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At least 901 records · Page 50

Nonadditive CO 2 Uptake of Type II Porous Liquids Based on Imine Cages

Type II porous liquids can potentially exploit the fluidity of liquids and sorption properties of porous sorbents, yet CO 2 uptake in porous liquids is still poorly understood. Molecular simulations and experiments are used to examine CO 2 uptake by a prototypical porous liquid composed of porous organic cages (CC13) in 2′-hydroxyacetophenone (2′-HAP). The simulations are in reasonable agreement with experimental measurements of CO 2 solubility and provide unambiguous information on the partitioning of CO 2 within microenvironments in the liquid. Analysis of CO 2 dynamics is performed using these simulations, including assessing the self-diffusivity of CO 2 in both the neat solvent and porous liquid. This offers insights into the kinetics of CO 2 uptake and transport in type II porous liquids based on imine cages. Experiments with type II porous liquids formed by dissolving CC13 in three different size-excluded solvents show nonadditive CO 2 absorption relative to predictions based on ideal volume additivity. This nonadditive absorption behavior is also observed in simulations. Nonadditive CO 2 uptake is also demonstrated in type II porous liquids based on another imine-based porous cage, CC19.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Methodology for Good Machine Learning with Multi‐Omics Data

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4‐year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio‐genomics‐based prognostic and predictive factors for HR+/HER− metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi‐omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as “maintaining effective communication” and “following good data science practices,” followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

Pharmacology & Pharmacy↗

Coping with cold: Sorghum cold stress from germination to maturity

Abstract Sorghum [ Sorghum bicolor (L.) Moench] is an important crop that is highly drought tolerant but susceptible to low temperatures. Many studies have begun to explore the genetic basis of variation in chilling sensitivity in the sorghum germplasm in an effort to improve sorghum's chilling tolerance. However, differences in genetic maps and updates to the sorghum reference genome have made comparing studies of chilling in sorghum challenging. Here, we review the current state of research on chilling tolerance and susceptibility in sorghum during germination and emergence, vegetative growth, and reproduction and harvest stages. Using the most recent sorghum reference genome (v3.1), we have standardized the locations of quantitative trait loci and marker‐trait associations for chilling tolerance traits across the literature. This revealed substantial overlap between quantitative trait loci/marker‐trait associations identified for similar traits across studies of different sorghum populations. Chromosomes 2, 3, and 6 contained particularly concentrated regions of markers associated with chilling tolerance traits. Although many studies have uncovered genetic variation for chilling responses in the sorghum germplasm, follow‐up studies are needed to confirm and characterize the molecular mechanisms responsible for variation in chilling tolerance in sorghum. We discuss potential molecular mechanisms for cold stress tolerance based on agreements between studies and address the challenges and opportunities for increasing chilling tolerance in sorghum and other next‐generation crops.

59 BASIC BIOLOGICAL SCIENCES↗

Computational Approach for Rapidly Predicting Temperature–Dependent Polymer Solubilities Using Molecular–Scale Models

One promising approach to recycle multicomponent plastic waste (e. g., multilayer plastic films) is selective dissolution. Selective dissolution is a solvent-mediated process in which differences in polymer solubility in a carefully chosen solvent system are exploited to recover a target polymer. Here, a computational approach was developed that rapidly predicts temperature-dependent polymer solubilities to guide the design of solvent systems for solvent-mediated polymer recycling. Polymer conformations were obtained from molecular dynamics simulations by modeling the polymer as a short oligomer and then used as input to the conductor-like screening model for real solvents (COSMO-RS) for solubility predictions. Using polyethylene (PE) and ethylene vinyl alcohol (EVOH) as representative polymers, the effect of simulation parameters was systematically studied, and predicted solubilities were found to be in good agreement with experimental measurements. Furthermore, the applicability of the approach was demonstrated by identifying selective solvents for PE and EVOH dissolution from a library of 524 solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulation of the impact of particle recycling on the plasma in MPS-LD device based on the BOUT++ LPD module

