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At least 1,207 records · Page 67

Data Imbalance, Uncertainty Quantification, and Transfer Learning in Data‐Driven Parameterizations: Lessons From the Emulation of Gravity Wave Momentum Transport in WACCM

Abstract Neural networks (NNs) are increasingly used for data‐driven subgrid‐scale parameterizations in weather and climate models. While NNs are powerful tools for learning complex non‐linear relationships from data, there are several challenges in using them for parameterizations. Three of these challenges are (a) data imbalance related to learning rare, often large‐amplitude, samples; (b) uncertainty quantification (UQ) of the predictions to provide an accuracy indicator; and (c) generalization to other climates, for example, those with different radiative forcings. Here, we examine the performance of methods for addressing these challenges using NN‐based emulators of the Whole Atmosphere Community Climate Model (WACCM) physics‐based gravity wave (GW) parameterizations as a test case. WACCM has complex, state‐of‐the‐art parameterizations for orography‐, convection‐, and front‐driven GWs. Convection‐ and orography‐driven GWs have significant data imbalance due to the absence of convection or orography in most grid points. We address data imbalance using resampling and/or weighted loss functions, enabling the successful emulation of parameterizations for all three sources. We demonstrate that three UQ methods (Bayesian NNs, variational auto‐encoders, and dropouts) provide ensemble spreads that correspond to accuracy during testing, offering criteria for identifying when an NN gives inaccurate predictions. Finally, we show that the accuracy of these NNs decreases for a warmer climate (4 × CO 2 ). However, their performance is significantly improved by applying transfer learning, for example, re‐training only one layer using ∼1% new data from the warmer climate. The findings of this study offer insights for developing reliable and generalizable data‐driven parameterizations for various processes, including (but not limited to) GWs.

54 ENVIRONMENTAL SCIENCES↗

Teaching a neural network to attach and detach electrons from molecules

Abstract Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2–3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions.

36 MATERIALS SCIENCE↗

Deep learning of dynamically responsive chemical Hamiltonians with semiempirical quantum mechanics

Conventional machine-learning (ML) models in computational chemistry learn to directly predict molecular properties using quantum chemistry only for reference data. While these heuristic ML methods show quantum-level accuracy with speeds several orders of magnitude faster than traditional quantum chemistry methods, they suffer from poor extensibility and transferability; i.e., their accuracy degrades on large or new chemical systems. Incorporating quantum chemistry frameworks into the ML models directly solves this problem. Here we take the structure of semiempirical quantum mechanics (SEQM) methods to construct dynamically responsive Hamiltonians. SEQM methods use empirical parameters fitted to experimental properties to construct reduced-order Hamiltonians, facilitating much faster calculations than ab initio methods but with compromised accuracy. By replacing these static parameters with machine-learned dynamic values inferred from the local environment, we greatly improve the accuracy of the SEQM methods. Trained on molecular energies and atomic forces, these dynamically generated Hamiltonian parameters show a strong correlation with atomic hybridization and bonding. Trained with only about 60,000 small organic molecular conformers, the resulting model retains interpretability, extensibility, and transferability when testing on much larger chemical systems and predicting various molecular properties. Overall, this work demonstrates the virtues of incorporating physics-based descriptions with ML to develop models that are simultaneously accurate, transferable, and interpretable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Competition response of cloud supersaturation explains diminished Twomey effect for smoky aerosol in the tropical Atlantic

The Twomey effect brightens clouds by increasing aerosol concentrations, which activates more droplets and decreases cloud supersaturation in response to more competition for water vapor. To quantify this competition response, we used marine low cloud observations in clean and smoky conditions at Ascension Island in the tropical South Atlantic during the Layered Aerosol Smoke Interactions with Cloud (LASIC) campaign. These observations show similar increases in droplet number for increased accumulation-mode particles from surface-based and satellite cloud retrievals, demonstrating the importance of below-cloud aerosol measurements for retrieving aerosol–cloud interactions (ACI) in clean and smoky aerosol conditions. Four methods for estimating cloud supersaturation from aerosol–cloud measurements were compared, with cloud scene-based and parcel-based methods showing sufficient variability for a strong dependence on both aerosol accumulation number concentration and cloud-base updraft velocities. Decomposing aerosol-related changes in cloud albedo and optical depth shows the calculated competition response accounts for dampening the activation response by 12 to 35%, explaining the diminished Twomey effect at high aerosol concentrations observed for smoky conditions at LASIC and previously around the world. This result was consistent for independent supersaturation retrievals by cloud scene-based droplet number and cloud condensation nuclei and parcel-based multimode size-resolving Lagrangian methods. Translating aerosol effects to local radiative forcing with clean conditions as a proxy for preindustrial and smoky conditions for present-day showed that the competition response reduces cooling from the Twomey radiative forcing by 12 to 35%, providing an essential process-specific constraint for improving the representation of aerosol competition in climate model simulation of indirect aerosol forcing.

