Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biological processing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37

A Global Repository for Planet-Sized Experiments and Observations

Greenland’s ice loss doubled between 1996 and 2005. Nine of the ten warmest years on record have occurred since 2000. Carbon dioxide levels in the air are at their highest in 650,000 years. Are these phenomena related, and if so, what can they tell us about the Earth’s climate in the coming years and decades? The answer will require sophisticated computer models—and a way of dealing with the data they produce. Past climate patterns can be discerned by examining variables such as temperature and precipitation records, lake sediments, tree rings, and ice cores. Projecting future regional and global climate patterns, however, requires computer models that can simulate the complex interplay between physical, chemical, and biological processes occurring in the atmosphere, ocean, and on land and sea ice. These models are extremely computationally demanding. Over the past several decades, an ongoing revolution in high-capacity, high-performance computing has accelerated climate modeling. In 1998, a 1-year simulation of global climate using a 300- kilometer grid could be run in a day. In 2002, it took 4 or 5 hours. In 2015, this same model can be run on a high-end desktop in minutes.

54 ENVIRONMENTAL SCIENCES↗

Data sets for Unraveling Iron Oxides as Abiotic Catalysts of Organic Phosphorus Recycling in Soil and Sediment Matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus species. The dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this hydrolytic cleavage. Limited evidence of this abiotic catalysis has relied on monitoring inorganic phosphate in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Experiments with various organic phosphorus compounds revealed up to 12-fold greater catalytic and adsorption reactivities with iron oxides than with the silicate and aluminosilicate minerals identified in the environmental samples. Remarkably, we obtained dephosphorylation rates by the iron oxides that are within reported enzymatic rates in soils. However, phosphorus cycle models do not yet include a quantitative account of the abiotic evolution of inorganic phosphate from organic phosphorus trapped on iron oxides in environmental matrices. Our findings imply a missing abiotic axiom for organic phosphorus mineralization in the phosphorus cycle.

54 ENVIRONMENTAL SCIENCES↗

Long-term stabilization of intensity-difference squeezing from four-wave mixing in rubidium vapor

Generation of quantum states of light through off-resonance four-wave mixing in rubidium vapor is a straightforward and well-established technique. However, achieving a sufficiently high and consistent level of intensity difference squeezing (IDS) and intrinsic quantum correlations between photon pairs over an extended timescale, necessary for quantum-light-based nonlinear optical spectroscopy and microscopy, remains challenging and largely unexplored. Here, we report a simple stabilization method combining an active periodic laser frequency retuning with an automatic control algorithm based on quantitatively assessing the factors affecting the IDS level and squeezed light intensity. Validation of our method was performed by acquiring data over a 5-hour period, and the results demonstrate a remarkably stable squeezing level of -7.8 dB in combination with a > 4× reduction of the standard deviation of IDS level from 0.46 dB to 0.10 dB. The achieved stabilization further enables us to quantitatively assess the IDS reduction due to the scattering in a polystyrene bead suspension as a function of sample transmission. Our approach should enable a variety of applications requiring an extended squeezing stability over multiple hours, especially for those following biological processes and chemical reactions in real time.

Allen, Christian Harry [Oak Ridge National Laborat↗

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 562 times compared to single-core CPM code execution on CPU. Over short timescales of up to 3 recursive evaluations, or 300 MCS, our model captures the emergent behaviors demonstrated by the original Cellular-Potts model such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as a step toward efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM simulations of biological processes.

