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DOE OSTI2024

He bubble-induced phase transformation of W grain boundaries revealed by accelerated molecular dynamics

The growth of He bubbles and the resulting impact on the microstructural evolution of W are of paramount importance to the plasma-facing materials community due to the application of W in Tokamak fusion reactors. Using accelerated molecular dynamics (AMD) techniques, we outline the structural evolution of grain boundaries (GBs) caused by growing He bubbles. It is discovered that when an alternative, low energy, high density GB structure or phase is available, He bubbles can induce a progressive phase transformation of the GB to the higher density phase by the continual nucleation of W Frenkel pairs. Here, we find that the resulting W self-interstitials migrate to sites at the GB which are structurally related to the higher density phase, leading to the transformation. We discuss the implications of this progressive microstructural evolution on the growing He bubble and consider in general how He bubbles will impact the structural evolution of an arbitrary W GB. These findings of GB phase transformation are predicted to impact other damage events in W such as recrystallization, GB migration and defect segregation which must take these findings into account in order to accurately simulate a realistic W microstructure and hence extract experimentally meaningful data.

36 MATERIALS SCIENCE↗

DOE OSTI2012

Toward fully self-consistent simulation of the interaction of E-Clouds and beams with WARP-POSINST

To predict the evolution of electron clouds and their effect on the beam, the high energy physics community has relied so far on the complementary use of 'buildup' and 'single/multi-bunch instability' reduced descriptions. The former describes the evolution of electron clouds at a given location in the ring, or 'station', under the influence of prescribed beams and external fields [1], while the latter (sometimes also referred as the 'quasi-static' approximation [2]) follows the interaction between the beams and the electron clouds around the accelerator with prescribed initial distributions of electrons, assumed to be concentrated at a number of discrete 'stations' around the ring. Examples of single bunch instability codes include HEADTAIL [3], QuickPIC [4, 5], and PEHTS [6]. By contrast, a fully self-consistent approach, in which both the electron cloud and beam distributions evolve simultaneously under their mutual influence without any restriction on their relative motion, is required for modeling the interaction of high-intensity beams with electron clouds for heavy-ion beam-driven fusion and warm-dense matter science. This community has relied on the use of Particle-In-Cell (PIC) methods through the development and use of the WARP-POSINST code suite [1, 7, 8]. The development of novel numerical techniques (including adaptive mesh refinement, and a new 'drift-Lorentz' particle mover for tracking charged particles in magnetic fields using large time steps) has enabled the first application of WARP-POSINST to the fully self-consistent modeling of beams and electron clouds in high energy accelerators [9], albeit for only a few betatron oscillations. It was recently observed [10] that there exists a preferred frame of reference which minimizes the number of computer operations needed to simulate the interaction of relativistic objects. This opens the possibility of reducing the cost of fully self-consistent simulations for the interaction of ultrarelativistic beams with electron cloud by orders of magnitude. The computational cost of the fully self-consistent mode is then predicted to be comparable to that of the quasi-static mode, assuming that several stations per betatron period are needed. During the workshop, there was some debate about the number of stations per betatron period that are needed when using the quasi-static mode. The argument was made that if there is less than one station per betatron period, then artificial resonances can be triggered and the resulting emittance growth provides an upper bound. The emittance growth thus obtained will fall either above or below the operational requirements of the machine. In the latter case, one can conclude that the electron effect that has been simulated is of no concern. However, if the emittance growth that was obtained is above the threshold, then the results become inconclusive, and simulations which resolve the betatron motion are then needed. In this case, according to [10], the fully self-consistent approach becomes an option. The aim of this paper is to investigate whether this option is indeed practical.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Advantages of a variable‐resolution global climate model in reproducing the seasonal evolution of East Asian summer monsoon

