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At least 541 records · Page 30

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implementation of a Three-Dimensional Planetary Boundary Layer Parameterization in a Coupled Modeling System and Evaluation of "Gray Zone" Simulations of a Wind-Wave Event Off the US California Coast Using Observations

A three-dimensional (3D) planetary boundary layer (PBL) parameterization was added to the Coupled Ocean Atmosphere Wave Sediment Transport (COAWST) model and the first coupled atmosphere/wave "gray zone" simulations were carried out using the 3D PBL parameterization. A case study of a significant wind-wave event from 4-8 November 2020 off the US west coast was examined, with a focus on the impacts of the event within an approximate 280x280 km central California coastal region covering the Bureau of Ocean Energy Management Morro Bay wind energy lease area. Simulations with both one-dimensional (1D; Yonsei University) and 3D PBL parameterizations were examined in this nest with ..delta..x=400 m. Two-way coupling was active, with near-surface winds feeding back to the wave model and bulk wave statistics feeding back to the atmospheric model. Both simulations compared favorably with buoy observations in capturing the timing and magnitude of wind speed, temperature, dewpoint, and significant wave height, as the front associated with the maritime weather system moved southward across coastal California. However, wind speed errors over land were larger. Time series of the vertical profile of winds below z=250 m from the simulations compared favorably with observations from the US Dept. of Energy Morro Bay Doppler lidar buoy. Differences between the coupled 1D and 3D PBL simulations were minor. The most notable difference was that the simulation using the 3D PBL parameterization had approximately 10 % weaker winds at the peak of the event causing 10 % lower significant wave heights. This difference was shown to be mostly due to differences in the vertical mixing treatment between the parameterizations, in particular the nonlocal downward mixing of higher momentum air in the 1D Yonsei University parameterization in convective conditions. Overall, this work demonstrates that the 3D PBL parameterization can be used in a coupled atmosphere/wave modeling framework with similar behaviors as traditional PBL parameterizations that do not provide horizontal turbulent variances and fluxes.

16 TIDAL AND WAVE POWER↗

Stochastic Parameterization of Subgrid-Scale Velocity Enhancement of Sea Surface Fluxes

Abstract Subgrid-scale (SGS) velocity variations result in gridscale sea surface flux enhancements that must be parameterized in weather and climate models. Traditional parameterizations are deterministic in that they assign a unique value of the SGS velocity flux enhancement to any given configuration of the resolved state. In this study, we assess the statistics of SGS velocity flux enhancement over a range of averaging scales (as a proxy for varying model resolution) through systematic coarse-graining of a convection-permitting atmospheric model simulation over the Indian Ocean and west Pacific warm pool. Conditioning the statistics of the SGS velocity flux enhancement on 1) the fluxes associated with the resolved winds and 2) the precipitation rate, we find that the lack of a separation between “resolved” and “unresolved” scales results in a distribution of flux enhancements for each configuration of the resolved state. That is, the SGS velocity flux enhancement should be represented stochastically rather than deterministically. The spatial and temporal statistics of the SGS velocity flux enhancement are investigated by using basic descriptive statistics and through a fit to an anisotropic space–time covariance structure. Potential spatial inhomogeneities of the statistics of the SGS velocity flux enhancement are investigated through regional analysis, although because of the relatively short duration of the simulation (9 days) distinguishing true inhomogeneity from sampling variability is difficult. Perspectives for the implementation of such a stochastic parameterization in weather and climate models are discussed.

54 ENVIRONMENTAL SCIENCES↗

Joint Bayesian Inference for Near-surface Explosion Yield

Geophysical observations of an explosion scale with the yield of the explosion. Guided by the principal of yield-scaling and observed relationships in the data, we defined and parameterized seismoacoustic forward models in Ford et al. [2014]. This work extends the model with additional data features of maximum velocity and positive phase duration for the seismic and acoustic data types, respectively, and a new optic data type. Parameters for the seismoacoustic models are estimated via Bayesian inference. The parameterized models can then be used to infer the yield of a new explosion.

58 GEOSCIENCES↗

Target Soil Impact Verification: Experimental Testing and Kayenta Constitutive Modeling.

This report details experimental testing and constitutive modeling of sandy soil deformation under quasi - static conditions. This is driven by the need to understand constitutive response of soil to target/component behavior upon impact . An experimental and constitutive modeling program was followed to determine elastic - plastic properties and a compressional failure envelope of dry soil . One hydrostatic, one unconfined compressive stress (UCS), nine axisymmetric compression (ACS) , and one uniaxial strain (US) test were conducted at room temperature . Elastic moduli, assuming isotropy, are determined from unload/reload loops and final unloading for all tests pre - failure and increase monotonically with mean stress. Very little modulus degradation was discernable from elastic results even when exposed to mean stresses above 200 MPa . The failure envelope and initial yield surface were determined from peak stresses and observed onset of plastic yielding from all test results. Soil elasto - plastic behavior is described using the Brannon et al. (2009) Kayenta constitutive model. As a validation exercise, the ACS - parameterized Kayenta model is used to predict response of the soil material under uniaxial strain loading. The resulting parameterized and validated Kayenta model is of high quality and suitable for modeling sandy soil deformation under a range of conditions, including that for impact prediction.

