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At least 667 records · Page 37

Semiclassical shell-structure micro-macroscopic approach for the level density

Level density ρ(E,A) is derived for a one-component nucleon system with a given energy E and particle number A within the mean-field semiclassical periodic-orbit theory beyond the saddle-point method of the Fermi gas model. We obtain ρ∝I ν (S)/S ν , with I ν (S) being the modified Bessel function of the entropy S. Within the micro-macro-canonical approximation (MMA), for a small thermal excitation energy U, with respect to rotational excitations E rot , one obtains ν = 3/2 for ρ(E,A). In the case of excitation energy U larger than E rot but smaller than the neutron separation energy, one finds a larger value of ν = 5/2. A role of the fixed spin variables for rotating nuclei is discussed. The MMA level density ρ reaches the well-known grand-canonical ensemble limit (Fermi gas asymptote) for large S related to large excitation energies, and also reaches the finite micro-canonical limit for small combinatorial entropy S at low excitation energies (the constant “temperature” model). Fitting the ρ(E,A) of the MMA to the experimental data for low excitation energies, taking into account shell and, qualitatively, pairing effects, one obtains for the inverse level density parameter K a value which differs essentially from that parameter derived from data on neutron resonances.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility

The binding free energy between a ligand and its target protein is an essential quantity to know at all stages of the drug discovery pipeline. Assessing this value computationally can offer insight into where efforts should be focused in the pursuit of effective therapeutics to treat a myriad of diseases. In this work, we examine the computation of alchemical relative binding free energies with an eye for assessing reproducibility across popular molecular dynamics packages and free energy estimators. The focus of this work is on 54 ligand transformations from a diverse set of protein targets: MCL1, PTP1B, TYK2, CDK2, and thrombin. These targets are studied with three popular molecular dynamics packages: OpenMM, NAMD2, and NAMD3 alpha. Trajectories collected with these packages are used to compare relative binding free energies calculated with thermodynamic integration and free energy perturbation methods. The resulting binding free energies show good agreement between molecular dynamics packages with an average mean unsigned error between them of 0.50 kcal/mol. The correlation between packages is very good, with the lowest Spearman’s, Pearson’s and Kendall’s tau correlation coefficients being 0.92, 0.91, and 0.76, respectively. Agreement between thermodynamic integration and free energy perturbation is shown to be very good when using ensemble averaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Roadmap on nanoscale magnetic resonance imaging

Abstract The field of nanoscale magnetic resonance imaging (NanoMRI) was started 30 years ago. It was motivated by the desire to image single molecules and molecular assemblies, such as proteins and virus particles, with near-atomic spatial resolution and on a length scale of 100 nm. Over the years, the NanoMRI field has also expanded to include the goal of useful high-resolution nuclear magnetic resonance (NMR) spectroscopy of molecules under ambient conditions, including samples up to the micron-scale. The realization of these goals requires the development of spin detection techniques that are many orders of magnitude more sensitive than conventional NMR and MRI, capable of detecting and controlling nanoscale ensembles of spins. Over the years, a number of different technical approaches to NanoMRI have emerged, each possessing a distinct set of capabilities for basic and applied areas of science. The goal of this roadmap article is to report the current state of the art in NanoMRI technologies, outline the areas where they are poised to have impact, identify the challenges that lie ahead, and propose methods to meet these challenges. This roadmap also shows how developments in NanoMRI techniques can lead to breakthroughs in emerging quantum science and technology applications.

Budakian, Raffi↗

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

Abstract Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N 6 -methyladenosine (m 6 A) modifications near the 3′ end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m 6 As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m 6 A ensembles, and maintaining multiple of these m 6 As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.

60 APPLIED LIFE SCIENCES↗

Data and code for Daily and Multi-Day Extreme Rainfall Analysis Under Future Climates Using Stochastic Storm Transposition and NEX-GDDP-CMIP6 Over CONUS

