Search NASA⌕ Search

SEARCH · Search NASA

Results for “assembly identification”

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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat

The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria ( Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (C i ), but some evidence indicates that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of C i incorporation into different taxa, mat samples were incubated with [ 13 C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13 C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13 C. Most 13 C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins associated with photosynthesis, C i fixation, and N 2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for C i fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to C i fixation. Other taxa showed much lower [ 13 C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven C i fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in C i fixation. Because this pathway imparts a lower degree of selection of isotopically heavy C i than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13 C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13 C/ 12 C ratios of mat biomass will help geochemists interpret the 13 C/ 12 C ratios of organic carbon in the fossil record.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The large-area hybrid-optics CLAS12 RICH: First years of data-taking

The CLAS12 deep-inelastic scattering experiment at the upgraded 12 GeV continuous electron beam accelerator facility of Jefferson Lab conjugates luminosity and wide acceptance to study the 3D nucleon structure in the yet poorly explored valence region, and to perform precision measurements in hadron spectroscopy. A large area ring-imaging Cherenkov detector has been designed to achieve the required hadron identification in the momentum range from 3 GeV/c to 8 GeV/c, with the kaon rate about one order of magnitude lower than the rate of pions and protons. The adopted solution comprises aerogel radiator and composite mirrors in a novel hybrid optics design, where either direct or reflected light could be imaged in a high-packed and high-segmented photon detector. The first RICH module was assembled during the second half of 2017 and installed at the beginning of January 2018, in time for the start of the experiment. The second RICH module, planned with the goal to be ready for the beginning of the operation with polarized targets, has been timely built despite the complications caused by the pandemic crisis and successfully installed in June 2022. Finally, the detector performance is here discussed with emphasis on the operation and stability during the data-taking, calibration and alignment procedures, reconstruction and pattern recognition algorithms, and particle identification.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile

Abstract Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-l-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.

Chemistry↗
DOE OSTI2024

Novel Instrumentation for Advanced Quantum Chromodynamics Studies with Flavor Sensitivity

The true nature of ordinary matter has always fascinated humankind, whose imagination has been pointed to the right direction since the 5th century BC with the first known atomic theory by Leucippus and Democritus. They described the matter as formed by small, invisible, indivisible, and eternal particles: the atoms. A long investigation followed them, including contributions from several of history?s greatest philosophers and scientists. The progress led to the understanding that atoms have an internal structure consisting of a central nucleus composed of protons and neutrons, surrounded by a cloud of electrons. About 50 years ago, scientists discovered that nucleons also have an internal structure. Through the Deep Inelastic Scattering (DIS) experiments, on which a lepton is scattered off a nucleon, it was possible to access the distribution of partons inside the nucleon along the longitudinal direction defined by the hard-scale probe. It was a crucial step in developing Quantum Chromodynamics (QCD), currently the best theory describing the subatomic matter. Ultimately, DIS was recognized as a limited tool to investigate the nucleon structure because it is mainly sensitive to observables at the probe?s energy scale. In recent decades, theoretical developments have allowed defining soft-scale observables by measuring more complex processes. Reactions such as Semi-Inclusive Deep Inelastic Scattering (SIDIS) with single or di-hadron production, can provide information about the momentum of parton inside the nucleon. In particular, polarized SIDIS allows access to the Transverse-Momentum-Dependent (TMD) parton distributions describing the correlations of the quark and gluon degrees of freedom in transverse momentum and spin. This study can provide three-dimensional imaging of nucleon structure and inner dynamics, as long as the hadronic component in the final state can be measured. Identifying the species of the produced particles provides information on the quark flavor and assumes a crucial role in this context. The thesis describes the work carried out by the author in preparing novel instrumentation for particle identification in the final state of DIS experiments, to support modern analysis of the parton dynamics within the basic confined object (nucleon) with flavor sensitivity. The work has been focused on the CLAS12 spectrometer in operation at Jefferson Laboratory (JLab), Newport News, VA, USA, and the ePIC experiment in preparation for the future Electron-Ion Collider (EIC) at Brookhaven National Laboratory (BNL), Long Island, NY, USA. CLAS12 is a fixed-target experiment using a 12 GeV beam of polarized electrons scattering off polarized nuclear targets. In 2018 and 2022, two Ring Imaging Cherenkov (RICH) detector modules were installed to improve the ?±/K± separation in the high-momentum region (3÷8 GeV/c) of the experiment. The author contributed to the assembly, installation, and com- missioning of the second RICH module, to the efficiency studies of the first module, and to the first SIDIS analysis with high-momentum kaons identified by the RICH. These studies led to the observation of the first spin asymmetry with high-momentum kaons from the CLAS12 experiment, and an initial assessment of the systematic error associated with the hadron identification. ePIC will be the first experiment at the future EIC, the new collider designed to expand the frontiers of QCD. The author was involved in the development of the dual-radiator Ring Imaging Cherenkov (dRICH). This detector will interpolate the measurements of the Cherenkov angles of photons produced by relativistic particles crossing two different radiators to identify charged hadrons. The author contributed to the studies conducted with the dRICH prototype, developing the reconstruction and analysis software and simulations, characterizing the aerogel radiator samples, and being responsible for the tracking system used during the beam tests. The performance obtained by the prototype has been progressively improved and the results are now comparable with the expectation derived from the simulation and satisfy the requirements of the experiment. In Chapter 1, the SIDIS theory is briefly introduced, outlying the connection with the experimental measurement. Chapter 2 includes the description of the CLAS12 RICH, its assembly and installation, and the efficiency study. In Chapter 3, the analysis of the Beam-Spin Asymmetry associated with SIDIS kaons is described. Chapter 4 describes the contribution to the dRICH for EIC, starting from a description of the ePIC experiment and focusing on the studies performed for the dRICH prototype. The conclusions of this work are summarized at the end.