54 ENVIRONMENTAL SCIENCES↗

Quantum friction in arbitrarily directed motion

In quantum friction, the electromagnetic fluctuation-induced frictional force decelerating an atom which moves past a macroscopic dielectric body, has so far eluded experimental evidence despite more than three decades of theoretical studies. Inspired by the recent finding that dynamical corrections to such an atom's internal dynamics are enhanced by one order of magnitude for vertical motion—compared with the paradigmatic setup of parallel motion—here we generalize quantum friction calculations to arbitrary angles between the atom's direction of motion and the surface in front of which it moves. Motivated by the disagreement between quantum friction calculations based on Markovian quantum master equations and time-dependent perturbation theory, we carry out our derivations of the quantum frictional force for arbitrary angles by employing both methods and compare them.

74 ATOMIC AND MOLECULAR PHYSICS↗

Hybrid Kohn-Sham+Thomas-Fermi scheme for high-temperature density functional theory

We report density functional theory has revolutionised our understanding of dense, strongly coupled systems in the condensed-matter limit. At elevated temperatures, such as those found in warm dense matter and dense plasma, the computational cost of calculating enough states to accurately describe a thermal ensemble of electrons is a major obstacle to practical Kohn-Sham calculations. This problem has recently been tackled from a number of approaches, including a plane-wave approximation for electrons at high energy. In this work, we demonstrate how the Thomas-Fermi density of states, equivalent to a local plane-wave approximation, can yield improved results for thermodynamic quantities, electron density profiles, and interatomic forces while requiring fewer states than existing methods.

36 MATERIALS SCIENCE↗

Maximally local two-nucleon interactions at N 3 LO in Δ -less chiral effective field theory

We present new maximally local two-nucleon interactions derived in Δ -less chiral effective field theory up to next-to-next-to-next-to-leading order ( N 3 LO ), which include all contact and pion-exchange contributions to the nuclear Hamiltonian up to this order. Our interactions are fit to nucleon-nucleon phase shifts using a Bayesian statistical approach, and explore a wide cutoff range from 0.6 – 0.9 fm ( ≈ 660 – 440 MeV ). These interactions can be straightforwardly employed in quantum Monte Carlo methods, such as the auxiliary field diffusion Monte Carlo method. Together with local three-nucleon forces, calculations with these new interactions will provide improved benchmarks for the structure of atomic nuclei and serve as crucial input to analyses of astrophysical phenomena of neutron stars, such as binary neutron-star mergers. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Trends of Neutron Skins and Radii of Mirror Nuclei from First Principles

The neutron skin of atomic nuclei impacts the structure of neutron-rich nuclei, the equation of state of nucleonic matter, and the size of neutron stars. Here we predict the neutron skin of selected light- and medium-mass nuclei using coupled-cluster theory and the auxiliary field diffusion Monte Carlo method with two- and three-nucleon forces from chiral effective field theory. We find a linear correlation between the neutron skin and the isospin asymmetry in agreement with the liquid-drop model and compare with data. We also extract the linear relationship that describes the difference between neutron and proton radii of mirror nuclei and quantify the effect of charge symmetry breaking terms in the nuclear Hamiltonian. In conclusion, our results for the mirror-difference charge radii and binding energies per nucleon agree with existing data.

79 ASTRONOMY AND ASTROPHYSICS↗

A Novel Framework for Parametric Analysis of Coastal Transition Zone Modeling

Abstract Vulnerability of coastal regions to extreme events motivates an operational coupled inland‐coastal modeling strategy focusing on the coastal transition zone (CTZ), an area between the coast and upland river. To tackle this challenge, we propose a top‐down framework for investigating the contribution of different processes to the hydrodynamics of CTZs with various geometrical shapes, different physical properties, and under several forcing conditions. We further propose a novel method, called tidal vanishing point (TVP), for delineating the extent of CTZs through the upland. We demonstrate the applicability of our framework over the United States East and Gulf coasts. We categorize CTZs in the region into three classes, namely, without estuary (direct river–coast connection), triangular‐, and trapezoidal‐shaped estuary. The results show that although semidiurnal tidal constituents are dominant in most cases, diurnal tidal constituents become more prevalent in the river segment as the discharge increases. Also, decreasing the bed roughness value promotes more significant changes in the results than increasing it by the same value. Additionally, the estuary promotes tidal energy attenuation and consequently decreases the reach of tidal signals through the upland. The proposed framework is generic and extensible to any coastal region.

