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DOE OSTI2023

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps

Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. Here, we quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.

3D alignment↗

DOE OSTI2020

Potential Impacts of Assimilating All-sky Satellite Infrared Radiances on Convection-Permitting Analysis and Prediction of Tropical Convection

Geostationary infrared satellite observations are spatially dense [< 1/(20 km)2] and temporally frequent (< 1/hour). These suggest the possibility of using these observations to constrain sub-synoptic features over data sparse regions, such as tropical oceans. In this study, the potential impacts of assimilating water vapor channel brightness temperature (WV-BT) observations from the geostationary Meteorological Satellite 7 (Meteosat-7) on tropical convection analysis and prediction were systematically examined through a series of ensemble data assimilation experiments. WV-BT observations were assimilated hourly into convection-permitting ensembles using Penn State’s ensemble square root filter (EnSRF). Comparisons against independently observed Meteosat-7 window channel brightness temperature (Window-BT) show that the assimilation of WV-BT generally improved the intensities and locations of large-scale cloud patterns at spatial scales larger than 100 km. However, comparisons against independent soundings indicate that the EnSRF analysis produced a much stronger dry bias than the no data assimilation experiment. This strong dry bias is associated with the use of the simulated WV-BT from the prior mean during the EnSRF analysis step. A stochastic variant of the ensemble Kalman filter (NoMeanSF) is proposed. The NoMeanSF algorithm was able to assimilate the WV-BT without causing such a strong dry bias and the quality of the analyses’ horizontal cloud pattern is similar to EnSRF’s analyses. Finally, deterministic forecasts initiated from the NoMeanSF analyses possess better horizontal cloud patterns above 500 km than those of the EnSRF. These results suggest that it might be better to assimilate all-sky WV-BT through the NoMeanSF algorithm than EnSRF algorithm.

Chan, Man-Yau↗

DOE OSTI2024

Evaluation of a Stochastic Mixing Scheme in the Deep Convective Gray Zone Using a Tropical Oceanic Deep Convection Case Study

Abstract A stochastic horizontal subgrid‐scale mixing scheme is evaluated in ensemble simulations of a tropical oceanic deep convection case using a horizontal grid spacing (Δ h ) of 3 km. The stochastic scheme, which perturbs the horizontal mixing coefficient according to a prescribed spatiotemporal autocorrelation scale, is found to generally increase mesoscale organization and convective intensity relative to a non‐stochastic control simulation. Perturbations applied at relatively short autocorrelation scales induce differences relative to the control that are more systematic than those from perturbations applied at relatively long scales that yield more variable outcomes. A simulation with mixing enhanced by a constant factor of 4 significantly increases mesoscale organization and convective intensity, while turning off horizontal subgrid‐scale mixing decreases both. Total rainfall is modulated by a combination of mesoscale organization, areal coverage of convection, and convective intensity. The stochastic simulations tend to behave more similarly to the constant enhanced mixing simulation owing to greater impacts from enhanced mixing as compared to reduced mixing. The impacts of stochastic mixing are robust, ascertained by comparing the stochastic mixing ensembles with a non‐stochastic mixing ensemble that has grid‐scale noise added to the initial thermodynamic field. Compared to radar observations and a higher resolution Δ h = 1 km simulation, stochastic mixing seemingly degrades the simulation performance. These results imply that stochastic mixing produces non‐negligible impacts on convective system properties and evolution but does not lead to an improved representation of convective cloud characteristics in the case studied here.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Deep Generative Models that Solve PDEs: Distributed Computing for Training Large Data-Free Models

Recent progress in scientific machine learning (SciML) has opened up the possibility of training novel neural network architectures that solve complex partial differential equations (PDEs). Several (nearly data free) approaches have been recently reported that successfully solve PDEs, with examples including deep feed forward networks, generative networks, and deep encoder-decoder networks. However, practical adoption of these approaches is limited by the difficulty in training these models, especially to make predictions at large output resolutions (≥1024×1024). Here we report on a software framework for data parallel distributed deep learning that resolves the twin challenges of training these large SciML models - training in reasonable time as well as distributing the storage requirements. Our framework provides several out of the box functionality including (a) loss integrity independent of number of processes, (b) synchronized batch normalization, and (c) distributed higher-order optimization methods. We show excellent scalability of this framework on both cloud as well as HPC clusters, and report on the interplay between bandwidth, network topology and bare metal vs cloud. We deploy this approach to train generative models of sizes hitherto not possible, showing that neural PDE solvers can be viably trained for practical applications. We also demonstrate that distributed higher-order optimization methods are 2-3× faster than stochastic gradient-based methods and provide minimal convergence drift with higher batch-size.