Vallarino, Simone↗
DOE OSTI2025

Identification of the Liquid Argon Scattering Experimental Discrepancies Using Simulation

Scintillation light analysis in liquid argon based neutrino detectors is restrained in capability due to uncertainty in fundamental constants critical to the analysis process. One such property is the Rayleigh scattering length of liquid argon. In the fall of 2023, the TallBo cryostat, located in the Proton Assembly Building at Fermilab, was used to study the scattering length of liquid argon in the Liquid Argon Scattering (LArS) experiment. Due to systematic errors unknown during measurement analysis, LArS’s measurements were quite uncertain. By simulating the LArS experiment, we found that the downturn in detector count rate as a function of liquid argon height at low heights was caused by a misplaced photo multiplier. With concentrated effort, we may be able to successfully correct this effect by understanding the relationship between the specified Rayleigh scattering length and the measured attenuation length. With this information and further progression in analysis, we may be able to extract corrected measurements from the LArS data and attain a tangible experimental measurement of the scattering length of liquid argon.

Breaux, Auto D. [Tulane U.; Fermilab]↗
DOE OSTI2022

Probing Electron Beam Induced Transformations on a Single-Defect Level via Automated Scanning Transmission Electron Microscopy

A robust approach for real-time analysis of the scanning transmission electron microscopy (STEM) data streams, based on ensemble learning and iterative training (ELIT) of deep convolutional neural networks, is implemented on an operational microscope, enabling the exploration of the dynamics of specific atomic configurations under electron beam irradiation via an automated experiment in STEM. Combined with beam control, this approach allows studying beam effects on selected atomic groups and chemical bonds in a fully automated mode. Here, in this study, we demonstrate atomically precise engineering of single vacancy lines in transition metal dichalcogenides and the creation and identification of topological defects in graphene. The ELIT-based approach facilitates direct on-the-fly analysis of the STEM data and engenders real-time feedback schemes for probing electron beam chemistry, atomic manipulation, and atom by atom assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Extension of SCALE/Sampler’s sensitivity analysis

Nuclear data are a major source of uncertainties in reactor physics calculations. The propagation of nuclear data uncertainties to important system responses is instrumental when determining appropriate safety margins in reactor safety analyses. It is also important to understand the major contributors to the observed uncertainties to make recommendations for further measurements and evaluations and aid in the understanding of the studied system. The SCALE code system allows for nuclear data uncertainty analysis based on the random sampling approach as implemented in SCALE’s Sampler sequence. Sampler was recently extended by a sensitivity analysis in terms of the calculation of two correlation-based sensitivity indices. This analysis allows for the identification of the top contributing nuclear reactions to any analyzed output uncertainty. This paper presents the sensitivity indices, along with their interpretation and limitations. It demonstrates the application in an eigenvalue and decay heat analysis for a boiling water reactor fuel assembly.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

