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DOE OSTI2021

Extreme metrics from large ensembles: investigating the effects of ensemble size on their estimates

Abstract. We consider the problem of estimating the ensemble sizes required to characterize the forced component and the internal variability of a number of extreme metrics. While we exploit existing large ensembles, our perspective is that of a modeling center wanting to estimate a priori such sizes on the basis of an existing small ensemble (we assume the availability of only five members here). We therefore ask if such a small-size ensemble is sufficient to estimate accurately the population variance (i.e., the ensemble internal variability) and then apply a well-established formula that quantifies the expected error in the estimation of the population mean (i.e., the forced component) as a function of the sample size n, here taken to mean the ensemble size. We find that indeed we can anticipate errors in the estimation of the forced component for temperature and precipitation extremes as a function of n by plugging into the formula an estimate of the population variance derived on the basis of five members. For a range of spatial and temporal scales, forcing levels (we use simulations under Representative Concentration Pathway 8.5) and two models considered here as our proof of concept, it appears that an ensemble size of 20 or 25 members can provide estimates of the forced component for the extreme metrics considered that remain within small absolute and percentage errors. Additional members beyond 20 or 25 add only marginal precision to the estimate, and this remains true when statistical inference through extreme value analysis is used. We then ask about the ensemble size required to estimate the ensemble variance (a measure of internal variability) along the length of the simulation and – importantly – about the ensemble size required to detect significant changes in such variance along the simulation with increased external forcings. Using the F test, we find that estimates on the basis of only 5 or 10 ensemble members accurately represent the full ensemble variance even when the analysis is conducted at the grid-point scale. The detection of changes in the variance when comparing different times along the simulation, especially for the precipitation-based metrics, requires larger sizes but not larger than 15 or 20 members. While we recognize that there will always exist applications and metric definitions requiring larger statistical power and therefore ensemble sizes, our results suggest that for a wide range of analysis targets and scales an effective estimate of both forced component and internal variability can be achieved with sizes below 30 members. This invites consideration of the possibility of exploring additional sources of uncertainty, such as physics parameter settings, when designing ensemble simulations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

De novo design of protein homodimers containing tunable symmetric protein pockets

Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A combined ensemble-volume average homogenization method for lattice structures with defects under dynamic and static loading

In the study of lattices structures, both experiments and numerical simulations are often conducted with small samples. Using combined ensemble and volume averaging, this work introduces a method to extract a macroscopic constitutive response of a lattice material from numerical simulations performed in periodic domains. The domain size needed to obtain statistically accurate results is investigated. Similar to molecular dynamics, the concept of the virial stress is introduced after homogenized equations are derived using the ensemble averaging method. Under static conditions, the virial stress is shown to agree with the volume averaged solid stress. Using the homogenization method, constitutive relations for this stress can be obtained from systems with uniform strains. Application of such obtained constitutive relations to more general cases results in an error proportional to the square of the ratio between the lattice length scale and the macroscopic length scale. Taking advantage of this property, numerical simulations are performed in systems with a uniform gradient of the average velocity. The volume average method is then used to accelerate convergence when studying lattices with defects. To avoid the artificial numerical time scale from the size of a representative volume element divided by the wave speed, a numerical scheme is developed to enforce a spatially uniform velocity gradient within the computational domain while allowing fluctuations of the velocity or displacement to develop naturally. To account for probability distribution of lattice defects, the stress is calculated as the ensemble-volume averaged value. For dynamic systems, energy dissipation properties are also studied.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Probing Microplasticity in Small-Scale FCC Crystals via Dynamic Mechanical Analysis

In small-scale metallic systems, collective dislocation activity has been correlated with size effects in strength and with a steplike plastic response under uniaxial compression and tension. Yielding and plastic flow in these samples is often accompanied by the emergence of multiple dislocation avalanches. Dislocations might be active preyield, but their activity typically cannot be discerned because of the inherent instrumental noise in detecting equipment. We apply alternate current load perturbations via dynamic mechanical analysis during quasistatic uniaxial compression experiments on single crystalline Cu nanopillars with diameters of 500 nm and compute dynamic moduli at frequencies 0.1, 0.3, 1, and 10 Hz under progressively higher static loads until yielding. By tracking the collective aspects of the oscillatory stress-strain-time series in multiple samples, we observe an evolving dissipative component of the dislocation network response that signifies the transition from elastic behavior to dislocation avalanches in the globally preyield regime. We postulate that microplasticity, which is associated with the combination of dislocation avalanches and slow viscoplastic relaxations, is the cause of the dependency of dynamic modulus on the driving rate and the quasistatic stress. We construct a continuum mesoscopic dislocation dynamics model to compute the frequency response of stress over strain and obtain a consistent agreement with experimental observations. The results of our experiments and simulations present a pathway to discern and quantify correlated dislocation activity in the preyield regime of deforming crystals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection

