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How Collective Phenomena Impact CO 2 Reactivity and Speciation in Different Media
CO 2 has attracted considerable attention in the recent years due to its role in the greenhouse effect and environmental management. While its reaction with water has been studied extensively, the same cannot be said for reactivity in supercritical CO 2 phase, where the conjugate acid/base equilibria proceed through different mechanisms and activation barriers. Furthermore, in spite of the apparent simplicity of the CO 2 + H 2 O reaction, the collective effect of different environments has drastic influence on the free energy profile. Enhanced sampling techniques and well-tailored collective variables provide a detailed picture of the enthalpic and entropic drivers underscoring the differences in the formation mechanism of carbonic acid in the gas, aqueous and supercritical CO 2 phases.
Whistler Chorus Amplification in the Magnetosphere: The Nonlinear Free‐Electron Laser Model and the Ginzburg‐Landau Equation
We present a novel nonlinear model for whistler-mode chorus amplification based on the free-electron laser (FEL) mechanism. First, we derive the nonlinear collective variable equations for the whistler-electron interaction. Consistent with in situ satellite observations, these equations predict that a small seed wave can undergo exponential growth, reaching a peak of a few hundred picoteslas after a few milliseconds, followed by millisecond timescale amplitude modulations. Next, we show that when one accounts for multiple wave frequencies and wave spatial variations, the amplitude and phase of the whistler wave can be described by the Ginzburg-Landau equation (GLE), providing a framework for the investigation of solitary wave behavior of chorus modes. These findings enhance our understanding of wave-particle interactions and space weather in the Van Allen radiation belts, deepen the connection between whistler-electron dynamics and FELs, and reveal a novel connection between whistler-mode chorus and the GLE.
Data-guided Multi-Map variables for ensemble refinement of molecular movies
Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.
Baseline Climate Variables for Earth System Modelling
The Baseline Climate Variables for Earth System Modelling (ESM-BCVs) are defined as a list of 135 variables which have high utility for the evaluation and exploitation of climate simulations. The list reflects the most frequently used elements of the Coupled Model Intercomparison Project Phase 6 (CMIP6) archive. Successive phases of CMIP have supported strong results in science and substantially influence international climate policy formulation. This paper responds to both interest in exploiting CMIP data standards in a broader range of climate modelling activities and a need to achieve greater clarity about the significance and intention of variables in the CMIP Data Request. As Earth system modelling archives grow in scale and complexity, there are emerging problems associated with weak standardisation at the variable collection level. That is, there are good standards covering how specific variables should be archived, but this paper fills a gap in the standardisation of which variables should be archived. The ESM-BCV list is intended as a resource for ESM intercomparison projects (MIPs) developing requests to enable greater consistency among MIPs and as a reference for modelling centres to enhance consistency within MIPs. Provisional planning for the CMIP7 Data Request exploits the ESM-BCVs as a core element. The baseline variable list includes 98 variables which have modest or minor data volume footprints and could be generated systematically when simulations are produced and archived for exploitation by the World Climate Research Programme (WCRP) community. A further 35 variables are classed as “high volume” and are only suitable for production when the resource implications are justified.
Misclassification in Workers’ Telecommuting Frequency Choices Using a Generalized Extreme Value Model
Telecommuting frequency is a response variable collected in travel surveys and is, therefore, prone to errors leading to mismeasurements or misclassification. Misclassification of explanatory variables is a common risk when using statistical modeling techniques. We define “misclassification” as a response reported or recorded in the wrong category; for example, a variable is recorded as a 1 when it should be 0. Here, in this context, this study aims to develop a statistical model to analyze telecommuting data which accounts for potential misclassification errors by building on existing literature in econometrics. The empirical analysis was undertaken using the 2017 National Household Travel Survey (NHTS) and the general extreme value (GEV) models available in the literature. Specifically, the frequency of telecommuting days was analyzed using the negative binomial (NB) model recast as the multinomial logit (MNL) model. By nature—and consistent with other studies—NHTS data are prone to errors that can be classified as intentional or unintentional misinformation provided by the person being interviewed. Ignoring these errors while modeling telecommuting frequencies using standard discrete count models can result in biased parameter estimates. The misclassification parameter was calculated for both over-reporting and under-reporting scenarios. The misclassification errors can be as high as 14% over-reported and 10% under-reported, particularly for the neighboring values. Statistical fit comparison between the models shows that models that ignore misclassification have worse data fit and biased parameter estimates with significant policy implications.
