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At least 1,711 records · Page 95
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large genetic circuit in different states: RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Biogeochemical modeling of CO 2 and CH 4 production in anoxic Arctic soil microcosms

Abstract. Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe the observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Process-based modeling of soil nitrous oxide emissions from United States corn fields under different management and climate scenarios coupled with evaluation using regional estimates

Direct emissions of soil nitrous oxide during a growing season (N 2 O gs ) can be quantified with process-based models considering interactions between management, climate, and soil moisture when key data are available. We used an adapted “parameterized CENTURY/DAYCENT-model” ( p CENTURY) calibrated with crop growth and soil organic matter decay coefficients at the county-level for the estimation of N 2 O gs in the United States Corn Belt. Model estimated N 2 O-emissions from corn-based biofuels scenarios considering crop rotation, fertilizer inputs, tillage, and weather were compared against meta-summary of field observations from 55 studies. Both model and meta-summary ranked N 2 O gs -emissions to be corn > wheat > soybean phase while model likely underestimated cover crop N 2 O gs -emissions. The N 2 O gs -emissions and the associated emission factors (EFs) were modeled and summarized to be greater after anhydrous ammonia than urea application and from conventional tilled than non-tilled fields. Modeled and observed N 2 O gs -emissions after organic and inorganic fertilizer amendment did not differ due to high variability associated with the treatments. However, the organic fertilizer associated EFs were greater according to meta-summary data because of N input rates. Regionalized weather scenarios indicate hotspots for N 2 O gs -emissions can occur where crop N uptake is limited during dry years and in eastern states also during normal or wet seasons. The p CENTURY-derived N 2 O gs EFs (0.91 ± 0.19%) for counties investigated were only slightly lower than literature (1.07 ± 0.57%) or Tier-1 (1%) values. Our preliminary evaluation of regional soil moisture estimates showed reasonable agreement between monthly soil moisture estimates and the North American Soil Moisture Dataset during the growing season, but overestimation of soil moisture in winter-spring can influence the estimates of annual N 2 O emissions so future work is needed to calibrate soil moisture-associated model parameters. Our work provided scenario-based estimates of climate and management impacts on soil N 2 O gs -emissions together with valuable spatial insights into EFs that will be improved by more accurate information of fertilizer inputs and more temporally refined model evaluation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

A Non-hydrostatic Variable Resolution Atmospheric Model in ACME

The Accelerated Climate Modeling for Energy (ACME) Project is designed to perform coupled climate simulations at high resolution on current and next generation DOE leadership class supercomputers. Prior to this project, the ACME atmospheric model employed the primitive equations of motion, which constrained its maximum resolution and limited the physical phenomena that it could resolve. Our team removed this constraint by implementing a non-hydrostatic (NH) atmospheric model in the ACME Framework. Collaboration with SciDAC FASTMath institutes facilitated improvements to key technologies needed for the non-hydrostatic model. This model was tested in a variable resolution framework, which enables high resolution simulation regions at reasonable computational costs. The correct performance of the NH model was verified with standard dynamical-core tests, and by demonstrating that it reproduced expected climate statistics in the hydrostatic regime. The completed model was applied to evaluate the limitations of existing turbulent mountain stress and gravity wave drag parameterizations, in order to demonstrate the power of the new nonhydrostatic model to model new phenomena and enhance the quality of present day 1/4 degree simulations.

Hall, David Matthew↗
DOE OSTI2015

ALMA OBSERVATIONS OF THE DEBRIS DISK AROUND THE YOUNG SOLAR ANALOG HD 107146

We present the Atacama Large Millimeter/submillimeter Array (ALMA) continuum observations at a wavelength of 1.25 mm of the debris disk surrounding the ∼100 Myr old solar analog HD 107146. The continuum emission extends from about 30 to 150 AU from the central star with a decrease in the surface brightness at intermediate radii. We analyze the ALMA interferometric visibilities using debris disk models with radial profiles for the dust surface density parameterized as (1) a single power law, (2) a single power law with a gap, and (3) a double power law. We find that models with a gap of radial width ∼8 AU at a distance of ∼80 AU from the central star, as well as double power-law models with a dip in the dust surface density at ∼70 AU provide significantly better fits to the ALMA data than single power-law models. We discuss possible scenarios for the origin of the HD 107146 debris disk using models of planetesimal belts in which the formation of Pluto-sized objects trigger disruptive collisions of large bodies, as well as models that consider the interaction of a planetary system with a planetesimal belt and spatial variation of the dust opacity across the disk. If future observations with higher angular resolution and sensitivity confirm the fully depleted gap structure discussed here, a planet with a mass of approximately a few Earth masses in a nearly circular orbit at ∼80 AU from the central star would be a possible explanation for the presence of the gap.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Low-cloud characteristics over the tropical western Pacific from ARM observations and CAM5 simulations

