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At least 487 records · Page 27

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DOE OSTI2019

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

Significance A major challenge in biology is characterizing the structural flexibility of intrinsically disordered proteins (IDPs). Ensemble-averaged experimental data do not provide the underlying protein structures. Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. We report that enhancing the sampling of the simulations can generate an ensemble of IDP structures in quantitative agreement with scattering and NMR, without the need for biasing the simulation or reweighting the results. The demonstration of established simulation technology that produces accurate physical models of flexible biosystems may pave the way to relating conformational flexibility to biological function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Internally Generated and Externally Forced Multidecadal Oceanic Modes and Their Influence on the Summer Rainfall over East Asia

Abstract Interdecadal oceanic variabilities can be generated from both internal and external processes, and these variabilities can significantly modulate climate on global and regional scales, including the warming slowdown in the early twenty-first century and rainfall in East Asia. By analyzing simulations from a unique Community Earth System Model (CESM) Large Ensemble (CESM-LE) project, it is shown that the interdecadal Pacific oscillation (IPO) is primarily an internally generated oceanic variability, while the Atlantic multidecadal oscillation (AMO) may be an oceanic variability generated by internal oceanic processes and modulated by external forcing in the twentieth century. Although the observed relationship between IPO and the Yangtze–Huaihe River valley (YHRV) summer rainfall in China is well simulated in both the preindustrial control and the twentieth-century ensemble simulation, none of the twentieth-century ensemble members can reproduce the observed time evolution of both the IPO and YHRV rainfall because of the unpredictable nature of IPO on multidecadal time scales. On the other hand, although CESM-LE cannot reproduce the observed relationship between the AMO and Huanghe River valley (HRV) summer rainfall of China in the preindustrial control simulation, this relationship in the twentieth-century simulations is well reproduced, and the chance of reproducing the observed time evolution of both AMO and HRV rainfall is about 30%, indicating the important role of the interaction between the internal processes and the external forcing to realistically simulate the AMO and HRV rainfall.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2012

Changes in winter precipitation extremes for the western United States under a warmer climate as simulated by regional climate models

We find a consistent and statistically significant increase in the intensity of future extreme winter precipitation events over the western United States, as simulated by an ensemble of regional climatemodels (RCMs) driven by IPCC AR4 global climate models (GCMs). All eight simulations analyzed in this work consistently show an increase in the intensity of extreme winter precipitation with the multi-model mean projecting an area-averaged 12.6% increase in 20-year return period and 14.4% increase in 50-year return period daily precipitation. In contrast with extreme precipitation, the multi-model ensemble shows a decrease in mean winter precipitation of approximately 7.5% in the southwestern US, while the interior west shows less statistically robust increases.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Realistic simulations of spin squeezing and cooperative coupling effects in large ensembles of interacting two-level systems

We describe an efficient numerical method for simulating the dynamics of interacting spin ensembles in the presence of dephasing and decay. The method builds on the discrete truncated Wigner approximation for isolated systems, which combines the mean-field dynamics of a spin ensemble with a Monte Carlo sampling of discrete initial spin values to account for quantum correlations. Here we show how this approach can be generalized for dissipative spin systems by replacing the deterministic mean-field evolution by a stochastic process, which describes the decay of coherences and populations while preserving the length of each spin. We demonstrate the application of this technique for simulating nonclassical spin-squeezing effects or the dynamics and steady states of cavity QED models with 10 5 interacting two-level systems. This opens up the possibility to perform accurate real-scale simulations of a diverse range of experiments in quantum optics or with solid-state spin ensembles under realistic laboratory conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Optimal Run Strategies in Monte Carlo Iterated Fission Source Simulations

The method of successive generations used in Monte Carlo simulations of nuclear reactor models is known to suffer from intergenerational correlation between the spatial locations of fission sites. One consequence of the spatial correlation is that the convergence rate of the variance of the mean for a tally becomes worse than O(N–1). In this work, we consider how the true variance can be minimized given a total amount of work available as a function of the number of source particles per generation, the number of active/discarded generations, and the number of independent simulations. We demonstrate through both analysis and simulation that under certain conditions the solution time for highly correlated reactor problems may be significantly reduced either by running an ensemble of multiple independent simulations or simply by increasing the generation size to the extent that it is practical. However, if too many simulations or too large a generation size is used, the large fraction of source particles discarded can result in an increase in variance. We also show that there is a strong incentive to reduce the number of generations discarded through some source convergence acceleration technique. Furthermore, we discuss the efficient execution of large simulations on a parallel computer; we argue that several practical considerations favor using an ensemble of independent simulations over a single simulation with very large generation size.

correlation↗

DOE OSTI2022

Hot and dense matter equation of state probability distributions for astrophysical simulations