International Meeting on Fuel Cell and Electrolyzer Quality Control: Summary Report

Quality control (QC) for both polymer electrolyte membrane fuel cell and electrolysis membrane electrode assembly (MEA) materials is a key challenge for scale-up and cost reduction. Developing methods for detecting defects, as well as measuring critical material properties and understanding the impact of as-manufactured variations in these materials on cell performance and lifetime, are critical barriers. To help address these needs, the National Research Council Canada (NRC), Fraunhofer Institute for Solar Energy Systems (ISE), and the National Renewable Energy Laboratory (NREL) have organized and facilitated a series of workshops on the topic, bringing together industry, academia, and research institutions from North America and Europe. Prior workshops in Canada and Germany have focused on the status of quality tool capabilities and identification of needed developments for fuel cells. These meetings have garnered an excellent response and follow-on attendance, with over 100 unique attendees.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2025

X-Ray and Particle Detection With the Si(Li) Tracker Module of the GAPS Experiment

Here, this work describes the architecture and the experimental results from the characterization of the lithium-drifted silicon (Si(Li)) detector module, which constitutes the building block of the tracker in the general antiparticle spectrometer (GAPS) experiment to search for dark matter. The instrument is designed for the identification of low-energy cosmic anti-nuclei (antiprotons, antideuterons, and antihelium) to be performed during an Antarctic long-duration balloon flight scheduled for late 2025. The GAPS Si(Li) tracker, that is the core of the instrument, is the assembly of 252 modules, each comprised of four Si(Li) detectors and a full custom-integrated circuit designed for detector readout and produced in a commercial 180-nm planar CMOS technology. A general overview of the detector module architecture and its components is provided, together with a description of the test setup and the experimental results obtained from the characterization of the low-noise analog readout channel. In order to verify the effective operation of the entire module, results concerning the detection of X-rays from a 241Am source and cosmic muons are also provided.

Manghisoni, Massimo [Università di Bergamo (Italy)↗
DOE OSTI2022

Re-evaluating the Systematics of Dendrolycopodium Using Restriction-Site Associated DNA-Sequencing

The genus Dendrolycopodium (Lycopodiaceae) includes four to five species across North America and East Asia. Species identification in Dendrolycopodium is difficult due to limited or inconsistent characters. In addition, plants with intermediate morphologies regularly occur, potentially indicative of interspecific hybridization. To determine the species relationships in Dendrolycopodium and investigate the existence of hybrids, we generated a draft genome assembly for D. obscurum and carried out double-digest restriction-site associated DNA sequencing (RADSeq) on 86 Dendrolycopodium specimens. Our sampling includes all the described species and 11 individuals with intermediate morphology. We find that the genus can be divided into four clades that largely correspond to the described taxa, as well as evidence of interspecific hybridization. Within these clades, our STRUCTURE analysis suggests that there are multiple finer subgroups, with evidence of hybridization and introgression between these subgroups. Given the limited availability of specimens collected from Asia, the status of the various Asian species remains uncertain and will require further study. In summary, our study confirms several hybrid relationships in Dendrolycopodium and provides a clear phylogenetic framework for future taxonomic revision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification of novel organic polar materials: A machine learning study with importance sampling

Recent advances in the synthesis of polar molecular materials have produced practical alternatives to ferroelectric ceramics, opening up exciting new avenues for their incorporation into modern electronic devices. However, in order to realize the full potential of polar polymer and molecular crystals for modern technological applications, it is paramount to assemble and evaluate all the available data for such compounds, identifying descriptors that could be associated with an emergence of ferroelectricity. In this paper, we utilized data-driven approaches to judiciously shortlist candidate materials from a wide chemical space that could possess ferroelectric functionalities. A machine learning study with importance sampling was employed to address the challenge of having a limited amount of available data on already-known organic ferroelectrics. Sets of molecular- and crystal-level descriptors were combined with a Random Forest Regression algorithm in order to predict the spontaneous polarization of the shortlisted compounds. First-principles simulations were performed to further validate the predictions obtained from the machine learning model.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Mapping thermal energy storage technologies with advanced nuclear reactors

