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At least 127 records · Page 7

Advantages of a variable‐resolution global climate model in reproducing the seasonal evolution of East Asian summer monsoon

Abstract The East Asian summer monsoon (EASM) is unique among monsoon systems that it features meridional evolution of the summer monsoon. In this study, we evaluate the performances of a Variable‐Resolution Community Earth System Model (VR‐CESM) regionally refined over eastern China (14 km) in reproducing the seasonal evolution of EASM precipitation over China. Compared with reference datasets, VR‐CESM shows better performance than the corresponding globally uniform coarse‐resolution model CESM (quasi‐uniform 1°), especially over western China where complex local topography exists. The northward monsoon migration is closely related to low‐level southerly flows and vertical moisture advection, which are more reasonably simulated in VR‐CESM. The four critical timings of the EASM (monsoon onset, withdrawal, peak, and duration) are also better captured in VR‐CESM than in CESM. The corresponding spatial Pearson correlation coefficients of the four critical timings with respect to reference datasets are about 0.1 higher in VR‐CESM than those in CESM. Both models are most accurate in simulating monsoon onset and least accurate at simulating the monsoon peak. The overestimated zonal thermal contrast in CESM is responsible for the earlier monsoon onset and excessive precipitation in September over the Yangtze River valley. Finer resolution in VR‐CESM, especially over the Tibetan Plateau (TP), appears to be a main factor in simulating better zonal thermal contrast and seasonal evolution of the EASM.

54 ENVIRONMENTAL SCIENCES↗

Kernel Manifolds: Nonlinear‐Augmentation Dimensionality Reduction Using Reproducing Kernel Hilbert Spaces

This paper generalizes recent advances on quadratic manifold (QM) dimensionality reduction by developing kernel methods-based nonlinear-augmentation dimensionality reduction. QMs, and more generally feature map-based nonlinear corrections, augment linear dimensionality reduction with a nonlinear correction term in the reconstruction map to overcome approximation accuracy limitations of purely linear approaches. While feature map-based approaches typically learn a least squares optimal polynomial correction term, we generalize this approach by learning an optimal nonlinear correction from a user-defined reproducing kernel Hilbert space. Our approach allows one to impose arbitrary nonlinear structure on the correction term, including polynomial structure, and includes feature map and radial basis function-based corrections as special cases. Furthermore, our method has relatively low training cost and has monotonically decreasing error as the latent space dimension increases. In conclusion, we compare our approach to proper orthogonal decomposition and several recent QM approaches on data from several example problems.

kernel methods↗

A neural network‐enhanced reproducing kernel particle method for modeling strain localization

Abstract Modeling the localized intensive deformation in a damaged solid requires highly refined discretization for accurate prediction, which significantly increases the computational cost. Although adaptive model refinement can be employed for enhanced effectiveness, it is cumbersome for the traditional mesh‐based methods to perform while modeling the evolving localizations. In this work, neural network‐enhanced reproducing kernel particle method (NN‐RKPM) is proposed, where the location, orientation, and shape of the solution transition near a localization is automatically captured by the NN approximation via a block‐level neural network (NN) optimization. The weights and biases in the blocked parameterization network control the location and orientation of the localization. The designed basic four‐kernel NN block is capable of capturing a triple junction or a quadruple junction topological pattern, while more complicated localization topological patters are captured by the superposition of multiple four‐kernel NN blocks. The standard RK approximation is then utilized to approximate the smooth part of the solution, which permits a much coarser discretization than the high‐resolution discretization needed to capture sharp solution transitions with the conventional methods. A regularization of the NN approximation is additionally introduced for discretization‐independent material responses. The effectiveness of the proposed NN‐RKPM is verified by a series of numerical verifications.

