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At least 1,477 records · Page 82

Reconstruction and analysis of the genome-scale metabolic model of schizochytrium limacinum SR21 for docosahexaenoic acid production

Schizochytrium limacinum SR21 is a potential industrial strain for docosahexaenoic acid (DHA) production that contains more than 30–40 % DHA among its total fatty acids. To resolve the DHA biosynthesis mechanism and improve DHA production at a systematic level, a genomescale metabolic model (GSMM), named iCY1170_DHA, which contains 1769 reactions, 1659 metabolites, and 1170 genes, was reconstructed. Results: Based on genome annotation results and literature reports, a new DHA synthesis pathway based on a polyketide synthase (PKS) system was detected in S. limacinum. Similarly to conventional fatty acid synthesis, the biosynthesis of DHA via PKS requires abundant acetyl-CoA and NADPH. The in silico addition of malate and citrate led to increases of 24.5 % and 37.1 % in DHA production, respectively. Moreover, based on the results predicted by the model, six amino acids were shown to improve DHA production by experiment. Finally, 30 genes were identified as potential targets for DHA over-production using a Minimization of Metabolic Adjustment algorithm. The reconstructed GSMM, iCY1170_DHA, could be used to elucidate the mechanism by which DHA is synthesized in S. limacinum and predict the requirements of abundant acetyl-CoA and NADPH for DHA production as well as the enhanced yields achieved via supplementation with six amino acids, malate, and citrate.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of High-Fidelity Ice Accretion Simulations on the Performance of a Full-Scale Airfoil Model

The simulation of ice accretion on a wing or other surface is often required for aerodynamic evaluation, particularly at small scale or low-Reynolds number. While there are commonly accepted practices for ice simulation, there are no established and validated guidelines. The purpose of this article is to report the results of an experimental study establishing a high-fidelity, full-scale, iced-airfoil aerodynamic performance database. This research was conducted as a part of a larger program with the goal of developing subscale aerodynamic simulation methods for iced airfoils. Airfoil performance testing was carried out at the ONERA F1 pressurized wind tunnel using a 72-in. (1828.8-mm) chord NACA 23012 airfoil over a Reynolds number range of 4.5x10(exp 6) to 16.0 10(exp 6) and a Mach number range of 0.10 to 0.28. The high-fidelity, ice-casting simulations had a significant impact on the aerodynamic performance. A spanwise-ridge ice shape resulted in a maximum lift coefficient of 0.56 compared to the clean value of 1.85 at Re = 15.9x10(exp 6) and M = 0.20. Two roughness and streamwise shapes yielded maximum lift values in the range of 1.09 to 1.28, which was a relatively small variation compared to the differences in the ice geometry. The stalling characteristics of the two roughness and one streamwise ice simulation maintained the abrupt leading-edge stall type of the clean NACA 23012 airfoil, despite the significant decrease in maximum lift. Changes in Reynolds and Mach number over the large range tested had little effect on the iced-airfoil performance.

Broeren, Andy P.↗

Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose

Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.

09 BIOMASS FUELS↗

A Physical Basis for M s -Yield Scaling in Hard Rock and Implications for Late-Time Damage of the Source Medium

Surface wave magnitude M s for a compilation of 72 nuclear tests detonated in hard rock media for which yields and burial depths have been reported in the literature is shown to scale with yield W as a + b × log[W], where a = 2.50 ± 0.08 and b = 0.80 ± 0.05. While the exponent b is consistent with an M s scaling model for fully coupled, normal containment-depth explosions, the intercept a is offset 0.45 magnitude units lower than the model. The cause of offset is important to understand in terms of the explosion source. Hard rock explosions conducted in extensional and compressional stress regimes show similar offsets, an indication that the tectonic setting in which an explosion occurs plays no role causing the offset. The scaling model accounts for the effects of source medium material properties on the generation of 20-s period Rayleigh wave amplitudes. Aided by thorough characterizations of the explosion and tectonic release sources, an extensive analysis of the 1963 October 26 Shoal nuclear test detonated in granite 27 miles southeast of Fallon NV shows that the offset is consistent with the predictions of a material damage source model related to non-linear stress wave interactions with the free surface. This source emits Rayleigh waves with polarity opposite to waves emitted by the explosion. The Shoal results were extended to analyse surface waves from the 1962 February 15 Hardhat nuclear test, the 1988 September 14 Soviet Joint Verification Experiment, and the anomalous 1979 August 18 northeast Balapan explosion which exhibits opposite polarity, azimuth-independent source component U1 compared to an explosion. Modelling these tests shows that Rayleigh wave amplitudes generated by the damage source are nearly as large as or larger than amplitudes from the explosion. As such, destructive interference can be drastic, introducing metastable conditions due to the sensitivity of reduced amplitudes to Rayleigh wave initial phase angles of the explosion and damage sources. This meta-stability is a likely source of scatter in M s -yield scaling observations. The agreement of observed scaling exponent b with the model suggests that the damage source strength does not vary much with yield, in contrast to explosions conducted in weak media where Ms scaling rates are greater than the model predicts, and the yield dependence of the damage source strength is significant. This difference in scaling behaviour is a consequence of source medium material properties.