PDEs↗

DOE OSTI2020

Evaluating and Improving Convective Parameterization for GCMs Using ARM Observations. Final report

This technical report summarizes the achievements during the project period funded by the Atmospheric System Research (ASR) program. The general goal of the project is to improve the representation of atmospheric deep convection in global climate models. By using DOE Atmospheric Radiation Measurement (ARM) program observations and a hierarchy of models from cloud-resolving to global climate models, we evaluated and improved many aspects of convection parameterization schemes, such as the trigger function for convection and closure condition to determine the amount of convection. We also incorporated the stochasticity of convection into a convection scheme. These improvements, when implemented into the National Center for Atmospheric Research (NCAR) Community Earth System Model (CESM) and the DOE Exascale Energy Earth System Model (E3SM), led to improved simulation of precipitation characteristics, including precipitation intensity, Intertropical Convergence Zone, and Madden-Julian oscillation. The project also improved the representation of microphysical processes in convective clouds. It enables the interaction of cloud microphysics with aerosols in weather and climate models.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2011

Allowing for Horizontally Heterogeneous Clouds and Generalized Overlap in an Atmospheric GCM

While fully accounting for 3D effects in Global Climate Models (GCMs) appears not realistic at the present time for a variety of reasons such as computational cost and unavailability of 3D cloud structure in the models, incorporation in radiation schemes of subgrid cloud variability described by one-point statistics is now considered feasible and is being actively pursued. This development has gained momentum once it was demonstrated that CPU-intensive spectrally explicit Independent Column Approximation (lCA) can be substituted by stochastic Monte Carlo ICA (McICA) calculations where spectral integration is accomplished in a manner that produces relatively benign random noise. The McICA approach has been implemented in Goddard's GEOS-5 atmospheric GCM as part of the implementation of the RRTMG radiation package. GEOS-5 with McICA and RRTMG can handle horizontally variable clouds which can be set via a cloud generator to arbitrarily overlap within the full spectrum of maximum and random both in terms of cloud fraction and layer condensate distributions. In our presentation we will show radiative and other impacts of the combined horizontal and vertical cloud variability on multi-year simulations of an otherwise untuned GEOS-5 with fixed SSTs. Introducing cloud horizontal heterogeneity without changing the mean amounts of condensate reduces reflected solar and increases thermal radiation to space, but disproportionate changes may increase the radiative imbalance at TOA. The net radiation at TOA can be modulated by allowing the parameters of the generalized overlap and heterogeneity scheme to vary, a dependence whose behavior we will discuss. The sensitivity of the cloud radiative forcing to the parameters of cloud horizontal heterogeneity and comparisons of CERES-derived forcing will be shown.

Lee, D.↗

NASA NTRS1997

Stochastic-Dynamical Modeling of Space Time Rainfall

The focus of this research work is the elucidation of the physical origins of the observed extreme-rainfall variability over tropical oceans. The quantitative results of this work may be used to establish links between deterministic models of the mesoscale and synoptic scale with statistical descriptions of the temporal variability of local tropical oceanic rainfall. In addition, they may be used to quantify the influence of measurement error in large-scale forcing and cloud scale observations on the accuracy of local rainfall variability inferences, important for hydrologic studies. A simple statistical-dynamical model, suitable for use in repetitive Monte Carlo experiments, is formulated as a diagnostic tool for this purpose. Stochastic processes with temporal structure and parameters estimated from observed large-scale data represent large-scale forcing.

