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At least 847 records · Page 47

Enhancing metaproteomics-The value of models and defined environmental microbial systems

Metaproteomics - the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time - added unique features and possibilities to study environmental microbial communities and to unravel these “black boxes”. New technical challenges arose which were not an issue for classical proteome analytics before and choosing the appropriate model system applicable to the research question can be difficult. Here, we reviewed different model systems for metaproteome analysis. Following a short introduction to microbial communities and systems, we discussed the most used systems ranging from technical systems over rhizospheric models to systems for the medical field. This includes acid mine drainage, anaerobic digesters, activated sludge, planted fixed bed reactors, gastrointestinal simulators and in vivo models. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial responses and ecological distribution of member organisms. In the future, novel improvements are necessary to fully engage complex environmental systems.

54 ENVIRONMENTAL SCIENCES↗

Sampling error study for rainfall estimate by satellite using a stochastic model

In a parameter study of satellite orbits, sampling errors of area-time averaged rain rate due to temporal sampling by satellites were estimated. The sampling characteristics were studied by accounting for the varying visiting intervals and varying fractions of averaging area on each visit as a function of the latitude of the grid box for a range of satellite orbital parameters. The sampling errors were estimated by a simple model based on the first-order Markov process of the time series of area averaged rain rates. For a satellite of nominal Tropical Rainfall Measuring Mission (Thiele, 1987) carrying an ideal scanning microwave radiometer for precipitation measurements, it is found that sampling error would be about 8 to 12 pct of estimated monthly mean rates over a grid box of 5 X 5 degrees. It is suggested that an observation system based on a low inclination satellite combined with a sunsynchronous satellite simultaneously might be the best candidate for making precipitation measurements from space.

Shin, Kyung-Sup↗

Development and Testing of CTF to Support Modeling of BWR Operating Conditions

This milestone supports developing and assessing COBRA-TF (CTF) for the modeling of boiling water reactors (BWRs). This is achieved in three stages. First, a new preprocessor utility that is capable of handling BWR-specic design elements (e.g., channel boxes and large water rods) is developed. A previous milestone (L3:PHI.CTF.P12.01) led to the development of this preprocessor capability for single assembly models. This current milestone expands this utility so that it is applicable to multi-assembly BWR models that can be modeled in either serial or parallel. The second stage involves making necessary modications to CTF so that it can execute these new models. Specically, this means implementing an outer-iteration loop, specic to BWR models, that equalizes the pressure loss over all assemblies in the core (which are not connected due to the channel boxes) by adjusting inlet mass ow rate. A third stage involves assessing the standard convergence metrics that are used by CTF to determine when a simulation is steady-state. The nal stage has resulted in the implementation of new metrics in the code that give a better indication of how steady the solution is at convergence. This report summarizes these eorts and provides a demonstration of CTF's BWR-modeling capabilities. CASL-U-2016-1030-000

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Large-scale molecular dynamics simulations of bubble collapse in water: Effects of system size, water model, and nitrogen

Molecular dynamics simulations in the microcanonical ensemble are performed to study the collapse of a bubble in liquid water using the single-site mW and the four-site TIP4P/2005 water models. To study system size effects, simulations for pure water systems are performed using periodically replicated simulation boxes with linear dimensions, L, ranging from 32 to 512 nm with the largest systems containing 8.7 × 10 6 and 4.5 × 10 9 molecules for the TIP4P/2005 and mW water models, respectively. The computationally more efficient mW water model allows us to reach converging behavior when the bubble dynamics results are plotted in reduced units, and the limiting behavior can be obtained through linear extrapolation in L –1 . Qualitative differences are observed between simulations with the mW and TIP4P/2005 water models, but they can be explained by the models’ differences in predicted viscosity and surface tension. Although bubble collapse occurs on time scales of only hundreds of picoseconds, the system sizes used here are sufficiently large to obtain bubble dynamics consistent with the Rayleigh–Plesset equation when using the models’ thermophysical properties as input. For the conditions explored here, extreme heating of the interfacial water molecules near the time of collapse is observed for the larger mW water systems (but the model underpredicts the viscosity), whereas heating is less pronounced for the TIP4P/2005 water systems because its larger viscosity contribution slows the collapse dynamics. The presence of nitrogen within the bubble only starts to affect bubble dynamics near the very end of the initial collapse, leading to an incomplete collapse and strong rebound for the mW water model. Although nitrogen is non-condensable at 300 K, it becomes highly compressed and reaches a liquid-like density near the collapse point. We find that the dissolution of nitrogen is much slower than the movement of the collapsing water front, and the re-expansion of the dense nitrogen droplet gives rise to bubble rebound. The incompatibility of the collapse and dissolution time scales should be considered for continuum-scale modeling of bubble dynamics. Finally, we also confirm that the diffusion coefficient for dissolved nitrogen is insensitive to pressure as the liquid transitions from a compressed to a stretched state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simplified predictive models for CO 2 sequestration performance assessment