54 ENVIRONMENTAL SCIENCES↗

Demonstration of Effects on Tropical Cyclone Forecasts with a High Resolution Global Model from Variation in Cumulus Convection Parameterization

The Goddard Earth Observing System Model, Version 5 (GEOS-5) is a system of models that have been developed at Goddard Space Flight Center to support NASA's earth science research in data analysis, observing system modeling and design, climate and weather prediction, and basic research. The work presented used GEOS-5 with 0.25o horizontal resolution and 72 vertical levels (up to 0.01 hP) resolving both the troposphere and stratosphere, with closer packing of the levels close to the surface. The model includes explicit (grid-scale) moist physics, as well as convective parameterization schemes. Results will be presented that will demonstrate strong dependence in the results of modeling of a strong hurricane on the type of convective parameterization scheme used. The previous standard (default) option in the model was the Relaxed Arakawa-Schubert (RAS) scheme, which uses a quasi-equilibrium closure. In the cases shown, this scheme does not permit the efficient development of a strong storm in comparison with observations. When this scheme is replaced by a modified version of the Kain-Fritsch scheme, which was originally developed for use on grids with intervals of order 25 km such as the present one, the storm is able to develop to a much greater extent, closer to that of reality. Details of the two cases will be shown in order to elucidate the differences in the two modeled storms.

Miller, Timothy L.↗

Simulations of isoprene: Ozone reactions for a general circulation/chemical transport model

A parameterized reaction mechanism has been created to examine the interactions between isoprene and other tropospheric gas-phase chemicals. Tests of the parameterization have shown that its results match those of a more complex reaction set to a high degree of accuracy. Comparisons between test runs have shown that the presence of isoprene at the start of a six day interval can enhance later ozone concentrations by as much as twenty-nine percent. The test cases used no input fluxes beyond the initial time, implying that a single input of a biogenic hydrocarbon to an airmass can alter its ozone chemistry over a time scale on the order of a week.

Makar, P. A.↗

Time-series machine-learning error models for approximate solutions to parameterized dynamical systems

This work proposes a machine-learning framework for modeling the error incurred by approximate solutions to parameterized dynamical systems. In particular, we extend the machine-learning error models (MLEM) framework proposed in Ref. Freno and Carlberg (2019) to dynamical systems. The proposed Time-Series Machine-Learning Error Modeling (T-MLEM) method constructs a regression model that maps features – which comprise error indicators that are derived from standard a posteriori error-quantification techniques – to a random variable for the approximate-solution error at each time instance. The proposed framework considers a wide range of candidate features, regression methods, and additive noise models. We consider primarily recursive regression techniques developed for time-series modeling, including both classical time-series models (e.g., autoregressive models) and recurrent neural networks (RNNs), but also analyze standard non-recursive regression techniques (e.g., feed-forward neural networks) for comparative purposes. Finally, numerical experiments conducted on multiple benchmark problems illustrate that the long short-term memory (LSTM) neural network, which is a type of RNN, outperforms other methods and yields substantial improvements in error predictions over traditional approaches.

42 ENGINEERING↗

Parameterized desert/clear atmosphere limb-darkening model derived from earth radiation budget satellite along-track measurements

A parameterized desert/clear atmosphere limb-darkening model was derived using longwave measurements from the Earth Radiation Budget Satellite operating in a unique along-track mode that allows all points along the ground track to be viewed over an entire range of viewing zenith angles at essentially constant solar zenith angle. Application of the model to radiances for scenes defined as clear desert by the Earth Radiation Budget Experiment data analysis algorithms shows that this parameterized model reflects the geographical and diurnal behavior expected for the limb-darkening phenomenon.

