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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Equation Discovery Using Fast Function Extraction: a Deterministic Symbolic Regression Approach

Advances in machine learning (ML) coupled with increased computational power have enabled identification of patterns in data extracted from complex systems. ML algorithms are actively being sought in recovering physical models or mathematical equations from data. This is a highly valuable technique where models cannot be built using physical reasoning alone. In this paper, we investigate the application of fast function extraction (FFX), a fast, scalable, deterministic symbolic regression algorithm to recover partial differential equations (PDEs). FFX identifies active bases among a huge set of candidate basis functions and their corresponding coefficients from recorded snapshot data. This approach uses a sparsity-promoting technique from compressive sensing and sparse optimization called pathwise regularized learning to perform feature selection and parameter estimation. Furthermore, it recovers several models of varying complexity (number of basis terms). FFX finally filters out many identified models using non-dominated sorting and forms a Pareto front consisting of optimal models with respect to minimizing complexity and test accuracy. Numerical experiments are carried out to recover several ubiquitous PDEs such as wave and heat equations among linear PDEs and Burgers, Korteweg–de Vries (KdV), and Kawahara equations among higher-order nonlinear PDEs. Additional simulations are conducted on the same PDEs under noisy conditions to test the robustness of the proposed approach.

42 ENGINEERING↗
DOE OSTI2026

Transfer learning for analysis of collective and non-collective Thomson scattering spectra

Thomson scattering (TS) diagnostics provide reliable, minimally perturbative measurements of fundamental plasma parameters, such as electron density (⁠n e ) and electron temperature (⁠T e ⁠). Deep neural networks can provide accurate estimates of ⁠n e and T e when conventional fitting algorithms may fail, such as when TS spectra are dominated by noise, or when fast analysis is required for real-time operation. Although deep neural networks typically require large training sets, transfer learning can improve model performance on a target task with limited data by leveraging pre-trained models from related source tasks, where select hidden layers are further trained using target data. We present five architecturally diverse deep neural networks, pre-trained on synthetic TS data and adapted for experimentally measured TS data, to evaluate the efficacy of transfer learning in estimating n e and T e in both the collective and non-collective scattering regimes. We evaluate errors in n e and T e estimates as a function of training set size for models trained with and without transfer learning, and we observe decreases in model error from transfer learning when the training set contains ≲ 200 experimentally measured spectra.

Artificial neural networks↗
DOE OSTI2023

A reference-area-free strain mapping method using precession electron diffraction data

Here, in this work, we developed a method using precession electron diffraction data to map the residual elastic strain at the nano-scale. The diffraction pattern of each pixel was first collected and denoised. Template matching was then applied using the center spot as the mask to identify the positions of the diffraction disks. Statistics of distances between the selected diffracted disks enable the user to make an informed decision on the reference and to generate strain maps. Strain mapping on an unstrained single crystal sapphire shows the standard deviation of strain measurement is 0.5%. With this method, we were able to successfully measure and map the residual elastic strain in VO 2 on sapphire and martensite in a Ni 50.3 Ti 29.7 Hf 20 shape memory alloy. This approach does not require the user to select a “strain-free area” as a reference and can work on datasets even with the crystals oriented away from zone axes. This method is expected to provide a robust and more accessible alternative means of studying the residual strain of various material systems that complements the existing algorithms for strain mapping.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Identifications of RR Lyrae Stars and Quasars from the Simulated Data of Mephisto-W Survey

We have investigated the feasibilities and accuracies of the identifications of RR Lyrae stars and quasars from the simulated data of the Multi-channel Photometric Survey Telescope (Mephisto) W Survey. Based on the variable sources light curve libraries from the Sloan Digital Sky Survey (SDSS) Stripe 82 data and the observation history simulation from the Mephisto-W Survey Scheduler, we have simulated the uvgriz multi-band light curves of RR Lyrae stars, quasars and other variable sources for the first-year observation of Mephisto W Survey. We have applied the ensemble machine learning algorithm Random Forest Classifier (RFC) to identify RR Lyrae stars and quasars, respectively. We build training and test samples and extract ~150 features from the simulated light curves and train two RFCs respectively for the RR Lyrae star and quasar classification. We find that, our RFCs are able to select the RR Lyrae stars and quasars with remarkably high precision and completeness, with purity = 95.4% and completeness = 96.9% for the RR Lyrae RFC and purity = 91.4% and completeness = 90.2% for the quasar RFC. In conclusion, we have also derived relative importances of the extracted features utilized to classify RR Lyrae stars and quasars.