Georgankakos, Konstantine P.↗

NASA NTRS2020

Assimilation of satellite microwave observations over the rainbands of tropical cyclones

A novel Bayesian Monte Carlo integration (BMCI) technique was developed to retrieve geophysical variables from satellite microwave radiometer data in the presence of tropical cyclones. The BMCI technique includes three steps: generating a stochastic database, simulating satellite brightness temperatures using a radiative transfer model, and retrieving geophysical variables such as profiles of temperature, relative humidity, and cloud liquid and ice water content from real observations. The technique also provides uncertainty estimates for each retrieval and can output the error covariance matrix of selected parameters. The measurements from the Advanced Technology Microwave Sounder (ATMS) on board Suomi National Polar-Orbiting Partnership (Suomi NPP) and the Global Precipitation Measurement (GPM) Microwave Imager (GMI) were used as input. A new technique was developed to correct the ATMS and GMI observations for the beam-filling effect, which is due to small-scale variability of precipitation and clouds when compared with the instrument footprint and also the nonlinear relation between the brightness temperature and precipitation. In addition, the assimilation of the BMCI retrievals into the NASA GEOS model is discussed for Hurricane Maria. The results show that assimilating the BMCI retrievals can influence the dynamical features of the cyclone, including a stronger warm core, a symmetric eye, and vertically aligned wind columns. Two possible factors that may limit the impact of the BMCI retrievals include 1) the resolution of the model (about 25 km), which was too coarse to show the potential of the BMCI data in improving the representation of tropical storms in the model forecast, and 2) the data assimilation system not being able to consider vertically correlated observation errors.

Isaac Moradi↗

DOE OSTI2020

On the Parameterization of Convective Downdrafts for Marine Stratocumulus Clouds

The role of nonlocal transport on the development and maintenance of marine stratocumulus (Sc) clouds in coarse-resolution models is investigated, with a special emphasis on the downdraft contribution. A new parameterization of cloud-top-triggered downdrafts is proposed and validated against large-eddy simulation (LES) for two Sc cases. The applied nonlocal mass-flux scheme is part of the stochastic multiplume eddy-diffusivity/mass-flux (EDMF) framework decomposing the turbulent transport into local and nonlocal contributions. The complementary local turbulent transport is represented with the Mellor–Yamada–Nakanishi–Niino (MYNN) scheme. This EDMF version has been implemented in the Weather Research and Forecasting (WRF) single-column model (SCM) and tested for three model versions: without mass flux, with updrafts only, and with both updrafts and downdrafts. In the LES, the downdraft and updraft contributions to the total heat and moisture transport are comparable and significant. The WRF SCM results show a good agreement between the parameterized downdraft turbulent transport and LES. While including updrafts greatly improves the modeling of Sc clouds over the simulation without mass flux, the addition of downdrafts is less significant, although it helps improve the moisture profile in the planetary boundary layer.

Wu, Elynn↗

DOE OSTI2022

Limitations of Bin and Bulk Microphysics in Reproducing the Observed Spatial Structure of Light Precipitation

Abstract Coarse-gridded atmospheric models often account for subgrid-scale variability by specifying probability distribution functions (PDFs) of process rate inputs such as cloud and rainwater mixing ratios ( q c and q r , respectively). PDF parameters can be obtained from numerous sources: in situ observations, ground- or space-based remote sensing, or fine-scale modeling such as large-eddy simulation (LES). LES is appealing to constrain PDFs because it generates large sample sizes, can simulate a variety of cloud regimes/case studies, and is not subject to the ambiguities of observations. However, despite the appeal of using model output for parameterization development, it has not been demonstrated that LES satisfactorily reproduces the observed spatial structure of microphysical fields. In this study, the structure of observed and modeled microphysical fields are compared by applying bifractal analysis, an approach that quantifies variability across spatial scales, to simulations of a drizzling stratocumulus field that span a range of domain sizes, drop concentrations (a proxy for mesoscale organization), and microphysics schemes (bulk and bin). Simulated q c closely matches observed estimates of bifractal parameters that measure smoothness and intermittency. There are major discrepancies between observed and simulated q r properties, though, with bulk simulated q r consistently displaying the bifractal properties of observed clouds (smooth, minimally intermittent) rather than rain while bin simulations produce q r that is appropriately intermittent but too smooth. These results suggest fundamental limitations of bulk and bin schemes to realistically represent higher-order statistics of the observed rain structure.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

A Comprehensive Analysis of Uncertainties in Warm-Rain Parameterizations in Climate Models Based on In Situ Measurements

