Preferred Orientation of a Physisorbed Molecular Catalyst and Implications for Selectivity
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Laurent, Guillaume P. [Division of Chemical and Bi↗
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A Preferences Corpus and Annotation Scheme for Human-Guided Alignment of Time-Series GPTs
The process of time-series forecasting such as predicting trajectories of silicon content in blast furnaces is a difficult task. Most time-series approaches today focus on scalar-type MSE loss optimization. This optimization approach, while widely common, could benefit from the use of human expert or process-level preferences. In this paper, we introduce a novel alignment and fine-tuning approach that involves learning from a corpus of preferred and dis-preferred time-series prediction trajectories. Our contributions include (1) a preference annotation pipeline for time-series forecasts, (2) the application of Score-based Preference Optimization (SPO) to train decoder-only transformers from preferences, and (3) results showing improvements in forecast quality. The approach is validated on both proprietary blast furnace data and the UCI Appliances Energy dataset. The proposed preference corpus and training strategy offer a new option for fine-tuning sequence models in industrial settings.
DPO↗
Microbes display broad diversity in cobamide preferences
ABSTRACT Cobamides, the vitamin B 12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli , Sinorhizobium meliloti , and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to those of previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function. IMPORTANCE Nearly all bacteria are found in microbial communities with tens to thousands of other species. Molecular interactions such as metabolic cooperation and competition are key factors underlying community assembly and structure. Cobamides, the vitamin B 12 family of enzyme cofactors, are one such class of nutrients, produced by only a minority of prokaryotes but required by most microbes. A unique aspect of cobamides is their broad diversity, with nearly 20 structural forms identified in nature. Importantly, this structural diversity impacts growth as most bacteria that have been tested show preferences for specific cobamide forms. We measured cobamide-dependent growth in several model bacteria and compared the results to those of previous analyses of cobamide preference. We found that cobamide preferences vary widely across bacteria, showing the importance of characterizing these aspects of cobamide biology to understand the impact of cobamides on microbial communities.
Mok, Kenny C. (ORCID:0000000252276987)↗
Analyzing users’ preferences between personal and pooled rideshare services using a mixed logit modeling approach
Ridesharing has become an increasingly popular transportation method over the past decade. Transportation network companies such as Uber and Lyft generally provide two types of rideshare services: personal rideshare, in which users ride alone or with individuals they know, and pooled rideshare, in which users ride with passengers they do not know but share similar routes. Pooled rideshare is capable of reducing energy consumption and traffic in the transportation system in comparison to personal rideshare. Despite the growth in trip volume, ridesharing usage is still low compared to other popular transportation methods in the U.S., particularly traveling in one’s own personal vehicle. Furthermore, pooled rideshare usage is lower than personal rideshare. To understand riders’ preferences, a national survey (N = 2884) was conducted in the U.S. to investigate users’ choice behaviors in rideshare services examining personal versus pooled rideshare. Each survey respondent completed 20 stated-preference scenarios where participants choose between a personal or pooled rideshare option. Based on the responses, a mixed logit model was developed to capture the choice behavior preferences of the participants. The model unveiled the impact of demographic and trip attribute variables on users’ rideshare preferences. The discussion encompassed insights into demographic backgrounds and trip attributes, accompanied by a set of policy recommendations aimed at enhancing future pooled rideshare utilization.