CO2 sequestration in deep saline formations is increasingly being considered as a viable strategy for the mitigation of greenhouse gas emissions from anthropogenic sources. In this context, detailed numerical simulation based models are routinely used to understand key processes and parameters affecting pressure propagation and buoyant plume migration following CO2 injection into the subsurface. As these models are data and computation intensive, the development of computationally-efficient alternatives to conventional numerical simulators has become an active area of research. Such simplified models can be valuable assets during preliminary CO2 injection project screening, serve as a key element of probabilistic system assessment modeling tools, and assist regulators in quickly evaluating geological storage projects. We present three strategies for the development and validation of simplified modeling approaches for CO2 sequestration in deep saline formations: (1) simplified physics-based modeling, (2) statisticallearning based modeling, and (3) reduced-order method based modeling. In the first category, a set of full-physics compositional simulations is used to develop correlations for dimensionless injectivity as a function of the slope of the CO2 fractional-flow curve, variance of layer permeability values, and the nature of vertical permeability arrangement. The same variables, along with a modified gravity number, can be used to develop a correlation for the total storage efficiency within the CO2 plume footprint. Furthermore, the dimensionless average pressure buildup after the onset of boundary effects can be correlated to dimensionless time, CO2 plume footprint, and storativity contrast between the reservoir and caprock. In the second category, statistical “proxy models” are developed using the simulation domain described previously with two approaches: (a) classical Box-Behnken experimental design with a quadratic response surface, and (b) maximin Latin Hypercube sampling (LHS) based design with a multidimensional kriging metamodel fit. For roughly the same number of simulations, the LHS-based metamodel yields a more robust predictive model, as verified by a k-fold cross-validation approach (with data split into training and test sets) as well by validation with an independent dataset. In the third category, a reduced-order modeling procedure is utilized that combines proper orthogonal decomposition (POD) for reducing problem dimensionality with trajectory-piecewise linearization (TPWL) in order to represent system response at new control settings from a limited number of training runs. Significant savings in computational time are observed with reasonable accuracy from the PODTPWL reduced-order model for both vertical and horizontal well problems – which could be important in the context of history matching, uncertainty quantification and optimization problems. The simplified physics and statistical learning based models are also validated using an uncertainty analysis framework. Reference cumulative distribution functions of key model outcomes (i.e., plume radius and reservoir pressure buildup) generated using a 97-run full-physics simulation are successfully validated against the CDF from 10,000 sample probabilistic simulations using the simplified models. The main contribution of this research project is the development and validation of a portfolio of simplified modeling approaches that will enable rapid feasibility and risk assessment for CO2 sequestration in deep saline formations.

54 ENVIRONMENTAL SCIENCES↗

Process Parameter Optimization in Refill Friction Spot Welding of 6061 Aluminum Alloys Using Response Surface Methodology

6061-T6 aluminum alloy joint was fabricated by refill friction stir spot welding (RFSSW) on which three process parameters of tool rotation speed, sleeve moving rate, and plunge depth make an important effect. The response surface methodology (RSM) was applied to establish a mathematical model to study the effect of process parameters on lap shear fracture load (LSFL) of the RFSSWed joints which were performed in Box–Behnken designs with three factors, three levels and 15 runs. Analysis of variance used to check the adequacy of the developed model indicates that the mathematical model is significant. LSFL increases with the increase in tool rotation speed, sleeve plunge depth, and sleeve moving rate to maximum and then decreases. Sleeve plunge depth makes the most effect on LSFL in all process parameters. The RFSSW process parameters were also optimized using RSM to predict maximize LSFL. The joint produced using a tool rotational speed of 1506 rpm, sleeve moving rate of 1.01 mm/s and sleeve plunge depth of 2.46 mm displays higher LSFL.

