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At least 163 records · Page 9

Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

Abstract Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN + ) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN + -based reducing power. This is based on an orthogonal, NMN + -dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN + . With a throughput of >10 6 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Two-Stage Reinforcement Learning Policy Search for Grid-Interactive Building Control

This paper develops an intelligent grid-interactive building controller, which optimizes building operation during both normal hours and demand response (DR) events. To avoid costly on-demand computation and to adapt to non-linear building models, the controller utilizes reinforcement learning (RL) and makes real-time decisions based on a near-optimal control policy. Learning such a policy typically amounts to solving a hard non-convex optimization problem. We propose to address this problem with a novel global-local policy search method. In the first stage, an RL algorithm based on zero-order gradient estimation is leveraged to search for the optimal policy globally, due to its scalability and the potential to escape some poor performing local optima. The obtained policy is then fine-tuned locally to bring the first-stage solution closer to that of the original unsmoothed problem. Experiments on a simulated five-zone commercial building demonstrate the advantages of the proposed method over existing learning approaches. They also show that the learned control policy outperforms a pragmatic linear model predictive controller (MPC) and approaches the performance of an oracle MPC in testing scenarios. Using a state-of-the-art advanced computing system, we demonstrate that the controller can be learned and deployed within hours of training.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Optimization of the Second Target Station cold source moderators using an automated workflow

The Second Target Station (STS) at the US Department of Energy’s Oak Ridge National Laboratory is designed to become the world’s highest peak-brightness spallation source of cold neutrons. Successful completion of the STS, which is currently in the preliminary design phase, will provide transformative new capabilities to examine novel materials for future technologies. At STS, neutrons will be generated by spallation reactions in a solid tungsten target. They will be moderated and thermalized in two cold (20 K) para-hydrogen moderators. Careful optimization of these moderators is essential to the project’s success. To find optimal moderator designs, an advanced optimization workflow integrates high-fidelity neutronics calculations using the Monte Carlo N-Particle (MCNP) transport code MCNP6.2 with state-of-the-art optimization algorithms in the Dakota optimization toolkit. For each design iteration, a parametrized solid CAD geometry is generated in Creo and automatically converted into an unstructured mesh geometry by Attila 4MC for the neutronics calculation with MCNP. Iterations repeat until optimal designs are found. Herein this paper presents the results of a sensitivity and optimization study for the cylindrical and tube moderators. Both moderators can be optimized for maximum peak brightness, maximum time-integrated brightness, or any combination between these extremes. Maximum peak brightness is achieved by using smaller optimal dimensions of the moderators, whereas maximum time-integrated brightness is achieved by using larger dimensions. A Pareto front details the designs that optimally balance both brightness metrics. The Pareto front can be found in only 40–110 iterations with 4–5 design parameters when using the efficient global and Pareto-set optimization algorithms in Dakota. Additionally, important engineering constraints can be taken into account, such as the coupling between the cylindrical moderator radius and aluminum vessel wall thicknesses required to ensure structural integrity of the vessels. This interaction has a significant impact on the resulting optimal designs. Our new, highly efficient, fully automated optimization workflow will be used to optimize additional STS components in the future and can be adopted for design and optimization studies at other experimental neutron and accelerator facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

LandScan Mosaic Time Series Version 1.0: 1975-2024

The LandScan Mosaic Annual Global Ambient Population Time Series, Version 1.0, provides annual high-resolution global ambient population estimates from 1975 to 2024. The dataset is distributed as one Cloud-Optimized GeoTIFF per year on a globally aligned 3 arc-second WGS 84 grid. The 2024 layer is the LandScan Mosaic benchmark reference year, while the 1975–2023 layers are historical estimates generated using the LandCast backcasting framework.

