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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Multiscale Electricity Modeling for Evaluating Carbon Capture and Sequestration Technologies (MEME-CCS)

This effort employs and adapts a rigorous multiscale electricity modeling platform at the National Renewable Energy Laboratory (NREL) to evaluate carbon capture and sequestration (CCS) and negative emissions technologies (NET) from the ARPA-E FLECCS program. NREL's modeling platform includes the Regional Energy Deployment System (ReEDS) electric sector capacity expansion model, which projects future electricity generation mixes at sub-state-level resolution that are downscaled to the unit-level to enable hourly, zonal or nodal electricity production cost modeling in the PLEXOS model. The ReEDS-PLEXOS modeling suite is well-established for examining electric sector futures with high renewable energy penetrations, energy storage, electrification, and distributed generation. The key advancement proposed herein utilizes collaboration with CCS experts at the University of Wyoming (U.WY) and the FLECCS technology development teams to create innovative methods for representing CCS and NET in the ReEDS and PLEXOS models. Expanded technology options and new operational parameterizations are integrated into these models to allow an unprecedented combination of scope and resolution for exploring the future of CCS and NET. The resulting capabilities permit wide-ranging scenario analysis to assess CCS and NET deployment under alternative scenarios of CO2 prices and competitiveness of flexible CCS and NET technologies. We demonstrate sample deployment and operational outcomes to show how these models are being used to assess the future potential for FLECCS technologies and their impacts on the U.S. electricity system. These products will help an emerging CCS/NET industry in the United States by providing economics-driven guidance to technology developers while informing policy and investment decisions in the public and private sectors.

capacity expansion↗
DOE OSTI2018

Large Ensemble Analytic Framework for Consequence-Driven Discovery of Climate Change Scenarios

An analytic scenario generation framework is developed based on the idea that the same climate outcome can result from very different socioeconomic and policy drivers. The framework builds on the Scenario Matrix Framework’s abstraction of “challenges to mitigation” and “challenges to adaptation” to facilitate the flexible discovery of diverse and consequential scenarios. We combine visual and statistical techniques for interrogating a large factorial data set of 33,750 scenarios generated using the Global Change Assessment Model. We demonstrate how the analytic framework can aid in identifying which scenario assumptions are most tied to user-specified measures for policy relevant outcomes of interest, specifically for our example high or low mitigation costs. We show that the current approach for selecting reference scenarios can miss policy relevant scenario narratives that often emerge as hybrids of optimistic and pessimistic scenario assumptions. We also show that the same scenario assumption can be associated with both high and low mitigation costs depending on the climate outcome of interest and the mitigation policy context. In the illustrative example, we show how agricultural productivity, population growth, and economic growth are most predictive of the level of mitigation costs. Formulating policy relevant scenarios of deeply and broadly uncertain futures benefits from large ensemble-based exploration of quantitative measures of consequences. To this end, we have contributed a large database of climate change futures that can support “bottom-up” scenario generation techniques that capture a broader array of consequences than those that emerge from limited sampling of a few reference scenarios.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Marine Corps Base Camp Lejeune New River Estuary - Acoustic Doppler Current Profiler (ADCP) Results

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of development pressures in surrounding areas, impairments due to other anthropogenic disturbances, and increasing requirements for compliance with environmental regulations. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and to optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a minimum 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the first six years of the program (DCERP1) are presented here.The overarching objectives of DCERP are to: (1) understand the effects of military training activities, infrastructure development, and other coastal military installations; (2) develop models, tools, and indicators to evaluate ecosystem health; and (3) recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.This data package contains a zipfile of results from Acoustic Doppler Current Profilers (ADCPs) used to collect current profiles throughout the New River Estuary in 2009: Teledyne RD Instrument’s acoustic Doppler current profilers (ADCPs) were deployed throughout the NRE to understand current flows and tidal extent. (Current velocity and water level data collected by the ADCPs were also used to validate a hydrodynamic model of the NRE.) Two ADCPS were deployed by Marker 12 and the Highway 172 bridge from late-February to early-July 2009. These ADCPs were attached to steel frames that rested on the sediment surface with the ADCP looking upward to make full water column profiles of water velocity minus a 1-m blanking between the instrument and sediment surface. Also attached to the steel frames were conductivity-temperature-depth (CTD) sensors, which provided concomitant salinity, temperature, and water depth data with the ADCP current measurements. Two ADCPS were also deployed in close proximity to the AVPs in Stones and Morgan Bays from mid-July to mid-December 2009. These ADCPs were deployed flush to the estuary floor to maximize the full vertical sampling capability at these shallow stations and the AVPs collected coincidental temperature, salinity, and depth measurements. For all deployments, the ADCPs were programmed in fast ping-rate mode 12 using 20 pings per ensemble and collected profiles in 10-cm bins every 6 minutes yielding a standard deviation in velocity measurements of 1.27 cm s-1. Current velocity and water level data were analyzed to understand the tidal influence on circulation within the NRE. Harmonic analyses were performed to extract the dominant tidal constituents from the velocity and depth records using T-tide run in MATLAB (Pawlowicz et al., 2002). These measurements of tidal amplitude and phase were then used to validate the high-resolution Advanced Circulation (ADCIRC) Model of the NRE region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

