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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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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Implementation of the D1S Methodology for Shutdown Dose Rate Calculations in the OpenMC Monte Carlo Particle Transport Code

We present an implementation of the direct one-step (D1S) methodology for shutdown dose rate (SDR) calculations in the OpenMC Monte Carlo particle transport code. In addition to being the first fully open-source D1S implementation, it is also the first to require no ad hoc source code or nuclear data library modifications. The code can seamlessly switch between production of prompt and decay photons based on a user input parameter, and the decay data needed for decay photon generation are made available through a depletion chain file, which is already used for OpenMC’s built-in depletion/activation solver. A set of Python functions significantly eases the burden of computing and applying time correction factors needed to properly account for the time dependence of radionuclide activity. To assess the accuracy of the D1S implementation, SDR calculations have been carried out for three problems: a prism of iron irradiated by 14-MeV neutrons, the ITER port plug computational benchmark, and the Frascati Neutron Generator (FNG) ITER dose rate benchmark problem from the Shielding INtegral Benchmark Archive and Database (SINBAD). For each of these problems, comparisons were made to calculations using the rigorous two-step (R2S) method. The results on the iron prism problem illustrate how the D1S method achieves superior spatial resolution compared to the R2S method without the need for spatial discretization of the activation regions. The D1S and R2S results for the ITER port plug benchmark agree well with previously reported results in the literature. While the D1S results are 10% to 15% lower than the R2S results, this may be due to stochastic uncertainty and/or spatial discretization in the R2S calculations. On the FNG dose rate benchmark problem, the D1S method produces dose rate estimates that are within 4% of the dose rates predicted using a cell-based R2S workflow. The D1S estimates of the SDR are also in reasonable agreement with the experimental measurements and show the same basic trends that have been observed in previous works. A qualitative analysis of the execution time and uncertainty for the R2S and D1S workflows suggests that the D1S method would attain a higher figure of merit.

D1S method↗
DOE OSTI2025

GIScience in the era of Artificial Intelligence: a research agenda towards Autonomous GIS

The advent of generative AI exemplified by large language models (LLMs) opens new ways to represent and compute geographic information and transcends the process of geographic knowledge production, driving geographic information systems (GIS) towards autonomous GIS. Leveraging LLMs as the decision core, autonomous GIS can independently generate and execute geoprocessing workflows to perform spatial analysis. In this vision paper, we further elaborate on the concept of autonomous GIS and present a conceptual framework that defines its five autonomous goals, five levels of autonomy, five core functions, and three operational scales. We demonstrate how autonomous GIS could perform geospatial data retrieval, spatial analysis, and map making with four proof-of-concept GIS agents. We conclude by identifying critical challenges and future research directions, including fine-tuning and self-growing decision-cores, autonomous modelling, and examining the societal and practical implications of autonomous GIS. By establishing the groundwork for a paradigm shift in GIScience, this paper envisions a future where GIS moves beyond traditional workflows to autonomously reason, derive, innovate, and advance geospatial solutions to pressing global challenges. Meanwhile, we emphasize that as we design and deploy increasingly intelligent geospatial systems, we carry a responsibility to ensure they are developed in socially responsible ways, serve the public good, and support the continued value of human geographic insight in an AI-augmented future.

Autonomous GI↗
DOE OSTI2026

Selection of a Pair of Experiments to Optimally Reduce Uncertainty in Targeted Nuclear Data

We propose a novel process to select a pair of differential and integral experiments that best reduce uncertainties in targeted 239 ⁢Pu nuclear data while compressing the current nuclear data pipeline from 20 to 3 years. 239⁢ Pu nuclear data are poorly understood for neutrons in the intermediate energy range due to sparsity and uncertainty in historical experiments. New experiments targeting this range will enable better understanding of these nuclear data, but choosing the ideal experiments to conduct is challenging. Beginning with a prior distribution represented by samples of nuclear data generated from theory, generalized least squares adjustments are made to incorporate data from historical experiments. To quantify potential uncertainty reduction obtainable from a pair of candidate experiments, we compute the D-optimality criterion of the posterior covariance of intermediate energy range nuclear data compared to the equivalent covariance after additional adjustment to the pair of candidate experiments. Repeating the process for each of many candidate pairs facilitates the final selection. Results support 63⁢ Cu total cross section measurements for differential experiments and alumina and alumina/graphite configurations for integral experiments. This analysis enables choosing differential and integral experiments to be executed concurrently while shortening decision times relative to the current nuclear data pipeline.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

