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Experimental protocol for phase 1 of the APARC QUOCA (QUasibiennial oscillation and Ozone Chemistry interactions in the Atmosphere) working group

The quasi-biennial oscillation (QBO) is the main mode of variability in the tropical stratosphere, influencing the predictability of other regions in the atmosphere through its teleconnections to the stratospheric polar vortices and coupling to surface tropical and extratropical variability. However, climate and forecasting models consistently underestimate QBO amplitudes in the lower stratosphere, likely contributing to their failure to simulate these teleconnections. One underexplored contributor to model biases is missing representation of ozone-radiative feedbacks, which enhance temperature variability in the lower stratosphere, particularly at periods at and greater than the QBO (>28 months). While previous studies suggest that ozone-radiative feedbacks can impact QBO periods, amplitudes and the associated secondary circulation in the lower stratosphere, the reported impacts differ widely among models and are hard to interpret due to differences in methodology. To this end, here we propose a coordinated experimental protocol – held joint between the Atmospheric Processes and their Role in Climate (APARC) Quasi-Biennial Oscillation Initiative (QBOi) and Chemistry Climate Modeling Initiative (CCMI) activities – which is aimed at assessing the coupling between stratospheric ozone, temperature and the circulation. We use the proposed experiments to define the ozone feedback on the QBO in both present-day and idealized (abrupt quadrupling of carbon dioxide) climates. While primary focus is on the QBO, the proposed protocol also enables analysis of other aspects of ozone-radiative-dynamical coupling in the atmosphere, including impacts on the Brewer-Dobson Circulation and tropospheric eddy-driven jet responses to future climate change. Here we document the scientific rationale and design of the QUOCA Phase 1 experiments, summarize the data request, and give a brief overview of participating models. Preliminary results using the NASA Goddard Institute for Space Studies E2-2 climate model are used to illustrate sensitivities to certain methodological choices.

Environmental sciences↗

Sparse Phase Ansatzes for Resource-Efficient Qudit State Preparation via the SNAP-Displacement Protocol

Efficient preparation of nonclassical bosonic states is a central requirement for quantum computing, simulation, and precision metrology. We study resource-efficient quantum state preparation in bosonic qudit systems using the SNAP-displacement (SD) protocol. Existing SD-based approaches typically require a large number of gates and SNAP phases, resulting in complex control pulses with longer ansatz durations and amplified impact of photon-loss and control errors. In this work, we focus on the near- to medium-term regime, in which noisy quantum devices impose trade-offs on the fidelity that can be achieved, which must be taken into account. Specifically, we propose to optimize only a subset of the SNAP phases and introduce three progressively more general sparse ansatzes. To provide fine-grained control and identify the most suitable ansatz for a given target fidelity, we further employ a scalarized multi-objective optimization that trades off fidelity against either the number of phases or the duration of the ansatz. Numerical results for several target states and qudit dimensions up to $d=64$, evaluated through the hypervolume of the Pareto frontiers, show that these sparse ansatzes achieve favorable trade-offs over the fully parameterized SD protocol in both ideal and noisy settings. The advantage is strongest and most consistent when minimizing the number of phases, while improvements in ansatz duration are smaller and more dependent on the target-state family and noise level, suggesting a practical route to more efficient near- and medium-term bosonic state preparation.

Ferrari Dacrema, Maurizio [Milan Polytechnic] (ORC↗

EnergyPlus-MCP: A model-context-protocol server for ai-driven building energy modeling

Traditional building energy modeling with the EnergyPlus building performance simulation engine requires domain expertise, programming skills, and intensive manual efforts limiting its effective adoption. This paper introduces EnergyPlus-MCP, the first open-source Model Context Protocol (MCP) server specifically designed for EnergyPlus simulation workflows, establishing a new foundational infrastructure for AI-driven building energy modeling. The MCP server implements a layered architecture with 35 specialized tools spanning model management, editing and analysis, HVAC and other systems configuration inspection, and simulation execution, enabling Large Language Models to interact with EnergyPlus through conversational interfaces. The server addresses critical workflow barriers by automating model validation, streamlining energy efficiency measures modification, and providing intelligent output management with interactive visualization. Through practical demonstrations using a multi-zone building retrofit analysis, we show how the EnergyPlus-MCP server significantly reduces manual efforts while maintaining full simulation rigor. By providing accessible natural language interfaces to sophisticated building energy analysis, this approach enables scalable deployment of simulation expertise across public and private organizations, educational institutions, and research teams, fundamentally transforming traditional building energy modeling practices.