Chegini, Taher↗

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis

Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses of Burkholderia thailandensis populations enriched for persisters via three methods: flow sorting for low proton motive force, meropenem treatment, and culture aging. Although the three persister-enriched populations generally displayed divergent gene expression profiles that reflect the multimechanistic nature of stress adaptations, there were several common gene pathways activated in two or all three populations. These include polyketide and nonribosomal peptide synthesis, Clp proteases, mobile elements, enzymes involved in lipid metabolism, and ATP binding cassette (ABC) transporter systems. In particular, identification of genes that encode polyketide synthases (PKSs) and fatty acid catabolism factors indicates that generation of secondary metabolites, natural products, and complex lipids could be part of the metabolic program that governs the persistence state. We also found that loss-of-function mutations in the PKS-encoding gene locus BTH_I2366, which plays a role in biosynthesis of histone deacetylase (HDAC) inhibitors, resulted in increased sensitivity to antibiotics targeting DNA replication. Furthermore, treatment of multiple bacterial pathogens with a fatty acid synthesis inhibitor, CP-640186, potentiated the efficacy of meropenem against the persister populations. Altogether, our results suggest that bacterial persisters may exhibit an outwardly dormant physiology but maintain active metabolic processes that are required to maintain persistence.

59 BASIC BIOLOGICAL SCIENCES↗

Specific Features of the Domain Structure of BaTiO{sub 3} Crystals during Thermal Heating and Cooling

This paper presents the results of the study of the domain structure of barium titanate crystals in a wide temperature range including the Curie point (T{sub C}) using the polarization-optical method in the reflected light and the force microscopy of the piezoelectric response. It is shown that a new a–c domain structure forms during cyclic heating of the crystal above T{sub C} and subsequent cooling to the ferroelectric phase. The role of uncompensated charges appeared on the crystal surface during the phase transition and their influence on the formation of the domain structure during cooling are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Biologically Active Hybrid Nanosystems Based on Zero-Valent Selenium Nanoparticles, Biocompatible Polymers, and Polyelectrolitic Complex

The molecular-conformal, morphological, and kinetic characteristics of selenium-containing nanosystems (NSs) based of biocompatible polymer matrices of different origins modified Se{sup 0} nanoparticles for the Se{sup 0} : polymer mass ratio ν = 0.1 have been analyzed using static and dynamic light scattering methods, UV spectroscopy, flow birefringence, and atomic force and transmission electron microscopies. We have determined the rate constants for the formation of selenium-containing NSs, the size characteristics of the corresponding nanostructures, as well as their shape, molecular mass, and density. It is found that isolated dense spherical polymolecular selenium-containing nanostructures are formed in the aqueous solution. Our results can be used as the physicochemical foundation for the modification of polymer materials with clearly manifested physiological activity by biogenic elements in the zero-valent form.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Sources of Uncertainty in Modeled Land Carbon Storage within and across Three MIPs: Diagnosis with Three New Techniques

Terrestrial carbon cycle models have incorporated increasingly more processes as a means to achieve more-realistic representations of ecosystem carbon cycling. Despite this, there are large across-model variations in the simulation and projection of carbon cycling. Several model intercomparison projects (MIPs), for example, the fifth phase of the Coupled Model Intercomparison Project (CMIP5) (historical simulations), Trends in Net Land–Atmosphere Carbon Exchange (TRENDY), and Multiscale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP), have sought to understand intermodel differences. Here in this study, the authors developed a suite of new techniques to conduct post-MIP analysis to gain insights into uncertainty sources across 25 models in the three MIPs. First, terrestrial carbon storage dynamics were characterized by a three-dimensional (3D) model output space with coordinates of carbon residence time, net primary productivity (NPP), and carbon storage potential. The latter represents the potential of an ecosystem to lose or gain carbon. This space can be used to measure how and why model output differs. Models with a nitrogen cycle generally exhibit lower annual NPP in comparison with other models, and mostly negative carbon storage potential. Second, a transient traceability framework was used to decompose any given carbon cycle model into traceable components and identify the sources of model differences. The carbon residence time (or NPP) was traced to baseline carbon residence time (or baseline NPP related to the maximum carbon input), environmental scalars, and climate forcing. Third, by applying a variance decomposition method, the authors show that the intermodel differences in carbon storage can be mainly attributed to the baseline carbon residence time and baseline NPP (>90% in the three MIPs). The three techniques developed in this study offer a novel approach to gain more insight from existing MIPs and can point out directions for future MIPs. Finally, since this study is conducted at the global scale for an overview on intermodel differences, future studies should focus more on regional analysis to identify the sources of uncertainties and improve models at the specified mechanism level.

