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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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DOE OSTI2018

ASC CSSE Level 2 Milestone #6362: Resilient Asynchronous Many Task Programming Model

This report is an outcome of the ASC CSSE Level 2 Milestone 6362: Analysis of Re- silient Asynchronous Many-Task (AMT) Programming Model. It comprises a summary and in-depth analysis of resilience schemes adapted to the AMT programming model. Herein, performance trade-offs of a resilient-AMT prograrnming model are assessed through two ap- proaches: (1) an analytical model realized by discrete event simulations and (2) empirical evaluation of benchmark programs representing regular and irregular workloads of explicit partial differential equation solvers. As part of this effort, an AMT execution simulator and a prototype resilient-AMT programming framework have been developed. The former permits us to hypothesize the performance behavior of a resilient-AMT model, and has undergone a verification and validation (V&V) process. The latter allows empirical evaluation of the perfor- mance of resilience schemes under emulated program failures and enabled the aforementioned V&V process. The outcome indicates that (1) resilience techniques implemented within an AMT framework allow efficient and scalable recovery under frequent failures, that (2) the abstraction of task and data instances in the AMT programming model enables readily us- able Application Program Interfaces (APIs) for resilience, and that (3) this abstraction enables predicting the performance of resilient-AMT applications with a simple simulation infrastruc- ture. This outcome will provide guidance for the design of the AMT programming model and runtime systems, user-level resilience support, and application development for ASC's next generation platforms (NGPs).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Open absorption cycle for combined dehumidification, water heating, and evaporative cooling

An absorption cycle system, which permits water heating, dehumidifying, and/or evaporative cooling, includes a desorber, absorber, heat exchanger, and, optionally, an evaporator, is constructed to heat a process water that is plumbed through the absorber, heat exchanger, and condenser. In the absence or isolation of the evaporator, the system can dehumidify ambient air to the absorber. The water vapor released by evaporative cooling at the evaporator can be provided to the absorber in a controlled manner to simultaneously maintain a desired humidity while cooling the air ambient by the evaporator. The absorption cycle system can be housed within a single unit or can be compartmentalized.

42 ENGINEERING↗
DOE OSTI2022

Interlinked tuples in coordination namespace

A system and method for supporting tuple record interlinking in one or more tuple space/coordinated namespace (CNS) extended memory storage systems. A system-wide CNS provides for efficient storing and communicating of data generated by local processes running at the nodes, and coordinated to generate a union/intersection of multiple CNS where tuple records are interlinked in multiple CNS hashtables, and/or share tuple data between two sets of processes that are part of different CNSs. Local node processes further generate multi-key tuples where two or more tuple records are interlinked within the same CNS hash table, thereby permitting a look up of the tuple data by either tuple name/keys. A CNS controller further provides a tuple iterator for a key-value storage in a CNS system that adds more links between tuples enables creation of iterator structures such as linked list or trees etc. of “different” tuples in a tuple database.

Jacob, Philip↗
DOE OSTI2020

Decontamination of urban surfaces contaminated with radioactive materials and consequent onsite recycling of the waste water

Enhancing rapid remediation strategies is paramount for recovery after a large-scale nuclear contamination event in an urban environment. Some current strategies recommend use of readily available equipment, materials, and facilities to expedite recovery. For example, applying pressurized water to contaminated surfaces may effectively remove radioactive contamination. In this study, a commercial power washer removes soluble forms of 152 Eu 3 + , 85 Sr 2 + , and 137 Cs + contamination from common porous building materials, and computer simulations characterize the recycling of the resultant contaminated wash water. Pressure washing the porous building materials under spray conditions typical with do-it-yourself units improved decontamination factors (DFs) for 152 Eu compared to low-pressure application of tap water (majority of two-tailed t-test p-values < 0.1), but pressure did not improve DFs for 137 Cs or 85 Sr. For both pressurized and low-pressure applications, adding potassium ions (K + ) to promote ion exchange reactions produced significantly higher DFs for tested radionuclides on asphalt, brick, and concrete. The resultant contaminated wash water can be processed through self-prepared chemical filtration beds of clay and sand. Modeled in a prior study, the beds yielded linear trends (R 2 > 0.98) in sensitivity analyses between most bed configuration variables and bed performance variables, permitting flexible ad-hoc bed design. The experimental and simulation results led to estimates of the remediation rate and waste generated after cleaning 250 m 2 of cesium-contaminated concrete from the combined deployment of a power washer and two different mobile treatment beds. Furthermore, the first treatment bed was designed to reduce treatment time and processed 1900 L of wash solution in 70 min using 880 kg of clay/sand infill material. Designed to reduce the solid waste generated, the second bed processed the same solution volume in 1040 min (17 h) using 170 kg of clay/sand infill material. The results of this analysis warrant further investigation of power washing with recycled salt solution as an effective rapid decontamination method with manageable waste.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Electrode manufacturing for lithium-ion batteries—Analysis of current and next generation processing