97 MATHEMATICS AND COMPUTING↗

A rapid methods development workflow for high-throughput quantitative proteomic applications

Recent improvements in the speed and sensitivity of liquid chromatography-mass spectrometry systems have driven significant progress toward system-wide characterization of the proteome of many species. These efforts create large proteomic datasets that provide insight into biological processes and identify diagnostic proteins whose abundance changes significantly under different experimental conditions. Yet, these system-wide experiments are typically the starting point for hypothesis-driven, follow-up experiments to elucidate the extent of the phenomenon or the utility of the diagnostic marker, wherein many samples must be analyzed. Transitioning from a few discovery experiments to quantitative analyses on hundreds of samples requires significant resources both to develop sensitive and specific methods as well as analyze them in a high-throughput manner. To aid these efforts, we developed a workflow using data acquired from discovery proteomic experiments, retention time prediction, and standard-flow chromatography to rapidly develop targeted proteomic assays. We demonstrated this workflow by developing MRM assays to quantify proteins of multiple metabolic pathways from multiple microbes under different experimental conditions. With this workflow, one can also target peptides in scheduled/dynamic acquisition methods from a shotgun proteomic dataset downloaded from online repositories, validate with appropriate control samples or standard peptides, and begin analyzing hundreds of samples in only a few minutes.

02 PETROLEUM↗

Investigating effects of soil chemicals on density of small mammal bioindicators using spatial capture-recapture models

Monitoring the ecological impacts of environmental pollution and the effectiveness of remediation efforts requires identifying relationships between contaminants and the disruption of biological processes in populations, communities, or ecosystems. Wildlife are useful bioindicators, but traditional comparative experimental approaches rely on a staunch and typically unverifiable assumption that, in the absence of contaminants, reference and contaminated sites would support the same densities of bioindicators, thereby inferring direct causation from indirect data. We demonstrate the utility of spatial capture-recapture (SCR) models for overcoming these issues, testing if community density of common small mammal bioindicators was directly influenced by soil chemical concentrations. By modeling density as an inhomogeneous Poisson point process, we found evidence for an inverse spatial relationship between Peromyscus density and soil mercury concentrations, but not other chemicals, such as polychlorinated biphenyls, at a site formerly occupied by a nuclear reactor. Although the coefficient point estimate supported Peromyscus density being lower where mercury concentrations were higher (β = –0.44), the 95% confidence interval overlapped zero, suggesting no effect was also compatible with our data. Estimated density from the most parsimonious model (2.88 mice/ha; 95% CI = 1.63–5.08), which did not support a density-chemical relationship, was within the range of reported densities for Peromyscus that did not inhabit contaminated sites elsewhere. Environmental pollution remains a global threat to biodiversity and ecosystem and human health, and our study provides an illustrative example of the utility of SCR models for investigating the effects that chemicals may have on wildlife bioindicator populations and communities.

36 MATERIALS SCIENCE↗

Virtual Observation System for Earth System Model: An Application to ACME Land Model Simulations

Investigating and evaluating physical-chemical-biological processes within an Earth system model (EMS) can be very challenging due to the complexity of both model design and software implementation. A virtual observation system (VOS) is presented to enable interactive observation of these processes during system simulation. Based on advance computing technologies, such as compiler-based software analysis, automatic code instrumentation, and high-performance data transport, the VOS provides run-time observation capability, in-situ data analytics for Earth system model simulation, model behavior adjustment opportunities through simulation steering. A VOS for a terrestrial land model simulation within the Accelerated Climate Modeling for Energy model is also presented to demonstrate the implementation details and system innovations.

58 GEOSCIENCES↗

Crystallization and assembly at interfaces: Celebrating the achievements of a vibrant research community

Crystallization is one of the cornerstones of modern materials science and engineering and plays a critical role in industries ranging from petroleum derivative manufacturing to microstructural engineering of structural materials and the defect-free growth of silicon single crystals for integrated chip technology. Also, in the realm of environmental and biological processes, the mineralization of diverse compounds has shaped the vast array of ecosystems we observe today. Conversely, understanding the crystallization and assembly of building blocks of various sizes at interfaces has broader impacts on materials synthesis, performance of energy storage devices, optimized processing conditions, and more.