Zimmer, Andrew [ORNL] (ORCID:0000000176838713)↗

Operational Focused Data Analytics for Optimizing Radiation Portal Monitor-Based Nuclear Smuggling Detection Systems at Global Ports of Entry

The National Nuclear Security Administration’s Office of Nuclear Smuggling Detection and Deterrence has deployed a fleet of radiation portal monitors (RPMs) across the world at global ports of entry including seaports, airports, and land border crossings. These RPMs are integrated into radiation detection systems (RDS) that also include fixed cameras, optical character recognition (OCR) systems, primary scanning systems (e.g., X-ray or gamma-ray), and secondary scanning systems (e.g., spectroscopic radiation portal monitors, portable radiation detection systems). The data from these sensing technologies is collected at the Central Alarm Station (CAS) where servers and computers reside to control and operate the system. Operators utilize the data collected by the CAS and declared cargo information to make decisions on how to respond to an alarm.This work explores the use of CAS-located data, looking at both the sensor data streams and operator inputs, to perform analysis which supports customs and border protection agencies to improve training capability and operational effectiveness. We focus on analyzing site level effectiveness and behavior by rolling up CAS-located data collected from individual occurrences. To-date, more than 15 sites (e.g., seaports, airports, border crossings) have been analyzed in this manner with the goal of understanding system operations to verify effectiveness and recommend potential improvements. This work first aims to provide background information on relevant CAS-located data sources and our current operational system analytics process including example results. After summarizing our current analytic techniques, we discuss how the future data analytics systems can provide key benefits to improving operational performance while minimizing the burden these detection systems place on operators.

Kuhn, Michael↗

A Brief Survey on High Performance Computing Systems Power Management

This paper provides a survey of software-based power management techniques in High Performance Computing (HPC) systems. Seven existing power management and monitoring tools and frameworks are discussed. These are: Variorum, dynamic energy-performance optimizer (DEPO), Powersched, Bull Dynamic Power Optimizer (BDPO), Energy Aware Runtime (EAR), Global Extensible Open Power Manager (GEOPM), and PoLiMEr. Each of these tools is evaluated based on hardware abstraction, optimization methods, usability, and experimental validation. This survey highlights the diversity of approaches in managing energy efficiency, from vendor-neutral APIs to algorithm-driven power capping, and dynamic frequency adjustments. Given that energy requirements for large computational systems is increasing quickly, the importance of integrating these tools into existing HPC environments and the need for further research in this rapidly evolving field is also discussed.

97 - MATHEMATICS AND COMPUTING↗

Convergence analysis for a nonlocal gradient descent method via directional Gaussian smoothing

We analyze the convergence of a nonlocal gradient descent method for minimizing a class of high-dimensional non-convex functions, where a directional Gaussian smoothing (DGS) is proposed to define the nonlocal gradient (also referred to as the DGS gradient). The method was first proposed in [Zhang et al., Enabling long-range exploration in minimization of multimodal functions, UAI 2021], in which multiple numerical experiments showed that replacing the traditional local gradient with the DGS gradient can help the optimizers escape local minima more easily and significantly improve their performance. However, a rigorous theory for the efficiency of the method on nonconvex landscape is lacking. In this work, we investigate the scenario where the objective function is composed of a convex function, perturbed by deterministic oscillating noise. We provide a convergence theory under which the iterates exponentially converge to a tightened neighborhood of the solution, whose size is characterized by the noise wavelength. Here, we also establish a correlation between the optimal values of the Gaussian smoothing radius and the noise wavelength, thus justifying the advantage of using moderate or large smoothing radii with the method. Furthermore, if the noise level decays to zero when approaching the global minimum, we prove that DGS-based optimization converges to the exact global minimum with linear rates, similarly to standard gradient-based methods in optimizing convex functions. Several numerical experiments are provided to confirm our theory and illustrate the superiority of the approach over those based on the local gradient.