As modern energy storage needs become more demanding, the manufacturing of lithium-ion batteries (LIBs) represents a sizable area of growth of the technology. Specifically, wet processing of electrodes has matured such that it is a commonly employed industrial technique. Despite its widespread acceptance, wet processing of electrodes faces a number of problems, including expensive and dangerous solvent recovery, cut-off waste, coating inconsistencies, and microstructural defects due to the solvent drying process. This review considers each of these issues and discusses which electrode slurry properties should be considered when optimizing wet slurry fabrication. Simultaneously, methods to replace traditional wet processing of electrodes are being extensively researched. Some of these novel electrode manufacturing techniques prioritize solvent minimization, while others emphasize boosting energy and power density by thickening the electrode and, subsequently, creating an organized pore structure to permit faster ion diffusion. This review contemplates the advantages and disadvantages of each of these approaches and provides a comprehensive outlook on the future of electrode manufacturing.

25 ENERGY STORAGE↗
DOE OSTI2019

Manufacturing of Advanced Alnico Magnets for Energy Efficient Traction Drive Motors CRADA Final Report

The primary theme of this Technology Commercialization Fund (TCF) project was refining the pre-alloyed powder processing approach (with alnico 8, modified for higher coercivity) of that came out of the previous Development of Radically Enhanced alnico Magnets (DREaM) project to permit full size net-shape alnico magnets to be produced in a reproducible manner that could allow testing in an advanced Permanent Magnet (PM) drive motor. Previously, a lack of sufficient coercivity in alnico magnets limits their energy product and their application in automotive traction drive motors, despite their high temperature stability. Use of enhanced sintered alnico magnets, instead of rare earth (RE) magnets or larger cast alnico magnets, could lower costs and decrease cooling needs of these motors. Conventional production of the best (aligned) alnico magnets (alnico 9) involves costly directional solidification (DS) and achieves good alignment, but modest energy product (10 MGOe), because of low coercivity. Other limitations of cast alnico 9 magnets are poor mechanical properties and difficulty in scaling special casting molds to mass production. In spite of these problems with alnico 9, a commercial electric motor company, UQM, developed a fully capable traction drive motor that met many 2022 DOE-VTO performance targets, except full speed operation, due to brittle mechanical behavior. While UQM demonstrated an advanced drive motor that used alnico 9, they also encouraged the development of improved alnico, especially for greater coercivity (seeking 2X) and improved mechanical properties. While commercial sintered alnico magnets are less brittle and have improved coercivity, they have an inferior energy product due to their non-aligned, fine-grained microstructure. Thus, full development and up-scaling of well-aligned alnico magnets with a further increase in coercivity and good mechanical properties by a low cost powder processing route became the theme of this TCF project. The processing route for this project involved high-pressure gas atomization, at Ames and Carpenter, of modified alnico 8 compositions, compression molding of the resulting pre-alloyed powders into bulk samples, de-binding and sintering the samples to full density, and a final magneto-thermal treatment of the resulting bulk magnets, at Ames and Arnold Magnetic Technologies, to produce aligned magnets, which were intended for motor testing at UQM and Ford.