Baek, Jonghyuk↗

Understanding Reproducibility of Sputter‐Deposited Metastable Ferroelectric Wurtzite Al 0.6 Sc 0.4 N Films Using In Situ Optical Emission Spectrometry

High‐Sc Al 1– x Sc x N thin films are of tremendous interest because of their attractive piezoelectric and ferroelectric properties, but overall film quality and reproducibility are widely reported to suffer as x increases. In this study, structural and electrical properties of metastable Al 0.6 Sc 0.4 N films are connected with plasma changes during film growth, identified via glow discharge optical emission spectroscopy (GD‐OES), and linked to the target mode changes. This in situ GD‐OES technique uses changes in the N 2 (I) intensity, correlated with DC bias hysteresis behavior of a Al 0.6 Sc 0.4 target in metallic and poisoned modes, to identify films that subsequently exhibit unacceptable structural and electrical performance. Two representative samples deposited under identical conditions but possessing distinct properties related to phases present in the films are focused on. Films sputtered under a poisoned target mode produce pure wurtzite ferroelectric Al 0.6 Sc 0.4 N with a reversible 80 μC cm −1 polarization and 3.1 MV cm −1 coercive field. When identical chamber settings are used but the process starts in metallic mode, a mixed wurtzite/rocksalt film is deposited which exhibits nanometer‐scale changes to the film microstructure and a nonferroelectric response. These results illustrate the utility of optical emission spectroscopy for tracking target mode fluctuations when fabricating metastable materials such as high‐Sc Al 1– x Sc x N films.

36 MATERIALS SCIENCE↗

Spontaneously supersaturated nucleation strategy for high reproducible and efficient perovskite solar cells

High-quality perovskite films are predominantly prepared by anti-solvent assisted spin-coating method. How- ever, small device size and narrow operation window limit their applications in practical and scalable production. Here, a spontaneously supersaturated nucleation strategy is developed to fabricate high-quality perovskite films without any antisolvents. The rapid precipitation behavior of the precursor solutions could be triggered by the volatilization of methylamine ethanol at the initial film formation stage, forming uniform and compact intermediate phase films. Mirror-like large area (10 cm × 10 cm) methylammonium lead triiodide (MAPbI 3 ) perovskite films with micrometer-sized grains can be achieved by phase transition via annealing. The average power conversion efficiency (PCE) of 19.4% is achieved for 0.1 cm 2 perovskite solar cells (PSCs). The 1 cm 2 device shows a PCE of 17.57% and retains 96.8% after aging for 39 days in the air with a relative humidity of 5–30%. The perovskite module based on the perovskite films prepared by our strategy exhibits a PCE of 13.13%. Here, the perovskite film fabrication method developed in this work shows high reproducibility of the fabrication process due to the spontaneous nucleation process. Meanwhile, it also exhibits significant potential in the application of scalable solution processing deposition techniques toward the commercialization of PSCs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interpretable and flexible non-intrusive reduced-order models using reproducing kernel Hilbert spaces

This paper develops an interpretable, non-intrusive reduced-order modeling technique using regularized kernel interpolation. Existing non-intrusive approaches approximate the dynamics of a reduced-order model (ROM) by solving a data-driven least-squares regression problem for low-dimensional matrix operators. Our approach instead leverages regularized kernel interpolation, which yields an optimal approximation of the ROM dynamics from a user-defined reproducing kernel Hilbert space. We show that our kernel-based approach can produce interpretable ROMs whose structure mirrors full-order model structure by embedding judiciously chosen feature maps into the kernel. The approach is flexible and allows a combination of informed structure through feature maps and closure terms via more general nonlinear terms in the kernel. We also derive a computable a posteriori error bound that combines standard error estimates for intrusive projection-based ROMs and kernel interpolants. In conclusion, the approach is demonstrated in several numerical experiments that include comparisons to operator inference using both proper orthogonal decomposition and quadratic manifold dimension reduction.