36 MATERIALS SCIENCE↗

Effects of oxidative stress on hyperglycaemia-induced brain malformations in a diabetes mouse model

Pregestational diabetes mellitus (PGDM) enhances the risk of fetal neurodevelopmental defects. However, the mechanism of hyperglycaemia-induced neurodevelopmental defects is not fully understood. In this study, several typical neurodevelopmental defects were identified in the streptozotocin-induced diabetes mouse model. The neuron-specific class III beta-tubulin/forkhead box P1-labelled neuronal differentiation was suppressed and glial fibrillary acidic protein-labelled glial cell lineage differentiation was slightly promoted in pregestational diabetes mellitus (PGDM) mice. Various concentrations of glucose did not change the U87 cell viability, but glial cell line-derived neurotrophic factor expression was altered with varying glucose concentrations. Mouse maternal hyperglycaemia significantly increased Tunel{sup +} apoptosis but did not dramatically affect PCNA{sup +} cell proliferation in the process. To determine the cause of increased apoptosis, we determined the SOD activity, the expression of Nrf2 as well as its downstream anti-oxidative factors NQO1 and HO1, and found that all of them significantly increased in PGDM fetal brains compared with controls. However, Nrf2 expression in U87 cells was not significantly changed by different glucose concentrations. In mouse telencephalon, we observed the co-localization of Tuj-1 and Nrf2 expression in neurons, and down-regulating of Nrf2 in SH-SY5Y cells altered the viability of SH-SY5Y cells exposed to high glucose concentrations. Taken together, the data suggest that Nrf2-modulated antioxidant stress plays a crucial role in maternal hyperglycaemia-induced neurodevelopmental defects. - Highlights: • Typical neurodevelopmental defects could be observed in STZ-treated mouse fetuses. • Nrf2 played a crucial role in hyperglycaemia-induced brain malformations. • The effects of hyperglycaemia on neurons and glia cells were not same.

60 APPLIED LIFE SCIENCES↗

Contribution of the Δ-isobar excitation mechanism to the pp → {pp}{sub s} π{sup 0} reaction

The differential cross section of the reaction pp → {pp}{sub s} π{sup 0}, where {pp}{sub s} is the proton pair in the {sup 1}S{sub 0} state at a small excitation energy E{sub pp} < 3 MeV, is calculated using the box diagram with the excitation of the Δ-isobar. The model demonstrates a clear bump observed in the experimental data at the beam energy of ∼0.6 GeV and the zero diproton outgoing angle; however, its absolute value strongly depends on the off-shell extrapolation of the πNΔ vertex factor and underestimates the data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Box truss development and applications

The development and applications of a box truss design for large space antennas are discussed. A kinematic model with a mesh reflector was constructed. A prototype cube is described. Details of fabrication are given.

Coyner, J. V., Jr.↗

Unsteady transonic flow simulation on a full-span-wing-body configuration

The presence of a body influences both the aerodynamic and aeroelastic performance of wings. Such effects are more pronounced in the transonic regime. To accurately account for the effect of the body, particularly when the wings are experiencing asymmetric modal motions, it is necessary to model the full configuration in the nonlinear transonic regime. In this study, full-span-wing-body configurations are simulated for the first time by a theoretical method that uses the unsteady potential equations based on the small-disturbance theory. The body geometry is modeled exactly as the physical shape, instead of as a rectangular box, which has been done in the past. Steady pressure computations for wing-body configurations compare well with the available experimental data. Unsteady pressure computations when the wings are oscillating in asymmetric modes show significant influence of the body.

Guruswamy, Guru P.↗

Space biology initiative program definition review. Trade study 1: Automation costs versus crew utilization

A significant emphasis upon automation within the Space Biology Initiative hardware appears justified in order to conserve crew labor and crew training effort. Two generic forms of automation were identified: automation of data and information handling and decision making, and the automation of material handling, transfer, and processing. The use of automatic data acquisition, expert systems, robots, and machine vision will increase the volume of experiments and quality of results. The automation described may also influence efforts to miniaturize and modularize the large array of SBI hardware identified to date. The cost and benefit model developed appears to be a useful guideline for SBI equipment specifiers and designers. Additional refinements would enhance the validity of the model. Two NASA automation pilot programs, 'The Principal Investigator in a Box' and 'Rack Mounted Robots' were investigated and found to be quite appropriate for adaptation to the SBI program. There are other in-house NASA efforts that provide technology that may be appropriate for the SBI program. Important data is believed to exist in advanced medical labs throughout the U.S., Japan, and Europe. The information and data processing in medical analysis equipment is highly automated and future trends reveal continued progress in this area. However, automation of material handling and processing has progressed in a limited manner because the medical labs are not affected by the power and space constraints that Space Station medical equipment is faced with. Therefore, NASA's major emphasis in automation will require a lead effort in the automation of material handling to achieve optimal crew utilization.