Background: In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. Results: To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. Conclusions: We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Filter Aerosol Measurements for ARM

The goal of this study was to determine the best filter media for use in Atmospheric Radiation Measurement (ARM) particle soot absorption photometers (PSAPs) following the manufacturer discontinuation of the current filter media. The study comprised multiple experiments to assess four potential replacement filter medium relative to the Pallflex E-70, which is being discontinued, and is documented in ARM’s ServiceNow system under ENG0003846. The experiments laid out in the document ‘180504 Filter Aerosol Measurements for ARM.docx’ and several subsequent tests suggest that the Pallflex Emfab media is the best candidate for ongoing ARM filter-based absorbance measurements. Other media were ruled out based on particle capture efficiency for small particles. In tests with Nigrosin, Emfab exceeded all other media. Tests were done measuring reported absorbance for all media in PSAPs operated in parallel sampling under several conditions: ambient air, three sizes of black-dyed PSL (polystyrene latex) spheres, and Nigrosin particles. These tests indicate a different factor of reported absorbance for each media relative to the original Pallflex E70 filter. The factor for the Azumi media was consistent with unpublished work by Ogren (National Oceanic and Atmospheric Administration [NOAA]). The tests described here were not exhaustive and were complicated by time-varying differences among the PSAPs used. However, it is concluded that they are sufficient to justify ARM switching to Emfab filter media for future ARM PSAP measurements. The remaining store of E70 will be reserved to quantitatively characterize differences between Emfab and E70 (and Azumi?) in both laboratory and field side-by-side tests as put forth in a succeeding ENG. This future work will empirically identify correction factors applicable to Emfab and quantify the uncertainty in comparing the historical E70 measurements with ongoing Emfab measurements. Comparison of PSAP measurements with an independent absolute ‘reference’ for aerosol absorbance, i.e., photo thermal interferometry or difference measurements of cavity attenuated phase shift extinction (CAPS) minus nephelometry scattering, would be valuable but exceed the scope of ARM Infrastructure. While the characterization of correction factors is required for maintaining and improving accuracy in future absorption measurements, it was beyond the scope of the current study.

aerosol observing system↗

NASA NTRS1972

The extrapolation of laboratory and aircraft radar sea return data to spacecraft altitudes

Laboratory measurements show that the spectra of capillary waves grow with wind speed over six orders of magnitude. The scatter in the data can be partially understood and predicted from a combination of turbulence theory, radar theory, and the small sample theory of statistical inference. When these results are applied to a prediction of the sea return values to be obtained by S193 on Skylab, it can be shown that the size of the illuminated patch effectively averages out the horizontal scales of gustiness, so that the measurement will correspond to the synoptic scale wind.

Pierson, W. J.↗

NASA NTRS1982

Altitude variations in stratospheric aerosols of a tropical region

To investigate the possibility that significant amounts of tropical tropospheric air may be convectively introduced into the stratosphere, aerosol samplings over Panama were made at various altitudes using a wire impactor collector. The percentage of particle sizes less than the mean mode decreases with height above the tropopause, suggesting depletion of small particles, possibly due to coagulation. Larger aerosols (greater than 0.3 micron in diam.) are more abundant farther above the tropopause, indicating growth, mainly by condensation. The total particle concentration decreases with increasing height above the tropopause, and also with increasing temperature. Aerosols containing smaller-size particles are thus found closer to the tropopause, and larger-size, more-evolved aerosols occur at higher altitudes. These data indicate that convective activity at the Intertropical Convergence Zone may be a source mechanism for stratospheric aerosols.

Goodman, J.↗

NASA NTRS1982

Corn and soybean Landsat MSS classification performance as a function of scene characteristics

In order to fully utilize remote sensing to inventory crop production, it is important to identify the factors that affect the accuracy of Landsat classifications. The objective of this study was to investigate the effect of scene characteristics involving crop, soil, and weather variables on the accuracy of Landsat classifications of corn and soybeans. Segments sampling the U.S. Corn Belt were classified using a Gaussian maximum likelihood classifier on multitemporally registered data from two key acquisition periods. Field size had a strong effect on classification accuracy with small fields tending to have low accuracies even when the effect of mixed pixels was eliminated. Other scene characteristics accounting for variability in classification accuracy included proportions of corn and soybeans, crop diversity index, proportion of all field crops, soil drainage, slope, soil order, long-term average soybean yield, maximum yield, relative position of the segment in the Corn Belt, weather, and crop development stage.