Data-driven model reduction↗

Interlaboratory Study: Testing Reproducibility of Solid Biofuels Component Identification Using Reflected Light Microscopy

Considering global market trends and concerns about climate change and sustainability, increased biomass use for energy is expected to continue. As more diverse materials are being utilized to manufacture solid biomass fuels, it is critical to implement quality assessment methods to analyze these fuels thoroughly. One such method is reflected light microscopy (RLM), which has the potential to complement and enhance current standard testing, leading to improving fuel quality assessment and, ultimately, preventing avoidable air pollution. An interlaboratory study (ILS) was conducted to test the reproducibility of biomass fuels component identification using a reflected light microscopy technique. The exercise was conducted on thirty photomicrographs showing biomass and various undesired components (like plastics or mineral matter), which were purposely added (by the ILS organizers) to contaminate wood pellets and charcoal-based grilling fuels. Forty-six participants had various levels of difficulty identifying the marked components, and as a result, the percentage of correct answers ranged from 52.2 to 94.4%. Among the most difficult components to distinguish were petroleum products and inorganic matter. Various reasons led to the misidentification, including insufficient morphological descriptions of the components provided to participants, ambiguities of the nomenclature, limitations of the analytical and exercise method, and insufficient experience of the participants. Overall, the results indicate that RLM has the potential to enhance the quality assessment of biomass fuels. However, they also demonstrate that the petrographic classification used in this exercise requires further refinement before it can be standardized. While a new simplified classification of solid biomass fuels components was created as an outcome of this study, future research is necessary to refine the nomenclature, develop a microscopic morphological description of the components, and verify the accuracy of component identification with a follow-up ILS.

biomass↗

Reproducibility of calculations on Li species with correlation-consistent basis sets

Here we have found that two different basis set series, both labeled cc-pVxZ, are widely available and widely used for calculation on Li compounds such that calculations that should be the same are different, causing a reproducibility problem. Here we study the magnitude of the disagreement of these nominally-the-same basis sets for wave function and density functional calculations of Li clusters. We find deviations among the basis sets of as large as 22 millihartrees. In most cases one obtains lower energies with the noncanonical choices. Therefore, it is important to specify which version of the basis set is used for calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility

The binding free energy between a ligand and its target protein is an essential quantity to know at all stages of the drug discovery pipeline. Assessing this value computationally can offer insight into where efforts should be focused in the pursuit of effective therapeutics to treat a myriad of diseases. In this work, we examine the computation of alchemical relative binding free energies with an eye for assessing reproducibility across popular molecular dynamics packages and free energy estimators. The focus of this work is on 54 ligand transformations from a diverse set of protein targets: MCL1, PTP1B, TYK2, CDK2, and thrombin. These targets are studied with three popular molecular dynamics packages: OpenMM, NAMD2, and NAMD3 alpha. Trajectories collected with these packages are used to compare relative binding free energies calculated with thermodynamic integration and free energy perturbation methods. The resulting binding free energies show good agreement between molecular dynamics packages with an average mean unsigned error between them of 0.50 kcal/mol. The correlation between packages is very good, with the lowest Spearman’s, Pearson’s and Kendall’s tau correlation coefficients being 0.92, 0.91, and 0.76, respectively. Agreement between thermodynamic integration and free energy perturbation is shown to be very good when using ensemble averaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Overcoming Variability: A Reproducible Approach to SERS Detection of Nanodiamonds

Detonation nanodiamonds (DNDs) are formed at specific pressures and temperatures during explosions. Different explosives produce varied yields of DNDs within their detonation soot, with Composition B producing the highest yield. Raman spectroscopy (RS) is often used for the characterization of sp 2 - and sp 3 -hybridized carbon allotropes in carbonaceous materials because of distinct disorder and graphitic bands. Bulk diamond also gives a distinct Raman peak at 1332 cm –1 . Furthermore, as bulk diamond decreases in size to nanometer-sized species, the peak red-shifts and broadens, becoming increasingly difficult to detect with RS using visible excitations. Therefore, surface-enhanced Raman spectroscopy (SERS) was used to enhance the diamond peak of DNDs, enabling better detection and faster examination of DNDs within detonation soot. Previous literature of the SERS of DNDs delivered inconsistent results in spectral signatures and SERS substrates. Herein, refining of the methodology for the acquisition of SERS spectra of DNDs was achieved. Before any SERS experiments, the DNDs were first characterized with normal Raman (NR) and scanning electron microscopy. Two routes for SERS enhancement were evaluated: colloidal noble metal nanoparticles and evaporated silver films. Silver films produced the best signal enhancement of DNDs with the best signal-to-noise and peak enhancements observed at 20–30 nm thick silver films at 5% (∼300 μW) laser power. Consistent, reproducible SERS spectra were acquired of small aggregates of DNDs down to ∼500 nm. NR and SERS mapping analysis of DNDs before and after evaporation of silver films revealed the improvements in the detection capabilities of SERS compared with NR.