Abstract The East Asian summer monsoon (EASM) is unique among monsoon systems that it features meridional evolution of the summer monsoon. In this study, we evaluate the performances of a Variable‐Resolution Community Earth System Model (VR‐CESM) regionally refined over eastern China (14 km) in reproducing the seasonal evolution of EASM precipitation over China. Compared with reference datasets, VR‐CESM shows better performance than the corresponding globally uniform coarse‐resolution model CESM (quasi‐uniform 1°), especially over western China where complex local topography exists. The northward monsoon migration is closely related to low‐level southerly flows and vertical moisture advection, which are more reasonably simulated in VR‐CESM. The four critical timings of the EASM (monsoon onset, withdrawal, peak, and duration) are also better captured in VR‐CESM than in CESM. The corresponding spatial Pearson correlation coefficients of the four critical timings with respect to reference datasets are about 0.1 higher in VR‐CESM than those in CESM. Both models are most accurate in simulating monsoon onset and least accurate at simulating the monsoon peak. The overestimated zonal thermal contrast in CESM is responsible for the earlier monsoon onset and excessive precipitation in September over the Yangtze River valley. Finer resolution in VR‐CESM, especially over the Tibetan Plateau (TP), appears to be a main factor in simulating better zonal thermal contrast and seasonal evolution of the EASM.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Environmental microbiome engineering for the mitigation of climate change

Abstract Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long‐term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high‐throughput technologies and modeling approaches, indicate that microbial inocula designed from the top‐down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Analytical model for chip formation in case of orthogonal machining process

The present work deals with the presentation of analytical methodology allowing the modelling of chip formation. For that a 'decomposition approach', based on assuming that the material removal is the summation of two contributions: ploughing and pure cut was adopted. Moreover, this analytical model was calibrated by a finite element model and experimental data in terms of temperature and forces evolutions. The global aim is to propose to the industrial community, an efficient rapid-execution analytical model concerning the material removal in the case of an orthogonal cutting process.

36 MATERIALS SCIENCE↗

DOE OSTI2011

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when applied to the manually curated training set. Applying this method to the data representing around a quarter of the fraction space for water soluble proteins in D. vulgaris, we obtained 854 reliable pair wise interactions. Further, we have developed algorithms to analyze and assign significance to protein interaction data from bait pull-down experiments and integrate these data with other systems biology data through associative biclustering in a parallel computing environment. We will 'fill-in' missing information in these interaction data using a 'Transitive Closure' algorithm and subsequently use 'Between Commonality Decomposition' algorithm to discover complexes within these large graphs of protein interactions. To characterize the metabolic activities of proteins and their complexes we are developing algorithms to deconvolute pure mass spectra, estimate chemical formula for m/z values, and fit isotopic fine structure to metabolomics data. We have discovered that in comparison to isotopic pattern fitting methods restricting the chemical formula by these two dimensions actually facilitates unique solutions for chemical formula generators. To understand how microbial functions are regulated we have developed complementary algorithms for reconstructing gene regulatory networks (GRNs). Whereas the network inference algorithms cMonkey and Inferelator developed enable de novo reconstruction of predictive models for GRNs from diverse systems biology data, the RegPrecise and RegPredict framework developed uses evolutionary comparisons of genomes from closely related organisms to reconstruct conserved regulons. We have integrated the two complementary algorithms to rapidly generate comprehensive models for gene regulation of understudied organisms. Our preliminary analyses of these reconstructed GRNs have revealed novel regulatory mechanisms and cis-regulatory motifs, as well asothers that are conserved across species. Finally, we are supporting scientific efforts in ENIGMA with data management solutions and by integrating all of the algorithms, software and data into a Knowledgebase. For instance, we have developed the RegPrecise database (http://regprecise.lbl.gov) which represents manually curated sets of regulons laying the basis for automatic annotation of regulatory interactions in closely related species. We are also in the midst of scaling up MicrobesOnline to handle the growing volume of sequence and functional genomics data. Over the last year our efforts have been focused on providing support for additional genomic and functional genomic data types. Similarly, we have developed several visualization tools to help with the exploration of complex systems biology datasets. A case in point is the Gaggle Genome Browser (GGB), which was enhanced with visualizations for plotting peptide detections and protein-DNA binding alongside transcriptome structure, plus the ability to interactively filter by signal intensity or p-value.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2002

The origin and evolution of model organisms

The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.