Abstract Because of the coarse grid size of Earth system models (ESMs), representing warm-rain processes in ESMs is a challenging task involving multiple sources of uncertainty. Previous studies evaluated warm-rain parameterizations mainly according to their performance in emulating collision–coalescence rates for local droplet populations over a short period of a few seconds. The representativeness of these local process rates comes into question when applied in ESMs for grid sizes on the order of 100 km and time steps on the order of 20–30 min. We evaluate several widely used warm-rain parameterizations in ESM application scenarios. In the comparison of local and instantaneous autoconversion rates, the two parameterization schemes based on numerical fitting to stochastic collection equation (SCE) results perform best. However, because of Jessen’s inequality, their performance deteriorates when grid-mean, instead of locally resolved, cloud properties are used in their simulations. In contrast, the effect of Jessen’s inequality partly cancels the overestimation problem of two semianalytical schemes, leading to an improvement in the ESM-like comparison. In the assessment of uncertainty due to the large time step of ESMs, it is found that the rainwater tendency simulated by the SCE is roughly linear for time steps smaller than 10 min, but the nonlinearity effect becomes significant for larger time steps, leading to errors up to a factor of 4 for a time step of 20 min. After considering all uncertainties, the grid-mean and time-averaged rainwater tendency based on the parameterization schemes is mostly within a factor of 4 of the local benchmark results simulated by SCE.

Meteorology & Atmospheric Sciences↗

DOE OSTI2021

Local limits of detection for anthropogenic aerosol-cloud interactions

Ship tracks are quasi-linear cloud patterns produced from the interaction of ship emissions with low boundary layer clouds. They are visible throughout the diurnal cycle in satellite images from space-borne assets like the Advanced Baseline Imagers (ABI) aboard the National Oceanic and Atmospheric Administration Geostationary Operational Environmental Satellites (GOES-R). However, complex atmospheric dynamics often make it difficult to identify and characterize the formation and evolution of tracks. Ship tracks have the potential to increase a cloud's albedo and reduce the impact of global warming. Thus, it is important to study these patterns to better understand the complex atmospheric interactions between aerosols and clouds to improve our climate models, and examine the efficacy of climate interventions, such as marine cloud brightening. Over the course of this 3-year project, we have developed novel data-driven techniques that advance our ability to assess the effects of ship emissions on marine environments and the risks of future marine cloud brightening efforts. The three main innovative technical contributions we will document here are a method to track aerosol injections using optical flow, a stochastic simulation model for track formations and an automated detection algorithm for efficient identification of ship tracks in large datasets.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

A Model for Ice Accretion Roughness Evolution and Spatial Variations

Over the past decade, multiple investigations of ice accretion roughness and spatial variations have been performed in the Icing Research Tunnel (IRT) at the NASA Glenn Research Center. The early investigations used models of NACA 0012 airfoils with different chord sizes and focused on temporal scaling and primary cloud scaling parameters such as stagnation point collection efficiency. Subsequent investigations included the effects of model sweep, airfoil shape, airfoil lifting condition, and freestream static temperature. To develop a predictive model for roughness evolution in generalized icing situations, the maximum roughness values for the airfoils and conditions used in the angle of attack and freestream temperature investigations were scaled to eliminate the temporal variations. LEWICE simulations were employed to identify the local collection efficiency at the locations of maximum roughness, and a two-dimensional panel-method code was used to identify the local static pressure at the location of the maximum roughness. Because of the stochastic nature of ice accretion roughness, a physics-directed approach was employed to develop a multi-dimensional correlation based on the local pressure coefficient, the local total temperature, the cloud properties, and the cloud exposure time. The resulting correlation predictions are compared to ice shapes measured in the IRT for both a 21-in. NACA 0012 airfoil model and a 60-in. HAARP-II model. The resulting predictions indicate that the local freezing fraction must be included in the roughness predictive model. Implications regarding icing heat transfer predictions using the resulting roughness model are also discussed.

Icing↗

NASA NTRS1984

Spiral structure and star formation. I - Formation mechanisms and mean free paths

The wide variety of optical appearances observed in spiral galaxies has encouraged the growth of two theoretical approaches to explain the spiral patterns exhibited by such young objects as OB associations, giant H II regions, and dark dust lanes. These approaches are related to the density wave theory of spiral structure and 'stochastic, self-propagating star formation'. Levinson and Roberts (1981) tried to reconcile these two theoretical approaches, and considered a disk filled with discrete gas clouds. The present investigation is concerned with refinements and extensions of the model of Levinson and Roberts. Attention is given to gravitational forces and dynamical propagation, cloud-cloud collisions, supernova interactions, computational models, a theory concerning the interactions of the gas cloud and stellar association systems, the time evolution of the gas cloud-stellar association systems, and aspects of collisionally triggered star formation.