A linear plasma device (LPD) module has been developed under the BOUT++ framework to simulate plasma transport in the MPS-LD. However, previously, the LPD module used a simplistic neutral particle model that only includes particle density and velocity, which prevents the full understanding of the plasma-neutrals interactions. In this work, we further optimize the neutral model by using a more complete neutral fluid model containing the continuity equation, momentum equation, and energy equation. The reactions such as charge exchange, excitation, and radiation collisions are included. Since the neutral particle source is mainly provided by particle recycling from the target, a particle recycling model is employed, which includes both fast reflection and slow thermal release. The upgraded LPD module is applied to simulate the argon (Ar) discharge experiment of MPS-LD, and the benchmark against experiment measurement and SOLPS-ITER simulation results are presented. Good agreements are obtained, showing the validation of the upgraded module. After that, the impact of particle recycling on Ar plasma is investigated. It is found that a higher recycling coefficient (R) promotes the achievement of high-density plasma at the target. In conclusion, the recycled Ar atoms change target plasma pressure as well as plasma-neutral collisions, which both contribute to plasma momentum loss, thus promoting the rollover of ion flux to the target.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

HL-2A's ELM cycle simulations by integrating BOUT++'s drift MHD and transport code

A new integrating model has been developed to couple tokamak edge multiscale magnetohydrodynamic (MHD) events and transport simulations, such as edge-localized mode (ELM) cycles. As a proof of principle, we first start from a set of three-field two-fluid model equations, which includes the pressure, current, and vorticity. Here, the equations are separated into the slowly evolving part of the axisymmetric component by taking a time average of the axisymmetric component. The time-averaged fluxes, which are quadratic in fluctuating quantities, act as driven terms for the time-averaged axisymmetric quantities that determine the plasma transport, and therefore the large-scale evolution of the plasma profiles. Then the HL-2A's ELM cycles are simulated using the model. Good agreements of ELM size and pedestal recovery time have been achieved for the solutions obtained from the coupled simulation compared with experiment. For one ELM cycle simulation, the coupled code can achieve a speedup of a factor of up to 30 over standalone code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Evidence of Free-Bound Transitions in Warm Dense Matter and Their Impact on Equation-of-State Measurements

Warm dense matter (WDM) is now routinely created and probed in laboratories around the world, providing unprecedented insights into conditions achieved in stellar atmospheres, planetary interiors, and inertial confinement fusion experiments. However, the interpretation of these experiments is often filtered through models with systematic errors that are difficult to quantify. Due to the simultaneous presence of quantum degeneracy and thermal excitation, transitions in which free electrons are de-excited into thermally unoccupied bound states transferring momentum and energy to a scattered x-ray photon become viable. Here we show that such free-bound transitions are a particular feature of WDM and vanish in the limits of cold and hot temperatures. The inclusion of these transitions into the analysis of recent X-ray Thomson Scattering experiments on WDM at the National Ignition Facility and the Linac Coherent Light Source is required to obtain a physically consistent temperature from the Chihara decomposition. This interpretation is corroborated by agreement with a recently developed model-free thermometry technique and presents an important step for precisely characterizing and understanding the complex WDM state of matter.