Here, this study evaluates the ability of the Community Atmospheric Model version 5 (CAM5) to reproduce low clouds observed by the Atmospheric Radiation Measurement (ARM) cloud radar at Manus Island of the tropical western Pacific during the Years of Tropical Convection. Here low clouds are defined as clouds with their tops below the freezing level and bases within the boundary layer. Low-cloud statistics in CAM5 simulations and ARM observations are compared in terms of their general occurrence, mean vertical profiles, fraction of precipitating versus nonprecipitating events, diurnal cycle, and monthly time series. Other types of clouds are included to put the comparison in a broader context. The comparison shows that the model overproduces total clouds and their precipitation fraction but underestimates low clouds in general. The model, however, produces excessive low clouds in a thin layer between 954 and 930 hPa, which coincides with excessive humidity near the top of the mixed layer. This suggests that the erroneously excessive low clouds stem from parameterization of both cloud and turbulence mixing. The model also fails to produce the observed diurnal cycle in low clouds, not exclusively due to the model coarse grid spacing that does not resolve Manus Island. Lastly, this study demonstrates the utility of ARM long-term cloud observations in the tropical western Pacific in verifying low clouds simulated by global climate models, illustrates issues of using ARM observations in model validation, and provides an example of severe model biases in producing observed low clouds in the tropical western Pacific.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Final Report for “Simulating the Arctic Winter Longwave Indirect Effects. A New Parameterization for Frost Flower Aerosol Salt Emissions” (DESC0006679) for 9/15/2011 through 9/14/2015

Description of the Project: This project has improved the aerosol formulation in a global climate model by using innovative new field and laboratory observations to develop and implement a novel wind-driven sea ice aerosol flux parameterization. This work fills a critical gap in the understanding of clouds, aerosol, and radiation in polar regions by addressing one of the largest missing particle sources in aerosol-climate modeling. Recent measurements of Arctic organic and inorganic aerosol indicate that the largest source of natural aerosol during the Arctic winter is emitted from crystal structures, known as frost flowers, formed on a newly frozen sea ice surface [Shaw et al., 2010]. We have implemented the new parameterization in an updated climate model making it the first capable of investigating how polar natural aerosol-cloud indirect effects relate to this important and previously unrecognized sea ice source. The parameterization is constrained by Arctic ARM in situ cloud and radiation data. The modified climate model has been used to quantify the potential pan-Arctic radiative forcing and aerosol indirect effects due to this missing source. This research supported the work of one postdoc (Li Xu) for two years and contributed to the training and research of an undergraduate student. This research allowed us to establish a collaboration between SIO and PNNL in order to contribute the frost flower parameterization to the new ACME model. One peer-reviewed publications has already resulted from this work, and a manuscript for a second publication has been completed. Additional publications from the PNNL collaboration are expected to follow.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Construction of deep-learning based WWBs parameterization for ENSO prediction

Westerly wind bursts (WWBs) significantly impact the occurrence and development of the El Niño-Southern Oscillation (ENSO). Current dynamical models, however, face significant challenges in representing WWBs. In this study, deep learning techniques were used to develop a new parameterization scheme for WWBs and further compared against two widely used schemes. Further, the results show that the scheme developed in this study has greater capability than previous schemes in reproducing WWBs characteristics, particularly in terms of occurrence probability, location, and duration. This improvement was mainly reflected in El Niño years, especially in strong events when the deep-learning-based scheme much realistically captures the location and strength of WWBs. It is expected that the new parameterization scheme will further improve ENSO prediction in dynamical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Reconstruction of interaction rate in holographic dark energy

The present work is based on the holographic dark energy model with Hubble horizon as the infrared cut-off. The interaction rate between dark energy and dark matter has been reconstructed for three different parameterizations of the deceleration parameter. Observational constraints on the model parameters have been obtained by maximum likelihood analysis using the observational Hubble parameter data (OHD), type Ia supernovab data (SNe), baryon acoustic oscillation data (BAO) and the distance prior of cosmic microwave background (CMB) namely the CMB shift parameter data (CMBShift). The interaction rate obtained in the present work remains always positive and increases with expansion. It is very similar to the result obtained by Sen and Pavon [1] where the interaction rate has been reconstructed for a parametrization of the dark energy equation of state. Tighter constraints on the interaction rate have been obtained in the present work as it is based on larger data sets. The nature of the dark energy equation of state parameter has also been studied for the present models. Though the reconstruction is done from different parametrizations, the overall nature of the interaction rate is very similar in all the cases. Different information criteria and the Bayesian evidence, which have been invoked in the context of model selection, show that the these models are at close proximity of each other.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Coupled Climate Simulations With E3SM‐MMF

