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DOE OSTI2014

Genomic Island Identification Software v 1.0

Genomic islands are key mobile DNA elements in bacterial evolution, that can distinguish pathogenic strains from each other, or distinguish pathogenic strains from non-pathogenic strains. Their detection in genomes is a challenging problem. We present 3 main software components that attack the island detection problem on two different bases: 1) the preference of islands to insert in chromosomal tRNA or tmRNA genes (islander.pl), and 2) islands' sporadic occurrence among closely related strains. The latter principle is employed in both an algorithm (learnedPhyloblocks.pl) and a visualization method (panGenome.pl). Component islander.pl finds islands based on their preference for a particular target gene type. We annotate each tRNA and tmRNA gene, find fragments of each such gene as candidates for the distal ends of islands, and filter candidates to remove false positives. Component learnedPhyloblocks.pl uses islands found by islander.pl and other methods as a training set to find new islands. Reference genomes are aligned using mugsy, then the "phylotypes" or patterns of occurrence in the reference set are determined for each position in the target genome, and those phylotypes most enriched in the training set of islands are followed to detect yet more islands. Component panGenome.pl produces a big-data visualization of the chromosomally-ordered "pan-genome", that includes every gene of every reference genome (x-axis, pan-genome order; y-axis, reference genomes; color-coding, gene presence/absence etc.), islands appearing as dark patches.

Williams, KellyPorter↗

DOE OSTI2014

Genomic Island Identification Software v 1.0

Source record↗

DOE OSTI2021

43-0434 Bridge Inspection Report 2021

The documentation includes the following: 1. 2021 NMDOT Bridge Inspection Report including Element Level Data Collection (in digital formats prepared by NMSU)--conforms to the National Bridge Inspection Standards and AASHTO Manual for Bridge Element Inspection; 2. 2021 Supplemental Report (in digital formats prepared by NMSU)--provides detailed information related to current condition of major bridge components; 3. 2021 Inspection Pictures (in digital format prepared by NMSU); 4. 2021 Delamination Map (in digital format prepared by LANL). During the 2021 inspection, three critical findings were reported to our LANL contact, Mr. Jonathan Stein, by text and/or email on June 26, 2021. 1. The south joint of the bridge had a modular section of the joint that could potentially come loose during the passing of vehicles. This was reported as a critical finding for safety. If the modular section becomes dislodged or deformed it could pose a serious hazard that could result in a punctured tire to vehicles, motorcyclists and/or bicyclist causing drivers/riders to lose control; 2. The bracket plate located at the north end of the bridge on the pedestrian walkway was corroded through and provides little protection to pedestrians and bicyclists. This was reported as a critical finding for safety to prevent injuries to people; 3. The north approach rail has three missing posts. These posts help ensure that traffic is redirected and the energy is absorbed by the rail. This was reported as a critical finding for safety. Additionally, the approach rail is on a curve with a nearby drop off. Immediate repair is recommended. Based on the 2021 inspection, the bridge deck is rated in "fair" condition. The chain drag performed on the deck identified several areas with delamination that are concentrated near the expansion joints, in the closure joint of the deck near the bridge centerline, and at the south end of the northbound lanes. The chain drag performed during the 2021 inspection revealed 215,333 sq. in. (1495 sq. ft) of delaminations and patched areas (not including the sidewalk). This is approximately a 600% increase from 2019. It is recommended that the delaminations and spalls with exposed rebar be repaired. The "delaminated area" map for the 2021 inspection is provided in the supplemental report.

42 ENGINEERING↗

DOE OSTI2018

Influence of dual nitrogen and phosphorus additions on nutrient uptake and saturation kinetics in a forested headwater stream