Batista, G. T.↗

NASA NTRS1985

Decomposition of ethylene on small Pd particles

New results have been obtained which contribute to the understanding of hydrocarbon reactions on the surface of highly dispersed metal systems. Small particle of Pd were grown by electron beam evaporation on cleavage planes of high purity natural mica under ultrahigh vacuum conditions. Samples were subsequently characterized by transmission electron microscopy. Average particle sizes ranged from about 1 to 10 nm diameter. The chemisoption and decomposition of C2H4 on the Pd particles was studied using Auger electron spectroscopy and flash thermal desorption. It is shown that (a) C2H4 decomposes on Pd particles at room temperature, (b) specific surface sites are causing decomposition, and (c) the proportion of such active sites is significantly greater for the smaller metal particles. This enhanced reactivity may be due to an increase in the density of step, corner, and edge sites with a decrease in particle size.

Durrer, W. G.↗

NASA NTRS1970

Solid State Studies of the Radiation Histosy of Lunar Samples

Particle track densities up to greater than 3 x 10(exp 9) per square centimeter have been measured in different samples. Rocks 17, 47, 57, and 58 have VH (Z greater than 22) galactic cosmic ray ages of 11, 14, 28, and 13 x 10(exp 6) years, respectively. Rock 57 has a calculated erosion rate of approximately less than 10(exp -7) centimeter per year. Near-surface track versus depth data in rock 17 can be fit with solar flare particles that have a differential energy spectrum alpha E(exp -s); lunar samples can be used to study the history of solar activity. The uranium in the crystalline rocks occurs principally in small regions less than 10 to approximately equal to 100 micrometers in size. The (low) thermoluminescence of the fines increases with depth in core 10004. With one possible exception, x-ray studies have not shown pronounced radiation damage effects. The total energy release upon heating is small up to 900 C and occurs in three broad regions.

Crozaz, G.↗

NASA NTRS2009

Presolar Organic Globules in Tagish Lake Meteorite, and other Astromaterials

Presolar grains were identified in meteorite residues 20 years ago based on their exotic isotopic compositions. Their study has provide new insights into stellar evolution and the first view of the original building blocks of the solar system. Organic matter in meteorites and IDPs is highly enriched in D/H and N-15/N-14 at micrometer scales, possibly due to presolar organic grains. These anomalies are ascribed to the partial preservation of presolar cold molecular cloud material. Identifying the carriers of these anomalies and elucidating their physical and chemical properties may give new views of interstellar chemistry and better understanding of the original components of the protosolar disk. However, identifying the carriers has been hampered by their small size and the inability to chemically isolate them. Thanks to immediate careful collection of Tagish Lake meteorite specimen, as well as major advances in nano-scale analytical techniques and advanced sample preparation, we were able to show that in the Tagish Lake meteorite, the principle carriers of these isotopic anomalies are sub-micrometer, hollow organic globules. The organic globules likely formed by photochemical processing of organic ices in a cold molecular cloud or the outermost regions of the protosolar disk. Organic globules with similar physical, chemical, and isotopic properties are also recently found from Bells CM2 carbonaceous chondrite, in IDPs and in the comet Wild-2 samples returned by Stardust. These results support the view that microscopic organic grains were widespread constituents of the protoplanetary disk. Their exotic isotopic compositions trace their origins to the outermost portions of the protosolar disk or a presolar cold molecular cloud.