An approach to urban waterway assessment using holistic values and reciprocity

Current aquatic ecosystem assessment methods and tools often focus on physical, chemical, and biological indicators of ecosystem health. This approach to ecosystem assessment is not always straightforward to execute in urban environments and ignores potential connectivity between social and environmental outcomes. During a workshop at the Symposium on Urbanization and Stream Ecology in Brisbane, Australia in 2023 (SUSE6), we developed an approach to urban aquatic ecosystem assessment that incorporates a holistic perspective. Specifically, our approach considers both environmental (biological, chemical, and physical integrity) and social (community connection, human safety, resource use) values of urban waterways. This approach is inclusive of Indigenous perspectives, such as the concept of reciprocity, whereby consideration of both the environment and society leads to a healthy ecosystem. Here, to highlight how this holistic assessment approach could be used, we present real-world examples that included assessing both environmental and societal values informed by reciprocity or balanced perspectives. This approach can be broadly applied and adapted to specific aquatic ecosystem conditions and projects, providing an inclusive, community-centered approach for assessing the health of waterways in urban environments.

Indigenous knowledge↗
DOE OSTI2024

Frequency-domain computing using nonlinear acoustic-wave device on lithium niobate

Abstract Multiply-accumulation are crucial computing operations in signal processing, numerical simulations, and machine learning. In recent years, optical analog approaches have demonstrated higher computing performance and better power efficiency than their digital counterparts. However, analog computing chips usually need large areas and complex structures for parallel computing, as a single device element only executes one computing operation at a single time. Here, we demonstrate frequency-domain computing using the nonlinear acoustic-wave devices on lithium niobate, featuring a normalized external second-harmonic generation conversion efficiency of ~ 5.7 × 10-4 W-1. The second-order sum-frequency nonlinear process of lithium niobate enables multiplication of inputs encoded in the frequency domain. Compared to the analog schemes, our device features a notably simpler design, and nanofabrication requires only one lift-off. Using a single acoustic-wave device within an area of 0.03 mm2, we can simultaneously conduct over 130,000 multiply-accumulation operations. Our acoustic-wave device shows applications in real and complex vector convolutions and image processing. This demonstration sets the stage for experimental realizations into frequency-domain integrated nonlinear acoustic computing systems, potentially shaping future developments in acoustic neural networks and quantum computing.

chai, mingzhao (ORCID:0009000466226341)↗
DOE OSTI2026

Diagnostic x-ray source using electrons produced by a 100 J-class picosecond laser

Many laser-based high-energy-density science (HEDS) facilities have one or more short-pulse (sub- to few-picosecond) laser beams for diagnostics. For the past decade, we have been developing a novel x-ray probing capability using such picosecond lasers interacting with an underdense plasma to produce relativistic electrons. The ultimate goal of these experiments is to demonstrate a new type of x-ray backlighter using the short-pulse ARC laser at the National Ignition Facility (NIF). Before this diagnostic is fielded at the NIF, it is critical to demonstrate the viability and reproducibility of the x-ray source on comparable high-power short-pulse laser systems. We present experiments that were carried out with the OMEGA EP laser at the University of Rochester’s laboratory for laser energetics. In these experiments, high-energy electrons are produced through a combination of the self-modulation instability and direct laser acceleration in an underdense gas jet. These electrons generate directional x-rays with characteristic energies up to several tens of keV as they execute betatron motion in the ion channel, and the inverse Compton scattering process generates even harder x-rays, with characteristic photon energies of 60–240 keV. When implemented on the OMEGA EP laser(s), this x-ray source yields results that are comparable to those obtained recently on the short-pulse Titan laser at the Jupiter Laser Facility at Lawrence Livermore National Laboratory, after accounting for differences in laser energy, peak intensity, focusing f/#, and plasma source. Applications of such an x-ray source for HEDS experiments are discussed.

backlighter↗
DOE OSTI2026

The inertial confinement fusion experimental platform and diagnostics for studies of nuclear reactions relevant to nuclear astrophysics

High energy density plasmas generated in laser-driven inertial confinement fusion implosions provide unparalleled laboratory conditions for studying stellar-relevant nuclear reactions: plasma environment; hot and dense; uniquely high achievable neutron flux. These experiments have the potential to address long-standing questions about plasma effects on nuclear reactions hitherto experimentally inaccessible, including nuclear rates with thermally distributed reactants, plasma screening, and reactions involving nuclei in excited states. The National Ignition Facility (NIF) and OMEGA lasers are two primary facilities for executing experiments of this type. Existing and future nuclear diagnostics, along with supporting diagnostics to characterize the platform, enable exploitation of these plasmas for such nuclear astrophysics-relevant experiments. Here, this review describes the nuclear diagnostic capabilities currently available for these types of experiments at the NIF and OMEGA, including neutron time-of-flight spectrometers, charged-particle detectors, gamma detectors and radiochemistry diagnostics, and briefly summarizes other available diagnostic capabilities used for platform characterization. Enabling tools not yet available are also identified, including a rapid radioactive sample retrieval system, a low-energy neutron spectrometer and a high-efficiency gamma spectrometer.