Nitrogen (N) and phosphorus (P) can limit autotrophic and heterotrophic metabolism in lotic ecosystems, yet most studies that evaluate biotic responses to colimitation focus on patch-scale (e.g., nutrient diffusing substrata) rather than stream-scale responses. In this study, we evaluated the effects of single and dual N and P additions on ambient nutrient uptake rates and saturation kinetics during two biologically contrasting seasons (spring, autumn) in Walker Branch, a temperate forested headwater stream in Tennessee, USA. In each season, we used separate instantaneous pulse additions to quantify nutrient uptake rates and saturation kinetics of N (nitrate) and P (phosphate). We then used steady-state injections to elevate background stream water concentrations (to low and then high background concentrations) of one nutrient (e.g., N) and released instantaneous pulses of the other nutrient (e.g., P). We predicted that elevating the background concentration of one nutrient would result in a lower ambient uptake length and a higher maximum areal uptake rate of the other nutrient in this colimited stream. Our prediction held true in spring, as maximum areal uptake rate of N increased with elevated P concentrations from 185 µg m –2 min –1 (no added P) to 354 µg m –2 min –1 (high P). This pattern was not observed in autumn, as uptake rates of N were not measurable when P was elevated. Further, elevating background N concentration in either season did not significantly increase P uptake rates, likely because adsorption rather than biotic uptake dominated P dynamics. Laboratory P sorption assays demonstrated that Walker Branch sediments had a high adsorption capacity and were likely a sink for P during most pulse nutrient additions. Furthermore, it may be difficult to use coupled pulse nutrient additions to evaluate biotic uptake of N and P in streams with strong P adsorption potential. Future efforts should use dual nutrient addition techniques to investigate reach-scale coupled biogeochemical cycles (C–N–P, and other elemental cycles [e.g., Fe, Mo]) across seasons, biomes, and land-use types and over longer time periods.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Metal oxide semiconductor thin-film transistors for flexible electronics

The field of flexible electronics has rapidly expanded over the last decades, pioneering novel applications, such as wearable and textile integrated devices, seamless and embedded patch-like systems, soft electronic skins, as well as imperceptible and transient implants. The possibility to revolutionize our daily life with such disruptive appliances has fueled the quest for electronic devices which yield good electrical and mechanical performance and are at the same time light-weight, transparent, conformable, stretchable, and even biodegradable. Flexible metal oxide semiconductor thin-film transistors (TFTs) can fulfill all these requirements and are therefore considered the most promising technology for tomorrow's electronics. This review reflects the establishment of flexible metal oxide semiconductor TFTs, from the development of single devices, large-area circuits, up to entirely integrated systems. First, an introduction on metal oxide semiconductor TFTs is given, where the history of the field is revisited, the TFT configurations and operating principles are presented, and the main issues and technological challenges faced in the area are analyzed. Then, the recent advances achieved for flexible n-type metal oxide semiconductor TFTs manufactured by physical vapor deposition methods and solution-processing techniques are summarized. In particular, the ability of flexible metal oxide semiconductor TFTs to combine low temperature fabrication, high carrier mobility, large frequency operation, extreme mechanical bendability, together with transparency, conformability, stretchability, and water dissolubility is shown. Afterward, a detailed analysis of the most promising metal oxide semiconducting materials developed to realize the state-of-the-art flexible p-type TFTs is given. Next, the recent progresses obtained for flexible metal oxide semiconductor-based electronic circuits, realized with both unipolar and complementary technology, are reported. In particular, the realization of large-area digital circuitry like flexible near field communication tags and analog integrated circuits such as bendable operational amplifiers is presented. The last topic of this review is devoted for emerging flexible electronic systems, from foldable displays, power transmission elements to integrated systems for large-area sensing and data storage and transmission. Finally, the conclusions are drawn and an outlook over the field with a prediction for the future is provided.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

Application of Field Evaluations of Ecological Resources at Hanford and Other DOE Sites for Consistency of Resource Protection and Sustainability - 16404