Tran, Hoang [Oak Ridge National Laboratory (ORNL),↗

On relaxations of the max k -cut problem formulations

Here, a tight continuous relaxation is a crucial factor in solving mixed integer formulations of many NP-hard combinatorial optimization problems. The (weighted) max k-cut problem is a fundamental combinatorial optimization problem with multiple notorious mixed integer optimization formulations. In this paper, we explore four existing mixed integer optimization formulations of the max k-cut problem. Specifically, we show that the continuous relaxation of a binary quadratic optimization formulation of the problem is: (i) stronger than the continuous relaxation of two mixed integer linear optimization formulations and (ii) at least as strong as the continuous relaxation of a mixed integer semidefinite optimization formulation. We also conduct a set of experiments on multiple sets of instances of the max k-cut problem using state-of-the-art solvers that empirically confirm the theoretical results in item (i). Furthermore, these numerical results illustrate the advances in the efficiency of global non-convex quadratic optimization solvers and more general mixed integer nonlinear optimization solvers. As a result, these solvers provide a promising option to solve combinatorial optimization problems. Our codes and data are available on GitHub.

97 MATHEMATICS AND COMPUTING↗

Domain Decomposition for Integer Optimal Control with Total Variation Regularization

Total variation integer optimal control problems admit solutions and necessary optimality conditions via geometric variational analysis. In spite of the existence of said solutions, algorithms which solve the discretized objective suffer from high numerical cost associated with the combinatorial nature of integer programming. Hence, such methods are often limited to small and medium-sized problems. We propose a globally convergent, coordinate descent–inspired algorithm that allows tractable subproblem solutions restricted to a partition of the domain. Our decomposition method solves relatively small trust-region subproblems that modify the control variable on a subdomain only. Given nontrivial subdomain overlap, we prove that a global first-order necessary optimality condition is equivalent to a first-order necessary optimality condition per subdomain. We additionally show that a sufficient decrease is achieved on a single subdomain by way of a trust-region subproblem solver using geometric measure–theoretic arguments, which we integrate with a greedy patch selection to prove convergence of our algorithm. In conclusion, we demonstrate the practicality of our algorithm on a benchmark large-scale, PDE-constrained integer optimal control problem and find that our method is faster than the state of the art.

domain decomposition↗

A constraint on historic growth in global photosynthesis due to rising CO 2

Theory predicts that rising CO 2 increases global photosynthesis, a process known as CO 2 fertilization, and that this is responsible for much of the current terrestrial carbon sink. The estimated magnitude of the historic CO 2 fertilization, however, differs by an order of magnitude between long-term proxies, remote sensing-based estimates and terrestrial biosphere models. Here we constrain the likely historic effect of CO 2 on global photosynthesis by combining terrestrial biosphere models, ecological optimality theory, remote sensing approaches and an emergent constraint based on global carbon budget estimates. Our analysis suggests that CO 2 fertilization increased global annual terrestrial photosynthesis by 13.5 ± 3.5% or 15.9 ± 2.9 PgC (mean ± s.d.) between 1981 and 2020. Our results help resolve conflicting estimates of the historic sensitivity of global terrestrial photosynthesis to CO 2 and highlight the large impact anthropogenic emissions have had on ecosystems worldwide.

54 ENVIRONMENTAL SCIENCES↗

Accelerating high-order mesh optimization using finite element partial assembly on GPUs

In this paper we present a new GPU-oriented mesh optimization method based on high order finite elements. Our approach relies on node movement with fixed topology, through the Target-Matrix Optimization Paradigm (TMOP) and uses a global nonlinear solve over the whole computational mesh, i.e., all mesh nodes are moved together. A key property of the method is that the mesh optimization process is recast in terms of finite element operations, which allows us to utilize recent advances in the field of GPU-accelerated high order finite element algorithms. For example, we reduce data motion by using tensor factorization and matrix-free methods, which have superior performance characteristics compared to traditional full finite element matrix assembly and offer advantages for GPU based HPC hardware. Furthermore, we describe the major mathematical components of the method along with their efficient GPU-oriented implementation. In addition, we propose an easily reproducible mesh optimization test that can serve as a performance benchmark for the mesh optimization community.