Choice model↗
Cosmological preference for a negative neutrino mass
The most precise determination of the sum of neutrino masses from cosmological data, derived from analysis of the cosmic microwave background (CMB) and baryon acoustic acoustic oscillations (BAO) from the Dark Energy Spectroscopic Instrument (DESI), favors a value below the minimum inferred from neutrino flavor oscillation experiments. We explore which data is most responsible of this puzzling aspect of the current constraints on neutrino mass and whether it is related to other anomalies in cosmology. We demonstrate conclusively that the preference for negative neutrino masses is a consequence of larger than expected lensing of the CMB in both the two- and four-point lensing statistics. Furthermore, we show that this preference is robust to changes in likelihoods of the BAO and CMB optical depth analyses given the available data. We then show that this excess clustering is not easily explained by changes to the expansion history and is likely distinct from the preference for for dynamical dark energy in DESI BAO data. Finally, we discuss how future data may impact these results, including an analysis of Planck CMB with mock DESI 5-year data. Here, we conclude that the negative neutrino mass preference is likely to persist even as more cosmological data is collected in the near future.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Preferred Practices Through a Project Template
In the realm of scientific software development, adherence to best practices is often advocated. However, implementing these can be challenging due to differing opinions. Certain aspects, such as software licenses and naming conventions, are typically left to the discretion of the development team. Our team has established a set of preferred practices, informed by, but not limited to, widely accepted best practices. These preferred practices are derived from our understanding of the specific contexts and user needs we cater to. To facilitate the dissemination of these practices among our team and foster standardization with collaborating domain scientists, we have created a project template for Python projects. This template serves as a platform for discussing the implementation of various decisions. This paper will succinctly delineate the components that constitute an effective project template and elucidate the advantages of consolidating preferred practices in such a manner.
Zhang, Chen↗
Pooled Rideshare in the U.S.: An Exploratory Study of User Preferences
Pooled ridesharing offers on-demand, one-way, cost-effective transportation for passengers traveling in similar directions via a shared vehicle ride with others they do not know. Despite its potential benefits, the adoption of pooled rideshare remains low in the United States. This exploratory study aims to evaluate potential service improvements and features that may increase users’ willingness to adopt the service. The study analyzed transportation behaviors, rideshare preferences, and willingness to adopt pooled rideshare services among 8296 U.S. participants in 2025, building on findings from a 2021 nationwide survey of 5385 U.S. participants. The study incorporated 77 actionable items developed from the results of the 2021 survey to assess whether addressing specific user-generated topics such as safety, reliability, convenience, and privacy can improve pooled rideshare use. A side-by-side comparison of the 2021 and 2025 data revealed shifts in transportation behavior, with personal rideshare usage increasing from 22% to 28%, public transportation from 21% to 27%, and pooled rideshare from 6% to 8%, while personal vehicle (79%) use remained dominant. Participants rated features such as driver verification (94%), vehicle information (93%), peak time reliability (93%), and saving time and money (92–93%) as most important for improving rideshare services. A pre-to-post analysis of willingness to use pooled rideshare utilizing the actionable items as per respondents’ preferences showed improvement: “definitely will” increased from 15.9% to 20.1% and “probably will” rose from 35.6% to 47.7%. These results suggest that well-targeted service improvements may meaningfully enhance pooled rideshare acceptance. This study offers practical guidance for Transportation Network Companies (TNCs) and policymakers aiming to improve pooled rideshare as well as potential future research opportunities.
Transportation Network Companies (TNCs)↗
Controlling Preferred Grain Orientation in Vapor-Deposited Metal-Halide Perovskite Thin Films
Metal-halide perovskites are promising semiconductor materials for light-absorber layers in solar cells due to their optimized band gap, defect tolerance, and relative ease of synthesis. In this work, we demonstrate the viability of vapor transport deposition (VTD), a solvent-free processing method, to realize polycrystalline films of both lead iodide (PbI 2 ) and methylammonium lead iodide (MAPbI 3 ) perovskites showing preferential crystallographic orientation. Notable is the difference in perovskite film texturing observed for sequentially and co-deposited VTD films of MAPbI 3 , as well as the lack of strong preferential orientation in solution-processed MAPbI 3 films. While sequential deposition of the perovskite precursors PbI 2 and methylammonium iodide (MAI) leads to a MAPbI 3 film with a limited preferential grain orientation, co-deposited MAPbI 3 films mirror the orientation of excess PbI 2 present in the film. The latter is confirmed by the similar dependence of preferential orientation for PbI 2 and co-deposited MAPbI 3 on underlayer roughness, as well as the emergence of preferential orientation in MAPbI 3 only when excess PbI 2 is present. Both MAPbI 3 and PbI 2 films show a strong preferred lattice orientation on smooth substrates, while on rougher substrates, this orientation is disrupted. Furthermore, these results are interpreted as excess PbI 2 frustrating the diffusion of MAI in the film, which would otherwise disrupt the preferred orientation, pointing to a notable difference in lattice orientation arising from processing technique and conditions.
