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Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis
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Digital Twin for Chemical Science: a case study on water interactions on the Ag(111) surface
Directly visualizing chemical trajectories offers insights into catalysis, gas-phase reactions and photoinduced dynamics. Tracking the transformation of chemical species is best achieved by coupling theory and experiment. Here we developed Digital Twin for Chemical Science (DTCS) v.01, which integrates theory, experiment and their bidirectional feedback loops into a unified platform for chemical characterization. DTCS addresses a core question: given a set of experimental conditions, what is the expected outcome and why? It consists of a forward solver that takes a chemical reaction network and predicts spectra under experimental conditions, and an inverse solver that infers kinetics from measured spectra. We applied DTCS to ambient-pressure X-ray photoelectron spectroscopy measurements of the Ag–H2O interface as an example. This approach enables real-time knowledge extraction and guides experiments until a stopping condition is met based on accuracy and degeneracy. As a step toward autonomous chemical characterization, DTCS provides mechanistic knowledge in a verified, standardized manner.
Importance sampling within configuration space integration for adsorbate thermophysical properties: a case study for CH 3 /Ni(111)
A new strategy is presented for computing anharmonic partition functions for the motion of adsorbates relative to a catalytic surface. Importance sampling is compared with conventional Monte Carlo.
Vertical gradient in atmospheric particle phase state: a case study over the alaskan arctic oil fields
The phase state of atmospheric particles impacts atmospheric processes like heterogeneous reactions, cloud droplet activation, and ice nucleation. This study highlights vertically resolved measurements of the phase state of individual particles.
Surface engineering of Pt nanocatalysts with transition metal oleates for selective catalysis: a case study on the hydrogenation of α,β-unsaturated aldehydes
Selective and active catalysts enable effective use of feedstocks, reduced energy consumption and waste generation. Tuning the electronic structure of heterogeneous metal nanocatalysts via their surface modifications is a promising strategy to design highly selective and active catalysts for the synthesis of harder to make and more cost-efficient products. Here, we introduce transition metal oleates as a new class of ligands to engineer the catalytically active and very selective surface in organic solvents. Using citral hydrogenation and 5 nm Pt NPs as a model reaction and model catalytic system, respectively, we show that surface engineering of Pt nanocatalysts with metal oleates allows synthesis of desired partially hydrogenated product (geraniol) with ∼90% conversion with selectivity over 93%. We demonstrate that the selective synthesis of the unsaturated alcohols catalyzed by Pt NPs modified by adsorption of the transition metal salts cannot be explained by the widely accepted mechanism of preferred coordination of C$=$O groups by Lewis acids (e.g. partially oxidized transition surface metals). Our results indicate that C$=$O groups prefer to bind to negatively charged surfaces. We propose the explanation on how the adsorption of transition metal oleates can result in the increased electron density at the surface of Pt nanoparticles. Our study not only provides reliable solutions to selective hydrogenation but opens a new possibility of using metal oleates for the electronic ligand effect.
Spatial Impacts of Electric Vehicle Charging on Power Grid Stability: A Downtown Atlanta Case Study
The rapid increase in electric vehicle (EV) charging demand poses a potential risk to power grid stability, particularly as the spatial distribution of this demand remains underexplored. Existing research often focuses on technical optimization models while overlooking the geographic and human dynamics that affect energy consumption. This study addresses this gap by incorporating mobility data to estimate both building energy use and EV charging demand while also considering geographic factors for a better understanding of grid load. Using agent-based simulations and the Open-Source Distribution System Simulator, the study evaluates the effect of various EV penetration scenarios on grid voltage and unbalance. The results show that, although voltage remains within acceptable limits at lower EV penetration rates, significant voltage drop and unbalance occur as EV penetration exceeds 40%, particularly in residential areas with high charging demand. This study offers a framework for integrating spatial analysis and mobility data in power network simulations, providing insights for future EV infrastructure planning.