42 ENGINEERING↗
DOE OSTI2017

Vegetation Demographics in Earth System Models: a review of progress and priorities

Numerous current efforts seek to improve the representation of ecosystem ecology and vegetation demographic processes within Earth System Models (ESMs). Furthermore, these developments are widely viewed as an important step in developing greater realism in predictions of future ecosystem states and fluxes. Increased realism, however, leads to increased model complexity, with new features raising a suite of ecological questions that require empirical constraints. We review the developments that permit the representation of plant demographics in ESMs, and identify issues raised by these developments that highlight important gaps in ecological understanding. These issues inevitably translate into uncertainty in model projections but also allow models to be applied to new processes and questions concerning the dynamics of real-world ecosystems. We also argue that stronger and more innovative connections to data, across the range of scales considered, are required to address these gaps in understanding. The development of first-generation land surface models as a unifying framework for ecophysiological understanding stimulated much research into plant physiological traits and gas exchange. Constraining predictions at ecologically relevant spatial and temporal scales will require a similar investment of effort and intensified inter-disciplinary communication.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Opposite Responses of the Dry and Moist Eddy Heat Transport Into the Arctic in the PAMIP Experiments

Given uncertainty in the processes involved in polar amplification, elucidating the role of poleward heat and moisture transport is crucial. The Polar Amplification Model Intercomparison Project (PAMIP) permits robust separation of the effects of sea ice loss from sea surface warming under climate change. We utilize a moist isentropic circulation framework that accounts for moisture transport, condensation, and eddy transport, in order to analyze the circulation connecting the mid-latitudes and the Arctic. In PAMIP's atmospheric general circulation model experiments, prescribed sea ice loss reduces poleward heat transport (PHT) by warming the returning moist isentropic circulation at high latitudes, while prescribed warming of the ocean surface increases PHT by strengthening the moist isentropic circulation. Inter-model spread of PHT into the Arctic reflects the tug-of-war between sea-ice and surface-warming effects.

58 GEOSCIENCES↗
DOE OSTI2018

Cascaded chirped photon acceleration for efficient frequency conversion

A cascaded sequence of photon acceleration stages using the instantaneous creation of a plasma density gradient by flash ionization allows the generation of coherent and chirped ultraviolet and x-ray pulses with independently tunable frequency and bandwidth. The efficiency of the cascaded process scales with 1/ω in energy, and multiple stages produce significant frequency up-conversion with gas-density plasmas. Lastly, chirping permits subsequent pulse compression to few-cycle durations, and output frequencies are not limited to integer harmonics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Automation of Nanoparticle Synthesis Processes in a Plasma Environment Using LabVIEW

This work presents an automated control system for the synthesis of nanomaterials by plasma-enhanced chemical vapor deposition (PECVD), implemented using the LabVIEW software environment. The main objective of the study is to develop an integrated hardware-software platform that enables sequential control of the key stages of the PECVD process, including vacuum chamber preparation, pressure monitoring, working gas supply, plasma ignition, power matching, cyclic nanomaterial growth, and optical monitoring of nanoparticles in the plasma environment. The use of LabVIEW made it possible to integrate actuator control, experimental parameter acquisition, and realtime process visualization within a single automated system. The automated cycle begins with evacuation of the reaction chamber to a predefined base pressure. Transition to the next stage is permitted only after the specified pressure threshold has been reached, ensuring reproducible initial conditions for each experiment. The program then controls the supply of the working gas through mass flow controllers (MFCs). In this work, two gas-flow control modes were considered: analog control using a 0-5 V voltage signal and digital communication via RS-232 interface. It was shown that the analog approach requires accurate scaling of the control voltage, since applying 5 V corresponds to full-scale opening of the controller and results in the maximum gas flow. In contrast, the RS232 interface enables the gas flow rate to be specified directly in sccm, improving the accuracy, flexibility, and convenience of gas-environment control. After pressure stabilization, LabVIEW initiates RF plasma ignition and executes the RF matching algorithm aimed at minimizing reflected power and improving the stability of the plasma process. A separate software module implements the cyclic nanomaterial growth mode, in which the plasma-on time, plasma duration, and total number of synthesis cycles are predefined. This approach makes it possible to control material accumulation on the substrate and to correlate the process parameters with the morphological characteristics of the resulting nanostructures. The final module of the system is designed for optical monitoring of the nanoparticle cloud density in dusty plasma. For this purpose, the change in the intensity of laser radiation passing through the plasma region is recorded using a photodetector and a Keithley 2401 measuring unit connected to LabVIEW via RS-232 interface. The difference between the initial and modified optical signal intensity is used as a diagnostic parameter characterizing the formation and temporal evolution of nanoparticles. The developed system demonstrates that LabVIEW can be effectively applied not only for the automation of individual instruments, but also for the implementation of a complete digital control cycle for PECVD-based nanomaterial synthesis.

