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At least 1,045 records · Page 58

Validating a microphysical prognostic stratospheric aerosol implementation in E3SMv2 using observations after the Mount Pinatubo eruption

Abstract. This paper describes the addition of a stratospheric prognostic aerosol (SPA) capability – developed with the goal of accurately simulating sulfate aerosol formation and evolution in the stratosphere – in the Department of Energy (DOE) Energy Exascale Earth System Model, version 2 (E3SMv2). The implementation includes changes to the four-mode Modal Aerosol Module microphysics in the stratosphere to allow for larger particle growth and more accurate stratospheric aerosol lifetime following the Pinatubo eruption. E3SMv2-SPA reasonably reproduces stratospheric aerosol lifetime, burden, aerosol optical depth, and top-of-atmosphere flux when compared to remote sensing observations. E3SMv2-SPA also has close agreement with the interactive chemistry–climate model CESM2-WACCM (Community Earth System Model version 2–Whole Atmosphere Community Climate Model) – which has a more complete chemical treatment – and the observationally constrained, prescribed volcanic aerosol treatment in E3SMv2. Global stratospheric aerosol size distributions identify the nucleation and growth of sulfate aerosol from volcanically injected SO2 from both major and minor volcanic eruptions from 1991 to 1993. The modeled aerosol effective radius is consistently lower than satellite and in situ measurements (max differences of ∼ 30 %). Comparisons with in situ size distribution samples indicate that this simulated underestimation in both E3SMv2-SPA and CESM2-WACCM is due to overly small accumulation and coarse-mode aerosols 6–18 months post-eruption, with E3SMv2-SPA simulating ∼ 50 % of the coarse-mode geometric mean diameters of observations 11 months post-eruption. Effective radii from the models and observations are used to calculate offline scattering and absorption efficiencies to explore the implications of smaller simulated aerosol size for the Pinatubo climate impacts. Scattering efficiencies at wavelengths of peak solar irradiance (∼ 0.5 µm) are 10 %–80 % higher for daily samples in models relative to observations through 1993, suggesting higher diffuse radiation at the surface and a larger cooling effect in the models due to the smaller simulated aerosol; absorption efficiencies at the peak wavelengths of outgoing terrestrial radiation (∼ 10 µm) are 15 %–40 % lower for daily samples in models relative to observations, suggesting an underestimation in stratospheric heating in the models due to the smaller simulated aerosol. These potential biases are based on aerosol size alone and do not take into account differences in the aerosol number. The overall agreement of E3SMv2-SPA with observations and its similar performance to the well-validated CESM2-WACCM makes E3SMv2-SPA a viable alternative to simulating climate impacts from stratospheric sulfate aerosols.

Brown, Hunter York (ORCID:0000000218147874)↗

Search for dark matter in association with an energetic photon in pp collisions at $ \sqrt{s} $ = 13 TeV with the ATLAS detector

A search for dark matter is conducted in final states containing a photon and missing transverse momentum in proton-proton collisions at s√ = 13 TeV. The data, collected during 2015–2018 by the ATLAS experiment at the CERN LHC, correspond to an integrated luminosity of 139 fb -1 . No deviations from the predictions of the Standard Model are observed and 95% confidence-level upper limits between 2.45 fb and 0.5 fb are set on the visible cross section for contributions from physics beyond the Standard Model, in different ranges of the missing transverse momentum. The results are interpreted as 95% confidence-level limits in models where weakly interacting dark-matter candidates are pair-produced via an s-channel axial-vector or vector mediator. Dark-matter candidates with masses up to 415 (580) GeV are excluded for axial-vector (vector) mediators, while the maximum excluded mass of the mediator is 1460 (1470) GeV. In addition, the results are expressed in terms of 95% confidence-level limits on the parameters of a model with an axion-like particle produced in association with a photon, and are used to constrain the coupling g a Z γ of an axion-like particle to the electroweak gauge bosons.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

