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At least 955 records · Page 53

A generalized platform for artificial intelligence-powered autonomous enzyme engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive tau-leaping methods for microscopic-lattice kinetic Monte Carlo simulations

Traditional Kinetic Monte Carlo (KMC) approaches, rooted in Gillespie’s stochastic simulation algorithm, become computationally demanding in systems with a large range of timescales. The goal of this work is to propose and study new adaptive lattice-KMC time integration strategies for spatially non-uniform systems. To that end, two novel adaptive tau-leaping methods and their corresponding time integration strategies are developed based on the idea of the “n-fold” direct KMC method. These strategies allow for the simultaneous execution of multiple reactions, advancing time by adaptively selected coarse increments. We present numerical experiments comparing the proposed methods with existing approaches in a catalytic surface kinetics application involving ammonia decomposition.

Bimolecular reactions↗

Hybrid Parameter Search and Dynamic Model Selection for Mixed-Variable Bayesian Optimization

Herein this article presents a new type of hybrid model for Bayesian optimization (BO) adept at managing mixed variables, encompassing both quantitative (continuous and integer) and qualitative (categorical) types. Our proposed new hybrid models (named hybridM) merge the Monte Carlo Tree Search structure (MCTS) for categorical variables with Gaussian Processes (GP) for continuous ones. hybridM leverages the upper confidence bound tree search (UCTS) for MCTS strategy, showcasing the tree architecture’s integration into Bayesian optimization. Our innovations, including dynamic online kernel selection in the surrogate modeling phase and a unique UCTS search strategy, position our hybrid models as an advancement in mixed-variable surrogate models. Numerical experiments underscore the superiority of hybrid models, highlighting their potential in Bayesian optimization.

97 MATHEMATICS AND COMPUTING↗

Accelerating the rate of discovery: toward high-repetition-rate HED science

As high-intensity short-pulse lasers that can operate at high-repetition-rate (HRR) (>10 H z ) come online around the world, the high energy density (HED) science they enable will experience a radical paradigm shift. The >10 3 increase in shot rate over today's shot-per-hour drivers translates into dramatically faster data acquisition, more experiments, and the ability to exploit machine learning, and thus the potential to significantly accelerate the advancement of HED science. A wide range of HED experiments, from opacity investigations to secondary source generation to plasma nuclear physics, will benefit from the increased statistics, precision, and exploration of phase space. Besides increasing the rate at which scientific experiments can be performed, HRR also allows for the rapid delivery of optimal experiments supported by simulations and modeling augmented by close coupling to empirical data. To fully realize such an HRR framework, numerous subsystems must be developed and brought together, including feedback laser control loops, high-throughput targetry and diagnostics, cognitive simulation, enhanced HED codes, and advanced data analytics. This paper describes the vision for an integrated HRR laser experimental HED system and outlines some of the major considerations and challenges for realizing it.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fault Detection via Occupation Kernel Principal Component Analysis

Reliable operation of automatic systems is heavily dependent on the ability to detect faults in the underlying dynamics. While traditional model-based methods have been widely used for fault detection, data-driven approaches have garnered increasing attention due to their ease of deployment and minimal need for expert knowledge. In this letter, we present a novel principal component analysis (PCA) method that uses occupation kernels. Occupation kernels result in feature maps that are tailored to the measured data, have inherent noise-robustness due to the use of integration, and can utilize irregularly sampled system trajectories of variable lengths for PCA. The occupation kernel PCA method is used to develop a reconstruction error approach to fault detection and its efficacy is validated using numerical simulations.