PECVD↗
DOE OSTI2017

Integrated Disposal Facility Performance Assessment: Modeling Consistency to Support Regulatory Decision Making at Hanford - 17398

Under DOE Order 435.1, 'Radioactive Waste Management', Washington River Protection Solutions, LLC and INTERA, Inc are currently preparing a performance assessment for the Hanford Integrated Disposal Facility, a near-surface low-activity waste disposal facility located on the Hanford Site in southeast Washington State. The disposal facility is expected to receive vitrified low-activity waste produced at the Hanford Waste Treatment and Immobilization Plant, as well as other secondary solid wastes generated during the treatment process. The performance assessment performs the analyses that will be relied upon to receive the Disposal Authorization Statement, establish waste acceptance criteria, modify the RCRA permit for the facility and make a waste-incidental-to-reprocessing determination for the vitrified tank waste. In January 2006 in the case State of Washington v. Bodman (Civil No. 2:03-cv-05018-AAM), DOE, the Washington State Department of Ecology (Ecology) and the State of Washington Attorney General's office reached a settlement agreement in Ecology's claim regarding off-site waste shipments to Hanford and the adequacy of modeling in the environmental impact statement. In response to the agreement, the DOE Office of Environmental Management set a policy to establish a consistent use of commercially available and public domain software for a vadose zone and groundwater model platform to support regulatory decisions at Hanford. In October 2012, the Associate Principal Deputy Assistant Secretary for Environmental Management released a memorandum to the manager of the Richland Operation Office directing how future environmental modeling activities to support regulatory decision making on the Hanford Site would be undertaken to be consistent with the 2006 settlement agreement. The preparation of the performance assessment must meet DOE Order 435.1 requirements and the additional direction provided by DOE. This paper will identify the approach taken to comply with the requirements in the 2012 memorandum. The paper will describe how environmental modeling performed for the 2017 Integrated Disposal Facility Performance Assessment was planned in a phased approach and how the current modeling is tied to the analyses that supported the decisions made in the environmental impact statement published in 2012. Additionally, the selection and qualification of the software selected to perform modeling activities for the performance assessment will be described. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

A substandard candle: the low-$$\nu $$ method at few-GeV neutrino energies

Abstract As accelerator-based neutrino oscillation experiments improve oscillation parameter constraints with more data, control over systematic uncertainties on the incoming neutrino flux and interaction models is increasingly important. The intense beams offered by modern experiments permit a variety of options to constrain the flux using in situ “standard candle” measurements. These standard candles must use very well understood interaction processes to avoid introducing additional interaction model dependence. One option often discussed in this context is the “low- $$\nu $$ ν ” method, which is designed to isolate neutrino interactions where there is low energy-transfer to the nucleus, such that the interaction cross section is expected to be approximately constant as a function of neutrino energy. The shape of the low-energy transfer event sample can then be used to extract the flux shape. Applications of the method at high neutrino energies (many tens of GeV) are well understood. However, the applicability of the method at the lower energies of current and future few-GeV accelerator neutrino experiments remains unclear due to the presence of nuclear and form-factor effects inherent in the interaction models.In this analysis we examine the prospects for improving constraints on the accelerator neutrino fluxes in situ with the low- $$\nu $$ ν method in an experiment-independent way, using (anti)neutrino interactions on argon and hydrocarbon targets from the GENIE, NEUT, NuWro and GiBUU event generators. We begin by investigating the extent to which deviations from the constant cross-section assumption are dependent on poorly understood aspects of the neutrino interaction model. We then assess whether a low energy-transfer event sample can be confidently identified using experimentally accessible observables. We finally consider how the practicalities of reconstructing the energy spectrum of interacting neutrinos in realistic detectors might further limit the utility of low- $$\nu $$ ν flux constraints. The results show that flux constraints from the low- $$\nu $$ ν method would be severely dependent on the interaction model assumptions used in an analysis of neutrinos with energies below 5 GeV, and anti-neutrinos below at least 15 GeV. The spread of model predictions show that a low- $$\nu $$ ν analysis is unlikely to offer much improvement on typical neutrino flux uncertainties, even with a perfect detector. Notably—running counter to the assumption inherent to the low- $$\nu $$ ν method—the model-dependence increases with decreasing energy transfer for experiments in the few-GeV region.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

