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At least 343 records · Page 19

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)↗

Inverse design of hypoeutectoid pearlite steel microstructures using a deep learning and genetic algorithm optimization framework

Goal-oriented microstructure design in metallic materials is a challenging task due to complex structure-property relationships. Traditional experimental and computational approaches are time-intensive and economically inefficient, limiting their applicability for large-scale design space exploration. Here, in this work, we propose an end-to-end framework that integrates deep learning models with genetic optimization to design microstructures with targeted mechanical properties. Deep learning models enable accurate forward design, while their integration with genetic optimization enables efficient inverse design within a few hours, compared to days or weeks using conventional finite element simulations. The framework combines experimental characterization and finite element modeling to analyze the influence of microstructural features on the mechanical behavior of hypoeutectoid steels. Data from both experiments and simulations are used to train the deep learning models. To demonstrate its effectiveness, we apply the framework to 0.63% carbon steel with proeutectoid ferrite and pearlite phases, commonly used in industrial applications. In this study, 2D microstructures were used for modeling, selected primarily for computational efficiency and to establish proof of concept. The framework successfully optimizes microstructures for targeted yield strength, ultimate strength, and stress concentration factors while significantly reducing computational time. Beyond hypoeutectoid steels, this scalable framework can be extended to other material systems and integrated with additive manufacturing, offering an efficient approach for accelerating microstructure design for specific engineering applications.

ConvLSTM↗

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

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

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

Niowave Power Converter Modeling and Testing

Niowave has designed, built and is now using in-beam a low power (up to 10 kW) lead bismuth eutectic (LBE) converter. In this concept, an electron beam is passed through a falling layer of LBE, converting the electron to neutrons which then pass into a vessel which is functionally a subcritical reactor configuration. A detailed report has been written by Niowave, entitled “LBE Neutron Converter Manual.” The LANL contribution has been modeling, followed by a flow visualization model made in quartz. The LANL contribution is reported herein.

43 PARTICLE ACCELERATORS↗

Target Optimization Study: Tolerance Sensitivity

A Work Package was initiated to investigate the potential for target optimization. The current design is made up of 82 disks 0.5 mm thick spaced 0.25 mm apart for helium coolant flow. This disk thickness and gap width are a result of continual increases is beam power and hence volumetric heating rate. Thickening the disks would mean higher disk temperatures, but this would be weighed against the prospect of fewer, thicker disks and wider coolant gap spaces, and the relaxed tolerances that would result. Fabrication of the target holder would be easier and less expensive, and target assembly would also be easier.

43 PARTICLE ACCELERATORS↗

Progress in Understanding the Origins of Excellent Corrosion Resistance in Metallic Alloys: From Binary Polycrystalline Alloys to Metallic Glasses and High Entropy Alloys

Some of the factors responsible for good corrosion resistance of select polycrystalline and emerging alloys in chloride solutions are discussed with a goal of providing some perspectives on the current status and future directions. Traditional metallic glass alloys, single phase high entropy alloys (HEAs), early metallic glasses, and high entropy metallic glasses are all emerging corrosion-resistant alloys (CRAs) that utilize traditional strategies for improved corrosion resistance as well as take advantage of some other novel beneficial attributes. These materials enjoy many degrees of freedom as far as choice of both composition and structure, providing great flexibility in the pursuit of superior corrosion resistance. The new materials depart from classical solvent-solute type polycrystalline binary or ternary alloys. Thus, such emerging materials provide significant opportunities to achieve even greater improvements in corrosion resistance in harsh environments. Several examples of the unique corrosion properties of selected materials in the context of modern theories of corrosion are discussed herein. Discussion is restricted to solid-solution binary or ternary polycrystalline alloys, several metallic glass alloys, and single phase HEAs. A common feature of many CRAs is that composition and microstructure often affect both passivity and resistance to localized corrosion that can be divided into initiation, stabilization, and propagation stages. Enormous complexities in protective oxide structures and chemistries and the large number of combinatorial possibilities in newer materials such as HEAs preclude trial-and-error approaches and perhaps even combinatorial experimental design. Computational materials methodologies will be required in the search for new corrosion-resistant alloys in these material classes. The search must consider the best scientific insights available regarding how major and minor alloy additions, as well as various microstructural attributes, contribute to corrosion mitigation. Additional scientific insights, as they emerge, will enable choices beyond the reliance on high concentrations of alloying elements that are known to affect passivity breakdown and pit stabilization. A challenge is to connect the “basic attributes” of an alloy with its properties. The strength of this connection will likely require new scientific principles enabling deep multiphysics insights in order to link feature(s) such as composition and metallurgical phases to the desired corrosion properties. Application of data informatics will likely also play a role given the plethora of variables that are important in corrosion and the difficulty in assessing all relationships. Here, the opportunity exists to accelerate the design of emerging materials for high corrosion resistance.