42 ENGINEERING↗

Visual Analytics of Crosstalk in Quantum Hardware

Crosstalk remains a major obstacle to building scalable and fault-tolerant quantum computers. Conventional diagnostic techniques-often based on numerical simulation or statistical modeling-struggle to scale with hardware complexity and offer limited interpretability. In this work, we present a visual analytics framework for diagnosing qubit crosstalk using lightweight, circuit-based models integrated with an interactive user interface. Our approach quantifies correlations between active and idle qubits under parameterized single- and twoqubit operations, enabling detection of both spatial and gateinduced crosstalk. The system incorporates qubit topology and gate performance data to support sector-based exploration and correlation mapping. This tool assists users in identifying correlated error sources, informing qubit placement strategies, and guiding noise-aware circuit design.

Chae, Junghoon [ORNL] (ORCID:0000000206016746)↗

Multi-Entity Simulation with CoSim Toolbox

Co-simulation is an analysis technique for linking multiple software models during runtime by facilitating data exchange and simulation time synchronization. There are numerous challenges when constructing an effective co-simulation including simulation tool installation, data management, and writing new models in a manner compatible with the co-simulation framework of choice. CoSim Toolbox is an integration of multiple pieces of software designed to make assembling such a co-simulation in HELICS easier. This report summarizes the existing capabilities of CoSim Toolbox and outlines future development plans.

97 MATHEMATICS AND COMPUTING↗

Develop and verify soil/structure interaction for pile/foundation interaction

Phase II of the Offshore Code Comparison Collaboration, Continued, with Correlation and unCertainty (OC6) project was used to verify the implementation of a new soil-structure interaction (SSI) model for use within offshore wind turbine modeling software. The REDWIN Macro-element model implemented and verified in this study enables a computationally efficient way to model the linear and nonlinear SSI problem, including hysteretic damping, of a monopile structure. The modeling approach was integrated into several modeling tools and a series of increasingly complex simulations was conducted using the IEA 10MW reference turbine mounted on a monopile support structure to verify the coupling between the tools and the REDWIN Macro-element SSI model. This campaign includes only numerical verification between various software and modeling approaches so no experimental measurements are available. The load cases (LC) considered include: LC1 – static response of the tower and substructure LC2 – frequency and mode-shape analysis of the tower and substructure LC3 – response of the tower and substructure due to wind-only loading LC4 – response of the tower and substructure due to wave-only loading LC5 – response of the tower and substructure due to wind and wave loading. Detailed properties of the modeled system are found in the following reference, “Bergua, Roger, Amy Robertson, Jason Jonkman, and Andy Platt. 2021. "Specification Document for OC6 Phase II: Verification of an Advanced Soil-Structure Interaction Model for Offshore Wind Turbines.” Golden, CO: National Renewable Energy Laboratory. NREL/TP-5000-79938. https://www.nlr.gov/docs/fy21osti/79938.pdf. Details on the results from the OC6 Phase II project can be found in the following reference, “Bergua R, Robertson A, Jonkman J, et al. OC6 Phase II: Integration and verification of a new soil–structure interaction model for offshore wind design.” Wind Energy. 2022;25(5):793-810. doi:10.1002/we.2698

17 WIND ENERGY↗

Shear strength and permeability of the cement-casing interface

Here, the shear strength and hydraulic permeability of the interface between well cement and casing was investigated using a triaxial direct shear apparatus. For the first time, these experiments provide measurements under controlled stress conditions with fluid flow measurements along the interface. The low cohesion (1.1 ± 1.1 MPa) and the high friction angle (43.4 ± 2.0°) indicates that the shear strength of the interface is provided by friction. This implies that the state of stress of the cement is critical to well integrity. The hydraulic aperture of the undamaged cement-steel samples was 6.8 ± 1.0 microns. Shear damage to the interface caused a decrease (-20 %) in hydraulic aperture for samples aged up to 1 month, and an increase (+300 %) for samples cured for two years. We performed numerical simulations to estimate the leakage potential from a carbon storage operation. This model predicts negligible leakage amounts (47 tonnes) in a shear-damaged well for the modeled injection of ~1.26 million tonnes of CO 2 . Thus, our measurements indicate that the cement-casing interface is not a significant leakage pathway in its intact or damaged state, and that shear-driven failure scenarios for this interface are not a significant risk to CO 2 storage security.