A multi‐variable framework for selecting WRF physics configurations at convection‐permitting scales: An Amazon wet‐season case study

Tropical convection over rainforests modulates atmospheric circulation and the energy and hydrological cycles across multiple scales. However, the scarcity of observations still limits our understanding of these processes. Although numerical models are utilized to investigate atmospheric physical processes, their performance depends on the choice of parameterizations and grid resolution. Here, in this work, we introduce and apply a multi‐variable, multi‐physics framework to evaluate and rank the Advanced Research Weather Research and Forecasting (WRF–ARW) configurations at 1‐km resolution over the central Amazon during the wet season. A 48‐member ensemble combines three land‐surface models (LSMs), four planetary boundary layer (PBL), and four microphysics (MP) schemes. Model performance for seven convection‐related near‐surface and boundary‐layer variables is assessed using Taylor diagrams and the Taylor skill score (TSS), analysis of variance (ANOVA)‐based sensitivity metrics, and non‐parametric rank tests. We then construct a combined, weighted TSS to identify configurations that are comparatively robust across variables. Results showed that most configurations reproduce near‐surface temperature, sensible and latent heat fluxes, and boundary‐layer height reasonably well, whereas humidity and rainfall remain challenging. LSM choice has the strongest impact on the surface fluxes and a secondary influence on near‐surface temperature and humidity, PBL schemes dominate boundary‐layer height, and MP schemes exert the largest control on rainfall. No single configuration is optimal for all variables, but the combination of Noah (LSM), Yonsei University (PBL), and Morrison (MP) emerges as the most robust configuration for this case, with the WRF single‐moment six‐class scheme (WSM6) providing a competitive, computationally cheaper MP alternative. The framework is general and can be applied to other regions, seasons, and convective regimes.

Amazon rainforest↗
DOE OSTI2020

Extended Finite Element Based Approach in Additive Manufacturing Modeling for Optimizing Highly Complex Manifold in Protonic Ceramic Electrochemical Cells

The objective of this project is to develop a novel numerical approach based on the extended finite element method (XFEM) for modeling moving boundaries of material deposited in additive manufacturing (AM) process with improved accuracy and reduced computational cost. One of the major challenges in simulating AM processes is that the boundaries of the computational domain need to change as material is deposited. Previous approaches have achieved this by activating new finite elements, but this requires a high level of mesh refinement to capture small movement of the boundary. XFEM allows the solution boundary to move independently of the mesh, permitting smooth representation of the evolution of the boundary as material is deposited. As a result, this new method will significantly improve the simulation accuracy while reducing the computational cost compared with existing approaches. Furthermore, this project will bring significant improvements for the design and AM process optimization in an iterative fashion among numerical simuation, parameter optimization, and experimental validation. Specifically, this project will support the protonic ceramic electrochemical cells (PCEC) stack development at INL by providing insights into the density, residual stress, thermal and mechanical properties of the PCEC manifold and interconnect, which is critical in enhancing the system lifetime and reducing the overall cost. Upon the success of proposed development and validation of the proposed approach, simulation will be applied to determine an optimal set of AM process parameters for the PCEC manifold production. This project will consolidate Idaho National Laboratory (INL)’s simulation capabilities provided by the MOOSE framework and the Valhalla AM simulation application, with encouraging expansion to emerging PCEC applications and AM technologies at INL and beyond.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Developing and testing capabilities for simulating cases with heterogeneous land/water surfaces in a novel atmospheric large eddy simulation code