Boehme, M [HZDR Dresden]↗

Comparative clumped isotope temperature relationships in freshwater carbonates

Lacustrine, riverine and spring carbonates represent archives of terrestrial climates and their geochemistry has been used to study palaeoenvironments. Clumped isotope thermometry is an emerging tool that has been applied to freshwater carbonates. Limited work has been done to evaluate comparative relationships between clumped isotopes and temperature in different types of modern freshwater carbonates. This study assembles an extensive calibration data set with 135 samples of modern freshwater carbonates from 96 sites and constrains the relationship between independent observations of water temperature and the clumped isotopic composition of carbonates (denoted by Δ 47 ), including new measurements, and recalculates published data in accordance with current community-defined standard values. For temperature reconstruction, the study reports a composite freshwater calibration and material-specific calibrations for biogenic carbonates (freshwater gastropods and bivalves), fine-grained carbonate (e.g. micrites), biologically mediated carbonates (microbialites and tufas) and travertines. Material-specific calibration trends show a convergence of slopes that are in agreement with recently published syntheses, but statistically significant differences in intercepts occur between some materials (e.g. some biogenics, fine-grained carbonates). These differences may arise due to unresolved seasonal biases, kinetic isotope effects and/or varying degrees of biological influence. The impact of different calibrations is shown through application to new data for glacial and deglacial age travertines from Austria and published data sets. While material-specific calibrations may yield more accurate results for biogenic and fine-grained carbonate samples, the use of material-specific and the composite freshwater calibrations generally produces values within 1.0–1.5°C of each other, and typically fall within calibration uncertainty given limitations of precision.

54 ENVIRONMENTAL SCIENCES↗

Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China)

1. Morphometrics are fundamental for the analysis of size and shape in fossils, particularly because soft parts or DNA are rarely preserved and hard parts such as shells are commonly the only source of information. Geometric morphometrics, that is, landmark analysis, is well established for the description of shape but it exhibits a couple of shortcomings resulting from subjective choices during landmarking (number and position of landmarks) and from difficulties in resolving shape at the level of micro-sculpture. 2. With the aid of high-resolution 3D scanning technology and analyses of fractal dimensions, we test whether such shortcomings of linear and landmark morphometrics can be overcome. As a model group, we selected a clade of modern viviparid gastropods from Lake Lugu, with shells that show a high degree of sculptural variation. Linear and landmark analyses were applied to the same shells in order to establish the fractal dimensions. 3. The genetic diversity of the gastropod clade was assessed. The genetic results suggest that the gastropod clade represents a single species. The results of all morphometric methods applied are in line with the genetic results, which is that no specific morphotype could be delimited. Apart from this overall agreement, landmark and fractal dimension analyses do not correspond to each other but represent data sets with different information. Generally, the fractal dimension values quantify the roughness of the shell surface, the resolution of the 3D scans determining the level. In our approach, we captured the micro-sculpture but not the first-order sculptural elements, which explains that fractal dimension and landmark data are not in phase. 4. We can show that analyzing fractal dimensions of gastropod shells opens a window to more detailed information that can be considered in evolutionary and ecological contexts. We propose that using low-resolution 3D scans may successfully substitute landmark analyses because it overcomes the subjective landmarking. Analyses of 3D scans with higher resolution than used in this study will provide surface roughness information at the mineralogical level. We suggest that fractal dimension analyses of a combination of differently resolved 3D models will significantly improve the quality of shell morphometrics.

54 ENVIRONMENTAL SCIENCES↗

δ 2 H isotopic offsets in xylem water measurements under cryogenic vacuum distillation: Quantifying and correcting wood‐water hydrogen exchange influences

Stable isotopes δ 18 O and δ 2 H are used to infer vegetation water sources. In some studies, significant xylem water δ 2 H offsets from potential source waters have been observed. The offsets appear to be more prevalent with cryogenic vacuum distillation (CVD) of plant water. Hypothesized mechanisms for these offsets include changes during plant water uptake and transport, and methodological problems. We propose that a large portion of the offsets are due to hydrogen isotope exchange between xylem water and non-crystalline hydroxyl groups of wood cellulose and hemicellulose during CVD. We present a method for estimating the hypothesized isotopic exchange between wood tissues and water, which is the result of Rayleigh and equilibrium fractionation. To estimate the exchange, we use published wood properties for North American tree species and isotope chemical relationships as a function of moisture content, CVD temperature and water extraction efficiency. A simple model of exchange between xylem water and hydroxyl groups captures the range of observations in studies in which CVD and non-CVD methods were compared. To evaluate the model, we compared observed δ 2 H offsets (sw-excess) values from two field datasets (90°C, n = 364, and 170°C, n = 43) to δ 2 H offsets estimated with our chemical model. We found good agreement between observed and estimated δ 2 H offsets for samples extracted at 90°C (r 2 = 0.69) but not for samples extracted at 170°C (r 2 = 0.20). The offset may be eliminated by increasing the extraction temperature to 229°C or by adding a standard sufficient to raise the moisture content to >150%. A correction can also be approximated by applying a theoretical calculation based on the extraction temperature, moisture content and water extraction efficiency.