Jackson, L. Neal↗

Performance Evaluation of the NASA/KSC Transmission System

NASA-KSC currently uses three bridged 100-Mbps FDDI segments as its backbone for data traffic. The FDDI Transmission System (FTXS) connects the KSC industrial area, KSC launch complex 39 area, and the Cape Canaveral Air Force Station. The report presents a performance modeling study of the FTXS and the proposed ATM Transmission System (ATXS). The focus of the study is on performance of MPEG video transmission on these networks. Commercial modeling tools - the CACI Predictor and Comnet tools - were used. In addition, custom software tools were developed to characterize conversation pairs in Sniffer trace (capture) files to use as input to these tools. A baseline study of both non-launch and launch day data traffic on the FTXS is presented. MPEG-1 and MPEG-2 video traffic was characterized and the shaping of it evaluated. It is shown that the characteristics of a video stream has a direct effect on its performance in a network. It is also shown that shaping of video streams is necessary to prevent overflow losses and resulting poor video quality. The developed models can be used to predict when the existing FTXS will 'run out of room' and for optimizing the parameters of ATM links used for transmission of MPEG video. Future work with these models can provide useful input and validation to set-top box projects within the Advanced Networks Development group in NASA-KSC Development Engineering.

Christensen, Kenneth J.↗

Orbital Debris Quarterly News, April 2020

Inside - Second Fragmentation of Fregat Upper Stage Debris - DAS v3.1 Release - Development of Experimental Hypervelocity Impact Capabilities with Non-Spherical Projectiles - Short-Term Satellite Breakup Risk Assessment Model Process - Two Recent Breakup Events Updated - Space Missions and Satellite Box Score

Orbital Debris↗

A two-dimensional radial outflow model of plasma at Jupiter

An analytic solution illustrating the behavior of incompressible irrotational plasma outflow in two dimensions is given for application to the Jovian magnetosphere. Plasma is assumed to emanate from the Alfven surface and is channeled downtail by the confining magnetopause surface. Conformal transformation methods are used to map this complex magnetotail geometry into a rectangular box for which the solution to Laplace's equation is expressed in simple form. The model suggests that a dipole layer is formed on the dawn side in the vicinity of the Alfven surface where the flow bifurcates into clockwise and counterclockwise motion. An electric field discontinuity of this type fixed in local time may be able to account for several anomalous spin-periodic phenomena, namely, the modulation of Io-independent radio emissions and the injection of energetic electrons into interplanetary space.

Barbosa, D. D.↗

Accurate predictions from small boxes: variance suppression via the Zel'dovich approximation

Simulations have become an indispensable tool for accurate modelling of observables measured in galaxy surveys, but can be expensive if very large dynamic range in scale is required. We describe how to combine Lagrangian perturbation theory models with N-body simulations to reduce the effects of finite computational volume in the prediction of ensemble average properties in the simulations within the context of control variates. In particular we use the fact that Zel'dovich displacements, computed during initial condition generation for any simulation, correlate strongly with the final density field. Since all the correlators of biased tracers can be computed with arbitrary precision for these displacements, pairing the Zel'dovich `simulation' with the N-body realization allows hundredfold reductions in sample variance for power spectrum or correlation function estimation. Additionally, Zel'dovich control variates can accurately extend matter or tracer field emulators to larger scales than previously possible, as well as improving measurements of statistics in simulations which are inherently limited to small volumes, such as hydrodynamical simulations of galaxy formation and reionization.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluating Subgrid-Scale Properties of Low Clouds over the Beaufort Sea in Arctic System Reanalysis using ARISE Airborne In Situ Observations

