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DOE OSTI2016

The Sphagnum Genome Project: a new model for ecological and evolutionary genomics. In: Genomes and Evolution of Charophytes, Bryophytes, Club Mosses and Ferns

The inception of the Sphagnum (peat moss) genome project marks the first plant-based sequencing project aimed specifically at carbon cycling genomics in a plant system relevant to ecological and evolutionary genomics. Sphagnum provides considerable intra- and interspecific variation at the nucleotide level, and in physiology, morphology, net production, decomposition and carbon accumulation (peat formation). Because of the large number of peat moss species, their diversity in mating systems, and clear patterns of niche differentiation, Sphagnum provides an exceptionally valuable complement to Physcomitrella patens and Ceratodon purpureus as moss models for genomic research. Here we review the organismal biology of Sphagnum including phylogeny, life cycle, mating systems, ecology and niche differentiation. We include the current state of Sphagnum genomic resources, in vitro methods and germplasm. A use-case is provided to address questions concerning epigenetics and reproduction.

Shaw, AJ↗

DOE OSTI2018

Projection-operator methods for classical transport in magnetized plasmas. Part 2. Nonlinear response and the Burnett equations [Projection-operator methods for classical transport in magnetized plasmas. Part 1. Nonlinear response and the Burnett equations]

The time-independent projection-operator formalism for the derivation of Burnett equations is extended and considered in the context of multispecies and magnetized plasmas. The procedure provides specific formulas for transport coefficients in terms of two-time correlation functions involving both two and three phase-space points. It is shown how to calculate those correlation functions in the limit of weak coupling. The results are used to demonstrate, with the aid of a particular non-trivial example, that the Chapman–Enskog methodology employed by Catto & Simakov (CS) (Phys. Plasmas, vol. 11, 2004, pp. 90–102) to calculate the contributions to the parallel viscosity driven by temperature gradients is consistent with formulas previously derived from the two-time formalism by Brey (J. Chem. Phys., vol. 79, 1983, pp. 4585–4598). Here, the work serves to unify previous work on plasma kinetic theory with formalism usually applied to turbulence. Additional contributions include discussions of (i) Braginskii-order interspecies momentum exchange from the point of view of two-time correlations; and (ii) a simple stochastic model, unrelated to many-body theory, that exhibits Burnett effects. Insights from that model emphasize the role of non-Gaussian statistics in the evaluation of Burnett transport coefficients, including the effects calculated by CS that stem from the nonlinear collision operator. Together, Parts 1 and 2 of this series provide an introduction to projection-operator methods that should be broadly useful in theoretical plasma physics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

Ligand-Enhanced Optical Response of Gold Nanomolecules and Its Fragment Projection Analysis: The Case of Au 30 (SR) 18

We investigate via first-principles simulations the optical absorption spectra of three different Au 30 (SR) 18 monolayer-protected clusters (MPC): Au 30 (StBu) 18 , Au 30 (SPh) 18 , and Au 30 (SPh-pNO 2 ) 18 . Au 30 (StBu) 18 is known in the literature, and its crystal structure is available. In contrast, Au 30 (SPh) 18 and Au 30 (SPh-pNO 2 ) 18 are two species that have been designed by replacing the tert-butyl organic residues of Au 30 (StBu) 18 with aromatic ones so as to investigate the effects of ligand replacement on the optical response of Au nanomolecules. By analogy to a previously studied Au 23 (SR)16– anionic species, despite distinct differences in charge and chemical composition, a substantial ligand enhancement of the absorption intensity in the optical region is also obtained for the Au 30 (SPh-pNO 2 ) 18 MPC. Furthermore, the use of conjugated aromatic ligands with properly chosen electron-withdrawing substituents and exhibiting steric hindrance so as to also achieve charge decompression at the surface is therefore demonstrated as a general approach to enhancing the MPC photoabsorption intensity in the optical region. In addition, we here subject the ligand-enhancement phenomenon to a detailed analysis based on the fragment projection of electronic excited states and on induced transition densities, leading to a better understanding of the physical origin of this phenomenon, thus opening avenues to its more precise control and exploitation.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Initial Land Use/Cover Distribution Substantially Affects Global Carbon and Local Temperature Projections in the Integrated Earth System Model

Initial land cover distribution varies among Earth system models, an uncertainty in initial conditions that can substantially affect carbon and climate projections. We use the integrated Earth System Model to show that a 3.9 M km2 difference in 2005 global forest area (9–14% of total forest area) generates uncertainties in initial atmospheric CO2 concentration, terrestrial carbon, and local temperature that propagate through a future simulation following the Representative Concentration Pathway 4.5. By 2095, the initial 6 ppmv uncertainty range increases to 9 ppmv and the initial 26 PgC uncertainty range in terrestrial carbon increases to 33 PgC. The initial uncertainty range in annual average local temperature of -0.74 to 0.96 °C persists throughout the future simulation, with a seasonal maximum in Dec-Jan-Feb. These results highlight the importance of accurately characterizing historical land use and land cover to reduce overall initial condition uncertainty.