Review, Academic↗

NASA NTRS2002

A Large-Magnitude Biological Source of H2 to the Archaean Atmosphere?

The appearance of photosynthetic microbial communities on Earth was a critical juncture in the chemical evolution of the oceans and atmosphere. The use of sunlight as an energy source frees life from a dependence on geochemical energy sources; global biospheric productivity, as well as the biological influence on planetary chemistry, can be greatly enhanced as a result. To understand the potential biogeochemical impacts of the transition to a photosynthetic biosphere, we examined chemical cycling in potential modern analogs of these Archaean photosynthetic communities - microbial mats from Baja California, Mexico. The primary role of photosynthetic members in the mat community is to extract reducing power (electrons) from water and use it to 'fix' carbon dioxide into organic carbon (biomolecules); however, when exposed to a simulated Archaean atmosphere of very low oxygen content, these organisms divert a substantial fraction of the captured reducing power into the production of molecular hydrogen. Globally, this mechanism of hydrogen production could have outstripped geologic sources by 2 to 4 orders of magnitude. A large-magnitude H2 flux to the environment offers the potential to enhance the global distribution and productivity of H2-consuming organisms, and also to contribute significantly to oxidation of the oceans and atmosphere by via escape to space.

Hoehler, Tori M.↗

NASA NTRS2016

InSitu SEM Investigation of Microstructural Damage Evolution and Strain Relaxation in a Melt Infiltrated SiC/SiC Composite

With CMC components poised to complete flight certification in turbine engines on commercial aircraft within the near future, there are many efforts within the aerospace community to model the mechanical and environmental degradation of CMCs. Direct observations of damage evolution are needed to support these modeling efforts and provide quantitative measures of damage parameters used in the various models. This study was performed to characterize the damage evolution during tensile loading of a melt infiltrated (MI) silicon carbide reinforced silicon carbide (SiC/SiC) composite. A SiC/SiC tensile coupon was loaded to a maximum global stress of 30 ksi in a tensile fixture within an SEM while observations were made at 5 ksi increments. Both traditional image analysis and DIC (digital image correlation) were used to quantify damage evolution. With the DIC analysis, microscale damage was observed at the fiber-matrix interfaces at stresses as low as 5 ksi. First matrix cracking took place between 20 and 25 ksi, accompanied by an observable relaxation in strain near matrix cracks. Matrix crack opening measurements at the maximum load ranged from 200 nm to 1.5 m. Crack opening along the fiber-matrix interface was also characterized as a function of load and angular position relative to the loading axis. This characterization was funded by NASA GRC and was performed to support NASA GRC modeling of SiC/SiC environmental degradation

testing↗

DOE OSTI2017

Sustainable Data Evolution Technology for Power Grid Optimization

The SDET Tool is used to create open-access power grid data sets and facilitate updates of these data sets by the community. Pacific Northwest National Laboratory (PNNL) and its power industry and software vendor partners are developing an innovative sustainable data evolution technology (SDET) to create open-access power grid datasets and facilitate updates to these datasets by the power grid community. The objective is to make this a sustained effort within and beyond the ARPA-E GRID DATA program so that the datasets can evolve over time and meet the current and future needs for power grid optimization and potentially other applications in power grid operation and planning.