54 ENVIRONMENTAL SCIENCES↗

Ventenata dubia projected to expand in the western United States despite future novel conditions

Abstract Distributions of both native and invasive species are expected to shift under future climate. Species distribution models (SDMs) are often used to explore future habitats, but sources of uncertainty including novel climate conditions may reduce the reliability of future projections. We explore the potential spread of the invasive annual grass ventenata ( Ventenata dubia ) in the western United States under both current and future climate scenarios using boosted regression tree models and 30 global climate models (GCMs). We quantify novel climate conditions, prediction variability arising from both the SDMs and GCMs, and the agreement among GCMs. Results demonstrate that currently suitable habitat is concentrated inside the invaded range of the northwest, but substantial habitat exists outside the invaded range in the Southern Rockies and southwestern US mountains. Future suitability projections vary greatly among GCMs, but GCMs commonly projected decreased suitability in the invaded range and increased suitability along higher elevations of interior mountainous areas. Climate novelty did not appear to undermine the prediction reliability in many cases where the climate–species relationship was fully represented by the occurrence data. GCM‐derived variability resulting from variation in future cool season precipitation and temperature seasonality was greatest in the Rocky Mountains. SDM‐derived variability was higher in currently suitable habitat, and few GCMs projections agreed that these areas would contain future suitable habitat. However, while prediction variability was high, many GCM projections agreed that parts of the Rocky, Wasatch, and Uinta Mountains would contain highly suitable habitat in the future. As disturbances in the interior mountains occur in coming decades, reducing some natural barriers to invasion, land managers, and conservationists will need to monitor for ventenata in post‐disturbance environments. Changes to invasion potential may not play out for several decades, but results related to current potential may have applications for early detection and rapid response planning.

Environmental Sciences & Ecology↗

Approximation of ice phenology of Maine lakes using Aqua MODIS surface temperature data

Studies of lake ice phenology have historically relied on limited in situ data. Relatively few observations exist for ice out and fewer still for ice in, both of which are necessary to determine the temporal extent of ice cover. Satellite data provide an opportunity to better document patterns of ice phenology across landscapes and relate them to the climatological drivers behind changing ice phenology. We developed a model, the Cumulative Sum Method (CSM), that uses daytime and nighttime surface temperature observations from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor on board the Earth-observing Aqua satellite to approximate ice in (the onset of ice cover) and ice out from training datasets of 13 and 58 Maine lakes, respectively, during the 2002/2003 through 2017/2018 ice seasons. Ice in was signaled by reaching a threshold of cumulative negative degrees following the first day of the season below 0°C. Ice out was signaled by reaching a threshold of cumulative positive degrees following the first day of the year above 0°C. The comparison of observed and remotely sensed ice-in dates showed relative agreement with a correlation coefficient of 0.71 and a mean absolute error (MAE) of 9.8 days. Ice-out approximations had a correlation coefficient of 0.67 and an MAE of 8.8 days. Lakes smaller in surface area and nearer the Atlantic coast had the greatest error in approximation. Application of the CSM to 20 additional lakes in Maine produced a comparable ice-out MAE of 8.9 days. Ice-out model performance was weaker for the warmest years; there was a larger MAE of 12.0 days when the model was applied to the years 2019–2023 for the original 58 lakes. The development of this model, which utilizes daily satellite data, demonstrates the promise of remote sensing for quantifying ice phenology over short, temporal scales, and wider geographic regions than can be observed in situ, and allows exploration of the influence of surface temperature patterns on the process and timing of ice in and ice out.