Di Vittorio, Alan↗

DOE OSTI2019

The Atmospheric River Tracking Method Intercomparison Project (ARTMIP): Quantifying Uncertainties in Atmospheric River Climatology

Atmospheric rivers (ARs) are now widely known for their association with high-impact weather events and long-term water supply in many regions. Researchers within the scientific community have developed numerous methods to identify and track of ARs—a necessary step for analyses on gridded data sets, and objective attribution of impacts to ARs. These different methods have been developed to answer specific research questions and hence use different criteria (e.g., geometry, threshold values of key variables, and time dependence). Furthermore, these methods are often employed using different reanalysis data sets, time periods, and regions of interest. The goal of the Atmospheric River Tracking Method Intercomparison Project (ARTMIP) is to understand and quantify uncertainties in AR science that arise due to differences in these methods. This paper presents results for key AR-related metrics based on 20+ different AR identification and tracking methods applied to Modern-Era Retrospective Analysis for Research and Applications Version 2 reanalysis data from January 1980 through June 2017. We show that AR frequency, duration, and seasonality exhibit a wide range of results, while the meridional distribution of these metrics along selected coastal (but not interior) transects are quite similar across methods. Furthermore, methods are grouped into criteria-based clusters, within which the range of results is reduced. AR case studies and an evaluation of individual method deviation from an all-method mean highlight advantages/disadvantages of certain approaches. For example, methods with less (more) restrictive criteria identify more (less) ARs and AR-related impacts. Finally, this paper concludes with a discussion and recommendations for those conducting AR-related research to consider.

Rutz, Jonathan J.↗

DOE OSTI2021

Graph Neural Network for Object Reconstruction in Liquid Argon Time Projection Chambers

This paper presents a graph neural network (GNN) technique for low-level reconstruction of neutrino interactions in a Liquid Argon Time Projection Chamber (LArTPC). GNNs are still a relatively novel technique, and have shown great promise for similar reconstruction tasks in the LHC. In this paper, a multihead attention message passing network is used to classify the relationship between detector hits by labelling graph edges, determining whether hits were produced by the same underlying particle, and if so, the particle type. The trained model is 84% accurate overall, and performs best on the EM shower and muon track classes. The model’s strengths and weaknesses are discussed, and plans for developing this technique further are summarised.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Implementation of a 1-2 keV point-projection x-ray spectrometer on the National Ignition Facility

A point-projection soft X-ray Opacity Spectrometer (OpSpec) has been implemented to measure X-ray spectra from ~1 to 2 keV on the National Ignition Facility (NIF). Measurement of such soft X-rays with open-aperture point-projection detectors is challenging because only very thin filters may be used to shield the detector from the hostile environment. OpSpec diffracts X-rays from 540 to 2100 eV off a potassium (or rubidium) acid phthalate (KAP or RbAP) crystal onto either image plates or, most recently, X-ray films. A “sacrificial front filter” strategy is used to prevent crystal damage, while 2 or 3 rear filters protect the data. Since May 2017, OpSpec has been recording X-ray transmission data for iron-magnesium plasmas on the NIF, at “Anchor 1” plasma conditions (temperature ~150 eV, density ~7 × 10 21 e - /cm 3 ). Upgrades improved OpSpec’s performance on 6 NIF shots in August and December 2017, with reduced backgrounds and 100% data return using filter stacks as thin as 2.9 μm (total). We conclude that photometric noise is beginning to meet requirements, and further work will reduce systematic errors.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

Projected coupled cluster theory: Optimization of cluster amplitudes in the presence of symmetry projection

Methods which aim at universal applicability must be able to describe both weak and strong electronic correlation with equal facility. Such methods are in short supply. The combination of symmetry projection for strong correlation and coupled cluster theory for weak correlation offers tantalizing promise to account for both on an equal footing. In order to do so, however, the coupled cluster portion of the wave function must be optimized in the presence of the symmetry projection. Finally, this paper discusses how this may be accomplished, and shows the importance of doing so for both the Hubbard model Hamiltonian and the molecular Hamiltonian, all with a computational scaling comparable to that of traditional coupled cluster theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

