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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"

This data package is associated with the publication "Organic Molecules are Deterministically Assembled in River Sediments" submitted to Scientific Reports (Stegen et al., 2024). The study applies community ecology methods to dissolved organic matter (DOM) chemistry from variably inundated riverbed sediments to uncover principles governing DOM composition at a reach-scale. This data package documents the workflow used to process and generate the main findings in the manuscript. The R scripts reference the raw, unprocessed Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data from another data package, available on ESS-DIVE at https://data.ess-dive.lbl.gov/view/doi:10.15485/1834208. The scripts then process the raw FTICR-MS data and generate the findings and figures presented in the associated manuscript. In brief, this study demonstrates that DOM assemblages in variably inundated sediments are primarily governed by deterministic variable selection, including sediment moisture effecting the degree of deterministic assembly. See the manuscript for more details pertaining to interpretation and implications of the findings. This data package is associated with the GitHub repository found at https://github.com/WHONDRS-Hub/ECA_2020_Sed.This data package is comprised of 6 scripts and 7 folders. The file-level metadata file (file ending in "flmd.csv") lists all files contained in this data package and descriptions for each. The data dictionary (file ending in "dd.csv) describes all tabular data columns and their respective definitions and units. The FTICR_Processing_Scripts produce the outputs found in the "Processed_Data" folder. The remaining scripts (located in the parent directory) produce the outputs found in the following four folders: (1) "MCD_Dendrograms", "MCD_Randomizations", "MCD_bNTI_Outcomes", and "OM_Null_Modeling". The fifth script additionally takes the three comma-separated values (CSV) files found in the parent directory as input ("VGC_texture.csv", "merged_weights.csv", and "ECA2_FTICR_BetaDisp.csv"). The outputs of each of the five scripts serve as the input to the following script, with the final outputs stored in the folder "OM_Null_Modeling".

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Data and scripts associated with “Non-random processes impacting organic matter chemistry are maximized in mid-order streams”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the publication “Non-random processes impacting organic matter chemistry are maximized in mid-order streams” submitted to Limnology and Oceanography (L&O) by Danczak et al. (in review). This package contains data and scripts used to investigate dissolved organic matter (DOM) molecular chemistry and diversification processes across 47 surface-water sampling sites in the Yakima River Basin, Washington, USA, during an August 2021 sampling campaign. The package contains analyses of ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), geochemical measurements, geospatial attributes, molecular diversity, and meta-metabolome ecological null models needed to reproduce the main manuscript results. The underlying field data were pulled from exising data packages at https://doi.org/10.15485/1892052 (Fulton et al., 2022) and https://doi.org/10.15485/1898914 (Grieger et al., 2022). For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. We thank the following organizations for providing access to field locations for sample collection: the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, the Confederated Tribes and Bands of the Yakama Nation, and the Cowiche Canyon Conservatory. Research was conducted under Washington State Parks and Recreation Commission Scientific Research Permit #210901. We are grateful to the Yakama Nation Tribal Council and Yakama Nation Fisheries for their collaboration in facilitating sample collection and ensuring data usage aligns with their values and worldview. This data package contains an R-Markdown file for analyses and five folders: (1) Data, (2) Geospatial Data, (3) Supplemental_Files, (5) Figures_pdf, (4) and src. The Data folder contains tabular inputs and derived files used in the manuscript analysis. The Geospatial Data folder contains climate and water-balance, hydrologic, land-cover, population/regional water-use, stream, topographic, and stream-order attribute CSV files. The src folder contains scripts used to process data, run analyses, and generate figures. The Figures_pdf folder contains manuscript figure outputs. The Supplemental_Files folder contains supplemental analysis products. All files are .csv, .pdf, .html, .png, .R, .Rmd, .svg, or .tre. This data package is associated with the rcfsa-RC2-SPS_Null_Modeling repository found at https://github.com/river-corridors-sfa/rcfsa-RC2-SPS_Null_Modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Field Testing of Compartmentalization Methods for Multifamily Construction

The 2012 IECC has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure for both single-family and multifamily construction in Climate Zones 3-8. Other programs (LEED, ASHRAE 189, ASHRAE 62.2) have similar or tighter compartmentalization requirements, driving the need for easier and more effective methods of compartmentalization in multifamily buildings. Builders and practitioners have found that fire-resistance rated wall assemblies are a major source of difficulty in air sealing/compartmentalization, particularly in townhouse construction. This problem is exacerbated when garages are “tucked in” to the units and living space is located over the garages. In this project, Building Science Corporation examined the taping of exterior sheathing details to improve air sealing results in townhouse and multifamily construction, when coupled with a better understanding of air leakage pathways. Current approaches are cumbersome, expensive, time consuming, and ineffective; these details were proposed as a more effective and efficient method. The effectiveness of these air sealing methods was tested with blower door testing, including “nulled” or “guarded” testing (adjacent units run at equal test pressure to null out inter-unit air leakage, or “pressure neutralization”). Pressure diagnostics were used to evaluate unit-to-unit connections and series leakage pathways (i.e., air leakage from exterior, into the fire-resistance rated wall assembly, and to the interior).