THE SINS/zC-SINF survey of z ∼ 2 galaxy kinematics: Rest-frame morphology, structure, and colors from near-infrared hubble space telescope imaging

We present the analysis of Hubble Space Telescope (HST) J- and H-band imaging for 29 galaxies on the star-forming main sequence at z ∼ 2, which have adaptive optics Very Large Telescope SINFONI integral field spectroscopy from our SINS/zC-SINF program. The SINFONI Hα data resolve the ongoing star formation and the ionized gas kinematics on scales of 1–2 kpc; the near-IR images trace the galaxies’ rest-frame optical morphologies and distributions of stellar mass in old stellar populations at a similar resolution. The global light profiles of most galaxies show disk-like properties well described by a single Sérsic profile with n∼1, with only ∼15% requiring a high n>3 Sérsic index, all more massive than 10{sup 10} M{sub ⊙}. In bulge+disk fits, about 40% of galaxies have a measurable bulge component in the light profiles, with ∼15% showing a substantial bulge-to-total ratio (B/T) B/T≳0.3. This is a lower limit to the frequency of z ∼ 2 massive galaxies with a developed bulge component in stellar mass because it could be hidden by dust and/or outshined by a thick actively star-forming disk component. The galaxies’ rest-optical half-light radii range between 1 and 7 kpc, with a median of 2.1 kpc, and lie slightly above the size–mass relation at these epochs reported in the literature. This is attributed to differences in sample selection and definitions of size and/or mass measurements. The (u−g){sub rest} color gradient and scatter within individual z ∼ 2 massive galaxies with ≳10{sup 11} M{sub ⊙} are as high as in z = 0 low-mass, late-type galaxies and are consistent with the high star formation rates of massive z ∼ 2 galaxies being sustained at large galactocentric distances.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

THE HAWAII INFRARED PARALLAX PROGRAM. I. ULTRACOOL BINARIES AND THE L/T TRANSITION

We present the first results from our high-precision infrared (IR) astrometry program at the Canada-France-Hawaii Telescope. We measure parallaxes for 83 ultracool dwarfs (spectral types M6-T9) in 49 systems, with a median uncertainty of 1.1 mas (2.3%) and as good as 0.7 mas (0.8%). We provide the first parallaxes for 48 objects in 29 systems, and for another 27 objects in 17 systems, we significantly improve upon published results, with a median (best) improvement of 1.7 times (5 times). Three systems show astrometric perturbations indicative of orbital motion; two are known binaries (2MASS J0518-2828AB and 2MASS J1404-3159AB) and one is spectrally peculiar (SDSS J0805+4812). In addition, we present here a large set of Keck adaptive optics imaging that more than triples the number of binaries with L6-T5 components that have both multi-band photometry and distances. Our data enable an unprecedented look at the photometric properties of brown dwarfs as they cool through the L/T transition. Going from Almost-Equal-To L8 to Almost-Equal-To T4.5, flux in the Y and J bands increases by Almost-Equal-To 0.7 mag and Almost-Equal-To 0.5 mag, respectively (the Y- and J-band 'bumps'), while flux in the H, K, and L' bands declines monotonically. This wavelength dependence is consistent with cloud clearing over a narrow range of temperature, since condensate opacity is expected to dominate at 1.0-1.3 {mu}m. Interestingly, despite more than doubling the near-IR census of L/T transition objects, we find a conspicuous paucity of objects on the color-magnitude diagram just blueward of the late-L/early-T sequence. This 'L/T gap' occurs at (J - H){sub MKO} 0.1-0.3 mag, (J - K){sub MKO} = 0.0-0.4 mag, and implies that the last phases of cloud evolution occur rapidly. Finally, we provide a comprehensive update to the absolute magnitudes of ultracool dwarfs as a function of spectral type using a combined sample of 314 objects.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Investigation of a Wedge Adhesion Test for Edge Seals