AlphaFold has recently become an important tool in providing models for experimental structure determination by X-ray crystallography and cryo-EM. Large parts of the predicted models typically approach the accuracy of experimentally determined structures, although there are frequently local errors and errors in the relative orientations of domains. Importantly, residues in the model of a protein predicted by AlphaFold are tagged with a predicted local distance difference test score, informing users about which regions of the structure are predicted with less confidence. AlphaFold also produces a predicted aligned error matrix indicating its confidence in the relative positions of each pair of residues in the predicted model. The phenix.process_predicted_model tool downweights or removes low-confidence residues and can break a model into confidently predicted domains in preparation for molecular replacement or cryo-EM docking. These confidence metrics are further used in ISOLDE to weight torsion and atom–atom distance restraints, allowing the complete AlphaFold model to be interactively rearranged to match the docked fragments and reducing the need for the rebuilding of connecting regions.

59 BASIC BIOLOGICAL SCIENCES↗

Estimating Energy Market Schedules Using Historical Price Data: Preprint

The global climate crisis is expected to reshape the energy generation landscape in the coming decades. Increasing integration of non-dispatchable renewable energy resources into energy infrastructures and markets increases uncertainty and creates new opportunities for flexible energy systems. To conduct proper economic evaluation of flexible energy systems, such as integrated energy systems (IES), advancements in modelling of market interactions, such as bidding, is crucial. This work presents a shortcut algorithm which uses two mixed integer linear programs to compute dispatch schedules (e.g., hourly power production targets) that are constrained by the resource's bid information and characteristics (e.g., minimum up and down times) based on historical locational marginal price (LMP) data. This is orders of magnitude less data than required for a market clearing calculation with a full production cost model (PCM). We find the shortcut simulator recapitulates generator dispatch signals for the Prescient PCM with approximately 4% error for the RTS-GMLC test system.

electricity generation↗

Estimating Energy Market Schedules using Historical Price Data

The global climate crisis is expected to reshape the energy generation landscape in the coming decades. Increasing integration of non-dispatchable renewable energy resources into energy infrastructures and markets creates uncertainty as well as new opportunities for flexible energy systems. To conduct proper economic evaluation of flexible energy systems, such as integrated energy systems (IES), advancements in modelling of market interactions, such as bidding, is crucial. This work presents a shortcut algorithm which uses two mixed integer linear programs to compute dispatch schedules (e.g., hourly power production targets) that are constrained by the resource's bid information and characteristics (e.g., minimum up and down times) based on historical locational marginal price (LMP) data. The proposed algorithm is approximately 100 times faster and uses orders of magnitude less data than a full production cost model (PCM). We find the shortcut simulator recapitulates generator dispatch signals for the Prescient PCM with approximately 4% error for the RTS-GMLC test system.

electricity generation↗

The total neutron cross section of liquid and solid ammonia

Ammonia is a material of interest for future neutron moderators at high-power sources due to its high hydrogen density, low melting point, and resistance to polymerization in an intense radiation field. Its performance in such applications cannot currently be calculated due to the absence of suitable computer models for the interaction of neutrons with ammonia under relevant conditions. In an effort to develop suitable scattering kernels for computer simulations of moderator performance, we have conducted a series of Density Functional Theory and Molecular Dynamics calculations of the molecular-level thermal properties of ammonia at various temperatures within both the solid and liquid phases. In this paper, we compare computer calculations for the energy-dependent total neutron cross section of ammonia, based on these models, to experimental measurements of those cross sections at temperatures of 221 K, 180 K, and 35 K. The experimental data were collected over an energy range from 0.1 meV to 10 eV using time-of-flight techniques at the Low Energy Neutron Source (LENS) facility at Indiana University. This comparison provides a first validation in the development of thermal scattering libraries for Monte Carlo source design simulations based on liquid and solid ammonia. In conclusion, we also provide some insights into where additional development of tools for creating such models may be needed.