Large eddy simulations (LES) are the primary computational tool used to simulate high Reynolds number three-dimensional turbulent flows. In the context of earth system sciences, particularly atmospheric science, LES are uniquely able to resolve the scales of atmospheric motion that are key for building process-level understanding of boundary layer turbulence, atmosphere-surface interaction, clouds, and cloud-aerosol-chemistry interaction, and are a core limited-area modeling capability. Increasing demands are being placed on LES code bases as growing high performance computing resources allow LES to address a wider range of scientific problems. In addition, LES are emerging as a source of high-quality machine learning training data. These demands necessitate an agile and extensible code base that allows the model to quickly adapt to emergent needs. However, LES have largely relied on legacy Fortran code bases that lack flexibility. A new, Python-based LES capability called Predicting INteractions of Aerosol and Clouds in Large Eddy Simulation (PINACLES) has been developed as part of the Department of Energy’s Earth System Model Development (ESMD) program area’s Enabling Aerosol-cloud interactions at Global convection-permitting scalES (EAGLES) project. PINACLES was developed from the ground up with a philosophy of maximizing scientific throughput, by attempting to optimize for both model throughput and software extensibility. The initial development of PINACLES delivered a state-of-the-art idealized LES capability solving the non-hydrostatic anelastic equations of motion with doubly periodic boundary conditions and idealized homogenous surface boundary conditions. Here we provide a final report on the outcomes of a fiscal year 2021 Seed Laboratory Directed Research Project that extended PINACLES in two key ways. First, PINACLES was coupled to a state-of-the-art land surface model enabling it to simulate spatially inhomogeneous land-atmosphere interactions that are known to control key atmospheric processes. Second, the dynamical core of PINACLES was modified to permit non-periodic boundary conditions. This model enhancement enables simulation of realistic cases with boundary conditions prescribed from atmospheric reanalysis and enables nested simulations conducted on a hierarchy of computational domains with increasing resolution. Together, these extensions to PINACLES make it a formidable modeling capability and expand its potential application to diverse components of DOE’s atmospheric science portfolio.

42 ENGINEERING↗
DOE OSTI2016

The influence of model resolution on the simulated sensitivity of North Atlantic tropical cyclone maximum intensity to sea surface temperature

Global climate models (GCMs) are routinely relied upon to study the possible impacts of climate change on a wide range of meteorological phenomena, including tropical cyclones (TCs). Previous studies addressed whether GCMs are capable of reproducing observed TC frequency and intensity distributions. This research builds upon earlier studies by examining how well GCMs capture the physically relevant relationship between TC intensity and SST. Specifically, the influence of model resolution on the ability of a GCM to reproduce the sensitivity of simulated TC intensity to SST is examined for the MRI-AGCM (20 km), the GFDL-HiRAM (50 km), the FSU-COAPS (0.94°) model, and two versions of the CAM5 (1° and 0.25°). Results indicate that while a 1°C increase in SST corresponds to a 5.5–7.0 m s -1 increase in observed maximum intensity, the same 1°C increase in SST is not associated with a statistically significant increase in simulated TC maximum intensity for any of the models examined. However, it also is shown that the GCMs all capably reproduce the observed sensitivity of potential intensity to SST. The models generate the thermodynamic environment suitable for the development of strong TCs over the correct portions of the Nort h Atlantic basin, but strong simulated TCs do not develop over these areas, even for models that permit Category 5 TCs. This result supports the notion that direct simulation of TC eyewall convection is necessary to accurately represent TC intensity and intensification processes in climate models, although additional explanations are also explored.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli

Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. In this paper, we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits, the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe 2 O 3 (s) reducing conditions. Overall and finally, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

Abstract Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