Verification of LANDSAT imagery for morphametric and topological studies of drainage basins in a section of the western plateau of Sao Paulo State: Tiete-Aguapei watershed
The potential of using LANDSAT MSS imagery for morphometric and topological studies of drainage basins was verified. Using Tiete and Aguapei watershed (Western Plateau) as the test site because of its homogeneous landscape. Morphometric variables collected for ten drainage basins include: circularity index; river density; drainage density; topographic texture; areal and index length; basin parameter; and main river length 1st order and 2nd order channel length. The topographical variables determined were: order; magnitude; bifuraction ratio; weighted bifuraction ratio; number of segments; number of linking; trajectory length; and topological diameter. Data were collected on topographical maps at the scale of 1:250,000 and 1:59,000 and on LANDSAT imagery at the scale of 1:250,000. The results which were summarized on tables for further analysis, show that LANDSAT imagery can supply the lack of topographic charts for drainage studies.
Data from: Understanding the biogeochemical and spatial drivers of methane and carbon dioxide fluxes in a large temperate reservoir
This dataset contains spatially resolved measurements of CO₂ and CH₄ fluxes and associated environmental variables collected across 200 sites in Douglas Reservoir (Tennessee, USA) between July 29-August 2, 2024. Measurements include diffusive fluxes of CO₂ and CH₄, CH₄ ebullition, and biogeochemical and spatial variables such as dissolved oxygen, temperature, conductivity, chlorophyll-a, pH, water depth, and distance from the dam. Sampling was conducted using a spatially balanced design to capture longitudinal and depth-related gradients throughout the reservoir. The dataset is structured to support analyses of spatial variability, flux pathway comparisons, and modeling approaches (e.g., spatial statistics and machine learning) aimed at understanding controls on reservoir CO₂ and CH₄ fluxes and improving upscaling to whole-reservoir and regional estimates.
Barrier penetration in a discrete-basis formalism
The dynamics of a many-particle system are often modeled by mapping the Hamiltonian into a Schrödinger equation. An alternative approach is to solve the Hamiltonian equations directly in a model space of many-body configurations. In a previous paper the numerical convergence of the two approaches was compared with a simplified treatment of the Hamiltonian representation. Here, we extend the comparison to the nonorthogonal model spaces that would be obtained by the generator-coordinate method. With a suitable choice of the collective-variable grid, a configuration-interaction Hamiltonian can reproduce the Schrödinger dynamics very well. Furthermore, the method as implemented here requires that the barrier height is not much larger than the zero-point energy in the collective coordinates of the configurations.
Studying the earth's poles from satellites
The use of satellite remote sensing is reviewed with respect to the investigation of polar regions and global meteorological processes. Data collected from previous and ongoing satellite missions sponsored by NASA and NOAA are discussed in terms of their ability to describe surface characteristics. Data relating to ocean/atmosphere heat transfer are obtained from microwave radiometers and synthetic aperture radars to give estimates of surface temperatures. Ocean color at several frequencies can be measured to estimate chlorophyll content, and optical and infrared sensors aid in the detection of short- and long-term variance in solar irradiance and earth radiation flux. The geophysical variables collected from satellite data at high latitudes can be used to understand the global climate, atmospheric warming, and other significant mechanisms.
