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Turbo-Turtle v0.12.1

A collection of solid body modeling tools for 2D sketched, 2D axisymmetric, and 3D revolved models. It also contains general purpose meshing and image generation utilities appropriate for any model, not just those created with this package. Implemented for Abaqus and Cubit as backend modeling and meshing software. Orginal implementation targeted Abaqus so most options and descriptions use Abaqus modeling concepts and language. Turbo-Turtle makes a best effort to maintain common behaviors and features across each third-party software’s modeling concepts. As much as possible, the work for each subcommand is performed in Python 3 to minimize solution approach duplication in third-party tools. The third-party scripting interface is only accessed when creating the final tool specific objects and output. The tools contained in this project can be expanded to drive other meshing utilities in the future, as needed by the user community. This project derives its name from the origins as a sphere partitioning utility following the turtle shell (or soccer ball) pattern.s.

Brindley, Kyle

Design and Analysis of a 25 MWe Supercritical CO2 Turbo Machine

This paper presents the design and analysis of a turbo machine operating with supercritical carbon dioxide (sCO2) in a 25 MWe Recompression Brayton Cycle (RCBC). The work was performed under US Department of Energy (DoE) program DE-EE-0010318. The design process involves the aerodynamic design of the compressor and turbine, including the initial layout of flowpaths and stage configurations to achieve high efficiency and performance. Additionally, a comprehensive rotodynamic analysis is performed to ensure the stability and reliability of the system. Conceptual designs for a high-speed motor and synchronous generator that match turbomachinery requirements are also developed from first principles.

42 ENGINEERING

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES

Characterization and Optimization of the Fitting of Quantum Correlation Functions

This case study presents a characterization and optimization of an application code for extracting parton distribution functions from high energy electron-proton scattering data. Profiling this application code reveals that the phase-space density computation accounts for 93% of the overall execution time for a single iteration on a single core. When executing multiple iterations in parallel on a multicore system, the application spends 78% of its overall execution time idling due to load imbalance. We address these issues by first transforming the application code from Python to C++ and then tackling the application load imbalance via a hybrid scheduling strategy that combines dynamic and static scheduling. These techniques result in a 62% reduction in CPU idle time and a 2.46x speedup in overall execution time per node. In addition, the typically enabled power-management mechanisms in supercomputers (e.g., AMD Turbo Core, Intel Turbo Boost, and RAPL) can significantly impact intra-node scalability when more than 50% of the CPU cores are used. This finding underscores the importance of understanding system interactions with power management, as they can adversely impact application performance, and highlights the necessity of intra-node scaling tests to identify performance degradation that inter-node scaling tests might otherwise overlook.

Chuang, Pi-Yueh [Virginia Tech,Dept. of Computer S

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine

Domain Knowledge Guided Bayesian Optimization For Autonomous Alignment Of Complex Scientific Instruments

Bayesian Optimization (BO) is a powerful tool for optimizing complex non-linear systems. However, its performance degrades in high-dimensional problems with tightly coupled parameters and highly asymmetric objective landscapes, where rewards are sparse. In such needle-in-a-haystack scenarios, even advanced methods like trust-region BO (TurBO) often lead to unsatisfactory results. We propose a domain knowledge guided Bayesian Optimization approach, which leverages physical insight to fundamentally simplify the search problem by transforming coordinates to decouple input features and align the active subspaces with the primary search axes. We demonstrate this approach's efficacy on a challenging 12-dimensional, 6-crystal Split-and-Delay optical system, where conventional approaches, including standard BO, TuRBO and multi-objective BO, consistently led to unsatisfactory results. When combined with an reverse annealing exploration strategy, this approach reliably converges to the global optimum. The coordinate transformation itself is the key to this success, significantly accelerating the search by aligning input co-ordinate axes with the problem's active subspaces. As increasingly complex scientific instruments, from large telescopes to new spectrometers at X-ray Free Electron Lasers are deployed, the demand for robust high-dimensional optimization grows. Our results demonstrate a generalizable paradigm: leveraging physical insight to transform high-dimensional, coupled optimization problems into simpler representations can enable rapid and robust automated tuning for consistent high performance while still retaining current optimization algorithms.

FOS: Computer and information sciences