We add an ensemble of nuclei to the equation of state for homogeneous nucleonic matter to generate a new set of models suitable for astrophysical simulations of core-collapse supernovae and neutron star mergers. We implement empirical constraints from (i) nuclear mass measurements, (ii) proton-proton scattering phase shifts, and (iii) neutron star observations. Our model is also guided by microscopic many-body theory calculations based on realistic nuclear forces, including the zero-temperature neutron matter equation of state from quantum Monte Carlo simulations and thermal contributions to the free energy from finite-temperature many-body perturbation theory. We ensure that the parameters of our model can be varied while preserving thermodynamic consistency and the connection to experimental or observational data, thus providing a probability distribution of the astrophysical hot and dense matter equation of state. Furthermore, we compare our results with those obtained from other available equations of state. While our probability distributions indeed represent a large number of possible equations of state, we cannot yet claim to have fully explored all of the uncertainties, especially with regard to the structure of nuclei in the hot and dense medium.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2017

On the Dependence of Cloud Feedbacks on Physical Parameterizations in WRF Aquaplanet Simulations

We investigate the effects of physical parameterizations on cloud feedback uncertainty in response to climate change. For this purpose, we construct an ensemble of eight aquaplanet simulations using the Weather Research and Forecasting (WRF) model. In each WRF‐derived simulation, we replace only one parameterization at a time while all other parameters remain identical. By doing so, we aim to (i) reproduce cloud feedback uncertainty from state‐of‐the‐art climate models and (ii) understand how parametrizations impact cloud feedbacks. Our results demonstrate that this ensemble of WRF simulations, which differ only in physical parameterizations, replicates the range of cloud feedback uncertainty found in state‐of‐the‐art climate models. We show that microphysics and convective parameterizations govern the magnitude and sign of cloud feedbacks, mostly due to tropical low‐level clouds in subsidence regimes. Finally, this study highlights the advantages of using WRF to analyze cloud feedback mechanisms owing to its plug‐and‐play parameterization capability.

Cesana, Gregory↗

NASA NTRS1991

A multicomputer simulation of the Galileo spacecraft command and data subsystem

A detailed simulation of the command and data subsystem of the Galileo spacecraft on a distributed memory multicomputer is described. The simulation is based on an ensemble of Inmos Transputers for simulating, to the bit level, the execution of instruction sequences for the six RCA 1802 microcomputers and the intricate bus traffic between them and other components of the spacecraft. Expressions were developed to estimate the performance of the simulator on a distributed system given the processor clock speed, memory access time, and communication characteristics.

Zipse, John E.↗

NASA NTRS2002

On Simulating the Mid-western-us Drought of 1988 with a GCM

The primary cause of the midwestern North American drought in the summer of 1988 has been identified to be the La Nina SST anomalies. Yet with the SST anomalies prescribed, this drought has not been simulated satisfactorily by any general circulation model. Seven simulation-experiments, each containing an ensemble of 4-sets of simulations, were conducted with the GEOS GCM for both 1987 and 1988. All simulations started from January 1 and continued through the end of August. In the first baseline case, Case 1, only the SST anomalies and some vegetation parameters were prescribed, while everything else (such as soil moisture, snow-cover, and clouds) was interactive. The GCM did produce some of the circulation features of a drought over North America, but they could only be identified on the planetary scales. The 1988 minus 1987 precipitation differences show that the GCM was successful in simulating reduced precipitation in the mid-west, but the accompanying circulation anomalies were not well simulated, leading one to infer that the GCM has simulated the drought for the wrong reason. To isolate the causes for this unremarkable circulation, analyzed winds and soil moisture were prescribed in Case 2 and Case 3 as continuous updates by direct replacement of the GCM-predicted fields. These cases show that a large number of simulation biases emanate from wind biases that are carried into the North American region from surroundings regions. Inclusion of soil moisture also helps to ameliorate the strong feedback, perhaps even stronger than that of the real atmosphere, between soil moisture and precipitation. Case 2 simulated one type of surface temperature anomaly pattern, whereas Case 3 with the prescribed soil moisture produced another.

Sud, Y. C.↗

NASA NTRS2004

Estimating the instability of a composite clock

A composite clock created from a local clock ensemble is known by its time offsets from the ensemble clocks. By a geometrical argument, estimate for the instability of the composite clock are calculated from the instabilities of the ensemble clocks, individually and against the composite clock. The method is illustrated by examples using simulated and real ensembles.

timescale↗

NASA NTRS1992

Role of a cumulus parameterization scheme in simulating atmospheric circulation and rainfall in the nine-layer Goddard Laboratory for Atmospheres General Circulation Model

The influence of a cumulus convection scheme on the simulated atmospheric circulation and hydrologic cycle is investigated by means of a coarse version of the GCM. Two sets of integrations, each containing an ensemble of three summer simulations, were produced. The ensemble sets of control and experiment simulations are compared and differentially analyzed to determine the influence of a cumulus convection scheme on the simulated circulation and hydrologic cycle. The results show that cumulus parameterization has a very significant influence on the simulation circulation and precipitation. The upper-level condensation heating over the ITCZ is much smaller for the experiment simulations as compared to the control simulations; correspondingly, the Hadley and Walker cells for the control simulations are also weaker and are accompanied by a weaker Ferrel cell in the Southern Hemisphere. Overall, the difference fields show that experiment simulations (without cumulus convection) produce a cooler and less energetic atmosphere.