Ammonia↗

A new bioenergy model that simulates the impacts of plant‐microbial interactions, soil carbon protection, and mechanistic tillage on soil carbon cycling

Abstract Advancing our predictive understanding of bioenergy systems is critical to design decision tools that can inform which feedstock to plant, where to plant it, and how to manage its production to provide both energy and ecosystem carbon (C) benefits. Here, we lay the foundation for that advancement by integrating recent developments in the science of belowground processes in shaping the C cycle into a new bioenergy model, FUN‐BioCROP (Fixation and Uptake of Nitrogen‐Bioenergy Carbon, Rhizosphere, Organisms, and Protection). We show that FUN‐BioCROP can approximate the historical trajectory of soil C dynamics as natural ecosystems were successively converted into intensive agriculture and bioenergy systems. This ability relies in part on a novel tillage representation that mechanistically models tillage as a process that increases microbial access to C. Importantly, the impacts of tillage and feedstock choice also influence FUN‐BioCROP simulations of warming responses with no‐till perennial feedstocks, miscanthus, and switchgrass, having more C that is unprotected and susceptible to warming than tilled annual feedstocks like corn–corn–soybean. However, this susceptibility to warming is balanced by a greater potential for increases in belowground C allocation to enhance soil C stocks in perennial systems. Collectively, our model results highlight the importance of belowground processes in evaluating the ecosystem C benefits of bioenergy production.

09 BIOMASS FUELS↗

Electric Field Analysis in a Cold-Ion Source Using Stark Spectroscopy of Rydberg Atoms

Here, we analyze electric fields in ion sources generated by quasicontinuous photoionization of cold Rb atoms trapped in the focal spot of a near-concentric, in-vacuum cavity for 1064-nm laser light. Ion streams are extracted with an external electric field, F. Stark effects of Rb 57F and of nearby high-angular-momentum Rydberg levels, which exhibit large, linear Stark shifts, are employed to study the net electric-field probability distribution within the ion-source region over an extraction-field range of 0 < F < 0.35 V/cm. For F = 0, we also investigate ion-field-induced Stark spectra of the 60P 1/2 state, which exhibits a (lesser) quadratic electric-field response that affords a simplified electric-field analysis. Experimental Rydberg spectra are compared with theoretical Stark spectra, which are weighted with net electric-field distributions obtained from classical ion-trajectory simulations that include Coulomb interactions. Experiments and models are in good agreement. At small F and high ion-source rates, the field approximately follows a Holtsmark distribution, and the ion streams are degraded by the Coulomb microfields. With increasing F and at lower ion-source rates, the fields become narrowly distributed around F, resulting in directional ion streams that are less degraded by microfields. Our results are of interest for monitoring cold-ion sources for focused-ion-beam applications, where Coulomb interactions are of concern, and for studies of electric fields in cold plasmas.

74 ATOMIC AND MOLECULAR PHYSICS↗

A novel ignition model for low velocity impact of heterogeneous explosives based on interacting hot spots

While numerous studies have focused on the ignition of explosives occurring in high velocity impact and the associated shock-to-detonation transition, there has been growing interest in developing computational models focused on low-velocity impact regimes. A predictive low-velocity impact ignition model will be important for analyzing high explosive safety and potential accident scenarios. This work introduces a novel ignition model based on the concept of thermally interacting hot spots to simulate low velocity impacted heterogeneous explosives where observed ignition times are on the order of milliseconds. The model asserts that relevant hot spots are micron-sized, the typical separation between neighboring hot spots is on the order of a hundred microns, and that neighbors interact thermally through heat conduction across the interstitial region between them. To achieve tractable numerical solutions, hot spots are assumed to form a periodic array as opposed to the highly irregular positioning in an actual explosive. This idealization allows a single two hotspot system to characterize the ignition process. Consequently, the model is referred to as the two hot spot Frank-Kamenetskii ignition model. In the present study, hot spots are modeled as constant heat sources terms, but this can be extended to include grain-scale phenomena like frictional heating of micron-sized growing cracks that are confined under high pressure. Because the micron-sized features are below the scale that can be efficiently resolved at a systems level, an efficient subscale scheme based on the Method of Weighted Residuals (MWR) is used to efficiently solve the equations. In conclusion, we carry out numerical examples and analytic predictions illustrating the accuracy and the functioning of the model.