54 ENVIRONMENTAL SCIENCES↗

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗

The importance of explicitly representing the streambed in watershed models

Abstract The streambed is the critical interface between the aquatic and terrestrial systems and hosts important biogeochemical hot spots within river corridors. Although the streambed characteristics are significantly different from those of its surrounding soil, the streambed itself has not been explicitly represented in watershed models. Here, we explicitly incorporated a streambed layer into an integrated hydrologic model through model parameterization and discretization. We examined the hydrological effects of streambed characteristics, including hydraulic conductivity ( K ), layer thickness, and resolution, on the exchange fluxes across the streambed as well as the streamflow at the watershed outlet. The numerical experiments were performed in the American River Watershed, a headwater, mountainous watershed within the Yakima River Basin in central Washington. Despite having a negligible effect on the watershed streamflow, an explicit representation of the streambed with distinctive properties dramatically changed the magnitude and variability of the exchange flux. In general, a larger streambed K along with a thicker streambed layer induced larger exchange fluxes. The exchange flux was most sensitive to the streambed resolution. A finer streambed resolution increased exchange fluxes per unit area while reducing the overall exchange volumes across the entire streambed. The amount of baseflow decreased by 6% as the streambed resolution increased from 250 to 50 m. This finding is important because these hydrological changes may, in turn, affect the exchange of nutrients and contaminants between surface water and groundwater and the associated biogeochemical processes. Our work demonstrated the importance of representing streambeds in fully distributed, process‐based watershed models to better capture the exchange flow dynamics in river corridors.

54 ENVIRONMENTAL SCIENCES↗

Expedited Walkdowns and Preparation of Cost Estimates for Decontamination and Demolition of Excess Facilities - 20335

Lawrence Livermore National Security, LLC (LLNS) is the prime contractor responsible for managing and operating Lawrence Livermore National Laboratory (LLNL). The mission of the LLNL is to strengthen security of the United States through development and application of world-class science and technology to enhance the nation's defense, reduce the global threat from terrorism and weapons of mass destruction, and respond with vision, quality, integrity, and technical excellence to scientific issues of national importance. To accomplish its mission, LLNL must plan and manage its campus space and facilities to optimize use of its relatively small one-square-mile footprint. LLNL currently has numerous excess facilities that require decontamination and demolition (D and D). The LLNL Legacy Facility Program is responsible for stewardship and risk reduction programs to effectively manage these excess assets at LLNL. The Legacy Facility Program identified 10 excess facilities at LLNL that were candidates for demolition based on risks from further degradation of the facilities, potential exposure to hazardous materials, or need for removal to make way for new program facilities. The buildings range from a structure built in 1943 to serve as a US Navy drill hall during World War II, to a facility that provided neutrons to study material properties for the fusion energy program. The National Nuclear Security Administration (NNSA) appropriated FY19 funding for the development of Class 3 estimates for these 10 excess facilities that would be used to develop a Program Management Plan for funding consideration. Class 3 estimates are not conceptual, nor overly detailed, but adequate to be used for budget and appropriation purposes. Using existing strategic sourcing agreements, LLNL was able to organize a team of senior subject matter experts (SMEs) with diverse technical backgrounds across the Department of Energy (DOE) Complex to complete extensive process knowledge (PK) reviews and walk-downs of each excess facility and to deliver accurate and complete estimates under an expedited schedule (i.e., within eight weeks). To facilitate the expedited schedule, LLNL was fully prepared for the arrival of the JGMS team, which consisted of the following companies: J.G. Management Systems, Inc. (JGMS); Strata-G, LLC; and Michael Baker International. LLNL provided background and PK information on the excess facilities, pictures, supporting historical documentation, and radiological survey history as well as escorted access to the facilities. The JGMS team has previous experience supporting Program Management Plans for excess facilities at the Y-12 National Security Complex. The team mobilized to LLNL and performed the facility walk-downs from January 22-25, 2019. Using a methodical evaluation process, expertise, and experience, the team was able to deliver walk-down draft reports and estimates to LLNL before their February 8, 2019 deadline. LLNL then in turn reviewed, completed the estimates by adding waste management costs and other LLNL costs, and delivered the estimates to NNSA by February 15, 2019. The completed final reports, including draft D and D estimates, were delivered to LLNL before their March 6, 2019 deadline. The work was successfully completed ahead of the expedited schedule required by LLNL, resulting in a commendation from the client. This paper describes how the partnership and collaboration as a fully integrated team comprised of the prime contractor, LLNS, and the JGMS team successfully met the needs of the US government, resulting in the performance of expedited site walk-downs, the development of summary evaluation reports, and the preparation of draft Class 3 estimates and preliminary schedules for the D and D of 10 excess facilities at LLNL. The efforts of the team will enable the D and D of the first excess facility in the 2020-2021 time frame. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Galaxy bispectrum in the spherical Fourier-Bessel basis