This data package provides inputs, codes, and outputs for a comprehensive analysis of projected changes in extreme precipitation across 10 regions of the continental United States, using 34 downscaled Earth System Models (ESMs) from the NASA Earth Exchange Global Daily Downscaled Projections, Coupled Model Intercomparison Project Phase 6 (NEX-GDDP-CMIP6) dataset. These models are part of the Coupled Model Intercomparison Project Phase 6 (CMIP6), a coordinated climate modeling framework widely used to assess climate change impacts. The analysis applies a stochastic storm transposition method to quantify changes in extreme rainfall under two Shared Socioeconomic Pathway (SSP) climate scenarios—SSP2-4.5 (moderate emissions) and SSP5-8.5 (high emissions)—compared to historical conditions (1995–2014 vs. 2081–2100). The dataset includes rainfall depth estimates for extreme events with return periods from 2 to 500 years across multiple storm durations (1, 3, and 5 days) for each of the 10 U.S. regions. Weighted ensemble statistics are derived from individual ESM performance against historical precipitation patterns, enabling robust uncertainty quantification through both sign-based and permutation-test-based model agreement assessments. Key analyses address: (1) relative changes in extreme precipitation for each climate scenario, (2) differences between SSP scenarios (SSP5-8.5 vs. SSP2-4.5), (3) contrasts between rare and frequent events, and (4) variations between multi-day and daily storm durations. The workflow produces ensemble statistics—median, 5th, 25th, 75th, and 95th percentiles—along with model agreement metrics that identify regions and event types with robust climate change signals. The dataset includes: processed rainfall depth outputs (netCDF format) from the RainyDay Python package, ESM weights from historical performance evaluation using DayMet observations, ensemble statistics across all storm dimensions, and figures summarizing key findings.

54 ENVIRONMENTAL SCIENCES↗

A machine learning approach to emulation and biophysical parameter estimation with the Community Land Model, version 5

Abstract. Land models are essential tools for understanding and predicting terrestrial processes and climate–carbon feedbacks in the Earth system, but uncertainties in their future projections are poorly understood. Improvements in physical process realism and the representation of human influence arguably make models more comparable to reality but also increase the degrees of freedom in model configuration, leading to increased parametric uncertainty in projections. In this work we design and implement a machine learning approach to globally calibrate a subset of the parameters of the Community Land Model, version 5 (CLM5) to observations of carbon and water fluxes. We focus on parameters controlling biophysical features such as surface energy balance, hydrology, and carbon uptake. We first use parameter sensitivity simulations and a combination of objective metrics including ranked global mean sensitivity to multiple output variables and non-overlapping spatial pattern responses between parameters to narrow the parameter space and determine a subset of important CLM5 biophysical parameters for further analysis. Using a perturbed parameter ensemble, we then train a series of artificial feed-forward neural networks to emulate CLM5 output given parameter values as input. We use annual mean globally aggregated spatial variability in carbon and water fluxes as our emulation and calibration targets. Validation and out-of-sample tests are used to assess the predictive skill of the networks, and we utilize permutation feature importance and partial dependence methods to better interpret the results. The trained networks are then used to estimate global optimal parameter values with greater computational efficiency than achieved by hand tuning efforts and increased spatial scale relative to previous studies optimizing at a single site. By developing this methodology, our framework can help quantify the contribution of parameter uncertainty to overall uncertainty in land model projections.

54 ENVIRONMENTAL SCIENCES↗

Assessing Global and Local Radiative Feedbacks Based on AGCM Simulations for 1980–2014/2017

In order to avoid contamination of unobservable and uncertain effective radiative forcing (ERF) on the diagnosis of radiative feedbacks based on short-term climate variability, we verify the Kernel-Gregory feedback calculation method using atmospheric model experiments with prescribed ERF. We show that both clear-sky radiative fluxes and all-sky radiative feedbacks have a closure between model simulations and kernel derivations. A near-zero global mean net cloud feedback is found in the simulation with prescribed ERF, which results in a more negative global net climate feedback, -2 W m -2 K -1 . Consistent with AMIP6 ensemble mean results, the lapse rate feedback is the largest contributor among all feedbacks to temperature amplification over the three poles (Arctic, Antarctic and Tibetan Plateau), followed by surface albedo feedback and Planck feedback deviation from its global mean. Except for the higher surface albedo feedback in the Antarctic, other feedbacks are almost same between the Arctic and Antarctic.