Brooks, David R.↗

Sensitivity of the MAR Regional Climate Model Snowpack to the Parameterization of the Assimilation of Satellite-Derived Wet-Snow Masks on the Antarctic Peninsula

Both regional climate models (RCMs) and remote sensing (RS) data are essential tools in understanding the response of polar regions to climate change. RCMs can simulate how certain climate variables, such as surface melt, runoff and snowfall, are likely to change in response to different climate scenarios but are subject to biases and errors. RS data can assist in reducing and quantifying model uncertainties by providing indirect observations of the modeled variables on the present climate. In this work, we improve on an existing scheme to assimilate RS wet snow occurrence data with the “Modèle Atmosphérique Régional” (MAR) RCM and investigate the sensitivity of the RCM to the parameters of the scheme. The assimilation is performed by nudging the MAR snowpack temperature to match the presence of liquid water observed by satellites. The sensitivity of the assimilation method is tested by modifying parameters such as the depth to which the MAR snowpack is warmed or cooled, the quantity of water required to qualify a MAR pixel as “wet” (0.1 % or 0.2 % of the snowpack mass being water), and assimilating different RS datasets. Data assimilation is carried out on the Antarctic Peninsula for the 2019–2021 period. The results show an increase in meltwater production (+66.7 % on average, or +95 Gt), along with a small decrease in surface mass balance (SMB) (−4.5 % on average, or −20 Gt) for the 2019–2020 melt season after assimilation. The model is sensitive to the tested parameters, albeit with varying orders of magnitude. The prescribed warming depth has a larger impact on the resulting surface melt production than the liquid water content (LWC) threshold due to strong refreezing occurring within the top layers of the snowpack. The values tested for the LWC threshold are lower than the LWC for typical melt days (approximately 1.2 %) and impact results mainly at the beginning and end of the melting period. The assimilation method will allow for the estimation of uncertainty in MAR meltwater production and will enable the identification of potential issues in modeling near-surface snowpack processes, paving the way for more accurate simulations of snow processes in model projections.

regional climate models↗

Atomistically resolved hot exciton relaxation dynamics in CdSe quantum dots: Experiment and theory

Semiconductor quantum dots (QDs) are well known to give rise to a quantum confined structure of excitons. Because of this quantum confinement, new physics of hot exciton relaxation dynamics arises. Decades of work using transient absorption (TA) spectroscopy have yielded initial simple observations, such as estimates of the cooling rate from single pump photon energy experiments. More detailed TA experiments employed variable pump photon energies to measure excitonic state-resolved transition rates. These TA measurements, usually the simplest form, have been employed to characterize QDs and their relaxation dynamics to this day. Yet, these TA measurements are fundamentally lacking in their ability to measure energy-resolved hot exciton cooling, which requires observation of the full cooling history through the real excitonic manifold. Here, we employ coherent multi-dimensional spectroscopy (CMDS) to perform an atomistically directed study of hot exciton cooling in CdSe QDs, revealing energy resolved relaxation dynamics. CMDS experiments are compared with simulations and prior TA measurements and simpler theories. Our findings reveal a hot exciton relaxation dynamics landscape. This relaxation dynamics landscape is a linear or sub-linear function of excess energy for different structures of QDs, with a strong size dependence. Our model simulations parameterized by the empirical pseudopotential model reproduces the experimental functional form and the dependence upon QD diameter and shell.

Atomistic simulations↗

Testing to Evaluate Processes Expected to Occur during MSR Salt Spill Accidents

Obtaining a license for a new nuclear reactor requires the identification and assessment of the potential consequences of specified accident scenarios, which are achieved using accident progression models. Those models need to be parameterized and validated using experimental data, but existing experimental data addressing processes relevant to molten salt reactor accidents are sparse. Specifically, experimental data that quantify the sensitives of important processes to the initial conditions of the spill, the ambient environment, and the containment features are needed to parameterize individual process models. Integrated experiments that simulate accident scenarios are also needed to provide data for model validation, but these experiments will require the use of proven methods to quantify the processes under evaluation. The overarching objectives of this work are to develop the methods for simulating the targeted processes, to determine the effectiveness of the methods in producing the data required for model development, to generate data that can be used to parameterize individual process models, and to provide key insights into the behavior of spilled molten salt that should be considered in models. Experimental methods were designed to quantify aspects of individual processes expected to occur during or after a molten salt spill accident that will affect the fate of spilled molten salt and the radionuclides within. These processes include 1) molten salt spreading and heat transfer, 2) molten salt flowing and freezing in tubing, 3) stainless steel corrosion kinetics in molten salt, and 4) molten salt splashing and aerosol generation. The initial tests described in this report were conducted using eutectic FLiNaK to demonstrate the test methods, the data that are generated, and the analyses of the data to derive values needed for modeling. The primary variables that were tested include initial salt temperature and the presence of volatile surrogate fission products (e.g., cesium and iodine). The developed methods are shown to be effective in quantifying the desired processes and can be applied to study more complex salt compositions of interest to molten salt reactor developers, a wide range of environmental conditions of interest to modelers, and additional variables relevant to salt spill accidents. The developed methods and insights gained from laboratory tests can also be incorporated in future large-scale integrated tests used to simulate molten salt spill accidents.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Mesoscale Simulations of a Florida Sea Breeze Using the PLACE Land Surface Model Coupled to a 1.5-Order Turbulence Parameterization