97 MATHEMATICS AND COMPUTING↗

Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference

Experimental Zika virus infection in non-human primates results in acute viral load dynamics that can be well-described by mathematical models. The inoculum dose that would be received in a natural infection setting is likely lower than the experimental infections and how this difference affects the viral dynamics and immune response is unclear. Here we study a dataset of experimental infection of non-human primates with a range of doses of Zika virus. We develop new models of infection incorporating both an innate immune response and viral interference with that response. We find that such a model explains the data better than models with no interaction between virus and the immune response. We also find that larger inoculum doses lead to faster dynamics of infection, but approximately the same total amount of viral production.

59 BASIC BIOLOGICAL SCIENCES↗

The TAMUTRAP facility: A Penning trap facility at Texas A&M University for weak interaction studies

The Texas A&M University Penning Trap (TAMUTRAP) facility aims to test the standard model of the electroweak interaction by measuring the β-ν correlation parameter, a βν , for β-delayed proton emitters in the atomic mass range 20 < A < 40. Precision measurements of this correlation parameter and, inextricably, the Fierz interference parameter, are a sensitive probe of physics beyond the standard model. Here, using off-line ion sources, the TAMUTRAP facility has been commissioned by demonstrating the ability to manipulate the trapped-ion motions as well as to perform precision mass measurements. Our novel cylindrical Penning trap – the world's largest – differs from typical designs in two key aspects: the electrode structure has an 180-mm inner diameter and an overall length of 334.89 mm leading to a uniquely small length/radius ratio l/r = 3.72; and we do not use the long end cap approximation, instead our short endcap electrodes are closed and capable of being placed at an arbitrary potential. This geometry is optimized for observing β-delayed proton decays, but is also well suited for other in-trap and post-trap precision decay experiments. In addition to presenting an overview of the TAMUTRAP facility, we demonstrate that our unique Penning trap is able to measure masses with a precision similar to typical trap designs.

47 OTHER INSTRUMENTATION↗

Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring the nexus of many-body theories through neural network techniques: the tangent model

Abstract In this paper, we present a physically informed neural network (NN) representation of the effective interactions associated with coupled-cluster downfolding models to describe chemical systems and processes. The NN representation not only allows us to evaluate the effective interactions efficiently for various geometrical configurations of chemical systems corresponding to various levels of complexity of the underlying wave functions, but also reveals that the bare and effective interactions are related by a tangent function of some latent variables. We refer to this characterization of the effective interaction as a tangent model. We discuss the connection between this tangent model for the effective interaction with the previously developed theoretical analysis that examines the difference between the bare and effective Hamiltonians in the corresponding active spaces.

97 MATHEMATICS AND COMPUTING↗

Measurement of exclusive 𝜋 + -argon interactions using ProtoDUNE-SP

We present the measurement of 𝜋 + -argon inelastic cross sections using the ProtoDUNE single-phase liquid argon time projection chamber in the incident 𝜋 + kinetic energy range of 500–800 MeV in multiple exclusive channels (absorption, charge exchange, and the remaining inelastic interactions). The results of this analysis are important inputs to simulations of liquid argon neutrino experiments such as the Deep Underground Neutrino Experiment and the Short Baseline Neutrino program at Fermi National Accelerator Laboratory. They will be employed to improve the modeling of final state interactions within neutrino event generators used by these experiments, as well as the modeling of 𝜋 + -argon secondary interactions within the liquid argon. This is the first measurement of 𝜋 + -argon absorption at this kinetic energy range as well as the first ever measurement of 𝜋 + -argon charge exchange.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Many‐body response of benzene at monolayer MoS 2 : Van der Waals interactions and spectral broadening