FIRE extended time/limited area observations at Palisades, New York
Downwelling shortwave and longwave irradiation are being continuously monitored at Palisades, New York as part of the First International Satellite Cloud Climatology Project (ISCCP) Regional Experiment (FIRE) Extended Time/Limited Area Initiative. In addition, fisheye (180 degree) sky photographs are taken at the times of NOAA 9 and LANDSAT satellite overpasses on select days, particularly when cirrus clouds are present. Measurements of incoming shortwave (0.28 to 2.80 microns) hemispheric and diffuse, hemispheric near infrared (0.7 to 2.80 microns), and downwelling hemispheric infrared (4.0 to 50.0 microns) irradiation have been made from a rooftop location on the grounds of the Lamont-Doherty Geological Observatory since December 1986. The three Eppley Precision Spectral Pyranometers and the Eppley Pyrgeometer used to measure these variables were calibrated with Colorado State University instruments at Madison, Wisconsin as part of the FIRE Intensive Laboratory. Pyrgeometer output contains an adjustment for body temperature but not for dome temperature. Data are transmitted to a Campbell CR-21 Digital Recorder, where one minute averages of ten second samples are stored and subsequently dumped to a cassette recorder. Using a Campbell C-20 Cassette Interface, these data are transferred to an Apple Macintosh computer for analysis and for archiving on floppy disks. In addition to the raw irradiances collected, variables derived from these data are generated and stored. These include: the ratio of near infrared irradiation to visible irradiation and the fraction of the full shortwave irradiation which is diffuse; and will soon include: shortwave transmissivity and optical depth in the shortwave. Sky photographs are taken with an Olympus OM2-N 35 mm camera and are timed to be coincident with overpassing NOAA and LANDSAT satellites. Palisades is within the field of view of the NOAA 9 daily in the middle to late afternoon. The satellite viewing angle is within 45 degrees of nadir over Palisades on approximately half of the passes.
Astronaut Preflight Cardiovascular Variables Associated with Vascular Compliance are Highly Correlated with Post-Flight Eye Outcome Measures in the Visual Impairment Intracranial Pressure (VIIP) Syndrome Following Long Duration Spaceflight
The detection of the first VIIP case occurred in 2005, and adequate eye outcome measures were available for 31 (67.4%) of the 46 long duration US crewmembers who had flown on the ISS since its first crewed mission in 2000. Therefore, this analysis is limited to a subgroup (22 males and 9 females). A "cardiovascular profile" for each astronaut was compiled by examining twelve individual parameters; eleven of these were preflight variables: systolic blood pressure, pulse pressure, body mass index, percentage body fat, LDL, HDL, triglycerides, use of anti‐lipid medication, fasting serum glucose, and maximal oxygen uptake in ml/kg. Each of these variables was averaged across three preflight annual physical exams. Astronaut age prior to the long duration mission, and inflight salt intake was also included in the analysis. The group of cardiovascular variables for each crew member was compared with seven VIIP eye outcome variables collected during the immediate post‐flight period: anterior-posterior axial length of the globe measured by ultrasound and optical biometry; optic nerve sheath diameter, optic nerve diameter, and optic nerve to sheath ratio‐ each measured by ultrasound and magnetic resonance imaging (MRI), intraocular pressure (IOP), change in manifest refraction, mean retinal nerve fiber layer (RNFL) on optical coherence tomography (OCT), and RNFL of the inferior and superior retinal quadrants. Since most of the VIIP eye outcome measures were added sequentially beginning in 2005, as knowledge of the syndrome improved, data were unavailable for 22.0% of the outcome measurements. To address the missing data, we employed multivariate multiple imputation techniques with predictive mean matching methods to accumulate 200 separate imputed datasets for analysis. We were able to impute data for the 22.0% of missing VIIP eye outcomes. We then applied Rubin's rules for collapsing the statistical results across our 200 multiply imputed data sets to assess the canonical correlation between the eye outcomes and the twelve astronaut cardiovascular variables available for all 31 subjects. Results: A highly significant canonical correlation was observed among the canonical solutions (p<.00001), with an average best canonical correlation of.97. The results suggest a strong association between astronauts' measures of cardiovascular health and the seven eye outcomes of the VIIP syndrome used in this analysis. Furthermore, the "joint test" revealed a significant difference in cardiovascular profile between male and female astronauts (Prob > F = 0.00001). Overall, female astronauts demonstrated a significantly healthier cardiovascular status. Individually, the female astronauts had significantly healthier profiles on seven of twelve cardiovascular variables than the men (p values ranging from <0.0001 to <0.05). Male astronauts did not demonstrate significantly healthier values on any of the twelve cardiovascular variables measured
Real-time dispatch optimization for concentrating solar power with thermal energy storage
Concentrating solar power (CSP) plants present a promising path towards utility-scale renewable energy. The power tower, or central receiver, configuration can achieve higher operating temperatures than other forms of CSP, and, like all forms of CSP, naturally pairs with comparatively inexpensive thermal energy storage, which allows CSP plants to dispatch electricity according to market price incentives and outside the hours of solar resource availability. Currently, CSP plants commonly include a steam Rankine power cycle and several heat exchange components to generate high-pressure steam using stored thermal energy. The efficiency of the steam Rankine cycle depends on the temperature of the plant's operating fluid, and so is a main concern of plant operators. However, the variable nature of the solar resource and the conservatism with which the receiver is operated prevent perfect control over the receiver outlet temperature. Therefore, during periods of solar variability, collection occurs at lower-than-design temperature. To support operator decisions in a real-time setting, we develop a revenue-maximizing non-convex mixed-integer, quadradically-constrained program which determines a dispatch schedule with sub-hourly time fidelity and considers temperature-dependent power cycle efficiency. The exact nonlinear formulation proves intractable for real-time decision support. Here we present exact and inexact techniques to improve problem tractability that include a hybrid nonlinear and linear formulation. Our approach admits solutions within approximately 3% of optimality, on average, within a five-minute time limit, demonstrating its usability for decision support in a real-time setting.