AI↗

Rephasing spectral diffusion in time-bin spin-spin entanglement protocols

Generating high-fidelity spin-spin entanglement is an essential task of quantum repeater networks for the distribution of quantum information across long distances. Solid-state-based spin-photon interfaces are promising candidates to realize nodes of a quantum network, but are often limited by spectral diffusion of the optical transition, which results in phase errors on the entangled states. Here, we introduce a method to correct phase errors from quasi-static frequency fluctuations after the entangled state is generated, by shelving the emitters in the excited state to refocus the unknown phase. For quasi-static frequency fluctuations, the fidelity is determined only by the lifetime of the excited state used for shelving, making it particularly suitable for systems with a long-lived shelving state with correlated spectral diffusion. Such a shelving state may be found in Kramers doublet systems such as rare-earth emitters and color centers in Si or SiC interfaced with nanophotonic cavities with a strongly frequency-dependent Purcell enhancement. Furthermore, the protocol can be used to generate high-fidelity entangled spin pairs without reducing the rate of entanglement generation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Active and Stable PtPd Diesel Oxidation Catalysts under Industry‐Defined Test Protocols

Nanoparticle-supported Pt and Pd catalysts are employed industrially to convert CO and hydrocarbon residue from incomplete diesel fuel combustion into more environmentally-benign products. However, these catalysts deactivate over time due to sintering, especially for Pt nanoparticles which readily generate volatile species under high operating temperatures. Here, we turned the detrimental vapor-mediated sintering of Pt into an advantage by using a physical mixture of Pt and Pd catalysts prepared using a raspberry-colloid-templating (RCT) method. The RCT method produced Pt/Al 2 O 3 and Pd/Al 2 O 3 catalysts with partially embedded NPs to inhibit surface-mediated sintering pathways. As validated using an industry-defined emission control test protocol, aging a physical mixture of Pt/Al 2 O 3 and Pd/Al 2 O 3 at high temperature produced an alloyed PtPd/Al 2 O 3 catalyst that outperformed the fresh catalyst mixture and both individual catalysts for hydrocarbon conversion, while exhibiting high catalytic stability and resistance to sintering and to SO 2 poisoning. X-ray photoelectron spectroscopy revealed that in the aged catalyst mixture, half of the Pd content existed in the more active metallic state, compared to the less active oxide forms in the fresh mixture and both individual catalysts, explaining the unusual activity enhancement. Our results represent a practical approach to producing active and stable PtPd/Al 2 O 3 diesel oxidation catalysts for emission control applications.

Lim, Kang Rui Garrick [Harvard University, Cambrid↗

Security Assessment of an LBP16-Protocol-Based Computer Numerical Control Machine

Subtractive manufacturing systems, specifically, computer numerical control machines, have revolutionized the manufacturing industry. Computer numerical control machining is the preferred method for producing finished parts due to its efficiency, speed and suitability for high-volume production. Securing computer numerical control machines is a priority. Compromises or disruptions of these machines can result in significant downtime, loss of productivity and financial loss. This study examines the vulnerabilities and risks associated with computer numerical control machines, in particular, systems utilizing the LBP16 protocol for controller-machine communications. The study reveals that an adversary can execute cyber-physical attacks such as sabotage and denial of service. The potential security threats emphasize the importance of implementing robust security measures to mitigate the cyber risks to computer numerical control machines.

Forihat, Yahya [Virginia Commonwealth University, ↗

Protocol for engineering poly(ethylene terephthalate) hydrolases via directed evolution using a high-throughput screening assay

Poly(ethylene terephthalate) (PET) hydrolases, which depolymerize PET to its monomers, have gained attention for their potential to facilitate bio-industrial recycling of this waste plastic. Here, we present a protocol for screening large, random mutagenesis enzyme libraries simultaneously for enhanced activity, solubility, and stability. We outline steps for library construction, screening using plate-based split GFP and model substrate assays, and determination of enzyme thermostability. We then detail procedures for validation assays on PET substrates and characterization of final variants.

59 BASIC BIOLOGICAL SCIENCES↗

Protocol for applying a network-enabled gene discovery pipeline to non-model plant species

Identifying upstream regulators of key genes is essential for understanding gene regulatory mechanisms and translating these insights into functional targets. Here, we present a protocol for applying the network-enabled gene discovery pipeline (NEEDLE) to non-model plant species. We describe steps for environment setup, data preparation, computational analysis, expected outputs, and parameter considerations. NEEDLE integrates RNA sequencing (RNA-seq) processing, weighted gene co-expression analysis (WGCNA), Gene Network Inference with Ensemble of trees (GENIE3), and promoter conservation analysis to prioritize candidate transcriptional regulators.