58 GEOSCIENCES↗

HPC-enabled computation of demand models at scale

The purpose of this project is to examine the energy impact of urban-scale traffic for the Los Angeles Basin by developing and implementing a scalable traffic assignment model. An energy optimization function will be posed and when integrated into the optimization code for travel assignment it can be mathematically proven to converge. The energy optimization function can then be compared to the typical travel time optimization that is traditionally used in traffic assignment models. The analysis will begin with static traffic assignment models with the routing for all origin and destinations computed in parallel on high performance computing facilities. Convergence of the numerical methods rely on the solution of convex programs (or extensions of these). This step will mostly consist of demonstrating the ability to parallelize the Frank Wolfe algorithm on various platforms.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Numerical simulations of turbulent thermal convection with differential rotation

The solar nebula, from which the planets in our solar system formed, featured a disk of gas and dust grains in rapid, differential rotation, and at some stage was likely to have been unstable to thermal convection. This situation is suspected by many to lead to significant turbulent Reynolds stress production and angular momentum transport in such systems, and estimates of transport rates have been attempted from unsubstantiated phenomenological models. In order to determine the circumstances and physical conditions under which our own planetary system formed and to explain recent observations of young stellar systems, it is necessary to develop realistic models of heat and angular momentum transport for such flows. Developing an understanding of complicated flows featuring thermal convection, rotation, and shear is also of wide interest in stellar astrophysics and in planetary and terrestrial atmospheric studies. The ultimate objective is to develop workable models based on the numerical simulations for constructing global solar nebula models; viz., relatively simple prescriptions for heat and angular momentum fluxes from given system parameters (e.g., ratios of rotation, shear, and convective lapse rates) are characterized, quantified, and developed. Toward this end, our program has been to attempt to understand the behavior of the direct numerical simulations of Boussinesq convection, which, despite the complexity of the results, is still an overly simplified approximation to the real system and should be more amenable to analysis. These results are also intended to be tested against turbulence models, especially those designed for atmospheric boundary layers, and may provide a basis for subgrid-scale models. In order to make the numerical simulations more realistic with regard to the solar nebula problem, a fully compressible code that will allow incorporation of large density stratifications and realistic thermodynamic and radiative properties is developed. In order to explore the properties of these flows at the very high values of Re found in natural systems and the very low values of Pr found in most astrophysical contexts, we will need to employ large-eddy simulations for which we want to determine the most appropriate subgrid-scale model to incorporate.

Cabot, William H.↗

Starobinsky-like inflation and neutrino masses in a no-scale SO(10) model

Using a no-scale supergravity framework, we construct an SO(10) model that makes predictions for cosmic microwave background observables similar to those of the Starobinsky model of inflation, and incorporates a double-seesaw model for neutrino masses consistent with oscillation experiments and late-time cosmology. We pay particular attention to the behaviour of the scalar fields during inflation and the subsequent reheating.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Acoustics and aerodynamics of over-the-wing thrust reversers

As part of the Quiet Clean Short-Haul Experimental Engine Program, model tests were conducted to determine the effects of thrust reverser geometric parameters on noise and reverse thrust. The acoustic tests used a 1/6 scale model thrust reverser while the aerodynamic performance tests used a 1/12 scale model reverser. Parameters which were varied in both tests include blocker spacing, blocker height, lip angle, and lip length. The impact of these parameters on peak sideline noise and reverse thrust performance is discussed.

Stimpert, D. L.↗

Experimental validation of a Kalman observer using linearized OpenFAST and a fully instrumented 1:70 model

Abstract To enable real‐time monitoring and control strategies for floating offshore wind turbines, accurate information about the state of the system is needed. This paper details the application of a Kalman filter to the UMaine VolturnUS‐S floating wind platform to provide accurate state estimates in real time using minimal system measurements. The midfidelity nonlinear simulation tool OpenFAST was used to generate the underlying linear state‐space model for the Kalman filter. This linear model and its limitations are demonstrated through comparison with experimental data collected on a 1:70 froude‐scaled model of the floating platform and tower. Using a selection of five measurements from the real system, a Kalman filter was developed to provide estimates for the remaining system states and measurements. These estimates were then validated against the experimental values collected from testing of the scale model. Validation of the Kalman filter produced accurate estimates of surge, heave, and tower base bending moment, measurements of which were not available to the Kalman filter. Performance of the Kalman filter was tested and validated over a range of sea conditions from rated wind speed to storm events and demonstrated robustness in the Kalman filter to maintain accuracy across all operating conditions despite significant error in the underlying linear model for extreme conditions.

