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Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

Artificial Intelligence/Machine Learning (AI/ML)

TechEdSat-13: The First Flight of an AI/ML Neuromorphic Processor

Neuromorphic processors, inspired by the wiring of the brain, permit certain classes of Artificial Intelligence/Machine Learning (AI/ML) algorithms to run far more efficiently. Ultimately, such systems will make the small- and nano-satellite platforms even more useful in terms of greatly improved power, communication and internal data management. In addition, on-board processing of images and data will help to not only rapidly interpret the information, but also reduce the amount of data that needs to be transmitted to ground stations. This initial flight experiment uses the Intel/ Loihi processor combined with a custom interface board and three communication channels to run the AI/ML scripts. These will vary with increasing length and complexity during the course of the mission. The algorithms will use the (at first) limited sensor data to ‘learn’ - with comparisons to similar architecture in comparable ground experiments. Some of the applications for successor flights in the TES-n flight series include Cognitive Communications, whereby the overall communication system is optimized per overflight – by optimizing timing and data transmission functions. Lastly, the performance of the Loihi 14nm process technology will be monitored for performance in the LEO radiation environment, thus looking for induced hardware and software errors. This information will help guide future radiation protection techniques to extend the lifetime and overall utility. The TES-13 is a 3U nanosat successfully launched by the Virgin Orbit Launcher-1 on January 13, 2022, and will presage more flights and AI/ML applications to come.

TechEdSat

Advances in additive manufacturing, materials, and applications with AI/ML

There is high interest in making digital manufacturing a central facet of the new manufacturing landscape. However, in the materials science world, there is much work and opportunity to realize the full potential of artificial intelligence/machine learning (AI/ML) with regard to the structure–composition–processing–property (SCPP) relationship. For polymers (thermoplastics, thermosets, elastomers) and composites (nanocomposites), the origin of their high performance and even recyclability starts with design and formulation. Processing methods enable more property development based on curing, shape-factor forming, and anisotropic directionality. In subtractive manufacturing, high-performance and engineering polymers can be shaped and milled to very high tolerance and specifications and used as replacements for metals and alloys. In conclusion, this typically relies on digital manufacturing methods but tends to be wasteful in materials.

Lara-Ceniceros, Tania E. [Centro de Investigación

TechEdSat-13: The First Flight of a Neuromorphic Processor

Neuromorphic processors, inspired by the wiring of the brain, permit certain classes of Artificial Intelligence/Machine Learning (AI/ML) algorithms to run far more efficiently. Ultimately, such systems will make the small- and nano-satellite platforms even more useful in terms of greatly improved power, communication and internal data management. In addition, on-board processing of images and data will help to not only rapidly interpret the information, but also reduce the amount of data that needs to be transmitted to ground stations. This initial flight experiment uses the Intel/Loihi processor combined with a custom interface board and three communication channels to run the AI/ML scripts. These will vary with increasing length and complexity during the course of the mission. The algorithms will use the (at first) limited sensor data to ‘learn’ - with comparisons to similar architecture in comparable ground experiments. Some of the applications for successor flights in the TES-n flight series include Cognitive Communications, whereby the overall communication system is optimized per overflight – by optimizing timing and data transmission functions. Lastly, the performance of the Loihi 14nm process technology will be monitored for performance in the LEO radiation environment, thus looking for induced hardware and software errors. This information will help guide future radiation protection techniques to extend the lifetime and overall utility. The TES-13 is a 3U nanosat successfully launched by the Virgin Orbit Launcher-1 on January 13, 2022, and will presage more flights and AI/ML applications to come.

TechEdSat

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence

Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides

Background: Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleaginous yeast as part of a global stress response. While research has demonstrated that post-translational modifications (PTMs), including phosphorylation and protein cysteine thiol oxidation (redox PTMs), are involved in signaling pathways that regulate stress responses in metazoa and algae, their role in oleaginous yeast remain understudied and unexplored. Results: Towards linking the yeast oleaginous phenotype to protein function, we integrated lipidomics, redox proteomics, and phosphoproteomics to investigate Rhodotorula toruloides under nitrogen-rich and starved conditions over time. Our lipidomics results unearthed interactions involving sphingolipids and cardiolipins with ER stress and mitophagy. Our redox and phosphoproteomics data highlighted the roles of the AMPK, TOR, and calcium signaling pathways in regulation of lipogenesis, autophagy, and oxidative stress response. As a first, we also demonstrated that lipogenic enzymes including fatty acid synthase are modified as a consequence of shifts in cellular redox states due to nutrient availability. Conclusions: We conclude that lipid accumulation is largely a consequence of carbon rerouting and autophagy governed by changes to PTMs, and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis. Our systems-level approach sets the stage for acquiring multidimensional data sets for protein structural modeling and predicting the functional relevance of PTMs using Artificial Intelligence/Machine Learning (AI/ML). Coupled to those bioinformatics approaches, the putative PTM switches that we delineate will enable advanced metabolic engineering strategies to decouple lipid accumulation from nitrogen limitation.