Arctic low clouds influence the evolution of the Arctic system through their effects on radiative fluxes, boundary layer mixing, stability, turbulence, humidity, and precipitation. Unfortunately, atmospheric models and retrospective analysis (reanalysis) products struggle to accurately simulate the occurrence and properties of low clouds in the Arctic. To better understand the magnitude and possible causes of this problem, we analyze the disagreements between the Arctic System Reanalysis version 2 (ASR) and data taken during the September 2014 Arctic Radiation-IceBridge Sea and Ice Experiment (ARISE) airborne campaign conducted over the Beaufort Sea. Previous analysis of grid scale-averaged meteorological variables revealed a lack of cloud water produced in ASR, related to warm/dry biases, a failure to produce sufficient cloud water in conditions that are observed to be favorable for large cloud water values, and sampling issues with the ARISE flight paths. However, ARISE collected meteorological observations at one second intervals, offering spatial data resolution comparable to the subgrid scale of ASR. Subgrid scale properties and processes must be parameterized in conventional atmospheric models and reanalyses such as ASR, and often rely on assumed distributions of meteorological variables about the grid box mean state. To enable an examination of the realism of ASR’s subgrid scale properties, we use high resolution data from ARISE determine the “subgrid scale” distributions of cloud water and thermodynamic variables in the real atmosphere. Preliminary results show that the subgrid scale distribution of thermodynamic variables about the grid scale mean resembles the triangular distribution assumed in many bulk microphysical parameterization schemes, but also with tails resembling Gaussian distributions. The main goal is to understand the partitioning of the total available atmospheric water into water vapor and cloud water. Models typically covert some percentage of total water in a grid box to cloud water based on the estimated amount of supersaturation from the assumed vapor distribution. The ARISE measurements can reveal the relationship between subgrid scale supersaturation and the partition between cloud water and water vapor.

Jason Brant Dodson↗

Quantifying the Impact of Vertical Resolution on the Representation of Marine Boundary Layer Physics for Global-Scale Models

Abstract While GCM horizontal resolution has received the majority of scale improvements in recent years, ample evidence suggests that a model’s vertical resolution exerts a strong control on its ability to accurately simulate the physics of the marine boundary layer. Here we show that, regardless of parameter tuning, the ability of a single-column model (SCM) to simulate the subtropical marine boundary layer improves when its vertical resolution is improved. We introduce a novel objective tuning technique to optimize the parameters of an SCM against profiles of temperature and moisture and their turbulent fluxes, horizontal winds, cloud water, and rainwater from large-eddy simulations (LES). We use this method to identify optimal parameters for simulating marine stratocumulus and shallow cumulus. The novel tuning method utilizes an objective performance metric that accounts for the uncertainty in the LES output, including the covariability between model variables. Optimization is performed independently for different vertical grid spacings and value of time step, ranging from coarse scales often used in current global models (120 m, 180 s) to fine scales often used in parameterization development and large-eddy simulations (10 m, 15 s). Uncertainty-weighted disagreement between the SCM and LES decreases by a factor of ∼5 when vertical grid spacing is improved from 120 to 10 m, with time step reductions being of secondary importance. Model performance is shown to converge at a vertical grid spacing of 20 m, with further refinements to 10 m leading to little further improvement. Significance Statement In successive generations of computer models that simulate Earth’s atmosphere, improvements have been mainly accomplished by reducing the horizontal sizes of discretized grid boxes, while the vertical grid spacing has seen comparatively lesser refinements. Here we advocate for additional attention to be paid to the number of vertical layers in these models, especially in the model layers closest to Earth’s surface where climatologically important marine stratocumulus and shallow cumulus clouds reside. Our experiments show that the ability of a one-dimensional model to represent physical processes important to these clouds is strongly dependent on the model’s vertical grid spacing.

Meteorology & Atmospheric Sciences↗

High-Fidelity Computational Aerodynamics of the Elytron 4S UAV

High-fidelity Computational Fluid Dynamics (CFD) have been carried out for the Elytron 4S Unmanned Aerial Vehicle (UAV), also known as the converticopter "proto12". It is the scaled wind tunnel model of the Elytron 4S, an Urban Air Mobility (UAM) concept, a tilt-wing, box-wing rotorcraft capable of Vertical Take-Off and Landing (VTOL). The three-dimensional unsteady Navier-Stokes equations are solved on overset grids employing high-order accurate schemes, dual-time stepping, and a hybrid turbulence model using NASA's CFD code OVERFLOW. The Elytron 4S UAV has been simulated in airplane mode and in helicopter mode.

High-Fidelity↗