Nakamura-Messenger, K.↗

NASA NTRS2014

Large-Scale Spacecraft Fire Safety Tests

An international collaborative program is underway to address open issues in spacecraft fire safety. Because of limited access to long-term low-gravity conditions and the small volume generally allotted for these experiments, there have been relatively few experiments that directly study spacecraft fire safety under low-gravity conditions. Furthermore, none of these experiments have studied sample sizes and environment conditions typical of those expected in a spacecraft fire. The major constraint has been the size of the sample, with prior experiments limited to samples of the order of 10 cm in length and width or smaller. This lack of experimental data forces spacecraft designers to base their designs and safety precautions on 1-g understanding of flame spread, fire detection, and suppression. However, low-gravity combustion research has demonstrated substantial differences in flame behavior in low-gravity. This, combined with the differences caused by the confined spacecraft environment, necessitates practical scale spacecraft fire safety research to mitigate risks for future space missions. To address this issue, a large-scale spacecraft fire experiment is under development by NASA and an international team of investigators. This poster presents the objectives, status, and concept of this collaborative international project (Saffire). The project plan is to conduct fire safety experiments on three sequential flights of an unmanned ISS re-supply spacecraft (the Orbital Cygnus vehicle) after they have completed their delivery of cargo to the ISS and have begun their return journeys to earth. On two flights (Saffire-1 and Saffire-3), the experiment will consist of a flame spread test involving a meter-scale sample ignited in the pressurized volume of the spacecraft and allowed to burn to completion while measurements are made. On one of the flights (Saffire-2), 9 smaller (5 x 30 cm) samples will be tested to evaluate NASAs material flammability screening tests. The first flight (Saffire-1) is scheduled for July 2015 with the other two following at six-month intervals. A computer modeling effort will complement the experimental effort. Although the experiment will need to meet rigorous safety requirements to ensure the carrier vehicle does not sustain damage, the absence of a crew removes the need for strict containment of combustion products. This will facilitate the first examination of fire behavior on a scale that is relevant to spacecraft fire safety and will provide unique data for fire model validation.

Combustion↗

DOE OSTI2018

On the freezing time of supercooled drops in developing convective clouds over tropical ocean

Ice generation and evolution in tropical maritime convective clouds are still poorly understood and challenging to model. Aircraft measurements during the Ice in Clouds-Tropical (ICE-T) project suggest that the observed ice particles in intense convective clouds are primarily small at relatively warm temperature (between -7 °C and -10 °C), and large frozen drops are detected at a temperature colder than -10 °C. However, the ice particle size distributions (PSDs) between -7 °C and -10 °C modelled using a parcel model with spectral bin microphysics scheme are much broader than the observation. To interpret the difference in the temperature-dependent ice PSD evolution between the model simulations and the observations, the freezing times and temperatures of supercooled drops are modelled and analyzed. The results indicate that the freezing time (from the initial nucleation to fully frozen) must be considered; it is not instantaneous, and is longer for large drops than for small drops. In strong updrafts, such as that sampled by the Learjet during ICE-T, large freezing drops may be carried upwards to a temperature lower than their nucleation temperature before they are fully frozen. This offers a feasible explanation for the temperature-dependent ice particle size evolution in strong updrafts observed during ICE-T. In models, drop freezing is normally assumed to be instantaneous, which is not realistic; the models yields broader ice PSDs between -7 °C and -10 °C than is observed. The results highlight the importance to consider the freezing time of supercooled drops in interpreting the observed and modelled ice PSDs in growing turrets and in modelling ice generation in cloud resolving models. To better understand the time-dependent drop freezing and its impact on the microphysics and dynamics of convective clouds, more field measurements and laboratory experiments, as well as modelling studies are needed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Magnetic Barkhausen noise characterization of two pipeline steels with unknown history

Highlights: • The hardness, microstructure, texture and MBN of two pipeline steels were analyzed. • The angular MBN results revealed possible manufacturing histories of the two pipelines. • The MBN is closely related to the processing history, microstructure and stress state. • The use of MBN technique can help address the integrity issues in the pipeline industry. Steel samples cut from two line pipes with unknown processing history were analyzed using magnetic Barkhausen noise (MBN), electron backscatter diffraction (EBSD) and Vickers hardness techniques on the pipe surface and on sections through the wall thickness. The results show that the MBN responses vary significantly not only between the two pipe steels, but also among different thickness layers of each steel. Both steels show considerable variations in MBN at different locations on the surfaces. For one steel, the surface MBN illustrates an inverse linear relationship with respect to the hardness, while the other does not depict such a relation since the variation in hardness at different locations is very small. Across the thickness, the microstructure (phase and grain size) of both steels is quite similar, but the texture shows significant differences. Again, there is a large difference in hardness across the thickness for one steel, while the other only shows very small variation in hardness across the thickness. The variations in average MBN across the wall thickness for both steels are quite large. Angular MBN measurements on the sectioned samples revealed significant discrepancies in the magnetic anisotropy in the two steels. Based on the analysis of the angular MBN data with respect to the single and dual easy axis models, one pipe can be determined to have been manufactured through a seam welding process, while the other may have been formed by spiral welding. Due to the residual stresses in the steel samples, the effect of the crystallographic texture on the anisotropy in MBN response has essentially been suppressed.