Source record↗

DOE OSTI2017

Sustainable Data Evolution Technology for Power Grid Optimization

Source record↗

DOE OSTI2013

D and D knowledge management information tool - a web based system developed to share D and D knowledge worldwide

Deactivation and decommissioning (D and D) work is a high risk and technically challenging enterprise within the U.S. Department of Energy complex. During the past three decades, the DOE's Office of Environmental Management has been in charge of carrying out one of the largest environmental restoration efforts in the world: the cleanup of the Manhattan Project legacy. In today's corporate world, worker experiences and knowledge that have developed over time represent a valuable corporate asset. The ever-dynamic workplace, coupled with an aging workforce, presents corporations with the ongoing challenge of preserving work-related experiences and knowledge for cross-generational knowledge transfer to the future workforce [5]. To prevent the D and D knowledge base and expertise from being lost over time, the DOE and the Applied Research Center at Florida International University (FIU) have developed the web-based Knowledge Management Information Tool (KM-IT) to capture and maintain this valuable information in a universally available and easily accessible and usable system. The D and D KM-IT was developed in collaboration with DOE Headquarters (HQ), the Energy Facility Contractors Group (EFCOG), and the ALARA [as low as reasonably achievable] Centers at Savannah River Sites to preserve the D and D information generated and collected by the D and D community. This is an open secured system that can be accessed from https://www.dndkm.org over the web and through mobile devices at https://m.dndkm.org. This knowledge system serves as a centralized repository and provides a common interface for D and D-related activities. It also improves efficiency by reducing the need to rediscover knowledge and promotes the reuse of existing knowledge. It is a community-driven system that facilitates the gathering, analyzing, storing, and sharing of knowledge and information within the D and D community. It assists the DOE D and D community in identifying potential solutions to their problem areas by using the vast resources and knowledge base available throughout the global D and D community. The D and D KM-IT offers a mechanism to the global D and D community for searching relevant D and D information and is focused on providing a single point of access into the collective knowledge base of the D and D community within and outside of the DOE. Collecting information from subject matter specialists, it builds a knowledge repository for future reference archiving Lessons Learned, Best Practices, ALARA reports, and other relevant documents and maintains a secured collaboration platform for the global D and D community to share knowledge. With the dynamic nature and evolution of the D and D knowledge base due to multiple factors such as changes in the workforce, new technologies and methodologies, economics, and regulations, the D and D KM-IT is being developed in a phased and modular fashion. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Investigating the Roughness and Advance Rate of the Weathering Interface (Final Report)

To understand geological systems that are important to our national well-being -- such as nuclear waste repositories or hydraulically fractured rocks -- requires the ability to make quantitative projections of the evolution of rock-water systems forward in time. A fundamental goal of much of our geochemical research was focused on development of numerical models of reactive transport to simulate the evolution of natural water-rock systems. The geochemical community has provided such models and they are rapidly being improved with field-model cross-testing. This project was especially impactful in field-model testing for well-constrained weathering systems to provide new conceptual understanding of how these systems function.

04 OIL SHALES AND TAR SANDS↗

NASA NTRS1985

Aerothermodynamic environment for a Titan probe with deployable decelerator

It is pointed out that further exploration of Titan, Saturn's largest moon, is of current interest to the scientific community, particularly from the standpoint of the organic chemical evolution of its atmosphere. For a suitable study of this Saturnian satellite, a mission involving a Titan atmospheric entry probe is to be conducted. The probe is to employ a deployable decelerator with the aim to allow scientific measurements in the haze layer. The present investigation is concerned with an assessment of the aerothermodynamic environment for the considered probe during its hypervelocity, low-Reynolds-number entry. Attention is given to the employed computational method, the Titan probe configuration, the Titan probe trajectory, the viscous-layer regime of the aerothermodynamic environment, and the incipient merged-layer regime.