54 ENVIRONMENTAL SCIENCES↗

Investigation of Gravity-Driven Infiltration Instabilities in Smooth and Rough Fractures Using a Pairwise-Force Smoothed Particle Hydrodynamics Model

In this work, we use a three-dimensional multiphase pairwise-force smoothed particle hydrodynamics (PF-SPH) method to simulate infiltration dynamics in smooth and rough fractures. We investigate the influence of roughness and injection rate on the fluid flow profile and flow velocity. Three types of fractures are considered with different degrees of roughness, including a smooth fracture. Both the rough and smooth fractures exhibit flow instability, fingering, and intermittent flow regimes for low infiltration rates. A stable fluid profile only is achieved for high fluxes when fractures are fully saturated. In all considered fractures, the mean flow velocity exponentially increases with increasing infiltration rate. To characterize the flow instability, we calculate standard deviations of the velocity in different sections of the fracture relative to the mean flow velocity. For the considered infiltration rates, we find that roughness decreases the flow velocity and increases the velocity standard deviations. Hence, we observe that the likelihood of discontinuities in flow regimes increases with the degree of roughness.

58 GEOSCIENCES↗

Strain Distributions and Structural Changes in Motor Driven Gels (Final Report)

The goal of this project was to study the effects of DNA-based, force-generating motor proteins on the structure and dynamics of a DNA hydrogel. Motor proteins are nanoscale transducers, converting chemical energy embedded in the solution into local mechanical work on hydrogel strands, and thus potentially driving structural changes and/or non-equilibrium dynamics within the gel material. To explore this, we used self-assembly to create condensed DNA phases, and activated the phases with proteins. The specific aim was to study the deformations (strain fields) generated within a DNA gel by motor forces. We succeeded in this aim, developing methods to experimentally create gel/motor systems, and measure strain with high spatio-temporal resolution. A key finding was that simple continuum strain-field models fail to describe the data. A second major outcome was the development of novel models of hydrogel elasticity incorporating solvent effects that can be used to model dynamic motor-driven strains. A third major outcome was to learn how to control the phase and structure of condensed DNA particles, including both liquid-crystalline behavior, and the formation of DNA liquids.

59 BASIC BIOLOGICAL SCIENCES↗

Integrated potential formulation of unsteady supersonic aerodynamics for interacting wings

A numerical integrated velocity potential method for the determination of unsteady aerodynamic forces on arbitrary interacting wings and tails in supersonic flow has been developed. Constant Mach number has been assumed throughout the flow field. Normalwash and sidewash integrals have been derived. The upwash integral remains to be derived. Singular integrals in the expressions for the velocity components have been evaluated in closed form. Lifting surfaces are represented by triangular elements defined by arbitrarily spaced characteristic lines and the true surface edges. The wake field is represented by rectangular strip elements. Velocity potential distributions and generalized aerodynamic coefficients have been compared.

Appa, K.↗

Modified lattice-statics approach to dislocation calculations. II - Application

The atomic structure of a screw dislocation core of the 110 line type in aluminum is calculated by the modified lattice-statics method developed in the preceding paper. The method includes anharmonic as well as harmonic forces and permits relaxation of the atoms in all three dimensions. All forces used in the present calculations were derived from a first-principles interatomic pair potential obtained via pseudopotential theory. Several significant differences from the ordinary lattice statics results are noted, including the displacement field, Peierl's energy barrier, and the equilibrium core-center location.

Esterling, D. M.↗

Aerodynamic stability analysis of NASA J85-13/planar pressure pulse generator installation

A digital computer simulation model for the J85-13/Planar Pressure Pulse Generator (P3 G) test installation was developed by modifying an existing General Electric compression system model. This modification included the incorporation of a novel method for describing the unsteady blade lift force. This approach significantly enhanced the capability of the model to handle unsteady flows. In addition, the frequency response characteristics of the J85-13/P3G test installation were analyzed in support of selecting instrumentation locations to avoid standing wave nodes within the test apparatus and thus, low signal levels. The feasibility of employing explicit analytical expression for surge prediction was also studied.

Chung, K.↗