36 MATERIALS SCIENCE↗

87 Sr/ 86 Sr Concentrations in the Appalachian Basin: A Review

This document reviews 87 Sr/ 86 Sr isotope data across the Appalachian Basin from existing literature to show spatial and temporal variation. Isotope geochemistry presents a means of understanding the geochemical effects hydraulic fracturing may have on shallow ground substrates. Isotope fractionation is a naturally occurring phenomenon brought about by physical, chemical, and biological processes that partition isotopes between substances; therefore, stable isotope geochemistry allows geoscientists to understand several processes that shape the natural world. Strontium isotopes can be used as a tool to answer an array of geological and environmental inquiries. In some cases, strontium isotopes are sensitive to the introduction of a non-native fluid into a system. This ability allows strontium isotopes to serve as tracers in certain systems. Recently, it has been demonstrated that strontium isotopes can serve as a monitoring tool for groundwater and surface water systems that may be affected by hydraulic fracturing fluids (Chapman et al., 2013; Kolesar Kohl et al., 2014). These studies demonstrated that 87 Sr/ 86 Sr values have the potential to monitor subsurface fluid migration in regions where extraction of Marcellus Shale gas is occurring. This document reviews publicly available strontium isotope data from 39 sample locations in the Appalachian Basin (Hamel et al., 2010; Chapman et al., 2012; Osborn et al., 2012; Chapman et al., 2013; Capo et al., 2014; Kolesar Kohl et al., 2014). The data is divided into two sets: stratigraphic (Upper Devonian/Lower Mississippi, Middle Devonian, and Silurian) and groundwater. ArcMap™ (ESRI, Inc.) was used to complete inverse distance weighting (IDW) analyses for each dataset to create interpolated surfaces in an attempt to find regional trends or variations in strontium isotopic values across the Appalachian Basin. 87 Sr/ 86 Sr varies up to ~ 0.011 across the Appalachian Basin, but the current publicly available data is limited in frequency and regional extent, causing artifacts and high uncertainty when interpolating data for locations far from sampling sites. These factors highlight the need for additional strontium isotope sampling across the region. Identifying potential contamination from hydraulic fracturing fluid in Appalachian Basin groundwater using strontium isotopes would require additional sampling. For a more comprehensive strontium isotope database, samples would need to be collected during prefracturing, syn-fracturing, and post-fracturing stages. This would add a temporal component to the spatial data and make tracing of fluid migration with strontium isotopes more accurate. Future research and modeling that incorporates subsurface geology and watershed data would also serve to increase the accuracy and certainty of the interpolations of these analyses. Prospective geospatial Appalachian Basin isotope studies would also benefit from the integration of geologic mapping because surface and subsurface geology influences observed strontium isotope values.

58 GEOSCIENCES↗

Identification of Promising Remediation Technologies for Iodine in the UP-1 Operable Unit

Iodine-129 (129I) generated at the U.S. Department of Energy (DOE) Hanford Site during plutonium production was released to the subsurface, resulting in several large, though dilute, plumes in the groundwater, including the plume in the 200-UP-1 operable unit (OU). Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited, though work is under way to better understand the fate and transport of 129I in the environment and the effectiveness of potential remediation technologies. The recent UP-1 Evaluation Plan for Iodine and report on the Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site provide information on the history of contamination in the 200-UP-1 OU, relevant controlling processes (biological and geochemical), risk, the conceptual site model, and potential remedial options, which provided a foundation for this study. In this study, available information was compiled and used to categorize potential remediation technologies, culminating in a recommendation of promising technologies for further evaluation. Approaches to improve the technical information about promising technologies are also recommended in this study so that a subsequent evaluation of potential remediation alternatives can assess these technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single-Molecule Interfacial Electron Transfer