Remediation and management of contaminated facilities, soil, sediment and biota is an essential element of the DOE-EM mission for site completion, contaminant footprint reduction, and protection of human health and the environment. Protecting ecological resources is an integral part of protecting human health because people are part of the ecosystem and rely on ecological resources for food, fiber, clean air and water, recreational, aesthetic, and cultural values. Evaluation and management require understanding the past and current conditions, as well as protecting, preserving, and enhancing ecological resources. Understanding past and current resources includes evaluation of individual and population health within a local and regional context. The objective of this research is to describe a field method of evaluating ecological resources, based on work at the Hanford Site, which can be applied to sustainability of ecological resources as another mandate of DOE. This requires objective methods to characterize and evaluate resources spatially, within a context of local and regional importance. The DOE complex is large, diverse, and multi-state. The habitats and ecological resources are diverse, and the relative importance of ecological resources to the local ecosystem, region, and human communities varies. Large and diverse sites such as Hanford, Idaho National Laboratory, Los Alamos, hold resources of substantial importance to local and regional ecosystems, as well as to the ecology and cultural values of Tribes and other residents. However, other smaller sites (e.g. Oak Ridge, Brookhaven) also hold key ecological resources to local and regional ecosystems, cultures, and economics. Understanding the relative importance of ecological resources on each remediation site at different spatial scales, within and among DOE-EM sites is critical to management, stewardship, and ensuring sustainability for generations to come. Without a standardized methodology it is difficult to develop sound remediation and management plans to protect human health and the environment. The Ecological Evaluation of Resources described in this paper is part of the Consortium for Risk Evaluation with Stakeholder Participation's (CRESP) Risk Review Project on the Hanford Site. It is an independent assessment based of on-site field evaluations that encompasses evaluations of site resources in comparison to the Columbia Basin Ecosystem prior evaluations made by DOE, the States of Washington and Oregon, Nature Conservancy and Tribes. The on-site field evaluations are the focus of the current paper. The on-site field evaluation methodology was developed to update existing information on habitat values in light of changing landscape features (edge, patch size and shape, connectivity) and the current presence of invasive species. Both aspects change with time, especially given that remediation of remediation units changes the landscape. That is, every time there is a remediation and restoration of an operable unit (remediation site) on a DOE site, it changes the adjacent landscape (and ecological resources). The changes are greater where new roads were built to access a remediation site, staging areas constructed, and as a function of the size and time-frame for the remediation. Since ecological resources form a continuum across the landscape, and activities from remediation on a given site can affect those on adjacent areas, we evaluated resources both on the remediation site itself, and on a buffer equal to the largest diameter of the remediation site. The field evaluation methodology developed at Hanford Site makes use of existing resource level maps (DOE/RL-96-32 2013) and field surveys and measurements of current vegetation and habitat conditions to evaluate potential ecological impacts associated with cleanup activities at the evaluation unit. Additional information used in the ecological resource evaluations include current Endangered and Threatened Species distribution data (both state and federal), aerial imagery, locations of waste sites and infrastructure, and species and habitats of special concern. We suggest that the field methodology developed for the Hanford Site could be used across the DOE complex to evaluate ecological resources. This would provide DOE-EM with a common data base to make long-term decisions about the protection and sustainability of resources on the DOE complex, and would provide Tribes and the public with information on ecological resources on DOE sites. Such information could be provided in a web-based format which DOE, regulators, Tribes, and the public could easily access. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Single-Bubble Flow Boiling Phenomena - Interface Tracking Simulation

Boiling, as one of the most efficient heat transfer mechanisms, is widely used in various engineering systems. Better understanding and modeling of this process remains a major challenge in multiphase flow research. The distribution of vapor in boiling system affects the heat transfer rate and may cause unfavorable conditions, such as heater burn-out. A number of flow regimes have been observed experimentally. In general, there are three regimes under boiling conditions: nucleate boiling, transition boiling, and film boiling. The nucleate boiling regime is categorized into partial boiling regime and fully developed nucleate boiling, according to behavior of bubble dynamics and heat transfer characteristics. In the first region, as the wall temperature increases, the fraction of the wall surface subject to nucleate boiling increases until bubble formation occupies the entire heated surface. Heat transfer in this region is a complex mixture of single-phase forced convection and nucleate boiling. As bubble density increases, bubbles turn to coalesce and form insulating vapor patches, which impedes liquid flow back to the surface. The heat transfer rate under this condition reduces dramatically. This point is called Critical Heat Flux (CHF), which leads to boiling crisis. The behavior of boiling crisis is dependent on local fluid conditions due to bubble growth and departure. Experiments are the ultimate tool for boiling model development and verification, but they still lack some capabilities needed for better understanding of the local mechanism of this phenomena. It's difficult to capture many important details at the pressure/temperature conditions of interest using experimental techniques, such as full three dimensional measurements of velocity and temperature distribution and estimates of heat flux partitioning during the boiling process. The interface tracking simulation (ITS) is one of the promising approaches to describe heat transfer of boiling phenomena and their underlying mechanisms. The advances of high performance computing (HPC) in recent years made it possible to apply DNS to a wide variety of adiabatic flows. Some work has been done to implement evaporation / condensation models as well. Lee and Nydahl performed a numerical simulation of bubble growth and departure assuming that the bubble has the shape of a truncated sphere and a micro-layer exists during bubble growth. A 2-D cylindrical bubbles simulation has been done by Son with a simplified model to predict the heat flux in a thin liquid micro-layer. A direct simulation of 2D film boiling is conducted by Juric and Tryggvason. The film boiling, below critical pressure with a modified Level Set Method, is studied by Son and Dhir. Ose and Kunugi have developed a boiling and condensation model on subcooled boiling phenomena. Fuchs performed numerical simulations of bubble growth and departure considering wall conduction effects. Fully transient heat and fluid flow is modeled with a free surface of a rising bubble and a periodic calculation of the whole cycling of a growing, detaching, and rising bubble. Mukherjee and Kandikar have done a numerical simulation of an evaporating meniscus on a moving heated surface with level set method. The heat transfer associated with the advancing and receding contact angle has been studied. To develop the capability of physics-based boiling process, in the presented work the energy and momentum equations are coupled to simulate single-bubble growth scenarios. For a single bubble simulation in infinite liquid, the analytical solution exists and can be compared with the numerical results for verification purposes. The presented capabilities will be utilized in the large scale DNS of boiling flows in the future. The finite-element based code, PHASTA is used for the simulation. It is a parallel, hierarchic, higher-order accurate, adaptive, stabilized, transient analysis flow solver, which has been shown to be an effective tool for a wide range of single and two-phase flow problems. It has been shown to be highly scalable on top supercomputers ({approx}85% scaling on up to 3 million mesh partitions using a 92 billion element mesh . PHASTA has been shown to reliably predict the details of adiabatic bubbly flows as well as single-phase flows with heat transfer. To develop the capability of physics-based boiling process, in the presented work the energy and momentum equations are coupled to simulate a single-bubble growth scenario. For a single bubble growth in superheated water, the analytical solution exists and can be compared with the numerical results for verification purposes. The second-order accurate spatial and time discretization is used for the flow solver in the presented work. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Design and Manufacture of Tunable Permanent Magnet Based Quadrupole for Next Generation Electron-Ion Colliders [Slides]