Dynamic embedding of effective harmonic normal mode vibrations in all-atomistic energy gap fluctuations: Case study of light harvesting 2 complex
Environmental effects in excitation energy transfer have mostly been modeled by baths of harmonic oscillators, but to what extent such modeling provides a reliable description of actual interactions between molecular systems and environments remains an open issue. Here, we address this issue by investigating fluctuations in the excitation energies of the light harvesting 2 complex using a realistic all-atomistic simulation of the potential energy surface. Our analyses reveal that molecular motions exhibit significant anharmonic features, even for underdamped intramolecular vibrations. In particular, we find that the anharmonicity contributes to the broadening of spectral densities and substantial overlaps between neighboring peaks, which complicates the meaning of mode frequencies constituting a bath model. Thus, we develop a strategy to construct a minimally underdamped harmonic bath that has a clear connection to all-atomistic dynamics by utilizing actual normal modes of molecules but optimizing their frequencies such that the resulting bath model can best reproduce the all-atomistic simulation results. By subtracting the underdamped contribution from the entire fluctuations, we also show that identifying a residual spectral density representing all other contributions with overdamped behavior is possible. We find that this can be fitted well with a well-established analytic form of a spectral density function or, alternatively, modeled as explicit time dependent fluctuations with muti-exponential or power law type correlation functions. We provide an assessment and the implications of these possibilities. The approach presented here can also serve as a general strategy to construct a simplified bath model that can effectively represent the underlying all-atomistic bath dynamics.
Improving equations of state calibrations in the toroidal DAC—The case study of molybdenum
We report an updated isothermal equation of state (EoS) of molybdenum (Mo) obtained by compression in beveled and toroidal diamond-anvil cells (DACs). For an improved compression environment, we developed a copper (Cu) pressure-transmitting medium (PTM) for the toroidal diamond-anvil cell samples, as it is a soft metal compared to Mo with a well calibrated EoS. A Ne PTM was used for the conventional beveled DAC samples. The unit-cell volumes of Mo were measured to 336(1) GPa in the Cu PTM and 231.2(6) GPa in the Ne PTM at room temperature. We additionally calculated elastic stiffness and compliance constants and evaluated the uniaxial stress of Mo and Cu with pressure. A new EoS for Mo is presented from data collected in all sample environments and compared to our theoretical predictions as well as previous compression studies of Mo. The (200) lattice plane of Mo produced the lowest volumes across the pressure range of this study for all compression environments, suggesting that it is less affected by nonhydrostatic stresses in the DAC compared to the other observed diffraction planes. The presented Mo EoS is compatible with extrapolations of EoS fits of Mo in helium (He) within ~1% at 330 GPa. Results from this work demonstrate that compressing a sample in a softer metal in the toroidal DAC can improve the compression environment and result in measured sample volumes comparable to those collected in noble-gas media at multi-megabar conditions.
Bulk cloud microphysical properties as seen from numerical simulation and remote sensing products: case study of a hailstorm event over the La Plata Basin
Hailstorms develop over the La Plata Basin, in south-eastern South America, more often during later winter and early austral spring, between September and October. These systems have significant socioeconomic impacts over the region. Thus, a better understanding of how atmospheric drivers modulate the formation of hailstorms is important to improve the forecast of such phenomena. In this study, we selected a hailstorm event observed over the eastern La Plata Basin during 14–15 July 2016 to evaluate the performance of the Brazilian developments on the Regional Atmospheric Modelling System (BRAMS) model. The ability of the model in simulating cloud microphysical properties was evaluated by comparing simulations driven by different global forcings against in situ and remote sensing observations. The model results showed good skill in capturing the basic characteristics of the thunderstorm, particularly in terms of the spatial distribution of hydrometeors. The simulated spatial distribution of hail covers locations where hail fall was reported. The BRAMS simulations suggest that, despite relatively low values of the convective available potential energy (CAPE) (700–1000 J kg -1 ), environments with strong 0–8-km bulk shear (60–70 kt, ~30.9–36.0 m s –1 ) can promote the formation of ice clouds and hail fall over the eastern La Plata Basin. To be more conclusive, however, further research is needed to understand how different combinations of CAPE and shear affect hail formation over the region.