National Ignition Facility↗
DOE OSTI2026

Real-time observation of toroidal current redistributions induced by three-dimensional MHD phenomena triggering vertical displacement events in tokamak plasmas

Three-dimensional MHD instabilities, including edge-localized modes (ELMs) and internal reconnection events (IREs), have been observed to precipitate loss of vertical stability in tokamak plasmas, resulting in vertical displacement events (VDEs). This vertical destabilization can occur due to toroidal current redistributions and/or shape changes resulting from these phenomena. Using a recently introduced method for rapidly reconstructing the two-dimensional toroidal plasma current density profile in real-time, results are presented that demonstrate the specific current distribution changes that occur during ELMs (on KSTAR) and IREs (on MAST-U) that lead to loss of vertical control. The method most efficiently reconstructs the toroidal current density profile by doing so on a basis of principal components of historical profiles. These principal components isolate dominant current profile dynamics, improving interpretability, increasing speed, and reducing dimensionality of the profile computation. On KSTAR, this computation is executed in the real-time plasma control system at a rate of 10 kHz (limited by available CPU cycle times), allowing the current profile evolution to be assessed at several times over the course of each ELM event. Further, by incorporating the reconstructions into a novel vertical stability metric, the contribution of specific current profile dynamics to the loss of vertical stability can be assessed in real-time for VDE avoidance and improved understanding of the causal relationship between three-dimensional MHD phenomena and VDEs. The success of this method in approximating toroidal current density profiles from kinetic equilibrium reconstructions is also presented ($R^2=0.990$), along with its capability to produce other equilibrium quantities of interest in real-time at high time resolution.

edge-localized modes↗
DOE OSTI2026

Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels

Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.

Kwok, Martin [Fermilab] (ORCID:0000000286936146)↗
DOE OSTI2026

High voltage delivery and distribution for the NEXT-100 Time Projection Chamber

A critical element in the realization of large liquid andgas time projection chambers (TPCs) is the delivery and distributionof high voltages into and around the detector. Such experimentsrequire of order tens of kilovolts to enable electron drift overmeter-scale distances. This paper describes the design andoperation of the cathode feedthrough and high voltage distributionthrough the field cage of the NEXT-100 experiment, an undergroundTPC that will search for neutrinoless double beta decay0νββ. The feedthrough has been demonstrated to holdpressures up to 20 bar and sustain voltages as high as -65 kV.The TPC is operating stably at its design high voltages. The systemhas been realized within the constraints of a stringent radiopuritybudget and is now being used to execute a suite of sensitive doublebeta decay analyses.

Adams, C. [Argonne]↗
DOE OSTI2024

Reducing measurement costs by recycling the Hessian in adaptive variational quantum algorithms

Abstract Adaptive protocols enable the construction of more efficient state preparation circuits in variational quantum algorithms (VQAs) by utilizing data obtained from the quantum processor during the execution of the algorithm. This idea originated with Adaptive Derivative-Assembled Problem-Tailored variational quantum eigensolver (ADAPT-VQE), an algorithm that iteratively grows the state preparation circuit operator by operator, with each new operator accompanied by a new variational parameter, and where all parameters acquired thus far are optimized in each iteration. In ADAPT-VQE and other adaptive VQAs that followed it, it has been shown that initializing parameters to their optimal values from the previous iteration speeds up convergence and avoids shallow local traps in the parameter landscape. However, no other data from the optimization performed at one iteration is carried over to the next. In this work, we propose an improved quasi-Newton optimization protocol specifically tailored to adaptive VQAs. The distinctive feature in our proposal is that approximate second derivatives of the cost function are recycled across iterations in addition to optimal parameter values. We implement a quasi-Newton optimizer where an approximation to the inverse Hessian matrix is continuously built and grown across the iterations of an adaptive VQA. The resulting algorithm has the flavor of a continuous optimization where the dimension of the search space is augmented when the gradient norm falls below a given threshold. We show that this inter-optimization exchange of second-order information leads the approximate Hessian in the state of the optimizer to be consistently closer to the exact Hessian. As a result, our method achieves a superlinear convergence rate even in situations where the typical implementation of a quasi-Newton optimizer converges only linearly. Our protocol decreases the measurement costs in implementing adaptive VQAs on quantum hardware as well as the runtime of their classical simulation.