42 ENGINEERING↗
NASA NTRS2004

Terrestrial Planet Finder cryogenic delay line development

Delay lines provide the path-length compensation that makes the measurement of interference fringes possible. When used for nulling interferometry, the delay line must control path-lengths so that the null is stable and controlled throughout the measurement. We report on a low noise, low disturbance, and high bandwidth optical delay line capable of meeting the TPF interferometer optical path length control requirements at cryogenic temperatures.

cryogenic↗
NASA NTRS2006

Broadband Performance of TPF's High-contrast Imaging Testbed: Modeling and Simulations

The broadband performance of the high-contrast imaging testbed (HCIT) at JPL is investigated through optical modeling and simulations. The analytical tool is an optical simulation algorithm developed by combining the HCIT's optical model with a speckle-nulling algorithm that operates directly on coronagraphic images, an algorithm identical to the one currently being used on the HCIT to actively suppress scattered light via a deformable mirror. It is capable of performing full three-dimensional end-to-end near-field diffraction analysis on the HCIT's optical system. By conducting speckle-nulling optimization, we clarify the HCIT's capability and limitations in terms of its broadband contrast performance under various realistic conditions. Considered cases include non-ideal occulting masks, such as a mask with optical density and wavelength dependent parasitic phase-delay errors (i.e., a not band-limited occulting mask) and the one with an optical-density profile corresponding to a measured, non-standard profile, as well as the independently measured phase errors of all optics. Most of the information gathered on the HCIT's optical components through measurement and characterization over the last several years at JPL has been used in this analysis to make the predictions as accurate as possible. The best contrast values predicted so far by our simulations obtainable on the HCIT illuminated with a broadband light having a bandwidth of 80nm and centered at 800nm wavelength are Cm=1.1x10-8 (mean) and C4=4.9x10-8 (at 4(lamda)/D), respectively. In this paper we report our preliminary findings about the broadband light performance of the HCIT.

integrated modeling↗
DOE OSTI2015

Tropospheric Biennial Oscillation (TBO) indistinguishable from white noise

Abstract Previous studies proposed that the year‐to‐year variability of seasonal monsoon indices is partly determined by a Tropospheric Biennial Oscillation (TBO). Invoking coupled ocean‐atmosphere‐land processes and the presence of an annual memory, the TBO mechanism describes how a relatively strong monsoon is followed by a year with weaker monsoon and vice versa. Here we revisit the issue of preferred biennial timescales in tropical monsoon systems, by testing the biennial tendencies in observed and simulated monsoon indices against the white noise null hypothesis. According to an analytical expression for the null hypothesis, we expect the probability for this biennial tendency to be 2/3, which is in close agreement with observations, reanalysis products, and Atmospheric Model Intercomparison Project/Coupled Model Intercomparison Project general circulation model simulations. Thus, it is concluded that biennial tendencies in these monsoon indices and the associated TBO are fully consistent with a white noise process and do not require the presence of a preferred biennial timescale.

Stuecker, Malte F.↗
DOE OSTI2020

Associations between cumulative environmental quality and ten selected birth defects in Texas

Abstract Background Causes of most birth defects are largely unknown. Genetics, maternal factors (e.g., age, smoking) and environmental exposures have all been linked to some birth defects, including neural tube, oral cleft, limb reduction, and gastroschisis; however, the contribution of cumulative exposures across several environmental domains in association with these defects is not well understood. Methods The Environmental Quality Index (EQI) and its domains (air, water, land, sociodemographic, built) were used to estimate county‐level cumulative environmental exposures from 2006–2010 and matched to birth defects identified from Texas Birth Defects Registry and live birth records from births in years 2007–2010 ( N = 1,610,709). Poisson regression models estimated prevalence ratios (PR) and 95% confidence intervals (CI) for associations between 10 birth defects and the EQI. Results We observed some positive associations between worst environmental quality and neural tube, anencephaly, spina bifida, oral cleft, cleft palate, cleft lip with and without cleft palate, and gastroschisis [PR range: 1.12–1.55], but near null associations with limb reduction defects. Among domain specific results, we observed the strongest positive associations with the sociodemographic domain across birth defects but varied positive associations among the air and water domains, and negative or null associations with the land and built domains. Overall, few exposure‐response patterns were evident. Conclusions Our results highlight the complexities of cumulative, simultaneous environmental exposures in the prevalence rates of 10 selected birth defects. We were able to explore the impact of overall and domain specific environmental quality on birth defects and identify potential domain specific drivers of these associations.