Deposition↗
Identifying critical features of iron phosphate particle for lithium preference
One-dimensional (1D) olivine iron phosphate (FePO 4 ) is widely proposed for electrochemical lithium (Li) extraction from dilute water sources, however, significant variations in Li selectivity were observed for particles with different physical attributes. Understanding how particle features influence Li and sodium (Na) co-intercalation is crucial for system design and enhancing Li selectivity. Here, we investigate a series of FePO 4 particles with various features and revealed the importance of harnessing kinetic and chemo-mechanical barrier difference between lithiation and sodiation to promote selectivity. The thermodynamic preference of FePO 4 provides baseline of selectivity while the particle features are critical to induce different kinetic pathways and barriers, resulting in different Li to Na selectivity from 6.2 × 10 2 to 2.3 × 10 4 . Importantly, we categorize the FePO 4 particles into two groups based on their distinctly paired phase evolutions upon lithiation and sodiation, and generate quantitative correlation maps among Li preference, morphological features, and electrochemical properties. By selecting FePO 4 particles with specific features, we demonstrate fast (636 mA/g) Li extraction from a high Li source (1: 100 Li to Na) with (96.6 ± 0.2)% purity, and high selectivity (2.3 × 10 4 ) from a low Li source (1: 1000 Li to Na) with (95.8 ± 0.3)% purity in a single step.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Expansion-history preferences of DESI DR2 and external data
We explore the origin of the preference of Dark Energy Spectroscopic Instrument (DESI) Data Release 2 (DR2) baryon acoustic oscillation measurements and external data from cosmic microwave background (CMB) and type Ia supernovae (SNIa) that dark energy behavior departs from that expected in the standard cosmological model with vacuum energy (Λ CDM). In our analysis, we allow a flexible scaling of the expansion rate with redshift that nevertheless allows reasonably tight constraints on the quantities of interest, and adopt and validate a simple yet accurate compression of the CMB data that allows us to constrain our phenomenological model of the expansion history. We find that data consistently show a preference for a 3%–4% increase in the expansion rate at 𝑧 ≃ 0.7 relative to that predicted by the standard Λ CDM model, in excellent agreement with results from the less flexible (𝑤 0 ,𝑤 𝑎 ) parametrization which was used in previous analyses. Even though our model allows a departure from the best-fit Λ CDM model at zero redshift, we find no evidence for such a signal. We also find no evidence (at greater than 1𝜎 significance) for a departure of the expansion rate from the Λ CDM predictions at higher redshifts for any of the data combinations that we consider. Altogether, our results strengthen the robustness of the findings using the combination of DESI, CMB, and SNIa data to dark-energy modeling assumptions.
Cosmological parameters↗
Which way does the dendrite grow? Competition among epitaxy, preferred growth direction, and thermal gradients in powder bed fusion additive manufacturing
The as-processed microstructure of metal alloy parts manufactured through laser powder bed fusion (LPBF) is heavily derived from the cellular dendritic solidification. The growth direction of dendrites within the melt pool is determined through competition among epitaxial growth, preferred growth directions, and maximum thermal gradients. However, the dominant factor and the specific role of each in developing melt pool microstructures remain unknown. Here, in this study, we performed single laser track scans on an SS316L single crystal substrate and combined experimental characterization of microstructure and crystal orientations with Computational Fluid Dynamics simulations of thermal gradients to evaluate the role of each factor in determining dendritic growth direction and evolution. Our results reveal that epitaxial growth dominates microstructure development by preferentially growing along a single 〈100〉 variant of the single crystal substrate adjacent to the melt pool boundary. Under LPBF’s highly curved and rapidly evolving thermal field, this preferential dendrite variant selection and its continued growth from the melt pool boundary to the centerline are governed by the local temperature gradient magnitude at the solid-liquid interface, rather than by the instantaneous maximum temperature gradient direction alone. Using these findings, we successfully predict changes in the dendrite growth direction with changing laser scan direction on a single crystal substrate, and show that the geometric melt pool centerline can deviate from the microstructural centerline because asymmetric local temperature gradient magnitudes transiently limit growth, resulting in different dendrite travel distances on each side of the melt pool.
36 MATERIALS SCIENCE↗
Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum
Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4–5 m in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified.