17 WIND ENERGY↗

Scaling of Floods With Geomorphologic Characteristics and Precipitation Variability Across the Conterminous United States

Abstract Accurate flood risk assessment requires a comprehensive understanding of flood sensitivity to regional drivers and climate factors. This paper presents the scaling of floods (duration, peak, volume) with geomorphologic characteristics of the basin (i.e., drainage area, slope, elevation) and precipitation patterns (rainfall accumulation, variability). Long‐term daily streamflow observations over the 20th and early 21st centuries from Hydro‐Climatic Data Network streamgages across the conterminous United States are used to create a flood event database based on their flood stage information. Antecedent daily rainfall accumulation and variability corresponding to these floods are computed using Global Historical Climatology Network daily data set. Two Bayesian scaling models are developed, and the spatial organization of scaling exponents is investigated. The baseline model quantifies the scaling of floods to geomorphologic characteristics. The dynamic model quantifies the scaling of floods to antecedent precipitation distribution which is further conditioned on geomorphologic characteristics. Results show that small and low‐elevation basins have a stronger response to antecedent rainfall distribution in amplifying flood peaks, while high‐elevation steeper basins have a lower response for flood duration and volume. The dynamic models demonstrate that there are significant variations in the flood scaling rates, with the largest rates up to 40% and 4.5% for flood duration, 64% and 44% for peak, and 98% and 40% for volume found across the Northeast, Coastal Southeast, and Northwest with intensifying rainfall accumulation and variability, respectively. This study advances flood predictions by better informing the flood attributes in the context of dynamical land‐atmosphere perturbations.

54 ENVIRONMENTAL SCIENCES↗

Uncertainty quantification in LES of channel flow

Here, in this paper, we present a Bayesian framework for estimating joint densities for large eddy simulation (LES) sub-grid scale model parameters based on canonical forced isotropic turbulence direct numerical simulation (DNS) data. The framework accounts for noise in the independent variables, and we present alternative formulations for accounting for discrepancies between model and data. To generate probability densities for flow characteristics, posterior densities for sub-grid scale model parameters are propagated forward through LES of channel flow and compared with DNS data. Synthesis of the calibration and prediction results demonstrates that model parameters have an explicit filter width dependence and are highly correlated. Discrepancies between DNS and calibrated LES results point to additional model form inadequacies that need to be accounted for.

97 MATHEMATICS AND COMPUTING↗

On the transferability of residence time distributions in two 10-km long river sections with similar hydromorphic units

Quantifying hydrologic exchange fluxes (HEFs) at the stream-groundwater interface and their residence time distributions (RTDs) in the subsurface are important for managing the water quality and ecosystem health in dynamic river corridors. However, direct simulating high-spatial resolution HEFs and RTDs can be time-consuming, especially for watershed-scale modeling. Efficient surrogate models linking RTDs to hydromorphic units (HUs) can be alternatives for simulating RTDs in large-scale models. A common concern of these surrogate models, though, is the transferability of the relationship between the RTDs and HUs from one river corridor to another. To address this issue, this work evaluates the HEFs and resulting RTD-HU relationships for two 10-km long river corridors along the Columbia River leveraging a one-way coupled three-dimensional transient surface-subsurface water transport modeling framework we previously developed. Applying such a framework at the two river corridors with similar HUs allows for quantitative comparisons of HEFs and RTDs using both statistical tests and machine learning classification models. Finally, our comparison shows that the similarity and transferability of the RTD-HU relationship is very low for the two investigated river sections, which suggests that devising a general algorithm to estimate RTDs based solely on surface water hydrodynamics and short-distance river channel topography data, as well as HU classification, might be nearly impossible.

54 ENVIRONMENTAL SCIENCES↗

Multi-scale planning model for robust urban drought response

Increasingly severe droughts are straining municipal water resources and jeopardizing urban water security, but uncertainty in their duration, frequency, and intensity challenges drought planning and response. We develop the Drought Resilient Interscale Portfolio Planning model (DRIPP) to generate optimal planning responses to urban drought. DRIPP is a generalizable multi-scale framework for optimizing dynamic planning strategies of long-term infrastructure deployment and short-term drought response. It integrates climate and hydrological variability with high-fidelity representations of urban water distribution, available technology options, and demand reduction measures to yield robust and cost-effective water supply portfolios that are location-specific. We apply DRIPP in Santa Barbara, California to assess how least cost water supply portfolios vary under different drought scenarios and identify portfolios that are robust across drought scenarios. In Santa Barbara, we find that drought intensity, not duration or frequency, drives cost increases, reliability risk, and regret of overbuilding infrastructure. Under uncertain drought conditions, a diversified technology portfolio that includes both rapidly deployable, decentralized technologies alongside larger centralized technologies minimizes water supply cost while maintaining high robustness to climate uncertainty.