Intra-annual variation in microclimatic conditions in relation to vegetation type and structure in two tropical dry forests undergoing secondary succession
Microclimate acts as a strong filter on species performance in restored and regenerating forests, particularly in seasonally dry tropical forests (SDTF). Yet few studies have measured microclimate patterns across succession in SDTF. Furthermore, although dynamic vegetation models simulate microclimate, evaluation of these simulated variables with field observations has been relatively uncommon. Here, we investigated the seasonal patterns of soil temperature and soil water in naturally regenerated and planted successional vegetation in SDTF in Costa Rica and Puerto Rico, using complementary approaches of intensive field observations and simulation modeling with the Ecosystem Demography model. We found that plots representing later successional stages were wetter on average, but only during the dry season. During the wet season, mean soil water did not differ across vegetation types, but open, early successional vegetation experienced more frequent extreme wet and dry conditions than older forest and plantations. Soil temperature tended to decline with forest structure, and later successional vegetation also experienced less extreme daily temperature fluctuations. Basal area and leaf area index were the best predictors of differences in soil water and temperature across plots. Model simulations were consistent with observations of wet season soil temperature and soil water, but the model failed to reproduce dry season soil moisture dynamics, suggesting that further work is needed to reduce model biases in microclimate variables. Collectively, our results imply that common assumptions about how microclimates influence successional processes in SDTF should be revisited.
Ab initio metadynamics calculations reveal complex interfacial effects in acetic acid deprotonation dynamics
Acid-base reactions play a central role in solution chemistry, with carboxylic acids being particularly important in atmospheric chemical processes. In this work, we harness metadynamics calculations with Born-Oppenheimer molecular dynamics (BOMD) simulations to understand deprotonation dynamics of acetic acid (CH 3 COOH) in both bulk and air-water interfacial environments. Collective variables are carefully chosen in our well-tempered metadynamics simulations to capture the deprotonation process in various aqueous configurations. Herein, our findings show that the free energy barrier for deprotonation of acetic acid at the air-water interface is lower than in the bulk, in accordance with the available experimental data. Furthermore, our well-tempered metadynamics calculations suggest that the variations in free energy are primarily due to intricate solvation shell effects.
Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package
Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.
A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning
A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.
Confinement effects and acid strength in zeolites
Chemical reactivity and sorption in zeolites are coupled to confinement and—to a lesser extent—to the acid strength of Brønsted acid sites (BAS). In presence of water the zeolite Brønsted acid sites eventually convert into hydronium ions. The gradual transition from zeolite Brønsted acid sites to hydronium ions in zeolites of varying pore size is examined by ab initio molecular dynamics combined with enhanced sampling based on Well-Tempered Metadynamics and a recently developed set of collective variables. While at low water content (1–2 water/BAS) the acidic protons prefer to be shared between zeolites and water, higher water contents (n > 2) invariably lead to solvation of the protons within a localized water cluster adjacent to the BAS. At low water loadings the standard free energy of the formed complexes is dominated by enthalpy and is associated with the acid strength of the BAS and the space around the site. Conversely, the entropy increases linearly with the concentration of waters in the pores, favors proton solvation and is independent of the pore size/shape.