Interfacial electron transfer (ET) plays an important role in many chemical and biological processes. Specifically, interfacial ET in TiO 2 -based systems is important to solar energy technology, catalysis, and environmental remediation technology. However, the microscopic mechanism of interfacial ET is not well understood with regard to atomic surface structure, molecular structure, bonding, orientation, and motion. In this project, we used two complementary methodologies; single-molecule fluorescence spectroscopy, and scanning-tunneling microscopy and spectroscopy (STM and STS) to address this scientific need. The goal of this project was to integrate these techniques and measure the molecular dependence of ET between adsorbed molecules and TiO 2 semiconductor surfaces and the ET induced reactions such as the splitting of water. The scanning probe techniques, STM and STS, are capable of providing the highest spatial resolution but not easily time-resolved data. Single-molecule fluorescence spectroscopy is capable of good time resolution but requires further development to match the spatial resolution of the STM. The integrated approach involving Peter Lu at Bowling Green State University (BGSU) and Wilson Ho at the University of California, Irvine (UC Irvine) produced methods for time and spatially resolved chemical imaging of interfacial electron transfer dynamics and photocatalytic reactions. An integral aspect of the joint research was a significant exchange of graduate students to work at the two institutions. This project bridged complementary approaches to investigate a set of common problems by working with the same molecules on a variety of solid surfaces, but using appropriate techniques to probe under ambient (BGSU) and ultrahigh vacuum (UCI) conditions. The molecular level understanding of the fundamental interfacial electron transfer processes obtained in this joint project will be important for developing efficient light harvesting, solar energy conversion, and broadly applicable to problems in interface chemistry and surface physics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Understanding the electron-water interaction at the molecular level: Integrating theory and experiment in the cluster regime

In this final technical report, we summarize our major accomplishments resulting from a combined experimental-theoretical approach that exploits the unique properties of molecular clusters to elucidate how local interactions at the molecular level drive the macroscopic behavior of materials and chemical transformations in liquids. The specific targets for our efforts have need to elucidate how charged entities are accommodated by hydrogen-bonding networks and to establish how the behavior of room temperature ionic liquids can be tailored for specific chemical applications. Because of their central importance in aqueous electrolyte chemistry, we have placed particular emphasis understanding the accommodation of excess electrons and protons by water. These surprisingly complex fundamental electrical charges play a fundamental role in a wide range of chemical and biological processes, and yet even a qualitative picture of their speciation in water and at the air-water interface has proven elusive. The main experimental diagnostic in our approach is to measure and analyze vibrational spectra of temperature and composition controlled molecular aggregates that isolate and amplify the spectral markers for local interactions that are often obscured in measurement on bulk or interfacial water. Our combined experimental-theoretical program has led to a greatly enhanced understanding of the nature of excess electrons and protons in water and in the process developed new and powerful methods of chemical analysis that are currently in use across the chemical sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Land Surface Modeling 2.0 for agricultural climate change impact assessments

Focus Area: This white paper addresses DOE AI4ESP focus area #2 by providing a sketch blueprint for a next generation, hybrid AI/process-based global Land Surface Modeling (LSM) framework to improve projections of climate change impacts on the land surface system including agriculture and the hydrological cycle. Science Challenge: Climate change impacts on agriculture are highly uncertain: -50% to +150% global production changes for major grains under high-end climate change, for example. The core challenge in land surface system predictability is the large gap between the scale at which the relevant biological processes act and the scale at which the risks need to be assessed. Conventional empirical and process-based modeling approaches are insufficient. A new multi-scale modeling paradigm which employs AI/ML to learn from new streams of remote sensing data and targeted ’gene-to-global’ simulations is needed.