Krajewski, Alison K.↗
DOE OSTI2022

Modelling of electrostatic ion-scale turbulence in divertor tokamaks with the gyrokinetic code $\mathrm{COGENT}$

Here, continuum gyrokinetic simulations of electrostatic ion scale turbulence are presented for the case of a diverted (single-null) tokamak geometry. The simulation model, implemented in the finite-volume code COGENT, solves the long-wavelength limit of the full-F gyrokinetic equation for ion species coupled to a vorticity equation for electrostatic potential variations, where a fluid model is used for an electron response. The model describes the ion scale ion temperature gradient (ITG) and resistive drift modes as well as neoclassical ion physics effects. Different turbulence regimes are observed depending on the plasma profiles, and the roles of a self-consistent background electric field and an X-point geometry are explored. In particular, increasing the pedestal density gradient and the corresponding radial electric field is demonstrated to suppress the ITG turbulence, whereas the same edge plasma background can still be destabilized by the resistive modes when the plasma resistivity is increased. The effects of X-point geometry are assessed by comparing cross-separatrix simulations with counterpart calculations performed for a toroidal annulus geometry. For the simulation parameters considered, similar global behaviour is observed in both cases, whereas strong local suppression of turbulence fluctuations is demonstrated near the X-point for the case of a single-null geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

Abstract Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms

Abstract Understanding protein structure and function relationships in cellulose synthase (CesA), including divergent isomers, is an important goal. Here, we report results from mutant complementation assays that tested the ability of sequence variants of AtCesA7, a secondary wall CesA of Arabidopsis thaliana , to rescue the collapsed vessels, short stems, and low cellulose content of the irx3‐1 AtCesA7 null mutant. We tested a catalytic null mutation and seven missense or small domain changes in and near the AtCesA7 FTVTSK motif, which lies near the catalytic domain and may, analogously to bacterial CesA, exist within a substrate “gating loop.” A low‐to‐high gradient of rescue occurred, and even inactive AtCesA7 had a small positive effect on stem cellulose content but not stem elongation. Overall, secondary wall cellulose content and stem length were moderately correlated, but the results were consistent with threshold amounts of cellulose supporting particular developmental processes. Vibrational sum frequency generation microscopy allowed tissue‐specific analysis of cellulose content in stem xylem and interfascicular fibers, revealing subtle differences between selected genotypes that correlated with the extent of rescue of the collapsing xylem phenotype. Similar tests on PpCesA5 from the moss Physcomitrium (formerly Physcomitrella ) patens helped us to synergize the AtCesA7 results with prior results on AtCesA1 and PpCesA5. The cumulative results show that the FTVTxK region is important for the function of an angiosperm secondary wall CesA as well as widely divergent primary wall CesAs, while differences in complementation results between isomers may reflect functional differences that can be explored in further work.

Burris, Jason N.↗
DOE OSTI2020

Global aspects of conformal symmetry and the ANEC in dS and AdS

Starting from the averaged null energy condition (ANEC) in Minkowski we show that conformal symmetry implies the ANEC for a conformal field theory (CFT) in a de Sitter and anti-de Sitter background. A similar and novel bound is also obtained for a CFT in the Lorentzian cylinder. Using monotonicity of relative entropy, we rederive these results for dS and the cylinder. As a byproduct we obtain the vacuum modular Hamiltonian and entanglement entropy associated to null deformed regions of CFTs in (A)dS and the cylinder. A third derivation of the ANEC in dS is shown to follow from bulk causality in AdS/CFT. Finally, we use the Tomita-Takesaki theory to show that Rindler positivity of Minkowski correlators generalizes to conformal theories defined in dS and the cylinder.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Discrete Max-Focusing

The Quantum Focusing Conjecture (QFC) lies at the foundation of holography and semiclassical gravity. The QFC implies the Bousso bound and the Quantum Null Energy Condition (QNEC). The QFC also ensures the consistency of the quantum extremal surface prescription and bulk reconstruction in AdS/CFT. However, the central object in the QFC — the expansion of lightrays — is not defined at points where geodesics enter or leave a null congruence. Moreover, the expansion admits three inequivalent quantum extensions in terms of the conditional max, min, and von Neumann entropies.