54 ENVIRONMENTAL SCIENCES↗

Aeroacoustic Simulations of the High-Lift Common Research Model and Validation with Experiment

Aerodynamic and acoustic data from unsteady numerical simulations of the High-Lift Common Research Model are compared with experimental measurements from an open-jet wind tunnel test of a 10\-scale model. Time-averaged surface pressure data is in good agreement for all of the configurations evaluated during the test. Unsteady surface pressure spectra from the leading-edge slat and the nose of the main element are presented, demonstrating that the highest levels are associated with the wakes of slat brackets. At these locations the simulations and experiment match reasonably well at low enough frequencies (f < 10 kHz based on the model scale) before excessive numerical dissipation leads to a rapid roll off in the predicted frequency spectra. The agreement is inconsistent at other locations on the slat and main-element surfaces, where the pressure fluctuation levels are lower. Noise predictions using a synthetic microphone array are compared with equivalent experimental results, and the changes in levels predicted between three configurations are similar to those measured. However, some details of the noise predictions are inconsistent with the experiment, and the use of solid- instead of porous-surface data for the acoustic processing of the simulations likely contributes to the discrepancies. All of the simulations were completed before the test, and, despite some shortcomings, they provided valuable insight into the aeroacoustic performance of the model that greatly aided test planning and execution. Hence, the post-test comparisons presented here allow an assessment of the predictive methodology in the context of a realistic high-lift configuration.

High-lift↗

Cosmological constraints from galaxy–lensing cross-correlations using BOSS galaxies with SDSS and CMB lensing

ABSTRACT We present cosmological parameter constraints based on a joint modelling of galaxy–lensing cross-correlations and galaxy clustering measurements in the SDSS, marginalizing over small-scale modelling uncertainties using mock galaxy catalogues, without explicit modelling of galaxy bias. We show that our modelling method is robust to the impact of different choices for how galaxies occupy dark matter haloes and to the impact of baryonic physics (at the $\sim 2{{\ \rm per\ cent}}$ level in cosmological parameters) and test for the impact of covariance on the likelihood analysis and of the survey window function on the theory computations. Applying our results to the measurements using galaxy samples from BOSS and lensing measurements using shear from SDSS galaxies and CMB lensing from Planck, with conservative scale cuts, we obtain $S_8\equiv \left(\frac{\sigma _8}{0.8228}\right)^{0.8}\left(\frac{\Omega _\mathrm{ m}}{0.307}\right)^{0.6}=0.85\pm 0.05$ (stat.) using LOWZ × SDSS galaxy lensing, and S8 = 0.91 ± 0.1 (stat.) using combination of LOWZ and CMASS × Planck CMB lensing. We estimate the systematic uncertainty in the galaxy–galaxy lensing measurements to be $\sim 6{{\ \rm per\ cent}}$ (dominated by photometric redshift uncertainties) and in the galaxy–CMB lensing measurements to be $\sim 3{{\ \rm per\ cent}}$, from small-scale modelling uncertainties including baryonic physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Design of scaled down structural models

In the aircraft industry, full scale and large component testing is a very necessary, time consuming, and expensive process. It is essential to find ways by which this process can be minimized without loss of reliability. One possible alternative is the use of scaled down models in testing and use of the model test results in order to predict the behavior of the larger system, referred to herein as prototype. This viewgraph presentation provides justifications and motivation for the research study, and it describes the necessary conditions (similarity conditions) for two structural systems to be structurally similar with similar behavioral response. Similarity conditions provide the relationship between a scaled down model and its prototype. Thus, scaled down models can be used to predict the behavior of the prototype by extrapolating their experimental data. Since satisfying all similarity conditions simultaneously is in most cases impractical, distorted models with partial similarity can be employed. Establishment of similarity conditions, based on the direct use of the governing equations, is discussed and their use in the design of models is presented. Examples include the use of models for the analysis of cylindrical bending of orthotropic laminated beam plates, of buckling of symmetric laminated rectangular plates subjected to uniform uniaxial compression and shear, applied individually, and of vibrational response of the same rectangular plates. Extensions and future tasks are also described.

Simitses, George J.↗