Green, M. J.↗

NASA NTRS1986

Microbial contributions to the Precambrian Earth

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

Margulis, L.↗

NASA NTRS1990

Path programmable logic: A structured design method for digital and/or mixed analog integrated circuits

The design of Integrated Circuits has evolved past the black art practiced by a few semiconductor companies to a world wide community of users. This was basically accomplished by the development of computer aided design tools which were made available to this community. As the tools matured into different components of the design task they were accepted into the community at large. However, the next step in this evolution is being ignored by the large tool vendors hindering the continuation of this process. With system level definition and simulation through the logic specification well understood, why is the physical generation so blatantly ignored. This portion of the development is still treated as an isolated task with information being passed from the designer to the layout function. Some form of result given back but it severely lacks full definition of what has transpired. The level of integration in I.C.'s for tomorrow, whether through new processes or applications will require higher speeds, increased transistor density, and non-digital performance which can only be achieved through attention to the physical implementation.

Taylor, B.↗

NASA NTRS2006

Modeling the Optical Properties of Biomass Burning Aerosols: Young Smoke Aerosols From Savanna Fires and Comparisons to Observations from SAFARI 2000

Annually, farmers in southern Africa manage their land resources and prepare their fields for cultivation by burning crop residual debris, with a peak in the burning season occurring during August and September. The emissions from these fires in southern Africa are among the greatest from fires worldwide, and the gases and aerosol particles produced adversely affect air quality large distances from their source regions, and can even be tracked in satellite imagery as they cross the Atlantic and Pacific Ocean basins. During August and September 2000 an international group of researchers participating in the Southern African Regional Science Initiate field experiment (SAFARI 2000) made extensive ground-based, airborne, and satellite measurements of these gases and aerosols in order to quantify their amounts and effects on Earth's atmosphere. In this study we interpreted the measurements of smoke aerosol particles made during SAFARI 2000 in order to better represent these particles in a numerical model simulating their transport and fate. Typically, smoke aerosols emitted from fires are concentrated by mass in particles about 0.3 micrometers in diameter (1,000,000 micrometers = 1 meter, about 3 feet); for comparison, the thickness of a human hair is about 50 micrometers, almost 200 times as great. Because of the size of these particles, at the surface they can be easily inhaled into the lungs, and in high concentrations have deleterious health effects on humans. Additionally, these particles reflect and absorb sunlight, impacting both visibility and the balance of sunlight reaching -Earth's surface, and ultimately play a role in modulating Earth's climate. Because of these important effects, it is important that numerical models used to estimate Earth's climate response to changes in atmospheric composition accurately represent the quantity and evolution of smoke particles. In our model, called the Community Aerosol and Radiation Model for Atmospheres (CARMA) we used estimates of smoke emissions based on field studies and observations made with the NASA Terra and TRMM satellites. The meteorology used to calculate the transport was based on an assimilation of observed meteorological conditions provided by the National Center for Atmospheric Research.

Matichuk, R. I.↗

NASA NTRS2013

OSIRIS-REx Will Return a Sample of Asteroid 1999 RQ36 for Astrochemistry

Origins, Spectral Interpretation, Resource Identification, Security, Regolith Explorer (OSIRIS-REx) is the third mission in NASA's New Frontiers program. OSIRIS-REx launches in 2016 and will return the first pristine samples of carbonaceous material from the surface of a primitive asteroid in 2023. The target, (101955) 1999 RQ36, is 1/2 km diameter roughly spherical Apollo near-Earth asteroid. It is expected to be carbonaceous, similar to CI or CM carbonaceous chondrites. This organic-rich remnant from the early Solar System is also among the most potentially hazardous asteroids known with a 1 in 2500 chance of impacting the Earth in the late 22nd century. OSIRIS-REx will measure the Yarkovsky effect to better constrain future orbit and impact potential of this and other asteroids. OSIRIS-REx will image, map, and spectrally characterize RQ36 from 0.4-50 icron. The returned sample of regolith will be >60g (and up to 2kg) and thus the largest extraterrestrial sample returned from space since Apollo 17. Unlike meteorites, the sample will come from a known, well-characterized source and will be collected and transported to Earth pristine from terrestrial contamination. It will be available for study by the global astrochemistry community to address fundamental questions about the origin and evolution of the solar system and the life it harbors.

organic-rich↗