36 MATERIALS SCIENCE↗

Construction of a New MgB 2 Coating System for 1.3-GHz Superconducting RF Cavities at LANL

After many years of evaluating MgB 2 films prepared with various techniques for the application to superconducting radio-frequency (SRF) cavities, we have decided to build a system to coat full-size 1.3-GHz elliptical cavities. This paper describes the design and construction of the system. Additionally, we briefly describe experimental results with a small system and first tests with the new large system. In conclusion, we were able to obtain superconducting samples with a T c of up to 38 K with the small system, but we have not been able to get any superconducting samples with the new system yet.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Beyond interpolation: Physics-inspired gating transformers for extrapolating irradiation conditions to novel nuclear fuels

The qualification of advanced nuclear fuels relies on irradiation experiments in test reactors that emulate commercial conditions. Designing these tests requires accurate prediction of key irradiation quantities, particularly heat generation rate and burnup, yet obtaining them typically involves computationally expensive multi-step simulation workflows. We propose a physics-inspired gating transformer (PIGT) that integrates an inverse-square, distance-based attenuation into the encoder representation to bias attention toward physically relevant spatial relationships while retaining data-driven flexibility. Using MiniFuel irradiation data from the High Flux Isotope Reactor at Oak Ridge National Laboratory, we benchmark against ensemble methods, feedforward and recurrent networks, convolutional models, and standard transformers. While baseline models perform well under interpolation, they exhibit a pronounced generalization gap when evaluated on fuels not included in the training set. The proposed model consistently improves extrapolative accuracy and stability, yielding the strongest performance on unseen fuel configurations. These results indicate that a lightweight physics structure embedded within attention mechanisms can substantially improve robustness, enabling more reliable surrogate predictions to accelerate the design of nuclear fuel irradiation experiments.

Fuel qualification↗

CALPHAD-based ICME design of single-step aging to enhance mechanical strength of WAAM Haynes 282

To match the strength of wire-arc additive manufactured Haynes 282 to its wrought counterpart via a single-step aging heat treatment, the CALPHAD (Calculation of Phase Diagrams) method is integrated with physics-based process-structure-property models and experimental validation. The integrated computational materials engineering (ICME) framework simulates the effects of aging on γ′ and M 23 C 6 precipitation and the resulting yield strength. To improve simulation reliability, the interfacial energies between γ/γ′ and γ/M 23 C 6 carbides were estimated by comparison with precipitation kinetic modeling and measured precipitate sizes. γ′ and M23C6 were found to precipitate simultaneously between 640 and 860 °C, producing microstructures similar to those produced by two-step aging. The optimal γ′ size for peak yield stress was calculated to be 20–23 nm. WAAM Haynes 282 aged at 780 °C for 50 h exceeded the mechanical performance of its wrought counterpart subjected to two-step aging, though desired properties can also be achieved at 800 °C for 16 h or less. The error in yield strength is less than 20 MPa, demonstrating good agreement between the modeling framework and experiments. Creep studies showed that WAAM Haynes 282 exceeded the calculated rupture time, reaching 481 h. This proposed methodology can accelerate the design of aging heat treatments for any γ′-strengthened nickel-base alloy, minimizing the resources required for trial-and-error experiments.