Many photovoltaic (PV) technologies have been found to be sensitive to moisture that diffuses into a PV package. Even with the use of impermeable frontsheets and backsheets, moisture can penetrate from the edges of a module. To limit this moisture ingress pathway from occurring, manufacturers often use a low permeability polyisobutylene (PIB) based edge seal filled with desiccant to further restrict moisture ingress. Moisture ingress studies have shown that these materials are capable of blocking moisture for the 25-year life of a module; but to do so, they must remain well-adhered and free of cracks. This work focuses on adapting the Boeing Wedge test for use with edge seals laminated using glass substrates as part of a strategy to assess the long-term durability of edge seals. The advantage of this method is that it duplicates the residual stresses and strains that a glass/glass module may have when the lamination process results in some residual glass bending that puts the perimeter in tension. Additionally, this method allows one to simultaneously expose the material to thermal stress, humidity, mechanical stress, and ultraviolet radiation. The disadvantage of this method generally is that we are limited by the fracture toughness of the glass substrates that the edge seal is adhered to. However, the low toughness of typical uncrosslinked or sparsely crosslinked PIB makes them suitable for this technique. We present data obtained during the development of the wedge test for use with PV edge seal materials. This includes development of the measuring techniques and evaluation of the test method with relevant materials. We find consistent data within a given experiment, along with the theoretical independence of fracture toughness measurements with wedge thickness. This indicates that the test methodology is reproducible. However, even though individual experimental sets are consistent, the reproducibility between experimental sets is poor. We believe this may be due to inconsistencies in sample history, sample batch, or small changes in sample preparation/assembly from one month to the next. Because the fracture strength of typical edge seal materials is so low, they cannot be relied upon for mechanical strength. A small stress or strain on the edge seal is capable of promoting delamination or tearing causing the edge seal to fail. Because of this, edge seals are very dependent on the processing and construction parameters in the full size PV module such that any long term evaluation of their durability must be conducted on full size modules to be accurate.

14 SOLAR ENERGY↗
DOE OSTI2018

Long‐term evaluation of fitness and demographic effects of a Chinook Salmon supplementation program

Abstract While the goal of supplementation programs is to provide positive, population‐level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive‐born individuals are fully integrated into the natural population. In order to evaluate the long‐term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook Salmon ( Oncorhynchus tshawytscha ), we genotyped tissue samples spanning a 19‐year period (1998–2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho, USA. We expanded upon previous estimates of relative reproductive success (RRS) to include grandparentage analyses and used generalized linear models to determine whether origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural‐origin broodstock provided a long‐term demographic boost to the population (mean of 4.56 times in the first generation and mean of 2.52 times in the second generation). Overall, when spawning in nature, hatchery‐origin fish demonstrated a trend toward lower RS compared to natural‐origin fish ( p < 0.05). However, when hatchery‐origin fish successfully spawned with natural‐origin fish, they had similar RS compared to natural by natural crosses (first‐generation mean hatchery by natural cross RRS = 1.11 females, 1.13 males; second‐generation mean hatchery by natural cross RRS = 1.03 females, 1.08 males). While origin, return year, and body length were significant predictors of fitness for both males and females ( p < 0.05), return day was significant for males but not females ( p > 0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long‐term fitness effects on wild populations.

Janowitz‐Koch, Ilana↗
DOE OSTI2014

Partial Breast Radiation Therapy With Proton Beam: 5-Year Results With Cosmetic Outcomes