Ramôa, Mafalda (ORCID:0000000302187801)↗
DOE OSTI2025

Digital quantum simulation of cavity quantum electrodynamics: insights from superconducting and trapped ion quantum testbeds

We explore the potential for hybrid development of quantum hardware where currently available quantum computers simulate open cavity quantum electrodynamical (CQED) systems for applications in optical quantum communication, simulation and computing. Our simulations make use of a recent quantum algorithm that maps the dynamics of a singly excited open Tavis–Cummings model containing N atoms coupled to a lossy cavity. We report the results of executing this algorithm on two noisy intermediate-scale quantum computers: a superconducting processor and a trapped ion processor, to simulate the population dynamics of an open CQED system featuring N = 3 atoms. By applying technology-specific transpilation and error mitigation techniques, we minimize the impact of gate errors, noise, and decoherence in each hardware platform, obtaining results which agree closely with the exact solution of the system. These results can be used as a recipe for efficient and platform-specific quantum simulation of cavity–emitter systems on contemporary and future quantum computers.

cavity QED↗
DOE OSTI2025

New Era Towards Autonomous Additive Manufacturing: A Review of Recent Trends and Future Perspectives

Abstract The Additive Manufacturing (AM) landscape has significantly transformed in alignment with Industry 4.0 principles, primarily driven by the integration of Artificial Intelligence (AI) and Digital Twin (DT). However, current Intelligent Additive Manufacturing (IAM) systems face limitations such as fragmented AI tool usage and suboptimal human-machine interaction (HMI). This paper reviews existing IAM solutions, emphasizing control, monitoring, process autonomy, and end-to-end integration, and identifies key limitations, such as the absence of a high-level controller for global decision-making. To address these gaps, we propose a transition from IAM to Autonomous Additive Manufacturing (AAM), featuring a hierarchical framework with four integrated layers: knowledge, generative solution, operational, and cognitive. In the cognitive layer, AI agents notably enable machines to independently observe, analyze, plan, and execute operations that traditionally require human intervention. These capabilities streamline production processes and expand the possibilities for innovation, particularly in sectors like in-space manufacturing (ISM). Additionally, this paper discusses the role of AI in self-optimization and lifelong learning, positing that the future of AM will be characterized by a symbiotic relationship between human expertise and advanced autonomy, fostering a more adaptive, resilient manufacturing ecosystem.

Fan, Haolin↗
DOE OSTI2025

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Decarbonization and technology cost drivers: considerations for potential future thermoelectric water use in the power sector

The power sector is currently undergoing significant changes, driven by a combination of factors, including decarbonization and technology innovation. This study aims to assess implications of these drivers on U.S. power sector technology futures and the associated water and environmental implications for cooling thermoelectric power plants. Specifically, we evaluate four decarbonization scenarios for the contiguous United States that vary in assumptions concerning demand growth and technology costs, with technology costs driving alternative outcomes that prioritize either technologies that require low amounts of water (such as wind, solar, and battery) or high amounts of water (such as nuclear and carbon capture and storage). These scenarios are executed in a power sector capacity expansion model and compared to two reference scenarios that assume status quo with policy and cost drivers. Our analysis indicates that future U.S. thermoelectric water withdrawals could decrease by 25%–60%, but water consumption could more than triple in some scenarios. These changes are driven by a combination of retirement of some power facilities, shifts in cooling technologies, and new technology deployment. The water use patterns vary across the United States, with the eastern regions demonstrating a lot more variability in water consumption across scenarios than western regions. However, local concerns can influence these possible investments, since increased water consumption can exacerbate water scarcity, leading to conflicts among competing users and affecting regional social, environmental, and economic dynamics. Future work should consider possible costs associated with alternate water sources, as well as improve the representation of water constraints within simulations. Inclusion of extreme events and alternate modeling platforms (e.g. production cost modeling and resource adequacy) may also be warranted to further stress test the robustness of these possible technology futures. Such assessments will be critical for ensuring decarbonization and other infrastructure-oriented investments lead to a reliable and resilient power grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Plasma phosphorylated tau217 strongly associates with memory deficits in the Alzheimer’s disease spectrum