54 ENVIRONMENTAL SCIENCES↗

Elucidating the Structure of the Eu‐EDTA Complex in Solution at Various Protonation States

Abstract Ethylenediaminetetraacetic acid (EDTA), which has two amine and four carboxylate protonation sites, forms stable complexes with lanthanide ions. This work analyzes the coordination structure, in atomic resolution, of the Eu 3+ ion complexed with EDTA in all its protonation states in aqueous solution. Eu‐EDTA complexes were modeled using classical molecular dynamics (MD) simulations using force field parameters optimized with ab initio molecular dynamics (AIMD) simulations. Structures from the MD simulations were used to predict extended X‐ray absorption fine structure (EXAFS) spectra and compared with EXAFS measurements of the Eu 3+ aqua ion and Eu‐EDTA complexes at pH 3 and 11. This work details how Eu‐EDTA complex coordination structures change with increasing protonation of the EDTA ligand in the complex, from the tightly bound unprotonated complex to the unbinding of the fully protonated EDTA ligand from the Eu 3+ ion as both become solvated by water. Agreement between predicted and measured EXAFS spectra supports the findings from simulation.

Chemistry↗

Integrated, Coordinated, Open, and Networked (ICON) Science to Advance the Geosciences: Introduction and Synthesis of a Special Collection of Commentary Articles

The sciences struggle with poor integration across disciplines, the absence of coordination within and across data generation and modeling activities, scarce or disconnected open data, and weaknesses of networks to engage diverse stakeholders within and beyond the scientific community. The American Geophysical Union (AGU) is divided into 25 sections intended to encompass the breadth of the geosciences. Here, we introduce a special collection of commentary articles spanning 19 AGU sections on the challenges and opportunities associated with the use of ICON science principles. These principles focus on research intentionally designed to be Integrated, Coordinated, Open, and Networked (ICON) with the goal of maximizing mutual benefit (among stakeholders) and cross-system transferability of science outcomes. This article summarizes the ICON principles; discusses the crowdsourced approach to creating the collection; and explores insights from across the articles. There were multiple common themes among the commentary articles, including the broad agreement that the benefits of using ICON principles outweigh the costs, but that using ICON principles has important risks that need to be understood and mitigated. It was also clear that the ICON principles are not monolithic or static, but should instead be considered a heuristic tool that can and should be modified to meet changing needs. As a whole, the collection is intended as a resource for scientists pursuing ICON science and represents an important inflection point in which the geosciences community has come together around ICON principles as a unified approach for improving how science is done across the geosciences and beyond.

58 GEOSCIENCES↗

Evaluation of hydrograph separation techniques with uncertain end-member composition

Hydrograph separation is one of many approaches used to analyse shifts in source water contributions to stream flow resulting from climate change in remote watersheds. Understanding these shifts is vital, as shifts in source water contributions to a stream can shape water management decisions. Because remote watersheds are often inaccessible and have poorly characterized contributing water sources, or end-members, it is critical to understand the implications of using different hydrograph separation techniques in these data-limited environments. To explore the uncertainty associated with different techniques, results from two hydrograph separation techniques, mass balance and principle component analysis, were compared using 3 years of aqueous geochemical data from the East River watershed located in the Elk Mountains of Central Colorado. Solute concentrations of the end-members were characterized by both a limited set of direct chemical measurements of different sources and detailed seasonal instream chemistry to examine the influences of uncertain end-member compositions in a data-limited environment. Annual volumetric end-member contributions to stream flow had relatively good agreement across separation techniques. Large variations in time were observed in the hydrograph separations, depending on the end-member type, and estimated flow contributions varied between the selected solutes. End-member concentrations characterized by stream chemistry showed several limitations including a reduced number of distinguishable end-members and differences in timing of flow contributions. Here the results highlight the benefits of using multiple hydrograph separation techniques by providing a ‘weight-of-evidence’ approach to environments with limited end-member concentration data.