Expert evaluation of LLM world models: A high-T c superconductivity case study
Large Language Models (LLMs) show great promise as a powerful tool for scientific literature exploration. However, their effectiveness in providing scientifically accurate and comprehensive answers to complex questions within specialized domains remains an active area of research. Using the field of high-temperature cuprates as an exemplar, we evaluate the ability of LLM systems to understand the literature at the level of an expert. We construct an expert-curated database of 1,726 scientific papers that covers the history of the field, and a set of 67 expert-formulated questions that probe deep understanding of the literature. We then evaluate six different LLM-based systems for answering these questions, including both commercially available closed models and a custom retrieval-augmented generation (RAG) system capable of retrieving images alongside text. Experts then evaluate the answers of these systems against a rubric that assesses balanced perspectives, factual comprehensiveness, succinctness, and evidentiary support. Among the six systems, two using RAG on curated literature outperformed existing closed models across key metrics, particularly in providing comprehensive and well-supported answers. We discuss promising aspects of LLM performances as well as critical short-comings of all the models. The set of expert-formulated questions and the rubric will be valuable for assessing expert level performance of LLM based reasoning systems.
Technoeconomic Design Optimization for Fast Reactors. Part I: Workflow Development and Case Study for Small LFR District Energy Application
The nuclear industry is developing small reactor designs that can target a variety of deployment locations and energy products. Smaller nuclear designs have traditionally struggled to handle the steep trade-offs between size and cost that have historically incentivized large reactors. This motivates computational optimization of small reactors to minimize costs and quantify the trade-off between size and cost. In this paper, the cost/size trade-off for a small fast reactor is derived using a multi-objective genetic algorithm optimization, with steady-state, transient, and cost analysis of the fast reactor being performed. Specifically, the method is demonstrated on a small 10- to 120-MW(thermal) U-Pu-Zr–fueled lead-cooled fast reactor with a 10-year core life for district energy applications, which can have a thermal load compatible with this range. The results reinforced that fast reactor cores at the lower end of this power range suffer cost penalties due to critical mass considerations. It was found that high power density cores with strong reactivity swings and many control rods were favored over designing to minimize reactivity swing. Furthermore, this contrasts with some traditional configurations designed using engineering judgment and demonstrates that optimizers can find nontraditional but realistic solutions, along with demonstrating the value of incorporating cost functions into whole-reactor design optimization.
Case study probing the potential drivers of Houston new particle formation and growth in a unique outdoor chamber
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Apomixis in Farmers’ Fields: Overview, Case Studies from Forage Grasses and Considerations for Future Apomictic Crops
Apomixis occurs naturally in several commercially important species from diverse plant families. While in some of these species apomixis is yet to be exploited in breeding schemes aimed at fixing heterosis, genetic progress and cultivar development, in other species apomixis has been integrated at different stages of breeding. Some of the most relevant examples come from the subfamily Panicoideae, the second largest subfamily of the Poaceae, and are the main focus of this review. The subfamily encompasses many tropical and sub-tropical grasses and grains of worldwide economic importance. Apomictic tropical forages are prime examples of how apomixis can be used and exploited in the development of marketable cultivars, which are essential to the meat and milk production industries globally. The main commercial forages used as grass pastures covering millions of hectares in tropical and sub-tropical regions are polyploids exhibiting gametophytic apomixis that belong to the genus Urochloa spp. (brachiariagrasses) and to the species Megathyrsus maximus (guineagrass). Buffel grass (Cenchrus ciliaris) and Paspalum spp. are other important apomictic forages bred and used in these regions. Breeding involves large germplasm collections from the centers of origin of the species, and for most of them, sexually reproducing diploid plants have been found. Chromosomically duplicated plants that maintain sexual reproduction are used in crosses with apomictic genotypes for the development and selection of cultivars to be marketed or used as progenitors in subsequent breeding cycles. The peculiarities of each genus/species breeding programs, the cultivars obtained from these programs, and the impact of use of marker assisted selection in cultivar development are presented. In addition, the test or implementation of new technologies such as high throughput phenotyping, and the use of machine learning methods for trait prediction and genomic selection are positively impacting the selection and speed of development of new polyploid apomictic cultivars. Furthermore, genetic transformation techniques, including genome editing, provide an additional layer for design of tailor-made, customer-oriented cultivars.