(galaxies:) quasars: general↗
DOE OSTI2017

An unstructured-mesh finite-volume MPDATA for compressible atmospheric dynamics

An advancement of the unstructured-mesh finite-volume MPDATA (Multidimensional Positive Definite Advection Transport Algorithm) is presented that formulates the error-compensative pseudo-velocity of the scheme to rely only on face-normal advective fluxes to the dual cells, in contrast to the full vector employed in previous implementations. This is essentially achieved by expressing the temporal truncation error underlying the pseudo-velocity in a form consistent with the flux-divergence of the governing conservation law. The development is especially important for integrating fluid dynamics equations on non-rectilinear meshes whenever face-normal advective mass fluxes are employed for transport compatible with mass continuity—the latter being essential for flux-form schemes. In particular, the proposed formulation enables large-time-step semi-implicit finite-volume integration of the compressible Euler equations using MPDATA on arbitrary hybrid computational meshes. Furthermore, it facilitates multiple error-compensative iterations of the finite-volume MPDATA and improved overall accuracy. The advancement combines straightforwardly with earlier developments, such as the nonoscillatory option, the infinite-gauge variant, and moving curvilinear meshes. A comprehensive description of the scheme is provided for a hybrid horizontally-unstructured vertically-structured computational mesh for efficient global atmospheric flow modelling. The proposed finite-volume MPDATA is verified using selected 3D global atmospheric benchmark simulations, representative of hydrostatic and non-hydrostatic flow regimes. Besides the added capabilities, the scheme retains fully the efficacy of established finite-volume MPDATA formulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Noise-Directed Adaptive Remapping for Integer Optimization: from qubits to (encoded) qudits

We extend Noise-Directed Adaptive Remapping (NDAR), a recently proposed heuristic meta-algorithm that leverages device noise as a computational resource, to optimization problems over discrete (integer) domains. While originally introduced for unconstrained binary optimization, the proposed generalization introduces additional gauge degrees of freedom at the logical level, such that the gauge transformation applied at each iteration is no longer unique, allowing tailoring to particular encodings or quantum hardware. We identify encoding-dependent requirements for NDAR beyond binary domains: feasibility of the noise attractor, existence of compatible gauge transformations that preserve an efficiently implementable circuit family, and a systematic way to select the transform to apply at each step. We analyze these criteria for qudit-native and for binary, one-hot, and domain-wall qubit encodings, using the Max-k-colorable subgraph problem as a running example. We demonstrate that these encodings can exhibit distinct advantages and tradeoffs when integrated within the NDAR framework, particularly in how noise-induced dynamics interact with the solution landscape and choice of encoding. Our results indicate that NDAR-guided noise considerations provide a new criterion for comparing device-level encoding choices for quantum optimization. Finally, we outline directions toward experimental realization in superconducting qudit devices and further algorithmic improvements.

Hadfield, Stuart [RIACS, Mtn. View] (ORCID:0000000↗
DOE OSTI2018

Cold Commissioning Simulant Selection for the Hanford Tank Waste Treatment Plant LAW Facility - 18465

Commissioning the Low-Activity Waste (LAW) Facility of the Hanford Tank Waste Treatment and Immobilization Plant (WTP) will require large volumes (∼2,000,000 liters) of a non-radioactive, chemically analogous waste simulant. Cold commissioning will provide for operator training in an integrated facility, demonstration of mechanical process equipment capacity, environmental performance demonstration of emissions control systems, and process control systems shakedown and tuning. Selection of the cold commissioning simulant is following a structured four-phase process to arrive at the preferred composition and recipe. Phases I, II and III are complete. Phase I laid the framework for decision making with preparation of a Project Management Plan, an update to the Simulant Development, Approval, Validation, and Documentation procedure, and a kickoff meeting to gather stakeholder input into the simulant definition and selection criteria. Phase II consisted of a comprehensive literature search and compilation of LAW simulant recipes, followed by initial screening against the selection criteria identified in Phase I. This process identified 72 candidate simulant recipes and down-selected 9 for further study. Phase III studies involved a) statistical comparisons of the similarity of candidate simulant compositions to the tank waste feed vector, b) process modelling of the commissioning sequence with each simulant to estimate glass former and simulant material consumption, offgas and effluent volumes and compositions, and product glass volumes and compositions, and c) evaluation of simulants against the immobilized LAW glass composition algorithm to determine allo able waste loading to ensure compliance with product specifications and process constraints. The results of these studies identified two of the candidate recipes to be carried forward to full-scale testing. Phase IV consists of testing these two recipes at vendor facilities to determine scalability, fabricability, and stability of the simulants when produced at industrial scale. Scalability is the ability to take a recipe from bench scale (1 to 40 liters) batch size to full scale (>35,000 liters) batch size. Fabricability is the ability of a recipe to be prepared in large batches without the need for complex or expensive mechanical equipment, heating, or cooling systems. Stability is the ability of a simulant to withstand long term storage and variations in environmental conditions without unacceptable changes in key characteristics (the set of chemical, physical, and rheological parameters that the simulant is intended to exhibit during cold commissioning tests). Simulants will also be tested for compatibility with other startup material (i.e., frit), tuning simulants, and environmental performance demonstration test spiking solutions to ensure against unexpected situations. Using a structured process is essential when making high impact decisions such as waste simulant selection. Proper planning and a clear explanation of how the decision process will unfold is key to obtaining stakeholder buy-in as more information is gathered. The documentation resulting from this structured selection process will be compiled and summarized in a Cold Commissioning Simulant Definition deliverable due to the Department of Energy 24 months before the start of Cold Commissioning. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Results of the first implementation of RF phase signature matching at LANSCE