Simulations of the recent historical period from 1950 to 2014 are conducted with E3SM‐MMF, which uses an embedded 2D cloud resolving model that runs efficiently on GPUs in place of traditional parameterizations for cloud and turbulence. Analysis of the climate and variability reveal several aspects where E3SM‐MMF produces smaller biases compared to E3SMv2, including better agreement with the observed evolution of global mean surface temperature, although the representation of ENSO is too weak and fast. Three idealized abrupt CO 2 experiments were also conducted to assess climate sensitivity and feedbacks. These yield three estimates of effective climate sensitivity (4.38, 5.21, and 6.06 K), with a corresponding spread in the shortwave cloud feedbacks. These estimates are on the higher end of sensitivity estimates from CMIP ensembles, and the spread indicates substantial state‐dependent feedbacks. These results demonstrate how multiscale modeling framework (MMF) models can be used for climate relevant experiments and projections by leveraging modern GPU enabled computational platforms. The unique qualities of E3SM‐MMF shown in previous literature are largely still present, but various instances of reduced biases suggest that MMF models have utility in improving future projections.

E3SM↗
DOE OSTI2023

Seasonal trends in leaf-level photosynthetic capacity and water use efficiency in a North American Eastern deciduous forest and their impact on canopy-scale gas exchange

Vegetative transpiration (E) and photosynthetic carbon assimilation (A) are known to be seasonally dynamic, with changes in their ratio determining the marginal water use efficiency (WUE). Despite an understanding that stomata play a mechanistic role in regulating WUE, it is still unclear how stomatal and nonstomatal processes influence change in WUE over the course of the growing season. As a result, limited understanding of the primary physiological drivers of seasonal dynamics of canopy WUE remains one of the largest uncertainties in earth system model projections of carbon and water exchange in temperate deciduous forest ecosystems. Here, we investigated seasonal patterns in leaf-level physiological, hydraulic, and anatomical properties, including the seasonal progress of the stomatal slope parameter (g 1 ; inversely proportional to WUE) and the maximum carboxylation rate (V cmax ). V cmax and g 1 were seasonally variable; however, their patterns were not temporally synchronized. g 1 generally showed an increasing trend until late in the season, while V cmax peaked during the midsummer months. Seasonal progression of V cmax was primarily driven by changes in leaf structural, and anatomical characteristics, while seasonal changes in g 1 were most strongly related to changes in V cmax and leaf hydraulics. Using a seasonally variable V cmax and g 1 to parameterize a canopy-scale gas exchange model increased seasonally aggregated A and E by 3% and 16%, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces

Understanding ion adsorption at electrified metal–electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, in this study, we systematically investigate the free energy profiles of Na + , Cl − , and F − ions at the Au(111)–water interface using enhanced sampling molecular dynamics with both classical force fields and machine-learned interatomic potentials (MLIPs). Our classical metadynamics results reveal a strong dependence of predicted ion adsorption on the Lennard-Jones parameters, highlighting that—without due care—standard mixing rules can lead to qualitatively incorrect descriptions of ion–metal interactions. We present a systematic methodology for tuning the cross term LJ parameters to control adsorption energetics in agreement with more accurate models. As a surrogate for an ab initio model, we employed the recently released Universal Models for Atoms MLIP, which validates classical trends and displays strong specific adsorption for chloride, weak adsorption for fluoride, and no specific adsorption for sodium, in agreement with experimental and theoretical expectations. By integrating molecular-level adsorption free energies into continuum models of the electric double layer, we show that specific ion adsorption substantially alters the interfacial ion population, the potential of zero charge, and the differential capacitance of the system. Our results underscore the critical importance of force field parameterization and advanced interatomic potentials for the predictive modeling of ion-specific effects at electrified interfaces and provide a robust framework for bridging molecular simulations and continuum electrochemical models.

Roncoroni, Fabrice [Lawrence Berkeley National Lab↗
DOE OSTI2020

Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.