CALPHAD↗

GPU Direct I/O with HDF5

Exascale HPC systems are being designed with accelerators, such as GPUs, to accelerate parts of applications. In machine learning workloads as well as large-scale simulations that use GPUs as accelerators, the CPU (or host) memory is currently used as a buffer for data transfers between GPU (or device) memory and the file system. If the CPU does not need to operate on the data, then this is sub-optimal because it wastes host memory by reserving space for duplicated data. Furthermore, this “bounce buffer” approach wastes CPU cycles spent on transferring data. A new technique, NVIDIA GPUDirect Storage (GDS), can eliminate the need to use the host memory as a bounce buffer. Thereby, it becomes possible to transfer data directly between the device memory and the file system. This direct data path shortens latency by omitting the extra copy and enables higher-bandwidth. To take full advantage of GDS in existing applications, it is necessary to provide support with existing I/O libraries, such as HDF5 and MPI-IO, which are heavily used in applications. In this paper, we describe our effort of integrating GDS with HDF5, the top I/O library at NERSC and at DOE leadership computing facilities. We design and implement this integration using a HDF5 Virtual File Driver (VFD). The GDS VFD provides a file system abstraction to the application that allows HDF5 applications to perform I/O without the need to move data between CPUs and GPUs explicitly. We compare performance of the HDF5 GDS VFD with explicit data movement approaches and demonstrate superior performance with the GDS method.

Ravi, J↗

Advanced data analysis in inertial confinement fusion and high energy density physics

Bayesian analysis enables flexible and rigorous definition of statistical model assumptions with well-characterized propagation of uncertainties and resulting inferences for single-shot, repeated, or even cross-platform data. This approach has a strong history of application to a variety of problems in physical sciences ranging from inference of particle mass from multi-source high-energy particle data to analysis of black-hole characteristics from gravitational wave observations. The recent adoption of Bayesian statistics for analysis and design of high-energy density physics (HEDP) and inertial confinement fusion (ICF) experiments has provided invaluable gains in expert understanding and experiment performance. In this Review, we discuss the basic theory and practical application of the Bayesian statistics framework. We highlight a variety of studies from the HEDP and ICF literature, demonstrating the power of this technique. Due to the computational complexity of multi-physics models needed to analyze HEDP and ICF experiments, Bayesian inference is often not computationally tractable. Two sections are devoted to a review of statistical approximations, efficient inference algorithms, and data-driven methods, such as deep-learning and dimensionality reduction, which play a significant role in enabling use of the Bayesian framework. We provide additional discussion of various applications of Bayesian and machine learning methods that appear to be sparse in the HEDP and ICF literature constituting possible next steps for the community. We conclude by highlighting community needs, the resolution of which will improve trust in data-driven methods that have proven critical for accelerating the design and discovery cycle in many application areas.

47 OTHER INSTRUMENTATION↗

OptiMX

OptiMX is a GUI-oriented program with principal aim to be an easy to use, yet comprehensive, interactive accelerator optics design and analysis tool. It was originally developed starting in the 1990s as an MS Windows centric application using the commercial Borland OWL framework. In the spring of 2014, a decision was made to port OptiM to Qt, a modern, portable and open framework. As much as possible, the original interface was preserved.While a significant amount of refactoring was required, the underlying physics has been for the most, left unchanged. The custom plots of the original application have been replaced with functional equivalents based on a stable and well-established library (qwt). With very few minor exceptions the new refactored OptiMX should be a drop-in replacement for the original OWL version.

Lebedev, ValeriA. [Joint Inst. for Nuclear Researc↗

Niowave Design and Analysis of a 200 kW Converter

LANL is providing support to Niowave Inc. on the design and analysis of a 200 kW converter. The current design of the 200 kW (40 MeV, 5 mA electron beam) converter consists of LBE flowing from the top to the bottom. When compared to the Mk.5 20 kW converter, which flowed LBE from the bottom, flowing over a divider plate to create a waterfall, the 200 kW converter eliminates the divider plate, which would otherwise have melted with the higher beam power. Because the LBE flows from the top to the bottom, alternate methods to the divider plate need to be utilized to ensure a stable flow that minimizes splashing at the bottom of the LBE waterfall, while maintaining a uniform LBE thickness at the beam, and steady LBE flow at the desired flow rate.