Abstract Plasma phosphorylated tau (p-tau) biomarkers open unprecedented opportunities for identifying carriers of Alzheimer’s disease pathophysiology in early disease stages using minimally invasive techniques. Plasma p-tau biomarkers are believed to reflect tau phosphorylation and secretion. However, it remains unclear to what extent the magnitude of plasma p-tau abnormalities reflects neuronal network disturbance in the form of cognitive impairment. To address this question, we included 103 cognitively unimpaired elderly and 40 cognitively impaired, amyloid-β-positive individuals from the TRIAD cohort, in addition to 336 cognitively unimpaired and 216 cognitively impaired, amyloid-β-positive older adults from the BioFINDER-2 cohort. Participants had tau PET scans, amyloid PET scans or amyloid CSF, p-tau217, p-tau181 and p-tau231 blood measures, structural T1-MRI and cognitive assessments. In this cross-sectional study, we used regression models and correlation analyses to assess the relationship between plasma biomarkers and cognitive scores. Furthermore, we applied receiver operating characteristic curves to assess cognitive impairment across plasma biomarkers. Finally, we categorized participants into amyloid (A), p-tau (T1) and tau PET (T2) positive (+) or negative (−) profiles and ran non-parametric comparisons to assess differences across cognitive domains. We found that plasma p-tau217 was more associated with cognitive performance than p-tau181 and p-tau231 and that this relationship was particularly strong for memory scores (TRIAD: βp-tau217 = −0.53, βp-tau181 = −0.35 and βp-tau231 = −0.24; BioFINDER-2: βp-tau217 = −0.52, βp-tau181 = −0.24 and βp-tau231 = −0.29). Associations in amyloid-β-positive participants resembled these results, but other cognitive scores also showed strong associations in cognitively impaired individuals. Moreover, plasma p-tau217 outperformed plasma p-tau181 and plasma p-tau231 in identifying memory impairment (area under the curve values for TRIAD: p-tau217 = 0.86, p-tau181 = 0.77 and p-tau231 = 0.75; and for BioFINDER-2: p-tau217 = 0.86, p-tau181 = 0.76 and p-tau231 = 0.81) and in identifying executive function impairment only in the BioFINDER-2 cohort (p-tau217 = 0.82, p-tau181 = 0.76 and p-tau231 = 0.76). Lastly, we showed that subtle memory deficits were present in A+T1+T2− participants for plasma p-tau217 (P = 0.007) and plasma p-tau181 (P = 0.01) in the TRIAD cohort and for all biomarkers across cognitive domains in A+T1+T2− and A+T1+T2− individuals (P < 0.001 in all) in the BioFINDER-2 cohort. The A+T1+T2− individuals showed cognitive deficits in both cohorts (P < 0.001 in all). Together, our results suggest that plasma p-tau217 stands out as a biomarker capable of identifying memory deficits attributable to Alzheimer’s disease and that memory impairment certainly occurs in amyloid-β- and plasma p-tau-positive individuals who have no significant amounts of tau in the neocortex.

Neurosciences & Neurology↗
DOE OSTI2024

The DYRKP1 kinase regulates cell wall degradation in Chlamydomonas by inducing matrix metalloproteinase expression

Abstract The cell wall of plants and algae is an important cell structure that protects cells from changes in the external physical and chemical environment. This extracellular matrix, composed of polysaccharides and glycoproteins, must be constantly remodeled throughout the life cycle. However, compared to matrix polysaccharides, little is known about the mechanisms regulating the formation and degradation of matrix glycoproteins. We report here that a plant kinase belonging to the dual-specificity tyrosine phosphorylation-regulated kinase (DYRKP1) family present in all eukaryotes regulates cell wall degradation after mitosis of Chlamydomonas reinhardtii by inducing the expression of matrix metalloproteinases. Without DYRKP1, daughter cells cannot disassemble parental cell walls and remain trapped inside for more than 10 days. On the other hand, the dual-specificity tyrosine phosphorylation-regulated kinase complementation lines show normal degradation of the parental cell wall. Transcriptomic and proteomic analyses indicate a marked downregulation of MMP gene expression and accumulation, respectively, in the dyrkp1 mutants. The mutants deficient in matrix metalloproteinases retain palmelloid structures for a longer time than the background strain, like dyrkp1 mutants. Our findings show that dual-specificity tyrosine phosphorylation-regulated kinase, by ensuring timely MMP expression, enables the successful execution of the cell cycle. Altogether, this study provides insight into the life cycle regulation in plants and algae.

Kim, Minjae (ORCID:0000000223561295)↗
DOE OSTI2024

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