59 BASIC BIOLOGICAL SCIENCES↗
Past Approaches for Spent Nuclear Fuel, Transuranic, and High-Level Waste Disposal in the United States—Part 2: Siting Process, Staged Development, and Public Preferences
This report presents pertinent aspects of the ~50-year United States experience in siting a mined geologic disposal repository for spent nuclear fuel (SNF), transuranic (TRU) waste, and high-level radioactive waste (HLW) as related to site selection and the staged process for site investigations as specified in the Nuclear Waste Policy Act of 1982 and generic and site-specific regulations of the US Department of Energy (DOE), US Environmental Protection Agency (EPA), and US Nuclear Regulatory Commission (NRC). The roles of the Environmental Impact Statement and guidance in international consensus standards by the International Atomic Energy Agency are also mentioned. The focus is on siting and developing the Waste Isolation Pilot Plant, an operating repository for TRU waste from atomic energy defense activities, and the proposed Yucca Mountain repository for commercial SNF and HLW. In the social dimension, the role of institutional stakeholders is described. Past national surveys related to waste management options for storage and disposal provide insight on public preferences of other stakeholders. The descriptions are intended to help other countries more fully understand the stages adopted for siting and developing repositories in the United States.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Understanding and Modeling Pooled Rideshare Acceptance: Influential Factors, Preferred User Experiences, and Implications
Ridesharing allows people to share a vehicle with others traveling in the same direction, which can reduce costs and traffic congestion. Pooled rideshare (PR) services, such as UberX Share and Lyft Shared, offer an economical and environmentally friendly alternative by matching passengers traveling similar routes. However, despite these benefits, PR adoption remains low due to concerns about safety, privacy, and convenience. This research explores the factors influencing PR adoption and provides recommendations to improve user acceptance. A nationwide survey of 5,385 participants across the U.S. was conducted to understand why people choose or avoid PR. The study identified five key factors influencing PR consideration: safety, service experience, privacy, traffic/environment, and time/cost. Additional research examined ways to optimize PR experiences by identifying four critical factors: comfort/ease of use, convenience, vehicle technology/accessibility, and passenger safety. To measure the impact of these factors, a statistical model called the Pooled Rideshare Acceptance Model (PRAM) was developed, providing insights into how each element influences PR adoption. Further analysis using the Pooled Rideshare Acceptance Model Multigroup Analyses (PRAMMA) revealed how demographic characteristics such as age, gender, income, and past rideshare experience shape PR perceptions. Some key findings from the multigroup analyses showed that younger users valued technological features and environmental benefits, while older users prioritized reliability and service transparency. Additionally, privacy concerns were more significant for female users, while convenience was critical for higher-income groups. These results emphasize that a 'onesize-fits-all' approach to PR service design is not effective, highlighting the need for tailored strategies to address different user segments. Further, workshops were conducted with researchers and students to translate the findings into real-world solutions. These workshops and 3 all the statistical analyses led to the development of 95 actionable recommendations. The recommendations focus on key areas such as safety, service reliability, user education, and accessibility, offering tangible improvements to PR services. The insights from this study provide valuable guidance for policymakers, transportation network companies (TNCs), and researchers aiming to make PR services safer, more accessible, and widely accepted. By addressing user concerns, PR can become a more viable transportation option, supporting sustainable urban mobility and reducing reliance on private vehicles. Additionally, these findings emphasize the importance of user-centric service design in encouraging broader PR adoption. Future research should explore evolving trends in PR preferences, technological advancements, and policy changes to ensure continued improvements. By implementing these recommendations, PR services can better align with user expectations, enhance trust in shared mobility, and contribute to a more efficient transportation ecosystem.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Understanding and Modeling Pooled Rideshare Acceptance: Influential Factors, Preferred User Experiences, and Implications
This dissertation explores factors influencing pooled rideshare (PR) adoption to provide actionable insights for transportation network companies (TNCs) and policymakers. PR allows travelers to share rides with unknown passengers, offering benefits such as cost reduction and congestion relief. However, adoption remains limited due to safety concerns, privacy issues, and trust in rideshare platforms. A national U.S. survey with 5,385 respondents examined transportation preferences and barriers to PR adoption. Exploratory and confirmatory factor analyses identified five key factors influencing PR consideration—safety, service experience, privacy, traffic/environment, and time/cost. Second factor analyses examined ways to optimize PR experiences, revealing four factors—comfort/ease of use, convenience, vehicle technology/accessibility, and passenger safety. Privacy concerns, for instance, using regression analysis, were found to reduce the likelihood of PR adoption by 77%, and convenience had the potential to increase it by 156%. The Pooled Rideshare Acceptance Model (PRAM), based on the Technology Acceptance Model, assessed the impact of these factors using the Structural Equation Model (SEM). Privacy, safety, trust, and convenience had a large effect (Cohen's f2 > 0.35) on PR acceptance, while multigroup analyses (PRAMMA) explored 16 demographic variables such as gender, generation, and income, emphasizing the need for tailored strategies. Based on all the statistical analysis and workshops using descriptive statistics, 95 actionable recommendations were made from the riders' perspective. Findings highlight the importance of customized services, user experience improvements, and policy interventions to enhance PR adoption. This dissertation provides a roadmap for future research and policy development, ensuring evidence-based, practical strategies to improve PR services in the U.S. and beyond.