43 PARTICLE ACCELERATORS↗

Niowave Ancillary Systems – FY21: In Partial Fulfillment of the Deliverable Requirement for Niowave Ancillary Systems Support by LANL

Niowave Inc. produces medical radioisotopes within the US. Lead-bismuth eutectic (LBE) is irradiated using an electron beam to produce neutrons that are used in the production of Molybdenum-99 (Mo-99). The medical community relies on a steady supply of Mo-99 which is primarily used in medical diagnostic imaging. The irradiation of LBE results in high temperatures within the molten metal, this work focusses on the design of ancillary systems associated with the liquid metal system. The LBE is initially at a temperature of 200°C and flows over a steel plate to create a waterfall. The electron beam is then aimed at the waterfall to generate neutrons. The peak temperatures of the LBE post irradiation depend on the beam energy of the LINAC. For a 15 MeV and 20 kW beam, the temperatures can range between 300°C and 350°C. The LBE is cycled through the system to create a closed loop that requires the post-irradiation LBE to be cooled back to 200°C. This work focuses on the heat exchanger and condenser system responsible for the cooling of the post-irradiation LBE.

36 MATERIALS SCIENCE↗

Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents

Deep eutectic solvents (DESs) are emerging as environmentally friendly designer solvents for mass transport and heat transfer processes in industrial applications; however, the lack of accurate tools to predict and thus control their viscosities under both a range of environmental factors and formulations hinders their general application. While DESs may serve as designer solvents, with nearly unlimited combinations, this unfortunately makes it experimentally infeasible to comprehensively measure the viscosities of all DESs of potential industrial interest. To assist in the design of DESs, we have developed several new machine learning (ML) models that accurately and rapidly predict the viscosities of a diverse group of DESs at different temperatures and molar ratios using, to date, one of the most comprehensive data sets containing the properties of over 670 DESs over a wide range of temperatures (278.15–385.25 K). Three ML models, including support vector regression (SVR), feed forward neural networks (FFNNs), and categorical boosting (CatBoost), were developed to predict DES viscosity as a function of temperature and molar ratio and contrasted with multilinear and two-factor polynomial regression baselines. Further, quantum chemistry-based, COSMO-RS-derived sigma profile (σ-profile) features were used as inputs for the ML models. The CatBoost model is excellent at externally predicting DES viscosity, as indicated by high R 2 (0.99) and low root-mean-square-error (RMSE) and average absolute relative deviations (AARD) (5.22%) values for the testing data sets, and 98% of the data points lie within the 15% of AARD deviations. Furthermore, SHapley additive explanation (SHAP) analysis was employed to interpret the ML results and rationalize the viscosity predictions. The result is an ML approach that accurately predicts viscosity and will aid in accelerating the design of appropriate DESs for industrial applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding

Antigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptides into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental data set from the Immune Epitope Database, and theoretical data sets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of nine neutral residues from a six-residue subset with an average R 2 coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an receiver operating characteristic (ROC) AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2 value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting seven neutral residues from an eight-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

LAMP Technical Readiness Evaluation Report (Rev. 1)

An internal preliminary evaluation of Critical Technology Elements (CTEs) for the LANSCE Modernization Project (LAMP) was completed. Corresponding Technical Readiness Levels (TRLs) were also determined for all subsystems using the criteria of DOE G 413.3-4A, Technical Readiness Assessment Guide. The scope of the evaluation was limited to the project Work Breakdown Structure (WBS) elements as defined for the RFQ Injector and Drift Tube Linac (DTL) systems only. Integration of Instrumentation and Controls (I&C) and Safety Systems was not considered, although specific technologies as related to the RFQ and DTL systems were included. Other elements of the project such as Shielding, System Design, Technical Management, and additional facility integration needed to enable off-line testing and pre-installation commissioning were also not evaluated. Each technical subsystem element was evaluated for technical readiness, however, not all were found to meet the criteria for a CTE. Only two subsystem elements were determined to meet the CTE criteria. Their associated TRLs are summarized in the table below. These subsystem elements of the project have the lowest technical readiness due to either being new, novel or modified, requiring additional R&D before being capable of meeting the project Key Performance Parameters (KPPs) and subsystem requirements, or present technology exists but has not yet been demonstrated in a relevant environment. All other subsystems were determined to have a TRL of 8, indicating that actual operating systems exist having similar performance requirements as needed for LAMP. Details of the technical readiness evaluation for each subsystem is given in the following sections of this report.

43 PARTICLE ACCELERATORS↗