The DarkSide project

DarkSide is a graded experimental project based on radiopure argon, and is now, and will be, used in direct dark matter searches. The present DarkSide-50 detector, operating at the Gran Sasso National Laboratory, is a dual-phase, 50 kg, liquid argon time-projection-chamber surrounded by an active liquid scintillator veto. It is designed to be background free in 3 years of operation. DS-50 performances, when filled with atmospheric argon, are reported. However DS-50 filled with underground argon, shows impressive reduction of the 39Ar isotope. The application of this powerful technology in a future generation of the DarkSide program is discussed.

Agnes, P.↗

DOE OSTI2017

Convolutional Neural Networks Applied to Neutrino Events in a Liquid Argon Time Projection Chamber

We present several studies of convolutional neural networks applied to data coming from the MicroBooNE detector, a liquid argon time projection chamber (LArTPC). The algorithms studied include the classification of single particle images, the localization of single particle and neutrino interactions in an image, and the detection of a simulated neutrino event overlaid with cosmic ray backgrounds taken from real detector data. These studies demonstrate the potential of convolutional neural networks for particle identifi-cation or event detection on simulated neutrino interactions. We also address technical issues that arise when applying this technique to data from a large LArTPC at or near ground level.

Acciarri, R↗

DOE OSTI2017

The electronics, trigger and data acquisition system for the liquid argon time projection chamber of the DarkSide-50 search for dark matter

The DarkSide-50 experiment at the Laboratori Nazionali del Gran Sasso is a search for dark matter using a dual phase time projection chamber with 50 kg of low radioactivity argon as target. Light signals from interactions in the argon are detected by a system of 38 photo-multiplier tubes (PMTs), 19 above and 19 below the TPC volume inside the argon cryostat. We describe the electronics which processes the signals from the photo-multipliers, the trigger system which identifies events of interest, and the data-acquisition system which records the data for further analysis. The electronics include resistive voltage dividers on the PMTs, custom pre-amplifiers mounted directly on the PMT voltage dividers in the liquid argon, and custom amplifier/discriminators (at room temperature). After amplification, the PMT signals are digitized in CAEN waveform digitizers, and CAEN logic modules are used to construct the trigger, the data acquisition system for the TPC is based on the Fermilab "artdaq" software. The system has been in operation since early 2014.

Agnes, P.↗

DOE OSTI2024

Coupled model intercomparison project phase 6 (CMIP6) high resolution model intercomparison project (HighResMIP) bias in extreme rainfall drives underestimation of amazonian precipitation

Abstract Extreme rainfall events drive the amount and spatial distribution of rainfall in the Amazon and are a key driver of forest dynamics across the basin. This study investigates how the 3-hourly predictions in the High Resolution Model Intercomparison Project (HighResMIP, a component of the recent Coupled Model Intercomparison Project, CMIP6) represent extreme rainfall events at annual, seasonal, and sub-daily time scales. TRMM 3B42 (Tropical Rainfall Measuring Mission) 3 h data were used as observations. Our results showed that eleven out of seventeen HighResMIP models showed the observed association between rainfall and number of extreme events at the annual and seasonal scales. Two models captured the spatial pattern of number of extreme events at the seasonal and annual scales better (higher correlation) than the other models. None of the models captured the sub-daily timing of extreme rainfall, though some reproduced daily totals. Our results suggest that higher model resolution is a crucial factor for capturing extreme rainfall events in the Amazon, but it might not be the sole factor. Improving the representation of Amazon extreme rainfall events in HighResMIP models can help reduce model rainfall biases and uncertainties and enable more reliable assessments of the water cycle and forest dynamics in the Amazon.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

How to optimally constrain galaxy assembly bias: supplement projected correlation functions with count-in-cells statistics