Carbon↗

Comparative Evaluation of the Ability of the MYNN‐EDMF PBL Scheme in WRF Model to Reproduce Near Surface Wind Speed Over Different Topographical Types

Abstract This study systematically evaluates the performance of the Mellor‐Yamada‐Nakanishi‐Niino‐Eddy‐Diffusion‐Mass‐Flux planetary boundary layer (PBL) scheme within the Weather Research and Forecasting (WRF) model in simulating near‐surface wind speeds across various topographies in New York State (NYS). Simulated wind speeds are compared with in‐situ measurements from 22 surface sites, grouped into six topographic categories: continental plain (CT), lakeside (LS), river valley (RV), Long Island (LI), Block Island (BI), and offshore ocean (OO). A quantitative evaluation based on Relative Euclidean Distance shows that wind speeds at the OO site are the most accurately reproduced, followed by those at LI sites, while the model performs less accurately for the remaining topographic groups. Wind speeds over CT sites tend to be overestimated by approximately 1 m/s, although their diurnal variability (DV) is well captured. In contrast, the model underestimates wind DV at LS, RV, LI, and BI sites, with the largest biases occurring at LI and BI, resulting in underestimated daytime wind speed and/or overestimated nighttime wind speed. The OO winds exhibit minimal diurnal variation, accurately captured by our WRF model. The surface wind diurnal variation is closely linked to PBL development. Among the indicators of PBL development, surface potential temperature biases most strongly correlate with wind speed biases. Our WRF model faces challenges in capturing the distinctions between winds influenced by local circulations and those over continental plains, and the significantly stronger winds at OO compared to BI. Potential causes for these biases are discussed, offering pathways for improving surface wind simulations in future.

54 ENVIRONMENTAL SCIENCES↗

Design-driven optimization of low-cost reagent formulations for reproducible and high-yielding cell-free gene expression

Access to recombinant proteins is vital in basic science and biotechnology research. Cell-free gene expression systems provide one approach to address this need, but widespread utilization remains limited by the cost, complexity, and inconsistency of current platforms. To address these limitations, we carry out a multi-dimensional definitive screening design to reduce the number of reagent components and remove costly secondary energy substrates. From 1,231 different reagent formulations, we discover a simple and reproducible system based on 12 components. The optimized reagent formulation can produce 2.4 ± 0.3 g/L of protein product at the 15-µL scale (~$\$60$/gprotein) and 3.7 ± 0.2 g/L (~$\$39$/gprotein) at the 4-mL scale with oxygen supplementation. This provides an average 95% reduction in cost over previous cell-free reagent formulations. We further show that the optimized reagent formulation can produce nucleoside triphosphates from nitrogenous bases and ribose and that it is robust to failure across batches of cell lysates, users/locations, and in the synthesis of more than 20 different proteins. For example, we demonstrate the production of fifteen therapeutically relevant products, including full-length aglycosylated monoclonal antibodies. We anticipate that our optimized reagent formulation will democratize the use of cell-free systems for protein manufacturing and synthetic biology applications.

Biologics↗

Accelerated, scalable and reproducible AI-driven gravitational wave detection

The development of reusable artificial intelligence (AI) models for wider use and rigorous validation by the community promises to unlock new opportunities in multi-messenger astrophysics. Here we develop a workflow that connects the Data and Learning Hub for Science, a repository for publishing AI models, with the Hardware-Accelerated Learning (HAL) cluster, using funcX as a universal distributed computing service. Using this workflow, an ensemble of four openly available AI models can be run on HAL to process an entire month's worth (August 2017) of advanced Laser Interferometer Gravitational-Wave Observatory data in just seven minutes, identifying all four binary black hole mergers previously identified in this dataset and reporting no misclassifications. This approach combines advances in AI, distributed computing and scientific data infrastructure to open new pathways to conduct reproducible, accelerated, data-driven discovery. By combining a repository for artificial intelligence models and a supercomputing cluster, an entire month's worth of advanced LIGO data is analysed in just 7 min, finding all binary black hole mergers previously identified in this dataset and reporting no misclassifications.