Plant Sciences↗

Assessing the Sensitivity of Pourbaix Diagrams to Computational Protocols: Electrochemical Stability of Ni Oxides as a Case Study

Pourbaix diagrams stand as a useful tool in assessing and visualizing materials’ electrochemical stability and are widely used for electrocatalyst design. However, their reliability hinges on the accuracy of the chemical potentials of involved phases, which may bear uncertainties and can be significantly impacted by decision-making steps in the computational protocol. Here, this study introduces a robust sensitivity analysis framework, exemplified through a detailed examination of the computational Pourbaix diagram of Ni, the oxides of which are used as high-activity and cost-friendly catalysts for many electrochemical reactions. Quantities of interest derived from the Pourbaix diagram include the appearance and stability domain of the catalytically active Ni oxide phases along with the onset electrochemical potentials of phase transitions. These metrics can guide the design of operational conditions for Ni oxide electrocatalysts. We find that the employed DFT exchange-correlation functional has the most significant influence on the computed Pourbaix diagram. Uncertainties on crystal structures, along with their related ab initio energetics, are also found to affect the size of the phase stability domain. Higher-order coupling among input parameters is found to play a crucial role in influencing the appearance and distribution of Ni phases in the diagram. Our findings suggest a need to consider variations and uncertainties associated with the computational procedures on predicted Pourbaix diagrams for materials design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aging matrix visualizes complexity of battery aging across hundreds of cycling protocols

To reliably deploy lithium-ion batteries, a fundamental understanding of cycling aging behavior is critical. Battery aging consists of complex and highly coupled phenomena, making it challenging to develop a holistic interpretation. In this work, we generate a diverse battery cycling dataset with a broad range of degradation trajectories, consisting of 359 high energy density commercial Li(Ni,Co,Al)O 2 /graphite + SiO x cylindrical 21 700 cells cycled across 207 unique cycling protocols. We consolidate aging via 16 mechanistic state-of-health (SOH) metrics, including cell-level performance metrics, electrode-specific capacities/state-of-charges (SOCs), and aging trajectory metrics. We develop a framework using interpretable machine learning and explainable features to generate an aging matrix that visually deconvolutes the complex battery degradation behavior. This generalizable data-driven mechanistic framework simplifies the complex interplay between cycling conditions, degradation modes, and SOH, acting as a hypothesis-generation tool to aid battery users in identifying key degradation regimes for further study and experimentation.

25 ENERGY STORAGE↗

Weighted active space protocol for multireference machine-learned potentials

Multireference methods such as multiconfiguration pair-density functional theory accurately capture electronic correlation in systems with strong multiconfigurational character, but their cost precludes direct use in molecular dynamics. Combining these methods with machine-learned interatomic potentials (MLPs) can extend their reach. However, the sensitivity of multireference calculations to the choice of the active space complicates the consistent evaluation of energies and gradients across structurally diverse nuclear configurations. To overcome this limitation, we introduce the weighted active space protocol (WASP), a systematic approach to assign a consistent active space for a given system across uncorrelated configurations. By integrating WASP with MLPs and enhanced sampling techniques, we propose a data-efficient active learning cycle that enables the training of an MLP on multireference data. We demonstrated the approach on the TiC + -catalyzed C–H activation of methane, a reaction that poses challenges for Kohn–Sham density functional theory due to its significant multireference character. This framework enables accurate and efficient modeling of catalytic dynamics, establishing a paradigm for simulating complex reactive processes beyond the limits of conventional electronic-structure methods.

enhanced sampling↗

Demonstration and Concept of Operations for a Zero-Knowledge Protocol Passive Imaging Measurement for Arms Control

Here, we present an imaging system that employs zero-knowledge protocols to protect sensitive geometrical information, along with procedures to increase confidence in the result. The goal of this work is to enable the inclusion of warhead confirmation measurements in future arms control treaties. We present a demonstration of both true positive and true negative measurements that validate models and establish authenticating procedures toward meeting acceptance requirements for use in nuclear facilities. We use a two-dimensional time-encoded fast neutron imaging system with an anti-symmetric mask pattern; the fast neutron count values exceeding minimum or maximum thresholds indicate that two measured items are not identical. Laboratory measurements over twenty trials show that alarm rates for negative confirmation measurements are within uncertainties of model predictions. Positive confirmation measurements indicate that alarm rates are large enough to encourage treaty compliance.