Abstract Models of surface enhancement of molecular electronic response properties are challenging for two reasons: (a) molecule‐surface interactions require a simultaneous solution of the molecular and the surface dynamic response (a daunting task), and (b) when solving for the electronic structure of the combined molecule + surface system, it is not trivial to single out the particular physical effects responsible for enhancement. To tackle this problem, in this work, we apply a formally exact decomposition of the system's response function into subsystem contributions by using subsystem density functional theory (DFT), which grants access to dynamic polarizabilities and optical spectra. In order to access information about the interactions between the subsystems, we extend a previously developed subsystem‐based adiabatic connection fluctuation‐dissipation theorem of DFT to separate the additive from the nonadditive correlation energy and identify the nonadditive correlation as the van der Waals interactions. As an example, we choose benzene adsorbed on monolayer MoS 2 . We isolate the contributions to benzene's dynamic response arising from the interaction with the surface, and for the first time, we evaluate the enhancements to the effectiveness of C 6 coefficients as a function of benzene‐MoS 2 distance and adsorption site. We also quantify the spectral broadening of the benzene's electronic excited states due to their interaction with the surface. We find that the broadening has a similar decay law with the molecule‐surface distance as the leading van der Waals interactions (ie, R −6 ) and that the surface enhancement of dispersion interactions between benzene molecules is less than 5% but is still large enough (0.5 kcal/mol) to likely play a role in the prediction of interface morphologies.

Umerbekova, Alina↗

Throughfall-Reduction Drying Effects on Soil Respiration, Moisture, and Temperature in Four Distinct Lowland Panamanian Forests from 2015-2022

Objectives: Climatic drying is predicted for many tropical forests, yet effects on soil properties across moisture and soil gradients within tropical forests remain poorly characterized, hampering predictions of forest-climate feedbacks. We hypothesized that throughfall reduction (i.e. chronic drying) would suppress soil CO2 fluxes (i.e., respiration) in already-drier tropical forests by further reductions in soil moisture, but increases CO2 fluxes in wetter tropical forests by alleviating anaerobiosis and soil saturation. We conducted a field study in four distinct lowland Panamanian forests that vary in background rainfall and soil fertility. In each forest we constructed throughfall reduction structures that reduce moisture inputs to plots by ~50% (see methods). In drying and paired control plots we measured soil CO2 fluxes, soil moisture (volume/volume), soil temperature (°C), air temperature (°C), and forest floor biomass during wet-dry cycles (2015 – 2022). We also collected litterfall biomass and surveyed all tree species for diameter at breast height (dbh), and identified tree species in 2018 and 2019.Results:We found that soil moisture peaked in the wet season and declined in the dry season. Measured soil CO2 fluxes declined in the dry season and peaked in the early wet season ahead of peak soil moisture, resulting in a lower soil moisture optimum for respiration than previously modeled. Chronic throughfall exclusion also suppressed soil moisture across the four forests, and also initially suppressed soil CO2 fluxes across forests. There was sustained suppression of soil CO2 fluxes after four years in the wettest forest only (-28 ± 4% during the dry season), but elevated soil CO2 fluxes in a fertile forest after four years (+75 ± 28% during the late wet season). The unexpected negative drying effect in the wettest, most infertile forest could have resulted from reduced vertical flushing of nutrients into soils, as the drying effect increased with time. Including hydro-nutrient interactions in ecosystem models could improve predictions of tropical forest-climate feedbacks. Datasets included: Datasets included here include .csv and .xls files for soil respiration (carbon dioxide flux) collected using the LiCor (see methods), air temperature °C , soil moisture (vl/vl), and soil temperature °C. Soil moisture and soil temperature were collected at 0-10cm depths using hand-held probes (see methods). Data are on ~3 week timescales from 2015-2022 with some gaps. There is also a .kml file that includes coordinates for all 32 plots included in the study of four forests (n = 4 throughfall reduction and n = 4 control plots per site). No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗

Throughfall-Reduction Drying Effects on Soil Moisture and Soil Temperature at 30-Minute Intervals Four Lowland Panamanian Forests