Sud, Y. C.↗

NASA NTRS2012

A Comparison of Perturbed Initial Conditions and Multiphysics Ensembles in a Severe Weather Episode in Spain

Ensembles of numerical model forecasts are of interest to operational early warning forecasters as the spread of the ensemble provides an indication of the uncertainty of the alerts, and the mean value is deemed to outperform the forecasts of the individual models. This paper explores two ensembles on a severe weather episode in Spain, aiming to ascertain the relative usefulness of each one. One ensemble uses sensible choices of physical parameterizations (precipitation microphysics, land surface physics, and cumulus physics) while the other follows a perturbed initial conditions approach. The results show that, depending on the parameterizations, large differences can be expected in terms of storm location, spatial structure of the precipitation field, and rain intensity. It is also found that the spread of the perturbed initial conditions ensemble is smaller than the dispersion due to physical parameterizations. This confirms that in severe weather situations operational forecasts should address moist physics deficiencies to realize the full benefits of the ensemble approach, in addition to optimizing initial conditions. The results also provide insights into differences in simulations arising from ensembles of weather models using several combinations of different physical parameterizations.

severe weather↗

DOE OSTI2019

Evaluating the Uncertainty of Terrestrial Water Budget Components Over High Mountain Asia

This study explores the uncertainties in terrestrial water budget estimation over High Mountain Asia (HMA) using a suite of uncoupled land surface model (LSM) simulations. The uncertainty in the water balance components of precipitation (P), evapotranspiration (ET), runoff (R), and terrestrial water storage (TWS) is significantly impacted by the uncertainty in the driving meteorology, with precipitation being the most important boundary condition. Ten gridded precipitation datasets along with a mix of model-, satellite-, and gauge-based products, are evaluated first to assess their suitability for LSM simulations over HMA. The datasets are evaluated by quantifying the systematic and random errors of these products as well as the temporal consistency of their trends. Though the broader spatial patterns of precipitation are generally well captured by the datasets, they differ significantly in their means and trends. In general, precipitation datasets that incorporate information from gauges are found to have higher accuracy with low Root Mean Square Errors and high correlation coefficient values. An ensemble of LSM simulations with selected subset of precipitation products is then used to produce the mean annual fluxes and their uncertainty over HMA in P, ET, and R to be 2.11 ± 0.45, 1.26 ± 0.11, and 0.85 ± 0.36 mm per day, respectively. The mean annual estimates of the surface mass (water) balance components from this model ensemble are comparable to global estimates from prior studies. However, the uncertainty/spread of P, ET, and R is significantly larger than the corresponding estimates from global studies. A comparison of ET, snow cover fraction, and changes in TWS estimates against remote sensing-based references confirms the significant role of the input meteorology in influencing the water budget characterization over HMA and points to the need for improving meteorological inputs.

Yoon, Yeosang↗

NASA NTRS2016

An Assessment of Multimodel Simulations for the Variability of Western North Pacific Tropical Cyclones and Its Association with ENSO

An assessment of simulations of the interannual variability of tropical cyclones (TCs) over the western North Pacific (WNP) and its association with El Niño-Southern Oscillation (ENSO), as well as a subsequent diagnosis for possible causes of model biases generated from simulated large-scale climate conditions, are documented in the paper. The model experiments are carried out by the Hurricane Work Group under the U.S. Climate Variability and Predictability Research Program (CLIVAR) using five global climate models (GCMs) with a total of 16 ensemble members forced by the observed sea surface temperature and spanning the 28-yr period from 1982 to 2009. The results show GISS and GFDL model ensemble means best simulate the interannual variability of TCs, and the multimodel ensemble mean (MME) follows. Also, the MME has the closest climate mean annual number of WNP TCs and the smallest root-mean-square error to the observation. Most GCMs can simulate the interannual variability of WNP TCs well, with stronger TC activities during two types of El Niño-namely, eastern Pacific (EP) and central Pacific (CP) El Niño-and weaker activity during La Niña. However, none of the models capture the differences in TC activity between EP and CP El Niño as are shown in observations. The inability of models to distinguish the differences in TC activities between the two types of El Niño events may be due to the bias of the models in response to the shift of tropical heating associated with CP El Niño.