The bispectrum, the three-point correlation in Fourier space, is a crucial statistic for studying many effects targeted by the next-generation galaxy surveys, such as primordial non-Gaussianity (PNG) and general relativistic (GR) effects on large scales. In this work we develop a formalism for the bispectrum in the spherical Fourier-Bessel (SFB) basis—a natural basis for computing correlation functions on the curved sky, as it diagonalizes the Laplacian operator in spherical coordinates. Working in the SFB basis allows for line-of-sight effects such as redshift space distortions and GR to be accounted for exactly, i.e., without having to resort to perturbative expansions to go beyond the plane-parallel approximation. Only analytic results for the SFB bispectrum exist in the literature given the intensive computations needed. We numerically calculate the SFB bispectrum for the first time, enabled by a few techniques: We implement a template decomposition of the redshift-space kernel Z 2 into Legendre polynomials, and separately treat the PNG and velocity-divergence terms. We derive an identity to integrate a product of three spherical harmonics connected by a Dirac delta function as a simple sum and use it to investigate the limit of a homogeneous and isotropic Universe. Furthermore, we present a formalism for convolving the signal with separable window functions and use a toy spherically symmetric window to demonstrate the computation and give insights into the properties of the observed bispectrum signal. While our implementation remains computationally challenging, it is a step toward a feasible full extraction of information on large scales via a SFB bispectrum analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

The APBS software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. APBS has enjoyed widespread adoption throughout the biomedical community and is used in numerous applications involving biomolecular structures. However, visualization of complex biomolecular electrostatic properties can be challenging for two-dimensional graphics systems. Therefore, advanced visualization and manipulation capabilities have been incorporated. In particular, APBS tools have been integrated with the UnityMolX virtual reality platform to provide an immersive experience for preparing biomolecular systems for calculations as well as visualizing and comparing calculated results.

electrostatics, molecular visualization, solvation↗

Multi-fidelity microstructure-induced uncertainty quantification by advanced Monte Carlo methods

Quantifying uncertainty associated with the microstructure variation of a material can be a computationally daunting task, especially when dealing with advanced constitutive models and fine mesh resolutions in the crystal plasticity finite element method (CPFEM). Numerous studies have been conducted regarding the sensitivity of material properties and performance to the mesh resolution and choice of constitutive model. However, a unified approach that accounts for various fidelity parameters, such as mesh resolutions, integration time-steps and constitutive models simultaneously is currently lacking. Further, this paper proposes a novel uncertainty quantification (UQ) approach for computing the properties and performance of homogenized materials using CPFEM, that exploits a hierarchy of approximations with different levels of fidelity. In particular, we illustrate how multi-level sampling methods, such as multi-level Monte Carlo (MLMC) and multi-index Monte Carlo (MIMC), can be applied to assess the impact of variations in the microstructure of polycrystalline materials on the predictions of homogenized materials properties. We show that by adaptively exploiting the fidelity hierarchy, we can significantly reduce the number of microstructures required to reach a certain prescribed accuracy. Finally, we show how our approach can be extended to a multi-fidelity framework, where we allow the underlying constitutive model to be chosen from either a phenomenological plasticity model or a dislocation-density-based model.