Most models for the statistical connection between galaxies and their haloes ignore the possibility that galaxy properties may be correlated with halo properties other than halo mass, a phenomenon known as galaxy assembly bias. And yet, it is known that such correlations can lead to systematic errors in the interpretation of survey data that are analysed using traditional halo occupation models. At present, the degree to which galaxy assembly bias may be present in the real Universe, and the best strategies for constraining it remain uncertain. We study the ability of several observables to constrain galaxy assembly bias from redshift survey data using the decorated halo occupation distribution (dHOD), an empirical model of the galaxy-halo connection that incorporates assembly bias. We cover an expansive set of observables, including the projected two-point correlation function w p ( r p ), the galaxy-galaxy lensing signal ΔΣ( r p ), the void probability function VPF( r ), the distributions of counts-in-cylinders P(NCIC), and counts-in-annuli P(NCIA), and the distribution of the ratio of counts in cylinders of different sizes P ( N 2 /N 5 ). We find that despite the frequent use of the combination w p ( r p ) + ΔΣ( r p ) in interpreting galaxy data, the count statistics, P ( N CIC ) and P ( N CIA ), are generally more efficient in constraining galaxy assembly bias when combined with w p ( r p ). Constraints based upon w p ( r p ) and ΔΣ(rp) share common degeneracy directions in the parameter space, while combinations of r p w p ( r p ) with the count statistics are more complementary. Therefore, we strongly suggest that count statistics should be used to complement the canonical observables in future studies of the galaxy-halo connection.

galaxies: evolution↗

DOE OSTI2017

First observation of low energy electron neutrinos in a liquid argon time projection chamber

Liquid argon time projection chambers (LArTPCs) produce remarkable fidelity in the observation of neutrino interactions. Here, the superior capabilities of such detectors to reconstruct the spatial and calorimetric information of neutrino events have made them the detectors of choice in a number of experiments, specifically those looking to observe electron neutrino ($\nu_e$) appearance. The LArTPC promises excellent background rejection capabilities, especially in this "golden" channel for both short and long baseline neutrino oscillation experiments. We present the first experimental observation of electron neutrinos and anti-neutrinos in the ArgoNeut LArTPC, in the energy range relevant to DUNE and the Fermilab Short Baseline Neutrino Program. Additionally, we present a demonstration of separation of electrons from gammas using neutrino data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes. The progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Therefore, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. We introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Earth Microbiome Project and Global Systems Biology

Recently, we published the first large-scale analysis of data from the Earth Microbiome Project (1, 2), a truly multidisciplinary research program involving more than 500 scientists and 27,751 samples acquired from 43 countries. These samples represent myriad specimen types and span a wide range of biotic and abiotic factors, geographic locations, and physicochemical properties. The database (https://qiita.ucsd.edu/emp/) is still growing, with over 90,000 amplicon datasets, >500 metagenomic runs, and metabolomics datasets from a similar number of samples. Importantly, the techniques, data and analytical tools are all standardized and publicly accessible, providing a framework to support research at a scale of integration that just 7 years ago seemed impossible.

Gilbert, Jack A.↗

DOE OSTI2015

Future particle-physics projects in the United States

Here, basic proposals of experiments aimed at precision measurements of Standard Model parameters and at searches for new particles, including dark-matter particles, are described along with future experimental projects considered by American Physical Society at the meeting in the summer of 2013 and intended for implementation within the next ten to twenty years.

43 PARTICLE ACCELERATORS↗

DOE OSTI2015

The Wind Forecast Improvement Project (WFIP): A Public–Private Partnership Addressing Wind Energy Forecast Needs

The Wind Forecast Improvement Project (WFIP) is a public–private research program, the goal of which is to improve the accuracy of short-term (0–6 h) wind power forecasts for the wind energy industry. WFIP was sponsored by the U.S. Department of Energy (DOE), with partners that included the National Oceanic and Atmospheric Administration (NOAA), private forecasting companies (WindLogics and AWS Truepower), DOE national laboratories, grid operators, and universities. WFIP employed two avenues for improving wind power forecasts: first, through the collection of special observations to be assimilated into forecast models and, second, by upgrading NWP forecast models and ensembles. The new observations were collected during concurrent year-long field campaigns in two high wind energy resource areas of the United States (the upper Great Plains and Texas) and included 12 wind profiling radars, 12 sodars, several lidars and surface flux stations, 184 instrumented tall towers, and over 400 nacelle anemometers. Results demonstrate that a substantial reduction (12%–5% for forecast hours 1–12) in power RMSE was achieved from the combination of improved numerical weather prediction models and assimilation of new observations, equivalent to the previous decade’s worth of improvements found for low-level winds in NOAA/National Weather Service (NWS) operational weather forecast models. Data-denial experiments run over select periods of time demonstrate that up to a 6% improvement came from the new observations. Ensemble forecasts developed by the private sector partners also produced significant improvements in power production and ramp prediction. Based on the success of WFIP, DOE is planning follow-on field programs.

17 WIND ENERGY↗