54 ENVIRONMENTAL SCIENCES↗

Spin-free formulation of the multireference driven similarity renormalization group: A benchmark study of first-row diatomic molecules and spin-crossover energetics

We report a spin-free formulation of the multireference (MR) driven similarity renormalization group (DSRG) based on the ensemble normal ordering of Mukherjee and Kutzelnigg (1997). This ensemble averages over all microstates of a given total spin quantum number, and therefore, it is invariant with respect to SU(2) transformations. As such, all equations may be reformulated in terms of spin-free quantities and they closely resemble those of spin-adapted closed-shell coupled cluster (CC) theory. The current implementation is used to assess the accuracy of various truncated MR-DSRG methods (perturbation theory up to third order and iterative methods with single and double excitations) in computing the constants of 33 first-row diatomic molecules. The accuracy trends for these first-row diatomics are consistent with our previous benchmark on a small subset of closed-shell diatomic molecules. We then present the first MR-DSRG application on transition-metal complexes by computing the spin splittings of the [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ molecules. A focal point analysis (FPA) shows that third-order perturbative corrections are essential to achieve reasonably converged energetics. The FPA based on the linearized MR-DSRG theory with one- and two-body operators and up to a quintuple- ζ basis set predicts the spin splittings of [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ to be –35.7 and –17.1 kcal mol –1 , respectively, showing good agreement with the results of local CC theory with singles, doubles, and perturbative triples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ensemble Kalman filter for data assimilation coupled with low-resolution computations techniques applied in fluid dynamics

This paper presents an innovative Reduced-order model (ROM) for merging experimental and simulation data using data assimilation (DA) to estimate the "True" state of a fluid dynamics system, leading to more accurate predictions. Our methodology introduces a novel approach by implementing the ensemble Kalman filter (EnKF) within a reduced-dimensional framework, grounded in a robust theoretical foundation and applied to fluid dynamics. To address the substantial computational demands of DA, the proposed ROM employs low-resolution (LR) techniques to drastically reduce computational costs. This innovative approach involves downsampling datasets for DA computations, followed by an advanced reconstruction technique based on low-cost singular value decomposition (lcSVD). The lcSVD method, a key innovation in this paper, has never been applied to DA before and offers a highly efficient way to enhance resolution with minimal computational resources. Our results demonstrate significant reductions in both computation time and RAM usage through these LR techniques without compromising the accuracy of the estimations. For instance, in a turbulent test case, for a data compression rate of 15.9, the LR approach can achieve a speed-up of 13.7 and a RAM compression of 90.9% while maintaining a low relative root mean square error (RRMSE) of 2.6%, compared to 0.8% in the high-resolution (HR) reference. Furthermore, we highlight the effectiveness of the EnKF in estimating and predicting the state of fluid flow systems based on limited observations and given low-fidelity numerical data. This paper highlights the potential of the proposed DA method in fluid dynamics applications, particularly for improving computational efficiency in CFD and related fields. Its ability to balance accuracy with low computational and memory costs makes it especially suitable for large-scale and real-time applications, such as environmental monitoring or engineering design. This method will be incorporated into ModelFLOWs-app.

Data Assimilation↗

National CO 2 budgets (2015–2020) inferred from atmospheric CO 2 observations in support of the global stocktake

Accurate accounting of emissions and removals of CO 2 is critical for the planning and verification of emission reduction targets in support of the Paris Agreement. Here, we present a pilot dataset of country-specific net carbon exchange (NCE; fossil plus terrestrial ecosystem fluxes) and terrestrial carbon stock changes aimed at informing countries' carbon budgets. These estimates are based on “top-down” NCE outputs from the v10 Orbiting Carbon Observatory (OCO-2) modeling intercomparison project (MIP), wherein an ensemble of inverse modeling groups conducted standardized experiments assimilating OCO-2 column-averaged dry-air mole fraction (X CO 2 ) retrievals (ACOS v10), in situ CO 2 measurements or combinations of these data. The v10 OCO-2 MIP NCE estimates are combined with “bottom-up” estimates of fossil fuel emissions and lateral carbon fluxes to estimate changes in terrestrial carbon stocks, which are impacted by anthropogenic and natural drivers. These flux and stock change estimates are reported annually (2015–2020) as both a global 1° x 1° gridded dataset and a country-level dataset and are available for download from the Committee on Earth Observation Satellites' (CEOS) website. Across the v10 OCO-2 MIP experiments, we obtain increases in the ensemble median terrestrial carbon stocks of 3.29–4.58 Pg CO2 yr -1 (0.90–1.25 Pg C yr -1 ). This is a result of broad increases in terrestrial carbon stocks across the northern extratropics, while the tropics generally have stock losses but with considerable regional variability and differences between v10 OCO-2 MIP experiments. We discuss the state of the science for tracking emissions and removals using top-down methods, including current limitations and future developments towards top-down monitoring and verification systems.