79 ASTRONOMY AND ASTROPHYSICS↗

An AI-accelerated pathway for reproducible and stable halide perovskites

Halide perovskites (HPs) have remarkable optoelectronic properties, and in the last decade their photovoltaic power conversion efficiency and light-emitting diode efficiency have skyrocketed. Despite the surge in research on these burgeoning materials, two key challenges in the field remain: material irreproducibility and instability. Their behavior is especially dynamic in response to environmental stressors, due to complex interactions with the perovskite crystal lattice. Here, in this review, we survey the latest achievements in HP materials research accomplished with the assistance of artificial intelligence (AI), through the implementation of automated experimentation and machine learning (ML) data analysis. Automated synthesis and characterization tackle problems with material irreproducibility by systematically controlling parameters with very high precision, creating massive datasets, and allowing methodical comparisons from which unbiased conclusions can be drawn. AI can reveal otherwise unnoticed trends, inform future experiments with the highest potential information gain, and forecast future performance. The review concludes with a forward viewpoint of how human-assisted closed-loop laboratories and shared databases allow halide perovskite materials’ processing, properties, and performance to be potentially optimized with AI, accelerating the development of highly reproducible and stable optoelectronic devices.

Hering, Abigail R. [Univ. of California, Davis, CA↗

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Controlling morphology and improving reproducibility of magnetized liner inertial fusion experiments

X-ray imaging indicates magnetized liner inertial fusion (MagLIF) stagnation columns have a complicated quasi-helical structure with significant variations in x-ray brightness along the column. In this work, we describe MagLIF experiments aimed at controlling these stagnation structures by varying the initial liner geometry and composition. First, by varying the initial aspect ratio of the liner, we demonstrate a change in the stagnation structures that is consistent with helical magneto Rayleigh–Taylor (MRT) instabilities feedthrough from the outer-to-inner surfaces of the liner. Second, to minimize the seed for such instabilities, we incorporate a dielectric coating on the outer surface of the beryllium liner, which has previously been shown to reduce the growth of the electrothermal instability, a likely seed for MRT growth. Using this coating, we achieve a stagnation column with significantly reduced helical structure and axial variation in x-ray brightness. We discuss how this coating changes the evolution of structures through stagnation along with the spatial uniformity of neutron production. Finally, we show that these more uniform stagnations also result in improved reproducibility in stagnation temperatures and primary DD neutron yield.

Ampleford, D. J. (ORCID:0000000237422421)↗

Where Is the Provenance? Ethical Replicability and Reproducibility in GIScience and Its Critical Applications

As replicability and reproducibility (R&R) crises develop within emerging convergent inquiry, ethical use of provenance information is central to the establishment and preservation of trust in critical applications of GIScience and geospatial technologies. Today large volumes of geospatial data are generated at high velocity from satellite sensors and unmanned aircraft systems, citizen sensors, geolocation-based data services, global navigation satellite systems, and so on. The extensive use of these data for applications such as disaster and humanitarian response raises the issue of R&R from competing perspectives of location privacy and geospatial data quality. Although geospatial data can be integrated and linked with contextual information to identify individuals’ movements, steps taken to ensure privacy can complicate the multiuser development of high-quality geospatial workflows. Provenance information as digital records of historical (retrospective) and potential future (prospective) geospatial processes is often overlooked, misunderstood, or inadequately addressed. We explore the relationship between provenance information, location privacy, and geospatial data quality in the context of R&R with a focus on disaster analytics. Here, we argue that in the era of big data and deep learning, GIScientists and associated institutions bear greater responsibility both for geospatial workflow quality and for location privacy. Given vastly heterogenous computational landscapes, we provide practical recommendations for ethically driven provenance and R&R research and development within the GIScience community and beyond.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