The LINAC at the Los Alamos Neutron Science Center (LANSCE) has been utilizing the Delta-t method to match the RF cavities to the design acceleration parameters since its commissioning in 1972. The differences in time-of-flight between two subsequent Beam Position and Phase Monitors (BPPMs) are measured with both accelerated and drifting beams, depending on the whether the module is set to on or off. The algorithm optimizes the module amplitude and phase via iterative measurements if the initial phase is in the vicinity of the design value. With an upgrade to a faster readout system, a scan over the whole RF cavity phase range requires relatively less time than the classical optimization procedure. The Phase Scan Signature Matching (PSSM) method provides a time-efficient method that ensures the phase selection lands on the bunching side and empowers future analyses to build module-specific models. The PSSM also utilizes a direct model to determine the correct amplitude to sub-percent level instead of using linearized matrices. Furthermore, lacking a reliable energy measurement method in the LINAC, we measure the beam phases at two downstream locations to increase the precision of energy measurements. In this letter, we also discuss the sensitivities of PSSM, error propagation, and the implementation results for the 2019 and 2020 beam cycles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Multistage mixed precision iterative refinement

Abstract Low precision arithmetic, in particular half precision (16‐bit) floating point arithmetic, is now available in commercial hardware. Using lower precision can offer significant savings in computation and communication costs with proportional savings in energy. Motivated by this, there has been a renewed interest in mixed precision iterative refinement schemes for solving linear systems , and new variants of GMRES‐based iterative refinement have been developed. Each particular variant with a given combination of precisions leads to different condition number‐based constraints for convergence of the backward and forward errors, and each has different performance costs. The constraints for convergence given in the literature are, as an artifact of the analyses, often overly strict in practice, and thus could lead a user to select a more expensive variant when a less expensive one would have sufficed. In this work, we develop a multistage mixed precision iterative refinement solver which aims to combine existing mixed precision approaches to balance performance and accuracy and improve usability. For a user‐specified initial combination of precisions, the algorithm begins with the least expensive approach and convergence is monitored via inexpensive computations with quantities produced during the iteration. If slow convergence or divergence is detected using particular stopping criteria, the algorithm switches to use a more expensive, but more reliable variant. A novel aspect of our approach is that, unlike existing implementations, our algorithm first attempts to use “stronger” GMRES‐based solvers for the solution update before resorting to increasing the precision(s). In some scenarios, this can avoid the need to refactorize the matrix in higher precision. We perform extensive numerical experiments on a variety of random dense problems and problems from real applications which confirm the benefits of the multistage approach.