54 ENVIRONMENTAL SCIENCES↗

Modelling the Effects of Wetland Restoration on Coastal Hydrology: A Case Study of Elkhorn Slough Watershed, California

ABSTRACT Coastal wetlands, some of the most productive ecosystems on Earth, provide critical ecosystem services, including support of biodiversity, carbon sequestration and flood protection. In recent decades, these ecosystems have experienced extensive coastal wetland loss. Coastal wetland restoration provides a beacon of hope, offering a chance to reclaim these important habitats. However, even with billions of dollars invested worldwide in restoring coastal wetlands, we still lack comprehensive knowledge about the effectiveness of these restoration efforts in recovering wetland ecosystem functions and how future climate change may affect these efforts. The ability to evaluate how these ecosystems will function in the future is vital for examining current investments and developing future protection and management plans. We selected Elkhorn Slough, a tidal estuary, in California, to investigate the impact of wetland restoration and sea level rise (SLR) on coastal hydrology using the process‐based coastal hydrologic model, Advanced Terrestrial Simulator (ATS), informed by site‐specific data. We designed a novel modelling workflow for incorporating wetland restoration features into land cover and soil properties for the model parameterization. The validation results demonstrate a strong agreement between modelled and observed data. We studied the characteristics of coastal watershed hydrology, then focused on the surface water dynamics at two wetland sites within Elkhorn Slough, a reference site and a restored site. Our simulation results indicate that the restored site successfully maintains surface elevation, resulting in reduced surface inundation. We also examined the impact of wetland restoration under expected SLR over the next few decades. The low‐lying Yampah Marsh, the reference site, is likely to be inundated due to future SLR when highest tides arrive, while a higher percentage of Hester Marsh, the restored site, would retain marsh vegetation in coming decades, regardless of tidal conditions. Our study provides important information for examining the outcome of restoration practices that include surface elevation in tidal wetlands under climate changes.

advanced terrestrial simulator↗

Bond Energies of UO + and UC + : Guided Ion Beam and Quantum Chemical Studies of the Reactions of Uranium Cation with O 2 and CO

Here, guided ion beam tandem mass spectrometry was used to examine the kinetic energy dependent reactions of U + with O 2 and CO. In the reaction of U + with O 2 , the UO + product is formed in a barrierless and exothermic process with a reaction efficiency at low energies of k/k col =1.1±0.2, but increases at higher collision energies. Formation of both UO + and UC + in the reaction of U + with CO is endothermic. 0 K bond dissociation energies (BDEs) of D 0 (U + -O)=7.88±0.09 eV and D 0 (U + -C)=4.03±0.13 eV were determined by analyzing the kinetic energy dependent cross sections in the latter endothermic reactions. These values are within experimental uncertainty of previously reported experimental values. Additionally, the electronic states of UO + and UC + and the potential energy surfaces for the reactions were explored by quantum chemical calculations. The former include a full Feller-Peterson-Dixon composite approach with correlation contributions up to CCSDT(Q) for UO and UO + , yielding D 0 (U-O)=7.82 eV and D 0 (U + -O)=7.99 eV, as well as more approximate CCSD(T) calculations where a semi-empirical model was used to estimate spin-orbit energy contributions, which are generally found to improve the agreement with experiment. Both experimental BDEs are observed to be close to those of their transition metal congeners, ScL + , YL + , and GdL + (L=O and C).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PyCDFT: A Python package for constrained density functional theory

In this paper, we present PyCDFT, a Python package to compute diabatic states using constrained density functional theory (CDFT). PyCDFT provides an object-oriented, customizable implementation of CDFT, and allows for both single-point self-consistent-field calculations and geometry optimizations. PyCDFT is designed to interface with existing density functional theory (DFT) codes to perform CDFT calculations where constraint potentials are added to the Kohn–Sham Hamiltonian. Here, we demonstrate the use of PyCDFT by performing calculations with a massively parallel first-principles molecular dynamics code, Qbox, and we benchmark its accuracy by computing the electronic coupling between diabatic states for a set of organic molecules. We show that PyCDFT yields results in agreement with existing implementations and is a robust and flexible package for performing CDFT calculations. The program is available at https://dx.doi.org/10.5281/zenodo.3821097.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