondly, there has been no comparison between localized, centralized, and decentralized forecasting methods for BTM PV production, and the trade-off between prediction accuracy and privacy has not been explored. Lastly, the computational time of data-driven prediction algorithms has not been examined. This article presents a FL power forecasting method for PVs, which uses federated learning as a decentralized collaborative modeling approach to train a single model on data from multiple BTM sites. The machine learning network used to design this FL-based BTM PV forecasting model is a multi-layered perceptron, which ensures privacy and security of the data. Comparing the suggested FL forecasting model to non-private centralized and entirely private localized models revealed that it has a high level of accuracy, with an RMSE that is 18.17% lower than localized models and 9.9% higher than centralized models.

14 SOLAR ENERGY↗
DOE OSTI2023

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes

Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family—pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization—including quantitative evaluation of allosteric regulation—of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Optimization and Multimachine Learning Algorithms to Predict Nanometal Surface Area Transfer Parameters for Gold and Silver Nanoparticles

Interactions between gold metallic nanoparticles and molecular dyes have been well described by the nanometal surface energy transfer (NSET) mechanism. However, the expansion and testing of this model for nanoparticles of different metal composition is needed to develop a greater variety of nanosensors for medical and commercial applications. In this study, the NSET formula was slightly modified in the size-dependent dampening constant and skin depth terms to allow for modeling of different metals as well as testing the quenching effects created by variously sized gold, silver, copper, and platinum nanoparticles. Overall, the metal nanoparticles followed more closely the NSET prediction than for Förster resonance energy transfer, though scattering effects began to occur at 20 nm in the nanoparticle diameter. To further improve the NSET theoretical equation, an attempt was made to set a best-fit line of the NSET theoretical equation curve onto the Au and Ag data points. An exhaustive grid search optimizer was applied in the ranges for two variables, 0.1≤C≤2.0 and 0≤α≤4, representing the metal dampening constant and the orientation of donor to the metal surface, respectively. Three different grid searches, starting from coarse (entire range) to finer (narrower range), resulted in more than one million total calculations with values C=2.0 and α=0.0736. The results improved the calculation, but further analysis needed to be conducted in order to find any additional missing physics. With that motivation, two artificial intelligence/machine learning (AI/ML) algorithms, multilayer perception and least absolute shrinkage and selection operator regression, gave a correlation coefficient, R2, greater than 0.97, indicating that the small dataset was not overfitting and was method-independent. This analysis indicates that an investigation is warranted to focus on deeper physics informed machine learning for the NSET equations.

Demers, Steven M. E. (ORCID:0000000192213246)↗