Oktay, Eda↗
DOE OSTI2026

Measurement of coherent exclusive J/ψ → μ+μ− production in ultraperipheral Pb+Pb collisions at sNN=5.36 TeV with the ATLAS detector

The ATLAS experiment has performed a measurement of coherent exclusive J/ψ → μ+μ− production in ultraperipheral Pb+Pb collisions at sNN=5.36$$ \sqrt{s_{\textrm{NN}}}=5.36 $$ TeV. The data was recorded at the Large Hadron Collider (LHC) during 2023, and corresponds to an integrated luminosity of 79 μb−1. Exclusive J/ψ candidates were selected with a dedicated track-sensitive trigger based on the ATLAS transition radiation tracker. The analysis involves reconstruction of the dimuon invariant mass based on muon tracks from the inner detector, as the muon transverse momentum range of interest precludes the use of the standard muon reconstruction and identification algorithms. Differential cross sections are measured as a function of J/ψ rapidity and are compared with theoretical predictions. After extrapolation to sNN=5.02$$ \sqrt{s_{\textrm{NN}}}=5.02 $$ TeV, they are also compared with previous measurements performed by other experiments using data from LHC Run 2. While the results agree reasonably well with theoretical predictions, they are in tension with previous Run-2 results for the central rapidity region.

Aad, G↗
DOE OSTI2024

Radiation image reconstruction and uncertainty quantification using a Gaussian process prior

We propose a complete framework for Bayesian image reconstruction and uncertainty quantification based on a Gaussian process prior (GPP) to overcome limitations of maximum likelihood expectation maximization (ML-EM) image reconstruction algorithm. The prior distribution is constructed with a zero-mean Gaussian process (GP) with a choice of a covariance function, and a link function is used to map the Gaussian process to an image. Unlike many other maximum a posteriori approaches, our method offers highly interpretable hyperparamters that are selected automatically with the empirical Bayes method. Furthermore, the GP covariance function can be modified to incorporate a priori structural priors, enabling multi-modality imaging or contextual data fusion. Lastly, we illustrate that our approach lends itself to Bayesian uncertainty quantification techniques, such as the preconditioned Crank–Nicolson method and the Laplace approximation. The proposed framework is general and can be employed in most radiation image reconstruction problems, and we demonstrate it with simulated free-moving single detector radiation source imaging scenarios. We compare the reconstruction results from GPP and ML-EM, and show that the proposed method can significantly improve the image quality over ML-EM, all the while providing greater understanding of the source distribution via the uncertainty quantification capability. Furthermore, significant improvement of the image quality by incorporating a structural prior is illustrated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Rapid Bayesian High Entropy Alloy Designs Fabricated via Wire Arc Additive Manufacturing