Purpose: We updated our previous report of a phase 2 trial using proton beam radiation therapy to deliver partial breast irradiation (PBI) in patients with early stage breast cancer. Methods and Materials: Eligible subjects had invasive nonlobular carcinoma with a maximal dimension of 3 cm. Patients underwent partial mastectomy with negative margins; axillary lymph nodes were negative on sampling. Subjects received postoperative proton beam radiation therapy to the surgical bed. The dose delivered was 40 Gy in 10 fractions, once daily over 2 weeks. Multiple fields were treated daily, and skin-sparing techniques were used. Following treatment, patients were evaluated with clinical assessments and annual mammograms to monitor toxicity, tumor recurrence, and cosmesis. Results: One hundred subjects were enrolled and treated. All patients completed the assigned treatment and were available for post-treatment analysis. The median follow-up was 60 months. Patients had a mean age of 63 years; 90% had ductal histology; the average tumor size was 1.3 cm. Actuarial data at 5 years included ipsilateral breast tumor recurrence-free survival of 97% (95% confidence interval: 100%-93%); disease-free survival of 94%; and overall survival of 95%. There were no cases of grade 3 or higher acute skin reactions, and late skin reactions included 7 cases of grade 1 telangiectasia. Patient- and physician-reported cosmesis was good to excellent in 90% of responses, was not changed from baseline measurements, and was well maintained throughout the entire 5-year follow-up period. Conclusions: Proton beam radiation therapy for PBI produced excellent ipsilateral breast recurrence-free survival with minimal toxicity. The treatment proved to be adaptable to all breast sizes and lumpectomy cavity configurations. Cosmetic results appear to be excellent and unchanged from baseline out to 5 years following treatment. Cosmetic results may be improved over those reported with photon-based techniques due to reduced breast tissue exposure with proton beam, skin-sparing techniques, and the dose fractionation schedule used in this trial.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

TH-AB-202-03: A Novel Tool for Computing Deliverable Doses in Dynamic MLC Tracking Treatments

Purpose: In tracked dynamic multi-leaf collimator (MLC) treatments, segments are continuously adapted to the target centroid motion in beams-eye-view. On-the-fly segment adaptation, however, potentially induces dosimetric errors due to the finite MLC leaf width and non-rigid target motion. In this study, we outline a novel tool for computing the 4d dose of lung SBRT plans delivered with MLC tracking. Methods: The following automated workflow was developed: A) centroid tracking, where the initial segments are morphed to each 4dCT phase based on the beams-eye-view GTV shift (followed by a dose calculation on each phase); B) re-optimized tracking, in which all morphed initial plans from (A) are further optimised (“warm-started”) in each 4dCT phase using the initial optimisation parameters but phase-specific volume definitions. Finally, both dose sets are accumulated to the reference phase using deformable image registration. Initial plans were generated according to the RTOG-1021 guideline (54Gy, 3-Fx, equidistant 9-beam IMRT) on the peak-exhale (reference) phase of a phase-binned 4dCT. Treatment planning and delivery simulations were performed in RayStation (research v4.6) using our in-house segment-morphing algorithm, which directly links to RayStation through a native C++ interface. Results: Computing the tracking plans and 4d dose distributions via the in-house interface takes 5 and 8 minutes respectively for centroid and re-optimized tracking. For a sample lung SBRT patient with 14mm peak-to-peak motion in sup-inf direction, mainly perpendicular leaf motion (0-collimator) resulted in small dose changes for PTV-D95 (−13cGy) and GTV-D98 (+18cGy) for the centroid tracking case compared to the initial plan. Modest reductions of OAR doses (e.g. spinal cord D2: −11cGy) were achieved in the idealized tracking case. Conclusion: This study presents an automated “1-click” workflow for computing deliverable MLC tracking doses in RayStation. Adding a non-deliverable re-optimized tracking scenario is expected to help quantify plan robustness for more challenging patients with anatomy deformations. We acknowledge support of the MLC tracking research from Elekta AB. MFF is supported by Cancer Research UK under Programme C33589/A19908. Research at ICR is also supported by Cancer Research UK under Programme C33589/A19727 and NHS funding to the NIHR Biomedical Research Centre at RMH and ICR.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