36 MATERIALS SCIENCE↗

NASA NTRS2013

Application of CO2 Snow Jet Cleaning in Conjunction with Laboratory Based Total Reflection X-Ray Fluorescence

The Genesis mission was the first mission returning solar material to Earth since the Apollo program [1,2]. Unfortunately the return of the space craft on September 8, 2004 resulted in a crash landing, which shattered the samples into small fragments and exposed them to desert soil and other debris. Thus only small fragments of the original collectors are available, each having different degrees of surface contamination. Thorough surface cleaning is required to allow for subsequent analysis of solar wind material embedded within. An initial cleaning procedure was developed in coordination with Johnson Space Center which focused on removing larger sized particulates and a thin film organic contamination acquired during collection in space [3]. However, many of the samples have additional residues and more rigorous and/or innovative cleaning steps might be necessary. These cleaning steps must affect only the surface to avoid leaching and re-distribution of solar wind material from the bulk of the collectors. To aid in development and identification of the most appropriate cleaning procedures each sample has to be thoroughly inspected before and after each cleaning step. Laboratory based total reflection X-ray fluorescence (TXRF) spectrometry lends itself to this task as it is a non-destructive and surface sensitive analytical method permitting analysis of elements from aluminum onward present at and near the surface of a flat substrate [4]. The suitability of TXRF has been demonstrated for several Genesis solar wind samples before and after various cleaning methods including acid treatment, gas cluster ion beam, and CO2 snow jet [5 - 7]. The latter one is non-invasive and did show some promise on one sample [5]. To investigate the feasibility of CO2 snow jet cleaning further, several flown Genesis samples were selected to be characterized before and after CO2 snow application with sample 61052 being discussed below.

Schmeling, M.↗

DOE OSTI2013

EVOLUTION OF THE SIZES OF GALAXIES OVER 7 < z < 12 REVEALED BY THE 2012 HUBBLE ULTRA DEEP FIELD CAMPAIGN

We analyze the redshift- and luminosity-dependent sizes of dropout galaxy candidates in the redshift range z ∼ 7-12 using deep images from the 2012 Hubble Ultra Deep Field (UDF12) campaign, which offers two advantages over that used in earlier work. First, we utilize the increased signal-to-noise ratio offered by the UDF12 imaging to provide improved measurements for known galaxies at z ≅ 6.5-8 in the HUDF. Second, because the UDF12 data have allowed the construction of the first robust galaxy sample in the HUDF at z > 8, we have been able to extend the measurement of average galaxy size out to higher redshifts. Restricting our measurements to sources detected at >15σ, we confirm earlier indications that the average half-light radii of z ∼ 7-12 galaxies are extremely small, 0.3-0.4 kpc, comparable to the sizes of giant molecular associations in local star-forming galaxies. We also confirm that there is a clear trend of decreasing half-light radius with increasing redshift, and provide the first evidence that this trend continues beyond z ≅ 8. Modeling the evolution of the average half-light radius as a power law, ∝(1 + z) {sup s}, we obtain a best-fit index of s=-1.30{sup +0.12}{sub -0.14} over z ∼ 4-12. A clear size-luminosity relation is evident in our dropout samples. This relation can be interpreted in terms of a constant surface density of star formation over a range in luminosity of 0.05-1.0 L{sub z=3}. The average star formation surface density in dropout galaxies is 2-3 orders of magnitude lower than that found in extreme starburst galaxies, but is comparable to that seen today in the centers of normal disk galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1999

Method and Apparatus for the Collection, Storage, and Real Time Analysis of Blood and Other Bodily Fluids

The present invention provides a method and apparatus for separating a blood sample having a volume of up to about 20 milliliters into cellular and acellular fractions. The apparatus includes a housing divided by a fibrous filter into a blood sample collection chamber having a volume of at least about 1 milliliter and a serum sample collection chamber. The fibrous filter has a pore size of less than about 3 microns, and is coated with a mixture including between about 1-40 wt/vol % mannitol and between about 0.1-15 wt/vol % of plasma fraction protein (or an animal or vegetable equivalent thereof). The coating causes the cellular fraction to be trapped by the small pores, leaving the cellular fraction intact on the fibrous filter while the acellular fraction passes through the filter for collection in unaltered form from the serum sample collection chamber.

Whiitson, Peggy A.↗