Lipid Signalling

Data From Experiments on Bubbling Fluidization of Zeolite in a Rectangular Bubbling Fluidized Bed

Fluidization experiments were conducted in a lab-scale rectangular bubbling fluidized bed with the objective of generating a high-quality dataset for model validation and artificial intelligence/machine learning (AI/ML) training. Zeolite was chosen as the bed material, and the fluidizing medium was air as supplied by a compressor. Three different flow rates at the inlet were chosen such that the particles were fluidized but not elutriated from the system. The test matrix involved randomization and replicates to provide uncertainty estimates as well as four different batches of zeolite as the bed material. The quantities of interest obtained from this study were statistics of differential pressures, interface heights, and particle velocities. Considering all the components of the elaborate test plan, the results obtained were consistent and reproducible. Characterization tests were performed to estimate particle properties including size, density, coefficient of friction, coefficient of restitution, and minimum fluidization velocity. In addition, the angle of repose from granular discharge experiments has been reported to account for rolling friction, though its effect on the overall process is expected to be negligible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

AI/ML-Enhanced Wind Forecasts for Reducing Uncertainty in Prescribed Fire Planning

Prescribed fire is a vital tool for ecosystem management and wildfire risk reduction but its escalation is constrained by overly conservative burn windows because of uncertainties, for instance, in wind forecasts. This review describes the state of the art in weather product use by fire/smoke models and identifies three priority research gaps that artificial intelligence/machine learning (AI/ML) is well positioned to address: (1) spatial and temporal downscaling to meter-scale, sub-hourly wind fields; (2) bias correction for systematic model errors in complex terrain; and (3) robust uncertainty quantification to inform ensemble-based simulations. Emerging AI/ML techniques offer promising frameworks to address all three challenges. By providing high-resolution, bias-corrected, and probabilistic wind fields, AI/ML-enhanced forecasts will allow for expanded burn windows, improved ignition strategy design and a reduced reliance on expert intuition, especially when a prescribed fire is introduced into new areas.

54 ENVIRONMENTAL SCIENCES

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)

A Newly Developing Community-Oriented Data System from NASA GES DISC

Data services are essential to facilitate data access and to aid efficiency of conducting research and application activities. With emerging technologies such as cloud computing and AI/ML (Artificial Intelligence/Machine Learning) leading the pace of the data world, the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), home to the permanent archive for multidisciplinary Earth Observation (EO) geospatial data to study atmospheric composition, weather and climate variability, and water and energy cycles is no exception.Interfacing directly with users as part of data center work, we understand the challenges for the required time and effort to discover, visualize, and analyze large varieties and quantities of Earth Observation information for research, monitoring, and decision-making, largely due to the existing data and information systems aim to support experienced users, but has been proved difficult for non-earth scientists and new users that are unfamiliar with the variety of formats and structures in which data, metadata, and information are stored, as well as the required methods to use them. To address these challenges, I will update our latest activities with regard to water-and energy-related products and community-oriented and user-friendly services at the GES DISC, including our plans for the emerging technologies.

Jennifer Wei

The Machine Learning Showroom: Presentation to OCIO Data Science Summit

Artificial Intelligence/Machine Learning (AI/ML) has become an indispensable tool for descriptive, predictive and prescriptive analytics. Demand for AI/ML models at NASA is outpacing Data Scientist staff. The AI/ML Showroom is an effort to empower NASA professionals to evaluate AI/ML solutions for their problems in a scalable self-help manner, relying on coding examples, reference use cases, digital assistant guides, jam sessions, video training, and pre-configured cloud resources.

machine learning

Virtual Resource Management Framework (CRADA Final Report)

There is a need for advanced and widespread business automation within the nuclear industry to drive down operational costs while sustaining or improving safe operations. While there are many business process automation platforms commercially available, the difficulty is that business processes typically rely on a mixture of resource types to accomplish the desired activities and there is no universal software framework virtualizing diverse resource types for the purpose of automation. In this context, we are referring to any capability, physical or intangible, that can be used by an organization to achieve its objectives as a resource. To deploy business automation broadly and enable integrated operations for nuclear (ION), a framework is needed to represent all resource types and their associated disparate data within a plant and to enable seamless flow of resource information to the technologies used for process automation and resource optimization.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Application of Artificial Intelligence/Machine Learning to Operations Research

This report examines the transformative impact of Artificial Intelligence (AI) and Machine Learning (ML) on operations research, private industry, and government sectors, highlighting their applications in automating processes, enhancing decision-making, and optimizing complex systems. AI/ML technologies have revolutionized industries through predictive maintenance, supply chain optimization, and autonomous systems, while also advancing public safety and defense operations. However, challenges such as data integrity, model transparency, and the need for human oversight persist, particularly in high-consequence environments. The report emphasizes the critical role of explainable AI (XAI) and human-computer interaction models like Human-in-the-Loop (HITL) and Human-on-the-Loop (HOTL) in fostering trust and accountability. Balancing automation with ethical responsibility and transparency is essential for the continued successful integration of AI/ML into operational and strategic decision-making frameworks.

97 MATHEMATICS AND COMPUTING