54 ENVIRONMENTAL SCIENCES↗

Storage and Diffusion of Carbon and Nitrogen in Crustal Materials

Nitrogen is a primary constituent of Earth’s atmosphere and an essential component of many biological processes. Recent developments in understanding N incorporation into silicate minerals suggest that the solid earth and lithosphere could provide a substantial reservoir for the planetary N budget. Furthermore, determining the concentration and distribution of low abundances of N in silicates presents a significant challenge in microanalysis. We tested capabilities for high spatial resolution quantification of low levels of N using EPMA with the goal of developing standards to be used in coupled N and noble gas analyses of silicate minerals. We investigated the concentration and distribution of N in a suite of ammonium-bearing silicate minerals that reflect the dominant N-bearing phases of the lithosphere: tobelite, buddingtonite, ammonioleucite, tsaregorodtsevite, and hyalophane. These minerals form during NH 4 -rich alteration of K-bearing silicate minerals, and the bonding environment of N in each mineral is likely to differ based on crystal structure. Using an optimized analytical routine for N quantification enables sensitivity approaching 0.02 weight% N and high-resolution quantitative mapping of sub-micron variations in N contents.

58 GEOSCIENCES↗

Enhanced Atmospheric Research at the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) (Final Report)

The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) was an international scientific expedition into the central Arctic sea ice to study the changing atmosphere-ice-ocean system and its key physical, chemical, and biological processes in a way that will support improved understanding and modeling of Arctic climate. The US Department of Energy’s Atmospheric Research Measurement (ARM) Program operated its second ARM Mobile Facility (AMF2) as a major contribution to the expedition, and the Atmospheric System Research (ASR) program supported this project to maximize the success of DOE’s involvement in MOSAiC. This project has enabled the successful collection of data through support of field operations plans, in-field operational implementation, oversight of real-time data quality, and representing DOE’s interests within the broader international MOSAiC endeavor. The project has promoted scientific research by facilitating and leading a number of efforts to develop value-added products that will support research, including products related to aerosol properties, trace gases, cloud properties, snowfall, the surface energy budget, and a merged product designed for model assessment. These products and related analyses have also contributed to numerous scientific publications on related themes as well as direct model evaluation. Lastly, the project has engaged in a great deal of communication and outreach activities that help to publicize and promote both MOSAiC and DOE’s specific contribution to a broad audience that includes the scientific community, program management, policy makers, and the general public.

54 ENVIRONMENTAL SCIENCES↗

Reviewing MACCS Capabilities for Assessing Tritium Releases to the Environment

Tritium has a unique physical and chemical behavior which causes it to be highly mobile in the environment. As it behaves similarly to hydrogen in the environment, it may also be readily incorporated into the water cycle and other biological processes. These factors and other environmental transformations may also cause the oxidation of an elemental tritium release, resulting in a multiple order of magnitude increase in dose coefficient and radiotoxicity. While source term development and understanding for advanced reactors are still underway, tritium may be a radionuclide of interest. It is thus important to understand how tritium moves through the environment and how the MACCS accident consequence code handles acute tritium releases in an accident scenario. Additionally, existing tritium models may have functionalities that could inform updates to MACCS to handle tritium. In this report tritium transport is reviewed and existing tritium models are summarized in view of potential updates to MACCS.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Brief Overview of Reactive Transport Codes Used in CO 2 Applications

Reactive transport modelling consists of computational and numerical models that describe the coupled physical, chemical, mechanical, and biological processes interacting with each other over a broad range of spatial and temporal scales. This report reviews some of the reactive transport codes available in the literature for carbon dioxide (CO 2 ) applications and can assist the scientific community with the applicability of each code to solve a specific problem. Approaches implemented in these codes can be categorized in three groups: (i) continuum-scale, (ii) pore-scale, and (iii) hybrid-scale approaches. Theoretical foundations, numerical implementations, and application examples using the models are described. In the continuum approach, flow and transport are formulated in terms of a representative control volume of the medium and coupled with geochemical reactions. The medium is characterized by bulk parameters such as porosity, permeability, or reactive surface area. In the pore-scale approach, each point of space in the pore network is occupied by either a fluid or solid phase. The pore-scale approach requires an exact knowledge of the spatial and temporal phase distribution. In the hybrid-scale approach, media are described by multiple characteristic length-scales, with some regions using a pore-scale approach while others used a continuum approach.

01 COAL, LIGNITE, AND PEAT↗