The Impact of Bias Row Noise to Photometric Accuracy: Case Study Based on a Scientific CMOS Detector
Abstract We tested a new model of CMOS detector manufactured by the Gpixel Inc, for potential space astronomical application. In laboratory, we obtain some bias images under the typical application environment. In these bias images, clear random row noise pattern is observed. The row noise also contains some characteristic spatial frequencies. We quantitatively estimated the impact of this feature to photometric measurements, by making simulated images. We compared different bias noise types under strict parameter control. The result shows the row noise will significantly deteriorate the photometric accuracy. It effectively increases the readout noise by a factor of 2–10. However, if it is properly removed, the image quality and photometric accuracy will be significantly improved.
Behavior and mechanisms of Doppler wind lidar error in complex terrain: stable flow case study at Perdigão
A numerical experiment is carried out investigating the magnitude of biases in ground-based lidar measurements in complex flow conditions. Biases assessed include those arising from flow curvature and from the interaction of turbulence with the wind field reconstruction (WFR) algorithms used by a WindCube lidars and anemometers. RANS-CFD and WRF-LES simulations were performed for the Perdig˜ao Field Experiment site for a range of atmospheric conditions. Virtual anemometer and lidar data were generated for four locations: two near exposed ridge tops and two in low-speed regions in the valley. The LES data at these four locations show that the scalar inflation terms (the relation between scalar and vector averaged wind speed) for virtual lidar and virtual cups agree very well with predictions using perturbation theory. While the lidar errors vary greatly with location and height, the contribution from the flow curvature tends to be larger than the differences arising from scalar inflation. For one lidar/mast pair near the ridge top, comparisons between simulations and measurements are carried out for a resonant mountain wave event on June 14th, 2017, and for the whole duration of the Perdigão campaign for winds perpendicular to the ridges. The lidar error during the mountain wave, a period of strong stability and low inversion height, is significantly larger than the campaign average. The sensitivity of the lidar error to atmospheric stability is confirmed by the RANS simulations, which suggests strong sensitivity of flow curvature error to stability conditions and to the shape of the wind speed profile near the top of the boundary layer.
Urban morphology and urban water demand: a case study in the land constrained Los Angeles region using urban growth modeling
The interactions between population growth, urban morphology, and water demand have important implications for water resources and supply in urban regions. Water use for irrigation comprises a significant fraction of urban water demand, and is potentially influenced by long-term changes in urban morphology. To investigate this, we used spatially explicit projections of urban land development intensity (fraction impervious area) generated from a 30 m resolution urban growth model for the Los Angeles (LA) region. Recent historical data on water use and high resolution landcover were used to establish relationships between green area, urban development intensity, and outdoor water demand. These relationships were then used to project outdoor and total water demand in 2100 using the urban growth model outputs. We considered two different population scenarios informed by the shared socioeconomic pathway (SSP) projections for the region (SSP3 and SSP5), and three scenarios of urban development intensification. Our analysis is resolved for over 80 water providers in the region, from the urban core to suburban fringe, and highlights diverse demand responses influenced by initial urban form and water demand attributes. Assumptions about outdoor water use factors based on recent water supply data were found to be nearly as influential on future outdoor demand as the urban growth scenario settings. Compared to previous studies, our work is unique in coherently linking high resolution SSP population scenarios, urban land cover evolution, and urban water demand projections, demonstrating the approach for the LA region—the largest population center in the western United States.
Emulation of Monthly Water Allocations Using LSTM Models: A Case Study of the Colorado River Basin in Texas
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