The goal of this project is to design and construct of a prototype of quadrupole permanent magnet for the magnet transport lattice for an electron-ion collider. The technical objectives are not only to achieve the field gradient of 34.42T/m in the region of interest, at a radius 16.0mm, relative to the quadrupole axis (z-axis), but also lower the unwanted field harmonics below one unit out of 10,000, especially for Sextupole, Octupole, and Decapole components. The innovation is 1) modular design for cost saving, and 2) adjusting mechanism of each modular magnet for field tuning. The 300-mm long, quadrupole magnet assembly consists of 12 modules of 100-mm long magnet. The magnetic field tuning was implemented by two ways: first, adjusting mechanically the pole tip position for a majority of field tuning, and second, applying the passive shims for a fine field tuning. The magnetic design and optimization of the quadrupole magnet was performed using finite element analysis. The permanent magnet choice was EEC-N44SH grade with the minimum coercivity of 987kA/m (12.4kOe), which has enhanced resistance to demagnetization due to the radiation. The 3D computer-aided design of quadrupole magnet assembly was created based on the magnetic design results. The overall dimensions are 514x500x300mm and its weight is ~470kg (1,050lbs). The weight and volume were minimized through the optimization. Electron Energy Corporation’s vertically integrated manufacturing capability and over 48-years magnet production experience enabled us to implement a “fast prototyping” process and build two quadrupole magnets. Using wire EDM machines, the pole tip profile was precisely fabricated within ±25µm tolerance. The field gradient 34.22T/m was measured using the real time data acquisition system and a 3D Hall probe mounted on the precision XYZ station with the resolution of 1µm (0.00004”). The magnetic field harmonics were measured using a harmonic coil at the Brookhaven National Laboratory, Upton, NY. Faro® laser tracker was used to track the position of each quadrupole while adjusting the pole location mechanically. The normal harmonics were measured up to 20-poles. Overall the 2 nd magnet test data is better than the 1st magnet because of a better symmetry. The adjusting pole technique was proved effective to lower the Sextupole harmonics from -3.14 to -0.71 unit. The Octupole harmonics was improved from -5.67 to -3.45 unit, still not satisfactory. It is found that the proposed approach is not practical and efficient in terms of the mass production although the modular concept can save the manufacturing cost. Another finding is in reality it is hard to adjust mechanically due to the limit of laser tracker resolution .001” and tweak magnetically the field due to the limited harmonics data. Importantly the Brookhaven National Laboratory’s harmonics data doesn’t indicate where the strong/weak field position, which requires another field map test at each measurement. To resolve these, two alternative solutions are introduced; 1) electromagnet correcting coils and 2) 8-pieces quadrupole magnet.

43 PARTICLE ACCELERATORS↗