54 ENVIRONMENTAL SCIENCES↗

A benchmark dataset for Hydrogen Combustion

The generation of reference data for deep learning models is challenging for reactive systems, and more so for combustion reactions due to the extreme conditions that create radical species and alternative spin states during the combustion process. Here, we extend intrinsic reaction coordinate (IRC) calculations with ab initio MD simulations and normal mode displacement calculations to more extensively cover the potential energy surface for 19 reaction channels for hydrogen combustion. A total of ~290,000 potential energies and ~1,270,000 nuclear force vectors are evaluated with a high quality range-separated hybrid density functional, ωB97X-V, to construct the reference data set, including transition state ensembles, for the deep learning models to study hydrogen combustion reaction.

08 HYDROGEN↗

Reversible Surface Energy Storage in Molecular-Scale Porous Materials

Forcible wetting of hydrophobic pores represents a viable method for energy storage in the form of interfacial energy. The energy used to fill the pores can be recovered as pressure–volume work upon decompression. For efficient recovery, the expulsion pressure should not be significantly lower than the pressure required for infiltration. Hysteresis of the wetting/drying cycle associated with the kinetic barrier to liquid expulsion results in energy dissipation and reduced storage efficiency. In the present work, we use open ensemble (Grand Canonical) Monte Carlo simulations to study the improvement of energy recovery with decreasing diameters of planar pores. Near-complete reversibility is achieved at pore widths barely accommodating a monolayer of the liquid, thus minimizing the area of the liquid/gas interface during the cavitation process. At the same time, these conditions lead to a steep increase in the infiltration pressure required to overcome steric wall/water repulsion in a tight confinement and a considerable reduction in the translational entropy of confined molecules. In principle, similar effects can be expected when increasing the size of the liquid particles without altering the absorbent porosity. While the latter approach is easier to follow in laboratory work, we discuss the advantages of reducing the pore diameter, which reduces the cycling hysteresis while simultaneously improving the stored-energy density in the material.

36 MATERIALS SCIENCE↗

Evaluating Sea Breezes and Associated Convective Cloud Evolution in the Model Gray Zone

We characterize convective clouds associated with sea‐breeze circulations (SBC) using multi‐agency observations and multi‐case ensemble model simulations. The focus is on assessing convective cloud lifecycle properties and their merging behavior, as well as the environmental conditions they are embedded in, particularly SBC features. In total, 46 SBC days over the Houston‐Galveston region are selected and simulated using the Weather Research and Forecasting (WRF) model at a gray zone scale with a forecast‐like parameterization setup. Advanced techniques, including change‐point detection, a Lagrangian cloud tracking method, and a newly developed cell merging and splitting detection algorithm, are applied and/or developed for this study. Our findings indicate that the WRF model at 1 km grid spacing well represents the thermodynamic conditions over the region, as well as SBC timing and intensity. However, for the associated convective cells, WRF overestimates the 30‐dBZ echo top height, cell area, and maximum radar reflectivity compared to radar observations. This overestimation is potentially due to under‐resolved entrainment processes, an overestimated merging frequency, and the overestimation of updraft intensity. Furthermore, the model exhibits a deficiency in simulating congestus clouds, showing a more rapid transition from shallow to deep convection compared to observed behavior. Moreover, observations indicate stronger, deeper, and wider clouds when merging happens. Conversely, in simulations, the merging process does not necessarily lead to higher or longer‐lived cells, as many cases experience rapid and frequent merging and splitting which may result in more variance in convective updraft velocity during the convection lifetime.

54 ENVIRONMENTAL SCIENCES↗

Path integral factorization and the gravitational effective action

Abstract We discuss the factorization and continuity properties of fields in the Euclidean gravitational path integral with higher dimension operators constructed from powers of the Riemann tensor. We construct the boundary terms corresponding to the microcanonical ensemble and show that the saddle point approximation to the path integral with a quasilocal energy constraint generally yields a saddle point with discontinuous temperature. This extends a previous result for the Euclidean Schwarzschild–de Sitter geometry in Einstein gravity and shows that it is robust against at least some types of quantum corrections from heavy fields. As an application, we compute the entropy of SdS in D = 4 using the BTZ method. Our result matches the entropy calculated using Wald’s formula.