36 MATERIALS SCIENCE↗

Reman Co-Design: A Combined Design and Remanufacturing Optimization Framework for the Sustainable Design of High-Value Components

Remanufacturing is a process that returns end-of-life equipment to as-new conditions and offers numerous environmental and economic benefits. To fully capitalize on remanufacturing, its synergistic interactions with design must be fully realized and addressed during the design stage. Although this fact is widely recognized in the literature, most of the current studies focus primarily either on the design or remanufacturing aspects of design for remanufacturing (DfRem). In an effort to offer a more integrated DfRem approach than those reported in the literature, we propose a new combined design and remanufacturing optimization (reman co-design) framework that takes a holistic approach by leveraging the intricate interplay between design and remanufacturing. Here, the aim of this formulation is to identify the optimal decisions that maximize the benefits of remanufacturing throughout the entire lifespan of a product. To showcase the utility of the new formulation, we are using a case study of a hydraulic manifold, (re)manufactured by John Deere. Using this industry example, we compare the results of reman co-design to the ones from a decoupled remanufacturing design approach. Results reveal that remanufacturing benefits are better realized and improved upon when using the developed reman co-design approach.

design for X↗

Community-Informed Urban Flood Modeling for Impact Mitigation

The intensification of the hydrologic cycle due to climate change poses a threat to aging and under-designed water infrastructure systems which cannot adequately manage intense storm events. Developing a comprehensive plan for managing rain-driven flooding events is challenging due to uncertainties in the magnitude and frequency of future storm events and conflicting stakeholder objectives. In the City of Baltimore, Maryland, stormwater infrastructure is struggling to keep up with rainfall-driven (pluvial) flooding events, which regularly damage housing and disrupt transportation for residents. In this study, a hybrid of community engagement, numerical modeling, and artificial intelligence techniques are employed to explore prospective urban flooding adaptations. Community engagement drives the development of an urban flooding model (EPA Storm Water Management Model) for the Baltimore Harbor watershed. The model integrates complex surface and subsurface stormwater infrastructure data from the City, high-resolution spatial data, insights from local public works experts, and the lived experiences of City residents. This co-developed model simulates adaptations of interest to stakeholders in the city, including green and grey infrastructure and operational management strategies. Stormwater management scenarios focused on inlet cleaning and spatially concentrated green infrastructure are found to be the most effective in reducing flood depths in community priority locations. Together, these adaptations can reduce the duration of intersection inundation by more than twenty minutes, allowing for quicker emergency response and restoration of typical transportation systems. Future work will combine this community engaged flooding model with the Deep Uncertainties Pathways framework to explore tradeoffs between adaptations and develop dynamic adaptations which align with community objectives, enhance climate resilience in Baltimore, and can be adjusted in response to changing future conditions.

Ava, Spangler [Pennsylvania State University]↗

Light-ray wave functions and integrability

Using integrability, we construct (to leading order in perturbation theory) the explicit form of twist-three light-ray operators in planar $\mathcal{N}$ = 4 SYM. This construction allows us to directly compute analytically continued CFT data at complex spin. We derive analytically the “magic” decoupling zeroes previously observed numerically. Using the Baxter equation, we also show that certain Regge trajectories merge together into a single unifying Riemann surface. Perhaps more surprisingly, we find that this unification of Regge trajectories is not unique. If we organize twist-three operators differently into what we call “cousin trajectories” we find infinitely more possible continuations. We speculate about which of these remarkable features of twist-three operators might generalize to other operators, other regimes and other theories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