A sophisticated land-surface model, PLACE, the Parameterization for Land Atmospheric Convective Exchange, has been coupled to a 1.5-order turbulent kinetic energy (TKE) turbulence sub-model. Both have been incorporated into the Penn State/National Center for Atmospheric Research (PSU/NCAR) mesoscale model MM5. Such model improvements should have their greatest effect in conditions where surface contrasts dominate over dynamic processes, such as the simulation of warm-season, convective events. A validation study used the newly coupled model, MM5 TKE-PLACE, to simulate the evolution of Florida sea-breeze moist convection during the Convection and Precipitation Electrification Experiment (CaPE). Overall, eight simulations tested the sensitivity of the MM5 model to combinations of the new and default model physics, and initialization of soil moisture and temperature. The TKE-PLACE model produced more realistic surface sensible heat flux, lower biases for surface variables, more realistic rainfall, and cloud cover than the default model. Of the 8 simulations with different factors (i.e., model physics or initialization), TKE-PLACE compared very well when each simulation was ranked in terms of biases of the surface variables and rainfall, and percent and root mean square of cloud cover. A factor separation analysis showed that a successful simulation required the inclusion of a multi-layered, land surface soil vegetation model, realistic initial soil moisture, and higher order closure of the planetary boundary layer (PBL). These were needed to realistically model the effect of individual, joint, and synergistic contributions from the land surface and PBL on the CAPE sea-breeze, Lake Okeechobee lake breeze, and moist convection.

Lynn, Barry H.↗

On alpha-particle transport in inertial fusion

Analytical theory and models of inertial fusion implosion use parameterized microphysics models. In this paper, we consider the DT alpha-particle transport, and report new parameterizations of the range, heating efficacy, and energy partition using modern stopping-power theory. Here, our resulting heating efficacy is lower than previously published results, which reduces the temperature and pressure generated by a dynamic implosion hot-spot evolution model, and shifts the burning-plasma regime boundary slightly farther from current experimental results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Tropical dry forest response to nutrient fertilization: a model validation and sensitivity analysis

Abstract. Soil nutrients, especially nitrogen (N) and phosphorus (P), regulate plant growth and hence influence carbon fluxes between the land surface and atmosphere. However, how forests adjust biomass partitioning to leaves, wood, and fine roots in response to N and/or P fertilization remains puzzling. Recent work in tropical forests suggests that trees increase fine root production under P fertilization, but it is unclear whether mechanistic models can reproduce this dynamic. In order to better understand mechanisms governing nutrient effects on plant allocation and improve models, we used the nutrient-enabled ED2 model to simulate a fertilization experiment being conducted in a secondary tropical dry forest in Costa Rica. We evaluated how different allocation parameterizations affected model performance. These parameterizations prescribed a linear relationship between relative allocation to fine roots and soil P concentrations. The slope of the linear relationship was allowed to be positive, negative, or zero. Some parameterizations realistically simulated leaf, wood, and fine root production, and these parameterizations all assumed a positive relationship between relative allocation to fine roots and soil P concentration. Model simulations of a 30-year timeframe indicated strong sensitivity to parameterization and fertilization treatment. Without P fertilization, the simulated aboveground biomass (AGB) accumulation was insensitive to the parameterization. With P fertilization, the model was highly sensitive to the parameterization and the greatest AGB accumulation occurred when relative allocation to fine roots was independent of soil P. Our study demonstrates the need for simultaneous measurements of leaf, wood, and fine root production in nutrient fertilization experiments and for longer-term experiments. Models that do not accurately represent allocation to fine roots may be highly biased in their simulations of AGB, especially on multi-decadal timescales.

Environmental Sciences & Ecology↗

Machine learning based approach to predict ductile damage model parameters for polycrystalline metals

Damage models for ductile materials typically need to be parameterized, often with the appropriate parameters changing for a given material depending on the loading conditions. This can make parameterizing these models computationally expensive, since an inverse problem must be solved for each loading condition. Using standard inverse modeling techniques typically requires hundreds or thousands of high-fidelity computer simulations to estimate the optimal parameters. Additionally, the time of a human expert is required to set up the inverse model. Machine learning has recently emerged as an alternative approach to inverse modeling in these settings, where the machine learning model is trained in an offline manner and new parameters can be quickly generated on the fly, after training is complete. Here, this work utilizes such a workflow to enable the rapid parameterization of a ductile damage model called TEPLA with a machine learning inverse model. The machine learning model can efficiently estimate the model parameters much faster, as compared to previously employed methods, such as Bayesian calibration. The results demonstrate good accuracy on a synthetic test dataset and is validated against experimental data.

36 MATERIALS SCIENCE↗