Astronomy & Astrophysics↗

Comparing different generations of idealized solar geoengineering simulations in the Geoengineering Model Intercomparison Project (GeoMIP)

Abstract. Solar geoengineering has been receiving increased attention in recent years as a potential temporary solution to offset global warming. One method of approximating global-scale solar geoengineering in climate models is via solar reduction experiments. Two generations of models in the Geoengineering Model Intercomparison Project (GeoMIP) have now simulated offsetting a quadrupling of the CO2 concentration with solar reduction. This simulation is idealized and designed to elicit large responses in the models. Here, we show that energetics, temperature, and hydrological cycle changes in this experiment are statistically indistinguishable between the two ensembles. Of the variables analyzed here, the only major differences involve highly parameterized and uncertain processes, such as cloud forcing or terrestrial net primary productivity. We conclude that despite numerous structural differences and uncertainties in models over the past two generations of models, including an increase in climate sensitivity in the latest generation of models, the models are consistent in their aggregate climate response to global solar dimming.

54 ENVIRONMENTAL SCIENCES↗

Deep Learning Provides Substantial Improvements to County‐Level Fire Weather Forecasting Over the Western United States

Abstract The recent wildfires in the western United States during 2018 and 2020 caused record‐breaking fire damage and casualties. Despite remarkable advances in fire modeling and weather forecasting, it remains challenging to anticipate catastrophic wildfire events and associated damage. One key missing component is a fire weather prediction system with sufficiently long lead time capable of providing useful regional details. Here, we develop a hybrid prediction model of wildfire danger called CFS with super resolution (CFS‐SR) as a proof of concept to fill that void. The CFS‐SR model is constructed by integrating the Climate Forecast System version 2 with a deep learning (DL) technique from Single Image Super Resolution, a method widely used in enhancing image resolution. We show that for the 2018–2019 fire season, the CFS‐SR model significantly improves accuracy in forecasting fire weather at lead times of up to 7 days with an enhanced spatial resolution up to 4 km. This level of high resolution provides county‐level fire weather forecast, making it more practical for allocating resources to mitigate wildfire danger. Our study demonstrates that a proper combination of ensemble climate predictions with DL techniques can boost predictability at finer spatial scales, increasing the utility of fire weather forecasts for practical applications.

54 ENVIRONMENTAL SCIENCES↗

Peculiarities of the formation of photonic nanojets by a matrix of dielectric microtoroids

We report the results of theoretical modelling of photonic nanojets (PNJs) formed by laser radiation scattering on a single-layer ordered assembly of dielectric microtoroids placed on the surface of a transparent matrix (silicone film). Using the method of computational electrodynamics (FDTD), the main PNJ parameters (length, width, peak intensity) are analysed under the conditions of mutual influence of the light fields of neighbouring microparticles. It is shown that the main factor affecting the PNJ characteristics under study is the spatial configuration of the radiation-scattering particle, namely, the internal diameter of its cross section. It is found that for certain configurations of toroid placement in a cluster, a PNJ ensemble is implemented with parameters significantly better than those for a single toroid. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Influence of inhomogeneous stochasticity on the falsifiability of mean-field theories and examples from accretion disc modelling

ABSTRACT Despite spatial and temporal fluctuations in turbulent astrophysical systems, mean-field theories can be used to describe their secular evolution. However, observations taken over time scales much shorter than dynamical time scales capture a system in a single state of its turbulence ensemble. Comparing with mean-field theory can falsify the latter only if the theory is additionally supplied with a quantified precision. The central limit theorem provides appropriate estimates to the precision only when fluctuations contribute linearly to an observable and with constant coherent scales. Here, we introduce an error propagation formula that relaxes both limitations, allowing for non-linear functional forms of observables and inhomogeneous coherent scales and amplitudes of fluctuations. The method is exemplified in the context of accretion disc theories, where inhomogeneous fluctuations in the surface temperature are propagated to the disc emission spectrum – the latter being a non-linear and non-local function of the former. The derived precision depends non-monotonically on emission frequency. Using the same method, we investigate how binned spectral fluctuations in telescope data change with the spectral resolving power. We discuss the broader implications for falsifiability of a mean-field theory.

79 ASTRONOMY AND ASTROPHYSICS↗