97 MATHEMATICS AND COMPUTING↗

Beyond Component Optimization: Systems Level Biodesign for Lanthanide Recovery

Global demand for lanthanides (Ln) is projected to rise sharply over the next decade, while geographically concentrated supply chains and the low concentrations and matrix complexity of secondary feedstocks limit the reach of conventional hydro- and pyrometallurgical separation. Engineered biological systems offer a selective, low-energy alternative, and component-level advances in Ln-binding proteins, AI-designed selective scaffolds, and cell-surface display platforms now rival synthetic chelators in affinity and selectivity. These components, however, remain functionally isolated. Currently, there are no engineered chassis coupling recognition, intracellular trafficking, accumulation, and controlled release into an end-to-end pipeline. Here, we outline how new biodesign strategies and chassis selection must move beyond bioleaching to encompass the full recovery pathway. Achieving this requires integrating AI/ML-guided design, genome-scale build tools, high-throughput phenotyping, and biophysical transport modeling within a Design–Build–Test–Learn cycle tuned to recognition, trafficking, accumulation, and release.

Biodesign↗

One Stomatal Model to Rule Them All? Toward Improved Representation of Carbon and Water Exchange in Global Models

Abstract Stomatal conductance schemes that optimize with respect to photosynthetic and hydraulic functions have been proposed to address biases in land‐surface model (LSM) simulations during drought. However, systematic evaluations of both optimality‐based and alternative empirical formulations for coupling carbon and water fluxes are lacking. Here, we embed 12 empirical and optimization approaches within a LSM framework. We use theoretical model experiments to explore parameter identifiability and understand how model behaviors differ in response to abiotic changes. We also evaluate the models against leaf‐level observations of gas‐exchange and hydraulic variables, from xeric to wet forest/woody species spanning a mean annual precipitation range of 361–3,286 mm yr −1 . We find that models differ in how easily parameterized they are, due to: (a) poorly constrained optimality criteria (i.e., resulting in multiple solutions), (b) low influence parameters, (c) sensitivities to environmental drivers. In both the idealized experiments and compared to observations, sensitivities to variability in environmental drivers do not agree among models. Marked differences arise in sensitivities to soil moisture (soil water potential) and vapor pressure deficit. For example, stomatal closure rates at high vapor pressure deficit range between −45% and +70% of those observed. Although over half the new generation of stomatal schemes perform to a similar standard compared to observations of leaf‐gas exchange, two models do so through large biases in simulated leaf water potential (up to 11 MPa). Our results provide guidance for LSM development, by highlighting key areas in need for additional experimentation and theory, and by constraining currently viable stomatal hypotheses.

54 ENVIRONMENTAL SCIENCES↗

Optimization of COMPASS-U Support Structure

The global support structure for Compass Upgrade (COMPASS-U) employs many bolted and pinned components to improve the manufacturability of the whole structures. This is a departure from other designs used for highly loaded tokamaks, like Alcator C-Mod which used large forgings. Modeling of the numerous connections and interfaces was a challenge. This article will describe how to optimize the C-frame support structure with the goal to eliminate differential displacements at those interfaces and, importantly, minimize toroidal mutual displacement at the sliding joint of the toroidal field (TF) coils. The global support structure consists of 16 C-frames, and it can be simplified as a 1/8th cyclic symmetry model due to the eight vertical rods mounting that connect bottom CS and PF1-3 assemblies to the C-frames. Structure variants with different connection webs between two neighboring C-frames have been analyzed. The preloading of bolts can be split into several preload substeps to simulate the real assembly process of the COMPASS-U support structure. Additionally, the TF crown and the wedge plate can be further improved to become a solid part to better hold the TF coils.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An Experimental and Numerical Study of Plasma Treatment Effects on Adhesive Joints of Metals, CFRTPs, and Metal–CFRTP Combinations