The Hunt for Green Every April: Factors Affecting Fitness in Switchgrass

This grant funded work was undertaken to develop fundamental biological knowledge of the factors affecting the complex plant trait “fitness” in switchgrass (Panicum virgatum L.), a plant being developed as a biomass crop. Using a diverse range of latitudinally-adapted switchgrass plants, genomic, molecular and physiological studies were performed to track a number of different aspects of plant genetics and physiology over the course of the growing season. Work was performed on both genetically unrelated and genetically related plants. Plants were established in the field from seedlings raised in a greenhouse, or from clones present in other field nurseries. Field grown plants were used as the source of all tissues. The three objectives of this proposal were:(1) Transcript Profiling, Metabolomics, and C and N Partitioning and Recycling in Crowns and Rhizomes of Switchgrass over two growing seasons; (2) Gene Profiling During Regreening and Dormancy of Bulked Segregants; (3) Extent of Linkage Disequilibrium in Populations for Adaptation and Fitness Traits Being Developed for Central and Northern USA, that Show Significant Heterosis. Objective 1 results: Plants were labeled using 13 CO2 (a stable isotope) using an acrylic chamber constructed specifically for this purpose. Plants became labeled with 13 C and label decayed in aerial tissues over the course of the growing season. Varying amounts of 13 C were recovered in the rhizomes. These data are being analyzed. Plants were also labeled with 15 N-urea. Plants absorbed significant amounts of label that was remobilized to the growing shoots. N-dynamics would suggest that a portion of the 15 N absorbed into the crowns and rhizomes is sequestered below ground. Variable amounts of 15 N were translocated from the shoots to the roots over the course of the growing season. Polar metabolites extracted from a diverse array of rhizomes were analyzed using GCMS. Data indicated that there was a significant shift in metabolite pools over the course of the growing season, and differences in the levels of specific metabolites could be linked to the progression of dormancy. Several metabolites that accumulate in dormant rhizomes were identified. Some of these metabolites could be potentially linked to winter-survival of switchgrass. Extensive high-throughput sequencing was conducted on crown and rhizome samples collected from field grown plants. Initial work was performed on a Roche 454 system. All later work was performed on an Illumina sequencing-by-synthesis system. Some of these datasets have been published as peer-reviewed papers, other data are currently being analyzed and being readied for publication. Objective 2 results: Genetically related but phenotypically divergent plants from an octaploid switchgrass population were grown in a replicated field nursery. Rhizomes were harvested at four different times over the course of the growing season from plants with high winter survival and those with lower winter survival. RNA-Seq was performed on harvested materials. Initial analysis suggests that plants with lowered winter survival experience a greater level of cellular stress in dormant tissues. This aspect of plant function is being probed in greater depth. Objective 3 results: A total of 592 individual clones with three clonal replications in a randomized complete block design from each of five populations used in Objective 1 studies were rated for heading date in 2012 and 2014, green-up day of year in 2013, anthesis date in 2012, and yield in 2012, they were also subjected to NIR spectroscopy to derive cell wall composition estimates based on prior NIR calibrations. Plants were genotyped via a genotyping by sequencing (GBS) approach from reduced representation libraries constructed with adaptors that identified each individual. Libraries generated with the restriction enzyme PstI and called SNPs using Samtools after alignment to version 1.1 of the switchgrass genome sequence. A total of approximately 40,000 SNPs were found. These were then further filtered to eliminate markers with a minor allele frequency of < 0.05. The results of population analysis using STRUCTURE with expected population sizes or cluster numbers (K), clearly shows the hybrid composition of the KxS population and discriminated easily between upland (Summer) and lowland (Kanlow) populations. Under an assumption of 5 distinct populations there were detectable differences in allele frequencies between subpopulations within the three Kanlow populations particularly with respect to Kanlow EM and Kanlow base. We detected 110 SNPs with an allele frequency difference of ≥ 0.2 between Kanlow EM and Kanlow base populations, while 120 SNPs showed an allele frequency difference of ≥ 0.15 between Kanlow N1 and Kanlow base populations. These data are being readied for publication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Isotopes and genes reveal freshwater origins of Chinook salmon Oncorhynchus tshawytscha aggregations in California’s coastal ocean

The ability of salmon to navigate from the ocean back to their river of origin to spawn acts to reinforce local adaptation and maintenance of unique and heritable traits among salmon populations. Here, the extent to which Chinook salmon Oncorhynchus tshawytscha from the same freshwater breeding groups associate together in the ocean at regional and smaller-scale aggregations prior to homeward migration is evaluated. Natural variation in salmon otolith daily growth bands, strontium isotopes ( 87 Sr/ 86 Sr), and microsatellite DNA were used as intrinsic tags to link the distributions of fish caught in the ocean with their freshwater origins. Adults were caught from vessels by hook and line in small aggregations (7-18 ind.) at the same geographic location (1-24 km of coastline) and time (4-36 h) from 3 ocean regions along central California, USA. Salmon caught together in aggregations were from the same genetic group, and to a lesser extent, of the same natal origin (individual rivers or hatcheries). However, at regional scales, adult salmon mixed. Central Valley winter-run Chinook salmon caught together in the ocean varied in the duration of freshwater rearing for up to 2-3 mo prior to seaward migration, suggesting associations within the group were not established in freshwater or maintained over the lifetime of the fish. Our findings are consistent with coarser information indicating stocks are distributed differently in time and space, but larger sample sizes are required to evaluate the consistency of patterns at smaller spatial scales. This study uncovers freshwater associations prior to homeward migration, a principle and undocumented prerequisite of the collective navigation hypothesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain

Abstract Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000 ) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of E. meliloti Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to Ensifer meliloti IAM 12611 T , Ensifer medicae A 321 T and Ensifer numidicus ORS 1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating Ensifer strains, but ≤93% with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419 , lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413–415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Differentiable Multiphysics Codes: A Breakthrough Technology for Simulation and Computing

This document summarizes the findings of a strategic planning exercise commissioned by the Weapons Simulation and Computing, Computational Physics (WSC/CP) program at the Lawrence Livermore National Laboratory (LLNL) in FY24. During the year, the committee met with multiple stakeholder communities to gather input, opinions, suggestions and concerns which have been incorporated throughout this document. The key findings from this exercise are summarized: • The development of multiphysics modelling and simulation (mod/sim) codes and software technologies, their deployment on exascale compute platforms, and their broad adoption across the NNSA is a major success of the Advanced Simulation and Computing (ASC) program and the Exascale Computing Project (ECP). Sustained investment in these core technologies is essential. • Today’s state of the art involves running ensembles of O(100K) simulations to perform uncertainty quantification (UQ) and design studies using multiple statistical methods such as Bayesian optimization to understand sensitivities of our models and explore parameterized design spaces. Even with exascale computing, we are practically limited to O(10) parameters in these studies since the number of simulations required to sample the space scales exponentially with the number of design parameters. • The data from these simulation ensembles is increasingly being used to train machine learned (ML) surrogates (or reduced order models, ROMs) which can then be used for optimization or real time design exploration. However, the trained surrogates are still limited in the number of parameters they can represent due to the sampling limitations previously noted. • Augmenting our suite of integrated multiphysics simulation codes, both current and emerging, with the ability to compute gradients (solution derivatives) of arbitrary simulation outputs with respect to (some or all) simulation inputs would be a breakthrough technology, opening the door to a new era of efficient and automated inverse design based on verified and validated mod/sim capabilities. • This capability, which we refer to as differentiable multiphysics codes (DMCs), would revolutionize both UQ and optimization studies by breaking the curse of dimensionality that presently limits our “gradient-free” ensemble based computing approach. A similar breakthrough occurred in the AI/ML community once the ability to compute gradients of arbitrary loss functions using back-propagation became commonplace. Gradient information from the multiphysics codes can also be used to dramatically improve the efficiency and scale of training of ML/ROM surrogates for rapid assessments. • Achieving this in our suite of codes will be a grand challenge, similar to the amount of effort that was required to transition from CPU to GPU computing. It will require buy-in from the entire WSC/CP program and beyond, including all integrated codes, physics and engineering models, third-party library dependencies and performance portability abstractions. It will also require investment in research and development of numerical methods for computing adjoints of coupled physics across multiple adaptively refined moving meshes and of stochastic (Monte Carlo) and mesh free (SPH) methods. • New software and numerical techniques, largely pioneered by the AI/ML community, make this feasible. Chief among these is automatic differentiation (AD), the ability to employ AD at point-wise locations in a physics calculation (instead of traditional black-box approaches) and the ability to perform “back-propagation in time” (or reverse mode AD) for non-linear partial differential equations (PDEs). Fundamentally, the conclusion of this strategic planning exercise is that the time is right to undertake a large scale effort in WSC, centered on the existing integrated codes, to continue the natural evolution of mod/sim in the age of AI/ML. Instead of attempting to replace mod/sim with purely data driven AI/ML models, we believe the key to success is to integrate AI/ML by building on top of the decades of hard-won knowledge and the verified/validated multiphysics modelling capability that is the hallmark of the ASC program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Dynamic Bottlebrush Polymer Networks: Self-Healing in Super-Soft Materials