H atom parameterization↗
DOE OSTI2026

Understanding the causes of satellite–model discrepancies in aerosol–cloud interactions using near-LES simulations of marine boundary layer clouds

Aerosol–cloud interactions (ACI) remain the largest source of uncertainty in model estimates of anthropogenic radiative forcing, primarily because of deficiencies in representing aerosol–cloud microphysical processes that lead to inconsistent cloud liquid water path (LWP) responses to aerosol perturbations between observations and models. To investigate this discrepancy, we conducted a series of large-eddy-scale simulations driven by realistic meteorology over the eastern North Atlantic, and evaluated LWP susceptibility, precipitation processes, and boundary layer thermodynamics using satellite and ground-based observations. Simulated LWP responses show a strong dependence on cloud state. Non-precipitating thin clouds exhibit a modest LWP decrease with increasing cloud droplet number concentration (N d ), consistent in sign but weaker in magnitude than satellite estimates, reflecting enhanced turbulent mixing and evaporation. The largest model-observation discrepancy occurs in non-precipitating thick clouds, where simulated LWP susceptibilities are strongly positive (+0.32) while observations indicate large negative values (−0.69). This discrepancy stems from excessive precipitation driven by underestimated entrainment, overly active accretion, and overly broad drop-size distributions in polluted conditions. While our high-resolution setup mitigates the excessive drizzling common in coarser models and captures key regime transitions, these biases persist – highlighting that improved parameterizations of cloud-top processes, precipitation, and aerosol effects are needed beyond simply increasing model resolution. Additionally, misrepresented moisture inversions in reanalysis introduce a moist bias in cloud-top relative humidity, further amplifying positive LWP susceptibility. Our results also suggest that large negative N d –LWP relationships in observations may reflect internal cloud processes rather than true ACI effects.

Aerosol-cloud interaction↗
DOE OSTI2022

Co-optimized machine-learned manifold models for large eddy simulation of turbulent combustion

Many modeling approaches in large eddy simulation (LES) of turbulent combustion employ a projection of the thermochemical state onto a low-dimensional manifold within state space to reduce the number of transported variables and hence computational cost. Flamelet-generated manifolds (FGM) is an example of a well-established, physics-based approach, but increasingly, principal component analysis (PCA) is being used as a data-driven method for generating manifold models. For both approaches, the nonlinear relationship between the location on the predefined manifold and the outputs of interest, such as reaction rates, can be tabulated or encoded in a neural network. This work proposes a new approach for manifold modeling that extends these existing approaches. A modified neural network structure simultaneously encodes the definition of the manifold variables, the nonlinear mapping, and the subfilter closure for LES. This allows all three of these aspects of the model to be co-optimized, generating a model from any source of combustion thermochemical state data. The manifold parameterizing variables are constrained to be linear combinations of species, as in FGM and PCA-based models, to aid in interpretability and implementation. For LES, subfilter variances of the manifold variables are also included as inputs. Two types of a priori analysis are performed to evaluate the new approach. In the first, the model is trained on data from one-dimensional premixed flames. In this case, the approach recovers the behavior of flamelet-based manifold approaches, and in fact slightly improves performance by identifying an optimized progress variable. The approach is also applied to data from direct numerical simulations of spherical ignition kernels in isotropic turbulence. For any specified manifold dimensionality, the new approach provides substantially lower prediction errors than a PCA-based model developed from the same data set. Additionally, the LES formulation of the new approach can provide accurate predictions for filtered reaction rates across a variety of filter widths.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Assessing the drivers of Isoprene SOA: laboratory studies, field observations and modeling (Final Technical Report)

This report describes the research results and products stemming from the funding award DE-SC0018221. The main goals of this project were to develop a quantitative understanding of the factors driving secondary organic aerosol (SOA) formation from biogenic volatile organic compounds, namely isoprene and monoterpenes, using a combination of laboratory measurements, field data analysis, and modeling. Specifically, we aimed to: 1) develop an observationally constrained volatility distribution of trace gases produced from the oxidation of biogenic hydrocarbons that can explain the formation of SOA from in situ observations made during DOE ASR/ARM field campaigns such as HI-SCALE and BAECC 2) use new and existing (e.g. DOE ASR funded SOAFFEE experiments) laboratory chamber experiments to develop detailed parameterizations of isoprene-derived epxoy diol (IEPOX) reactive uptake, including product branching, product volatility, and solubility constants, as well as SOA formation generally from the formation of highly oxygenated organic molecules (HOM) formed from isoprene and monoterpene photo-oxidation that can be directly incorporated into models. 3) collaborate with PNNL modeling teams to incorporate new parameterizations into detailed box models, such as MOSAIC, and regional or Earth System models such as WRF.

54 ENVIRONMENTAL SCIENCES↗