This work investigates the effects of plasma surface treatment on both the local adherend–adhesive interfacial strength and the global lap shear strength (LSS) of adhesively-bonded joints composed of metals, CFRTPs, and metal-CFRTP combinations, using AA6061 and CFRPPA as representative examples. Experimental and computational results show that plasma treatment improved the ratio of CFRPPA–adhesive interfacial normal strength to adhesive tensile strength (sint,n/scri,t,adhesive) from 0.59–1.00 to 0.91–1.73, leading to an average 90% increase in LSS for CFRPPA-related joints. In contrast, the LSS and sint,n/scri,t,adhesive values of AA6061–AA6061 joints (>=2.27) remained nearly unchanged after plasma treatment. The enhanced joint bonding was further supported by post-failure surface morphologies from three-dimensional profilometry and simulations, showing a transition from dominant interfacial failure to mixed modes involving interfacial, cohesive, and slight fiber-peeling failures. The LSS evolution with respect to sint,n/scri,t,adhesive was numerically established until the saturation of the LSS of various joints, and the behavior of AA6061–CFRPPA T-joints with varying interfacial strengths was also modeled. This study highlights the importance of local interfacial bonding strength, rather than global LSS, for understanding and optimizing the mechanical performance of adhesively-bonded composite–metal and composite-composite structures via different surface modification strategies.

Qiao, Yao (ORCID:0000000265867604)↗

Exact signed distance fields using parallel Fast Sweeping Method

Signed distance fields are often used in multiphysics simulations to track material interfaces. We present a simple methodology based on the fast sweeping method to generate the exact signed distance from triangular meshes and linear paths on Cartesian grids. The methodology propagates the closest primitive to the boundary to the rest of the domain following the characteristics. A local upwind criterion is used to decide between the new and existing closest primitive at each grid point while capturing the correct sign of the global function. The methodology has optimal computational complexity and runs efficiently in distributed-memory architectures. We include 2D and 3D test cases along with a resolution study up to 0.512 trillion zones and 1,000 computer cores. The solution strategy can also be applied to other types of meshes or collections of primitives.

97 MATHEMATICS AND COMPUTING↗

PyFLEXTRKR: a flexible feature tracking Python software for convective cloud analysis

Abstract. This paper describes the new open-source framework PyFLEXTRKR (Python FLEXible object TRacKeR), a flexible atmospheric feature tracking software package with specific capabilities to track convective clouds from a variety of observations and model simulations. This software can track any atmospheric 2D objects and handle merging and splitting explicitly. The package has a collection of multi-object identification algorithms, scalable parallelization options, and has been optimized for large datasets including global high-resolution data. We demonstrate applications of PyFLEXTRKR on tracking individual deep convective cells and mesoscale convective systems from observations and model simulations ranging from large-eddy resolving (∼100s m) to mesoscale (∼10s km) resolutions. Visualization, post-processing, and statistical analysis tools are included in the package. New Lagrangian analyses of convective clouds produced by PyFLEXTRKR applicable to a wide range of datasets and scales facilitate advanced model evaluation and development efforts as well as scientific discovery.

54 ENVIRONMENTAL SCIENCES↗

Control co-design under uncertainty for offshore wind farms: Optimizing grid integration, energy storage, and market participation

Offshore wind farms (OWFs) are set to significantly contribute to global decarbonization efforts. Developers often use a sequential approach to optimize design variables and market participation for grid-integrated offshore wind farms. However, this method can lead to sub-optimal system performance, and uncertainties associated with renewable resources are often overlooked in decision-making. Here, this paper proposes a control co-design approach, optimizing design and control decisions for integrating OWFs into the power grid while considering energy market and primary frequency market participation. Additionally, we introduce optimal sizing solutions for energy storage systems deployed onshore to enhance revenue for OWF developers over time. This framework addresses uncertainties related to wind resources and energy prices. We analyze five U.S. west-coast offshore wind farm locations and potential interconnection points, as identified by the Bureau of Ocean Energy Management (BOEM). Results show that optimized control co-design solutions can increase market revenue by 3.2% and provide flexibility in managing wind resource uncertainties.

Control Co-design↗