Purpose: This project seeks to demonstrate a new high-throughput (rapid) alloy design technique applied to creating new high entropy alloys (HEAs) for extreme environments. High entropy alloys shift the design paradigm from being focused on a single principal element (e.g. nickel-based alloys) to target alloys that include high atomic fractions (X >10%) of multiple elements. These HEA materials can exhibit sluggish diffusion and enhanced corrosion resistance, ideal for potential applications in advanced ultra supercritical (A-USC) steam cycles for power generation. Scope: The addition of multiple elements in high atomic fractions creates an enormous design space that cannot easily be investigated by traditional material design strategies such as designed of experiments (DOE). This project utilizes a Bayesian machine learning algorithm that has been modified to work with calculation of phase diagrams (CALPHAD) software. This Bayesian algorithm reduces manual inputs and increase the likelihood of achieving an optimal solution. Compositional inputs to this algorithm will be assessed using existing material property models for high temperature strength and corrosion resistance. The target for alloy performance will be a 15% (~100 ⁰C) increase in allowable service temperature beyond heat-resistant stainless steels while maintaining or improving alloy cost and corrosion resistance. Haynes 230 was selected as a baseline, which is 57 wt% Ni with 22 wt% Cr 14 wt% W, and 2 wt% Mo as solid solution strengtheners. In addition to rapid design via Bayesian machine learning, the alloys were rapidly fabricated using a multi-wire arc additive manufacturing (mWAAM) technique which allows for precise control of alloy composition and assessing of alloy design “windows” to study composition effects. Build speeds for wire-arc additive processes are among the highest for additive technologies enabling rapid and reliable sample fabrication when compared to conventional methods such as arc button melting. The mWAAM samples will be rapidly characterized via instrumented indentation for room temperature modulus and strength and for elevated temperature strength via hot hardness tests. After being screened with hardness testing, potential alloys will be further evaluated with conventional microscopy techniques including scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to assess agreement with modeling results. The most promising compositions will also be evaluated by printing full sized tensile specimens for mechanical behavior tests at elevated temperatures. Results: Bayesian machine learning of a single performance function was initially used to optimize five performance metrics: 1) single phase stability, 2) yield strength, 3) creep resistance (low diffusion coefficient), 4) freezing range (weldability), and 5) material cost. The single performance function was suboptimal as assumptions had to be made about the results while formulating the optimization. A goal-oriented Bayesian optimization strategy (Hanaoka, 2021) was implemented with CALPHAD for use with the five metrics above. This multi-objective Bayesian optimization (MOBO) enabled the design of NiCrCoFe alloys with V and W additions. A base composition of NiCoCr was selected as Ni provides a stable FCC matrix, Cr aids corrosion/oxidation resistance, and Co is a solid-solutions strengthener that also improves creep by increasing the activation energy. Fe helps reduce diffusion coefficients and cost. Finally, V and W were selected for their reasonable solubility and high atomic misfit to aid in solid solution strengthening. Cracking of the mWAAM specimens was an early issue, and the Easton solidification cracking model (Easton et al., 2014a) was selected for addition to the MOBO function. High performing alloys fabricated by mWAAM included Ni 28 Cr 25 Co 26 Fe 15 V 8 and Ni 62 Cr 18 Co 1 Fe 3 W 15 . It was observed that even after adapting the mWAAM process for W, the W did not fully dissolve. To fully evaluate the Ni 62 Cr 18 Co 1 Fe 3 W 15 composition, a cored wire (80-20 NiCr sheath/powder core) was manufactured and printed via WAAM, and HIP’ing was utilized to homogenize and densify the printed alloy. The V and W alloys produced met metrics 1 (solid solution), 4 (solidification cracking), and 5 (cost). However, an unmodeled mechanism of thermal stress cracking was identified in the WAAM produced materials, perhaps exacerbated by the lack of grain boundary strengthening elements (B, C). Conclusions & Recommendations: A high-throughput (rapid) alloy design technique was applied to designing and manufacturing new high entropy alloys (HEAs) for extreme environments utilizing MOBO and mWAAM. The developed process was rapid and effective in addressing the mechanisms included in the model. The lack of grain boundary strengthening element additions (e.g., B, C) was a simplification that likely produced thermal stress cracking that turned into a large part of the investigation. Additions on the order of 0.005 wt% B and 0.05 wt% C likely would have minimized thermal stress grain boundary cracking. Overall, the high throughput design strategy is promising for rapid design of metrics-driven alloys for advanced ultra supercritical (A-USC) steam cycles for power generation. The MOBO and mWAAM process could be commercialized to accelerate metrics-driven alloy design. In addition, the cored-wire process utilized for scale-up is a promising high-volume process for WAAM alloy development and scale-up.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Real-Time Artificial Intelligence for Particle Reconstruction and Higgs Physics

With the discovery of the Higgs boson at the CERN LHC, the world's highest-energy particle accelerator complex, scientists have acquired an important tool to study the fundamental building blocks of the universe. Precision measurements of Higgs bosons produced with large momentum allow for unique insights into the structure of the interactions of the Higgs boson with other particles that may shed light on physics beyond the standard model. While experimentally challenging, exploring such interactions with novel artificial intelligence (AI) methods can advance our understanding of the Higgs sector, including the Higgs boson's self-interaction. Moreover, the LHC is undergoing a major upgrade to further increase its particle collision rate and thereby operate for an additional decade. The experimental detectors at the upgraded facility must process at least a factor of ten more data at rates of hundreds of terabytes per second all under challenging conditions. New AI techniques are required to reconstruct and select, or trigger on, the most physics-sensitive events in real-time to handle the resulting avalanche of data. The proposed research will achieve the goals of the LHC program at the CMS experiment by developing a sub-microsecond event reconstruction system using real-time AI algorithms that employ field-programmable gate array technologies. By harnessing sophisticated AI techniques, this research focuses on measuring the production of Higgs bosons at large momentum while enhancing particle reconstruction methods in the trigger and beyond. Overall, the proposed research has broader implications for the use of AI in resource-constrained, low-latency embedded applications across all fields of science.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

A comparison of eight optimization methods applied to a wind farm layout optimization problem