Here, we introduce a design strategy to expand the range of accessible mechanical properties in covalent adaptable networks (CANs) using bottlebrush polymer building blocks. Well-defined bottlebrush polymers with rubbery poly(4-methylcaprolactone) side-chains were crosslinked in formulations that include a bislactone and strong Lewis acid (tin ethylhexanoate). The resulting materials exhibit tunable stress relaxation rates at elevated temperatures (160–180 °C) due to dynamic ester crosslinks that undergo transesterification with residual hydroxy groups. Varying the crosslinker loading or bottlebrush backbone degree of polymerization yields predictable low-frequency shear moduli ca. 10–100 kPa, well below values typical of linear polymer CANs (1 MPa). These extensible networks can be stretched to strains as large as 350% before failure and undergo efficient self-healing to recover >85% of their original toughness upon repeated fracture and melt processing. In summary, molecular architecture creates new opportunities to tailor the mechanical properties of CANs in ways that are otherwise difficult to achieve.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

ROTATIONAL VELOCITIES OF INDIVIDUAL COMPONENTS IN VERY LOW MASS BINARIES

We present rotational velocities for individual components of 11 very low mass (VLM) binaries with spectral types between M7 and L7.5. These results are based on observations taken with the near-infrared spectrograph, NIRSPEC, and the Keck II laser guide star adaptive optics system. We find that the observed sources tend to be rapid rotators (v sin i > 10 km s{sup -1}), consistent with previous seeing-limited measurements of VLM objects. The two sources with the largest v sin i, LP 349-25B and HD 130948C, are rotating at {approx}30% of their break-up speed, and are among the most rapidly rotating VLM objects known. Furthermore, five binary systems, all with orbital semimajor axes {approx}<3.5 AU, have component v sin i values that differ by greater than 3{sigma}. To bring the binary components with discrepant rotational velocities into agreement would require the rotational axes to be inclined with respect to each other, and that at least one component is inclined with respect to the orbital plane. Alternatively, each component could be rotating at a different rate, even though they have similar spectral types. Both differing rotational velocities and inclinations have implications for binary star formation and evolution. We also investigate possible dynamical evolution in the triple system HD 130948A-BC. The close binary brown dwarfs B and C have significantly different v sin i values. We demonstrate that components B and C could have been torqued into misalignment by the primary star, A, via orbital precession. Such a scenario can also be applied to another triple system in our sample, GJ 569A-Bab. Interactions such as these may play an important role in the dynamical evolution of VLM binaries. Finally, we note that two of the binaries with large differences in component v sin i, LP 349-25AB and 2MASS 0746+20AB, are also known radio sources.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Robust parallel iterative solvers for linear and least-squares problems (Final Technical Report)

The primary goal of this project is to study and develop robust iterative methods for solving linear systems of equations and least squares systems. The focus of the Minnesota team is on algorithms development, robustness issues, and on tests and validation of the methods on realistic problems. 1. The project begun with an investigation on how to practically update a preconditioner obtained from an ILU-type factorization, when the coefficient matrix changes. 2. We investigated strategies to improve robustness in parallel preconditioners in a specific case of a PDE with discontinuous coefficients. 3. We explored ways to adapt standard preconditioners for solving linear systems arising from the Helmholtz equation. These are often difficult linear systems to solve by iterative methods. 4. We have also worked on purely theoretical issues related to the analysis of Krylov subspace methods for linear systems. 5. We developed an effective strategy for performing ILU factorizations for the case when the matrix is highly indefinite. The strategy uses shifting in some optimal way. The method was extended to the solution of Helmholtz equations by using complex shifts, yielding very good results in many cases. 6. We addressed the difficult problem of preconditioning sparse systems of equations on GPUs. 7. A by-product of the above work is a software package consisting of an iterative solver library for GPUs based on CUDA. This was made publicly available. It was the first such library that offers complete iterative solvers for GPUs. 8. We considered another form of ILU which blends coarsening techniques from Multigrid with algebraic multilevel methods. 9. We have released a new version on our parallel solver - called pARMS [new version is version 3]. As part of this we have tested the code in complex settings - including the solution of Maxwell and Helmholtz equations and for a problem of crystal growth.10. As an application of polynomial preconditioning we considered the problem of evaluating f(A)v which arises in statistical sampling. 11. As an application to the methods we developed, we tackled the problem of computing the diagonal of the inverse of a matrix. This arises in statistical applications as well as in many applications in physics. We explored probing methods as well as domain-decomposition type methods. 12. A collaboration with researchers from Toulouse, France, considered the important problem of computing the Schur complement in a domain-decomposition approach. 13. We explored new ways of preconditioning linear systems, based on low-rank approximations.

97 MATHEMATICS AND COMPUTING↗