climate models↗

DOE OSTI2013

Two-Way Integration of WRF and CCSM for Regional Climate Simulations

Under the support of the DOE award DE-SC0004670, we have successfully developed an integrated climate modeling system by nesting Weather Research and Forecasting (WRF) model within the Community Climate System Model (CCSM) and the ensuing new generation Community Earth System Model (CESM). The integrated WRF/CESM system is intended as one method of global climate modeling with regional simulation capabilities. It allows interactive dynamical regional downscaling in the computational flow of present or future global climate simulations. This capability substantially simplifies the process of dynamical downscaling by avoiding massive intermediate model outputs at high frequency that are typically required for offline regional downscaling. The inline coupling also has the advantage of higher temporal resolution for the interaction between regional and global model components. With the aid of the inline coupling, a capability has also been developed to ingest other global climate simulations (by CESM or other models), which otherwise may not have necessary intermediate outputs for regional downscaling, to realize their embedded regional details. It is accomplished by relaxing the global atmospheric state of the integrated model to that of the source simulations with an appropriate time scale. This capability has the potential to open a new venue for ensemble regional climate simulations using a single modeling system. Furthermore, this new modeling system provides an effective modeling framework for the studies of physical and dynamical feedbacks of regional weather phenomena to the large scale circulation. The projected uses of this capability include the research of up-scaling effect of regional weather system, and its use as an alternative physical representation of sub-scale processes in coarser-resolution climate models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Can nudging be used to quantify model sensitivities in precipitation and cloud forcing?

Efficient simulation strategies are crucial for the development and evaluation of high resolution climate models. This paper evaluates simulations with constrained meteorology for the quantification of parametric sensitivities in the Community Atmosphere Model version 5 (CAM5). Two parameters are perturbed as illustrating examples: the convection relaxation time scale (TAU), and the threshold relative humidity for the formation of low-level stratiform clouds (rhminl). Results suggest that the fidelity and computational efficiency of the constrained simulations depend strongly on 3 factors: the detailed implementation of nudging, the mechanism through which the perturbed parameter affects precipitation and cloud, and the magnitude of the parameter perturbation. In the case of a strong perturbation in convection, temperature and/or wind nudging with a 6-hour relaxation time scale leads to non-negligible side effects due to the distorted interactions between resolved dynamics and parameterized convection, while a 1-year free running simulation can satisfactorily capture the annual mean precipitation sensitivity in terms of both global average and geographical distribution. In the case of a relatively weak perturbation the large-scale condensation scheme, results from 1-year free-running simulations are strongly affected by noise associated with internal variability, while nudging winds effectively reduces the noise, and reasonably reproduces the response of precipitation and cloud forcing to parameter perturbation. These results indicate that caution is needed when using nudged simulations to assess precipitation and cloud forcing sensitivities to parameter changes in general circulation models. We also demonstrate that ensembles of short simulations are useful for understanding the evolution of model sensitivities.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

The role of pressure in inverse design for assembly

Isotropic pairwise interactions that promote the self-assembly of complex particle morphologies have been discovered by inverse design strategies derived from the molecular coarse-graining literature. While such approaches provide an avenue to reproduce structural correlations, thermodynamic quantities such as the pressure have typically not been considered in self-assembly applications. In this work, we demonstrate that relative entropy optimization can be used to discover potentials that self-assemble into targeted cluster morphologies with a prescribed pressure when the iterative simulations are performed in the isothermal-isobaric ensemble. The benefits of this approach are twofold. First, the structure and the thermodynamics associated with the optimized interaction can be controlled simultaneously. Second, by varying the pressure in the optimization, a family of interparticle potentials that all self-assemble the same structure can be systematically discovered, allowing for a deeper understanding of self-assembly of a given target structure and providing multiple assembly routes for its realization. Selecting an appropriate simulation ensemble to control the thermodynamic properties of interest is a general design strategy that could also be used to discover interaction potentials that self-assemble structures having, for example, a specified chemical potential.

74 ATOMIC AND MOLECULAR PHYSICS↗

NASA NTRS1992

Infrared, microwave, and spaceborne radar simulations of a deep convective system using a 3-D cloud ensemble method

A 3D cloud model is used to simulate the storm structure, and the results are linked to microwave and infrared radiative transfer models for simulation of aircraft observations. Spaceborne radar data are also simulated along the aircraft flight track. The cloud and radiative model simulations are studied and compared with aircraft observations. The initial results indicate that the 3D cloud model is capable of simulating the major features of observed storm systems when given a representative atmospheric sounding to initialize the convective systems. The simulations of infrared and microwave radiances provide reasonably good comparisons with the observations.

Yeh, H.-Y. M.↗