Sweany, Melinda Dominique [Sandia National Laborat↗

Investigating parameter trainability in the SNAP-displacement protocol of a qudit system

Here, in this study, we explore the universality of Selective Number-dependent Arbitrary Phase (SNAP) and Displacement gates for quantum control in qudit-based systems. However, optimizing the parameters of these gates poses a challenging task. Our main focus is to investigate the sensitivity of training any of the SNAP parameters in the SNAP-Displacement protocol. We analyze conditions that could potentially lead to the Barren Plateau problem in a qudit system and draw comparisons with multi-qubit systems. The parameterized ansatz we consider consists of blocks, where each block is composed of hardware operations, namely SNAP and Displacement gates [Fösel et al 2020 Efficient cavity control with snap gates arXiv:2004.14256]. Applying Variational Quantum algorithm (VQA) with observable and gate cost functions, we utilize techniques similar to those in [McClean et al 2018 Barren plateaus in quantum neural network training landscapes Nat. Commun.9 1–6] and [Cerezo et al 2021 Cost function dependent barren plateaus in shallow parametrized quantum circuits. Nat. Commun.12 1–12] along with the concept of t − design. Through this analysis, we make the following key observations: (a) The trainability of a SNAP-parameter does not exhibit a preference for any particular direction within our cost function landscape, (b) By leveraging the first and second moments properties of Haar measures, we establish new lemmas concerning the expectation of certain polynomial functions, and (c) utilizing these new lemmas, we identify a general condition that indicates an expected trainability advantage in a qudit system when compared to multi-qubit systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Moment extraction using an unfolding protocol without binning

Deconvolving (“unfolding”) detector distortions is a critical step in the comparison of cross-section measurements with theoretical predictions in particle and nuclear physics. However, most existing approaches require histogram binning while many theoretical predictions are at the level of statistical moments. We develop a new approach to directly unfold distribution moments as a function of another observable without having to first discretize the data. Our moment unfolding technique uses machine learning and is inspired by Boltzmann weight factors and generative adversarial networks (GANs). We demonstrate the performance of this approach using jet substructure measurements in collider physics. With this illustrative example, we find that our moment unfolding protocol is more precise than bin-based approaches and is as or more precise than completely unbinned methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tuning the spin dynamics and magnetic phase transitions of the Cantor alloy via composition and sample processing protocols: A muon spin relaxation study

CrMnFeCoNi, also called the Cantor alloy, is a well-known high-entropy alloy whose magnetic properties have recently become a focus of attention. Here, we present a detailed muon spin relaxation study of the influence of chemical composition and sample processing protocols on the magnetic phase transitions and spin dynamics of several different Cantor alloy samples. Specific samples studied include a pristine equiatomic sample, samples with deficient and excess Mn content, and equiatomic samples magnetized in a field of 9 T or plastically deformed in pressures up to 0.5 GPa. The results confirm the sensitive dependence of the transition temperature on composition and demonstrate that post-synthesis pressure treatments cause the transition to become significantly less homogeneous throughout the sample volume. In addition, we observe critical spin dynamics in the vicinity of the transition in all samples, reminiscent of canonical spin glasses and magnetic materials with ideal continuous phase transitions. Application of an external magnetic field suppresses the critical dynamics in the Mn-deficient sample, while the equiatomic and Mn-rich samples show more robust critical dynamics. The spin-flip thermal activation energy in the paramagnetic phase increases with Mn content, ranging from 3.1⁢(3) × 10 -21 J for 0% Mn to 1.2⁢(2) × 10 -20 J for 30% Mn content. These results shed light on critical magnetic behavior in environments of extreme chemical disorder and demonstrate the tunability of spin dynamics in the Cantor alloy via chemical composition and sample processing.

36 MATERIALS SCIENCE↗

Flash electropolishing for TEM: Reducing FIB‐induced defects in tungsten with protocols for new materials

Focused ion beam (FIB) milling has become the dominant approach for site-specific transmission electron microscopy (TEM) specimen preparation; however, FIB damage remains a critical limitation for reliable microstructural characterisation, particularly in radiation effects studies. Tungsten is especially susceptible to FIB damage due to its high nuclear stopping power, which promotes the formation and strong diffraction contrast of FIB-induced ‘black spot’ defects that are indistinguishable from very fine irradiation-induced loops/defects resulting from low to intermediate temperature neutron irradiation. In this work, flash electropolishing is systematically evaluated as a post-FIB treatment for minimising preparation-induced artefacts for TEM analysis of tungsten-based alloys. Using a range of non-, ion-, and neutron-irradiated tungsten materials, the effectiveness of flash electropolishing has been assessed through direct comparison with conventional FIB and plasma-FIB preparation including low-energy Ga, Ar, Xe ion cleaning. The results demonstrate that flash electropolishing effectively removes FIB-damaged layers and ‘black spot’ defects, thereby enabling reliable observation of irradiation-induced dislocation structures. Key processing parameters governing flash electropolishing quality – including lamella thickness, applied voltage, polishing duration, electrolyte chemistry, and cathode geometry – have been systematically evaluated, and clear criteria were established for determining when flash electropolishing is required to ensure reliable microstructural analysis. This work also provides practical guidance for implementing flash electropolishing as an artefact-controlled specimen-preparation approach for TEM characterisation of FIB-produced specimens. The systematic protocol can be extended to other, non-tungsten materials.

TEM sample preparation↗

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Novak, Vlastimil↗