Objectives: Climatic drying is predicted for many tropical forests, yet effects on soil properties across moisture and soil gradients within tropical forests remain poorly characterized, hampering predictions of forest-climate feedbacks. We hypothesized that drying would suppress soil CO2 fluxes (i.e., respiration) in already-drier tropical forests by further reductions in soil moisture, but increases CO2 fluxes in wetter tropical forests by alleviating anaerobiosis and soil saturation. We measured soil CO2 fluxes, soil moisture, soil temperature, and forest floor biomass during wet-dry cycles (2015 – 2022) in four Panamanian forests that vary in rainfall and soil fertility. We also surveyed all tree species and identified to species in 2018 and 2019.Results: We found that soil moisture peaked in the wet season and declined in the dry season. Measured soil CO2 fluxes declined in the dry season and peaked in the early wet season ahead of peak soil moisture, resulting in a lower soil moisture optimum for respiration than previously modeled. Chronic throughfall exclusion also suppressed soil moisture across the four forests, and also initially suppressed soil CO2 fluxes across forests. There was sustained suppression of soil CO2 fluxes after four years in the wettest forest only (-28 ± 4% during the dry season), but elevated soil CO2 fluxes in a fertile forest after four years (+75 ± 28% during the late wet season). The unexpected negative drying effect in the wettest, most infertile forest could have resulted from reduced vertical flushing of nutrients into soils, as the drying effect increased with time. Including hydro-nutrient interactions in ecosystem models could improve predictions of tropical forest-climate feedbacks (Cusack et al. 2023). Datasets included: Datasets here include .csv and .xls files for volumetric soil moisture (volume/volume) and soil temperature (°C). Data were taken at 30-minute intervals at 5cm and 20cm depths using permanent probes and data loggers (see methods). Data presented are from 2018-2019. There is also a .kml file that includes coordinates for all 32 plots included in the study of four forests (n = 4 throughfall reduction and n = 4 control plots per site). No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗

Tropical Tree Species Identity and Diameter at Breast Height in a Throughfall-Reduction Drying Experiment in Four Lowland Panamanian Forests

Objectives: Climatic drying is predicted for many tropical forests, yet effects on soil properties across moisture and soil gradients within tropical forests remain poorly characterized, hampering predictions of forest-climate feedbacks. We hypothesized that drying would suppress soil CO2 fluxes (i.e., respiration) in already-drier tropical forests by further reductions in soil moisture, but increases CO2 fluxes in wetter tropical forests by alleviating anaerobiosis and soil saturation. We measured soil CO2 fluxes, soil moisture, soil temperature, and forest floor biomass during wet-dry cycles (2015 – 2022) in four Panamanian forests that vary in rainfall and soil fertility. We also surveyed all tree species and identified to species in 2018 and 2019.Results: We found that soil moisture peaked in the wet season and declined in the dry season. Measured soil CO2 fluxes declined in the dry season and peaked in the early wet season ahead of peak soil moisture, resulting in a lower soil moisture optimum for respiration than previously modeled. Chronic throughfall exclusion also suppressed soil moisture across the four forests to 20cm depths, and also initially suppressed soil CO2 fluxes across forests. There was sustained suppression of soil CO2 fluxes after four years in the wettest forest only (-28 ± 4% during the dry season), but elevated soil CO2 fluxes in a fertile forest after four years (+75 ± 28% during the late wet season). The unexpected negative drying effect in the wettest, most infertile forest could have resulted from reduced vertical flushing of nutrients into soils, as the drying effect increased with time. Including hydro-nutrient interactions in ecosystem models could improve predictions of tropical forest-climate feedbacks (results presented in Cusack et al. 2023). Datasets included: Datasets included here include .csv and .xls files for tree species identity and diameter at breast height (dbh) in the study plots. There is also a .kml file that includes coordinates for all 32 plots included in the study of four forests (n = 4 throughfall reduction and n = 4 control plots per site). No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