Roberts, W. W., Jr.↗

DOE OSTI2020

Simulating the mechanisms of serrated flow in interstitial alloys with atomic resolution over diffusive timescales

Abstract The Portevin-Le Chatelier (PLC) effect is a phenomenon by which plastic slip in metallic materials becomes unstable, resulting in jerky flow and the onset of inhomogeneous deformation. The PLC effect is thought to be fundamentally caused by the dynamic interplay between dislocations and solute atoms. However, this interplay is almost always inaccessible experimentally due to the extremely fine length and time scales over which it occurs. In this paper, simulations of jerky flow in W-O interstitial solid solutions reveal three dynamic regimes emerging from the simulated strain rate-temperature space: one resembling standard solid solution strengthening, another one mimicking solute cloud formation, and a third one where dislocation/solute coevolution leads to jerky flow as a precursor of dynamic strain aging. The simulations are carried out in a stochastic framework that naturally captures rare events in a rigorous manner, providing atomistic resolution over diffusive time scales using no adjustable parameters.

36 MATERIALS SCIENCE↗

NASA NTRS1988

The influence of supernovae and passing stars on comets in the Oort cloud

It is demonstrated here that the passage of luminous stars through the Oort Cloud over the age of the solar system will subject all comets to heating episodes up to at least 16 K, and a sizeable fraction to 30 K. Stochastic supernovae have even more striking effects during monthlong events; conservative estimates of the supernovae are in the Galactic disk suggest that most comets have been heated to 45 K, and a fraction to about 60 K. These results imply that comets are not fully pristine relics of solar system formation.

Stern, S. Alan↗

DOE OSTI2025

Conveyor-belt magneto-optical trapping of molecules

Abstract Laser cooling is used to produce ultracold atoms and molecules for quantum science and precision measurement applications. Molecules are more challenging to cool than atoms due to their vibrational and rotational internal degrees of freedom. Molecular rotations lead to the use of type-II transitions ( F ⩾ F ′ ) for magneto-optical trapping (MOT). When typical red detuned light frequencies are applied to these transitions, sub-Doppler heating is induced, resulting in higher temperatures and larger molecular cloud sizes than realized with the type-I MOTs most often used with atoms. To improve type-II MOTs, Jarvis et al (2018 Phys. Rev. Lett. 120 083201) proposed a blue-detuned MOT to be applied after initial cooling and capture with a red-detuned MOT. This was successfully implemented (Burau et al 2023 Phys. Rev. Lett. 130 193401; Jorapur et al 2024 Phys. Rev. Lett. 132 163403; Li et al 2024 Phys. Rev. Lett. 132 233402), realizing colder and denser molecular samples. Very recently, Hallas et al (2024 arXiv:2404.03636) demonstrated a blue-detuned MOT with a ‘1+2’ configuration that resulted in even stronger compression of the molecular cloud. Here, we describe and characterize theoretically the conveyor-belt mechanism that underlies this observed enhanced compression. We perform numerical simulations of the conveyor-belt mechanism using both stochastic Schrödinger equation and optical Bloch equation approaches. We investigate the conveyor-belt MOT characteristics in relation to laser parameters, g -factors and the structure of the molecule, and find that conveyor-belt trapping should be applicable to a wide range of laser-coolable molecules.

Li, Grace K. (ORCID:0000000277223355)↗

NASA NTRS1991

A statistical rain attenuation prediction model with application to the advanced communication technology satellite project. 3: A stochastic rain fade control algorithm for satellite link power via non linear Markow filtering theory

The dynamic and composite nature of propagation impairments that are incurred on Earth-space communications links at frequencies in and above 30/20 GHz Ka band, i.e., rain attenuation, cloud and/or clear air scintillation, etc., combined with the need to counter such degradations after the small link margins have been exceeded, necessitate the use of dynamic statistical identification and prediction processing of the fading signal in order to optimally estimate and predict the levels of each of the deleterious attenuation components. Such requirements are being met in NASA's Advanced Communications Technology Satellite (ACTS) Project by the implementation of optimal processing schemes derived through the use of the Rain Attenuation Prediction Model and nonlinear Markov filtering theory.

Manning, Robert M.↗