Abstract. Selecting a wind farm layout optimization method is difficult. Comparisons between optimization methods in different papers can be uncertain due to the difficulty of exactly reproducing the objective function. Comparisons by just a few authors in one paper can be uncertain if the authors do not have experience using each algorithm. In this work we provide an algorithm comparison for a wind farm layout optimization case study between eight optimization methods applied, or directed, by researchers who developed those algorithms or who had other experience using them. We provided the objective function to each researcher to avoid ambiguity about relative performance due to a difference in objective function. While these comparisons are not perfect, we try to treat each algorithm more fairly by having researchers with experience using each algorithm apply each algorithm and by having a common objective function provided for analysis. The case study is from the International Energy Association (IEA) Wind Task 37, based on the Borssele III and IV wind farms with 81 turbines. Of particular interest in this case study is the presence of disconnected boundary regions and concave boundary features. The optimization methods studied represent a wide range of approaches, including gradient-free, gradient-based, and hybrid methods; discrete and continuous problem formulations; single-run and multi-start approaches; and mathematical and heuristic algorithms. We provide descriptions and references (where applicable) for each optimization method, as well as lists of pros and cons, to help readers determine an appropriate method for their use case. All the optimization methods perform similarly, with optimized wake loss values between 15.48 % and 15.70 % as compared to 17.28 % for the unoptimized provided layout. Each of the layouts found were different, but all layouts exhibited similar characteristics. Strong similarities across all the layouts include tightly packing wind turbines along the outer borders, loosely spacing turbines in the internal regions, and allocating similar numbers of turbines to each discrete boundary region. The best layout by annual energy production (AEP) was found using a new sequential allocation method, discrete exploration-based optimization (DEBO). Based on the results in this study, it appears that using an optimization algorithm can significantly improve wind farm performance, but there are many optimization methods that can perform well on the wind farm layout optimization problem, given that they are applied correctly.

17 WIND ENERGY↗
DOE OSTI2017

NSR&D FY17 Report: CartaBlanca Capability Enhancements

Over the last several years, particle technology in the CartaBlanca code has been matured and has been successfully applied to a wide variety of physical problems. It has been shown that the particle methods, especially Los Alamos's dual domain material point method, is capable of computing many problems involves complex physics, chemistries accompanied by large material deformations, where the traditional finite element or Eulerian method encounter significant difficulties. In FY17, the CartaBlanca code has been enhanced with physical models and numerical algorithms. We started out to compute penetration and HE safety problems. Most of the year we focused on the TEPLA model improvement testing against the sweeping wave experiment by Gray et al., because it was found that pore growth and material failure are essentially important for our tasks and needed to be understood for modeling the penetration and the can experiments efficiently. We extended the TEPLA mode from the point view of ensemble phase average to include the effects of nite deformation. It is shown that the assumed pore growth model in TEPLA is actually an exact result from the theory. Alone this line, we then generalized the model to include finite deformations to consider nonlinear dynamics of large deformation. The interaction between the HE product gas and the solid metal is based on the multi-velocity formation. Our preliminary numerical results suggest good agreement between the experiment and the numerical results, pending further verification. To improve the parallel processing capabilities of the CartaBlanca code, we are actively working with the Next Generation Code (NGC) project to rewrite selected packages using C++. This work is expected to continue in the following years. This effort also makes the particle technology developed with CartaBlanca project available to other part of the laboratory. Working with the NGC project and rewriting some parts of the code also given us an opportunity to improve our numerical implementations of the method and to take advantage of recently advances in the numerical methods, such as multiscale algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Functional protein mining with conformal guarantees

Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model. Our method (1) lets users select many biologically-relevant loss metrics (i.e. false discovery rate) and assigns reliable functional probabilities for annotating genes of unknown function; (2) achieves state-of-the-art performance in enzyme classification without training new models; and (3) robustly and rapidly pre-filters proteins for computationally intensive structural alignment algorithms. Our framework enhances the reliability of protein homology detection and enables the discovery of uncharacterized proteins with likely desirable functional properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Combining chemistry and protein engineering for new-to-nature biocatalysis

Biocatalysis, the application of enzymes to solve synthetic problems of human import, has blossomed into a powerful technology for chemical innovation. In the past decade, a threefold partnership, where nature provides blueprints for enzymatic catalysis, chemists introduce innovative activity modes with abiological substrates, and protein engineers develop new tools and algorithms to tune and improve enzymatic function, has unveiled the frontier of new-to-nature enzyme catalysis. In this Perspective, we highlight examples of interdisciplinary studies, which have helped to expand the scope of biocatalysis, including concepts of enzymatic versatility explored through the lens of biomimicry, to achieve activities and selectivities beyond those currently possible with chemocatalysis. We indicate how modern tools, such as directed evolution, computational protein design and machine learning-based protein engineering methods, have already impacted and will continue to influence enzyme engineering for new abiological transformations. As a result, a sustained collaborative effort across disciplines is anticipated to spur further advances in biocatalysis in the coming years.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs.

59 BASIC BIOLOGICAL SCIENCES↗