Gangadharaiah, Rakesh↗
Operationally induced preferred basis in unitary quantum mechanics
The preferred-basis problem and the definite-outcome aspect of the measurement problem persist even if the detector is modeled unitarily, because experimental data are necessarily represented in a Boolean event algebra of mutually exclusive records whereas the theoretical description is naturally formulated in a noncommutative operator algebra with continuous unitary symmetry. This change of mathematical type constitutes the core of the 'cut': a structurally necessary interface from group-based kinematics to set-based counting. In the presented view the basis relevant for recorded outcomes is not determined by the system Hamiltonian alone; it is induced by the measurement mapping, i.e., by the detector channel together with the coarse-grained readout that defines an instrument. The probabilistic mapping is anchored in symmetry and measure theory: by Gleason-type uniqueness (Gleason for projections in $d>2$ and Busch's extension for Positive Operator-Valued Measures (POVMs) including $d=2$), the trace rule is the unique probability measure consistent with additivity over exclusive events and basis-independence of the unitary sector. A compact qubit--pointer model yields an induced unsharp POVM $E_\pm=\tfrac12(\id\pm η\,σ_z)$ with $η$ fixed by pointer resolution, displaying explicitly how the detector induces the relevant basis. Finally, nested-observer paradoxes are tightened into a non-composability lemma: joint assignment of outcome propositions is obstructed unless a joint instrument exists. This relocates the origin of randomness to the stochasticity of the transition rules.
Pronskikh, Vitaly [Fermilab] (ORCID:00000002518174↗
In–context promoter bashing of the Sorghum bicolor gene models functionally annotated as bundle sheath cell preferred expressing phosphoenolpyruvate carboxykinase and alanine aminotransferase
In-context promoter bashing via genome editing is a route to identify and characterize critical regulatory regions that govern expression of genes of interest. The outcomes of in-context promoter bashing can be used to inform editing strategies to modulate the expression of selected gene models in a desired fashion. Here, we employed in-context promoter bashing to characterize the proximal upstream regulatory regions of sorghum genes encoding phosphoenolpyruvate carboxykinase bundle sheath (SbPEPCK.BS, SbiTx430.01G455400) and alanine aminotransferase bundle sheath (SbAlaAT.BS, SbiTx430.02G006600), two proteins involved in the PCK C 4 pathway. Characterized germinal edits within the targeted regions upstream of these two genes ranged in size from 138 up to 1790 bp. A 138 bp within the SbPEPCK.BS upstream region and a 1643 bp element within the SbAlaAT.BS upstream region were determined to be important for maintenance of transcription levels. No change in development or various physiological parameters was observed in characterized lineages carrying promoter edits. However, significant changes in seed reserves and a reduction in 100-seed weight were consistently observed, under both greenhouse and field environments, in plants carrying an edit in the promoter of SbPEPCK.BS gene, which were significantly reduced in transcript accumulation for this gene.
60 APPLIED LIFE SCIENCES↗
Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning
Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.
Lipo-chitooligosaccharides↗