AdS-CFT Correspondence↗
DOE OSTI2016

Entanglement conservation, ER=EPR, and a new classical area theorem for wormholes

We consider the question of entanglement conservation in the context of the ER=EPR correspondence equating quantum entanglement with wormholes. In quantum mechanics, the entanglement between a system and its complement is conserved under unitary operations that act independently on each; ER=EPR suggests that an analogous statement should hold for wormholes. We accordingly prove a new area theorem in general relativity: for a collection of dynamical wormholes and black holes in a spacetime satisfying the null curvature condition, the maximin area for a subset of the horizons (giving the largest area attained by the minimal cross section of the multi-wormhole throat separating the subset from its complement) is invariant under classical time evolution along the outermost apparent horizons. The evolution can be completely general, including horizon mergers and the addition of classical matter satisfying the null energy condition. In conclusion, this theorem is the gravitational dual of entanglement conservation and thus constitutes an explicit characterization of the ER=EPR duality in the classical limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

(2, 2) Scattering and the celestial torus

Analytic continuation from Minkowski space to (2, 2) split signature spacetime has proven to be a powerful tool for the study of scattering amplitudes. Here we show that, under this continuation, null infinity becomes the product of a null interval with a celestial torus (replacing the celestial sphere) and has only one connected component. Spacelike and timelike infinity are time-periodic quotients of AdS 3 . These three components of infinity combine to an S 3 represented as a toric fibration over the interval. Privileged scattering states of scalars organize into SL(2, $\mathbb{R}$) L ×SL(2, $\mathbb{R}$) R conformal primary wave functions and their descendants with real integral or half-integral conformal weights, giving the normally continuous scattering problem a discrete character.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Mutual information superadditivity and unitarity bounds

We derive the property of strong superadditivity of mutual information arising from the Markov property of the vacuum state in a conformal field theory and strong subadditivity of entanglement entropy. We show this inequality encodes unitarity bounds for different types of fields. These unitarity bounds are precisely the ones that saturate for free fields. This has a natural explanation in terms of the possibility of localizing algebras on null surfaces. A particular continuity property of mutual information characterizes free fields from the entropic point of view. We derive a general formula for the leading long distance term of the mutual information for regions of arbitrary shape which involves the modular flow of these regions. We obtain the general form of this leading term for two spheres with arbitrary orientations in spacetime, and for primary fields of any tensor representation. For free fields we further obtain the explicit form of the leading term for arbitrary regions with boundaries on null cones.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Entropy variations and light ray operators from replica defects

We study the defect operator product expansion (OPE) of displacement operators in free and interacting conformal field theories using replica methods. We show that as n approaches 1 a contact term can emerge when the OPE contains defect operators of twist d - 2. For interacting theories and general states we give evidence that the only possibility is from the defect operator that becomes the stress tensor in the n → 1 limit. This implies that the quantum null energy condition (QNEC) is always saturated for CFTs with a twist gap. As a check, we show independently that in a large class of near vacuum states, the second variation of the entanglement entropy is given by a simple correlation function of averaged null energy operators as studied by Hofman and Maldacena. This suggests that sub-leading terms in the defect OPE are controlled by a defect version of the spin-3 non-local light ray operator and we speculate about the possible origin of such a defect operator. For free theories this contribution condenses to a contact term that leads to violations of QNEC saturation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

2D Kac-Moody symmetry of 4D Yang-Mills theory

Scattering amplitudes of any four-dimensional theory with nonabelian gauge group G may be recast as two-dimensional correlation functions on the asymptotic twosphere at null in nity. The soft gluon theorem is shown, for massless theories at the semiclassical level, to be the Ward identity of a holomorphic two-dimensional G-Kac-Moody symmetry acting on these correlation functions. Holomorphic Kac-Moody current insertions are positive helicity soft gluon insertions. Furthermore, the Kac-Moody transformations are a CPT invariant subgroup of gauge transformations which act nontrivially at null in nity and comprise the four-dimensional asymptotic symmetry group.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Segmented strings in AdS 3

We study segmented strings in flat space and in AdS 3 . In flat space, these well known classical motions describe strings which at any instant of time are piecewise linear. In AdS 3 , the worldsheet is composed of faces each of which is a region bounded by null geodesics in an AdS 2 subspace of AdS 3 . The time evolution can be described by specifying the null geodesic motion of kinks in the string at which two segments are joined. The outcome of collisions of kinks on the worldsheet can be worked out essentially using considerations of causality. We study several examples of closed segmented strings in AdS 3 and find an unexpected quasi-periodic behavior. Here, we also work out a WKB analysis of quantum states of yo-yo strings in AdS 5 and find a logarithmic term reminiscent of the logarithmic twist of string states on the leading Regge trajectory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