Advanced nuclear power plants (NPPs) will potentially need to operate in environments where power generation flexibility is more highly valued than the stability or baseload generation capability for conventional demand curves. Thermal energy storage (TES) systems would enable NPPs to respond nimbly to market variability and could also position advanced NPPs to participate differently in restructured markets, thus further enhancing their economic competitiveness. TES systems could also benefit the electric grid by eliminating the need for peaking plants, as well as by improving the economic performance of baseload NPPs. While TES technologies afford a unique opportunity to address many of these challenges, the applicability of these systems is also complicated by the fact that various advanced NPPs are designed differently, each with its own temperature range, size, operating fluids, and operating conditions. Hence, TES systems face significant barriers to investment, as more information on their compatibility and performance metrics is needed to quantify the advantages provided by each, as well as the challenges these technologies might face if coupled with a particular type of advanced NPP. This study explores the possibility of integrating a wide variety of TES technologies with various categories of advanced NPPs, based on their operating characteristics. To help decision makers, users and developers decide which TES technology is best suited to a particular category of advanced NPPs, this research present a Phenomena Identification and Ranking Table (PIRT) analysis of 10 TES systems that could potentially be coupled with advanced NPPs, which themselves are divided into nine categories based on their operating conditions. Then, each advanced NPP category is evaluated for compatibility with the 10 TES systems by assembling and discussing a database of information concerning 10 engineering questions, defined herein in as figures of merit (FOMs), such as: technology readiness level (TRL), temperature compatibility, energy density, size, cycle frequency, ramp time, realignment frequency, geographic needs, environmental impact, and interventions. By assembling a database of information concerning the TES technologies' compatibility with various advanced NPP systems, this study can help developers acquaint themselves with a particular TES technology before choosing to build a new integrated installation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Development of the Mobile Systems for Conditioning of Disused Sealed Radioactive Sources in Serbia - 20105

Sealed radioactive sources (SRS) are being used worldwide in the field of medicine, agriculture, industry and research. They can be found in mobile as well as stationary devices. SRS contains radioactive material that is (a) permanently sealed in a capsule or (b) closely bounded and in a solid form. The capsule or material of an SRS should be strong enough to maintain leak tightness under the conditions of use and purpose for which the source was designed, also in case of accidents. In this case only emitted radiation is utilized. Firstly, the hazard from external radiation has to be considered, but the possibility of contamination due to fracture of the capsule should not be disregarded. The radioactive sources are composed of the radiating isotope contained in the filling medium, the single or double isotope holder that partially or totally surrounds the filling medium, the outer cover that contains the parts mentioned above and the capsule closed airtightly by welding or using some other method. The capsule must be tested for leakage periodically. If the SRS is no longer needed (e.g. replaced by a different technique) or it becomes useless for the intended application (e.g. the activity becomes too weak, the equipment containing the source works poorly or becomes obsolete, the source is damaged or leaking) it is considered disused. Disused sealed radioactive sources (DSRS) are typically conditioned and disposed if a facility is available. If the disposal option is not available, conditioned DSRS should be stored under proper conditions. In some cases, the radionuclide(s) in DSRS can be recovered/recycled or the DSRS can be repurposed for other applications. Conditioning of DSRS ensures containment of the radioactive material, provides confinement for leaking sources, provides sufficient radiation shielding, reduces storage/disposal volume by allowing consolidation of multiple sources into a single storage/disposal container, facilitates transport operations and contributes to safety and security as well. Typically, conditioning technologies are deployed either as permanently installed stationary systems in centralized or mobile on-site waste processing facilities, or in a mobile configuration. Centralized stationary facilities provide a single processing location for multiple users that requires transport of the waste to the facility. On the other hand, mobile systems may be provided for the selection and application of the optimum technology for a specific waste stream (such as DSRS) by bringing the process to the point where the waste is generated. In addition, mobile systems could offer additional flexibility by sharing equipment among multiple waste generating sites for processing campaigns that vary in duration, from very short periods to several years. The term 'mobile processing system' refers to any radioactive waste processing system or component which is designed to be transportable and which is not considered permanently installed. Two mobile system for conditioning of disused sealed radioactive sources are developed in the Public Company Nuclear Facilities of Serbia. Development of these mobile systems was supported by SRB9005 national project via Technical Cooperation of the IAEA. The first mobile system, built inside the 20 feet ISO container, will be used for conditioning of DSRS category 3 to 5. The second mobile system, built inside the 7 m long vehicle (Iveco Daily Van), will be used for dismantling of ionizing smoke detectors mostly with Am-241 sources. Designs of the mobile systems were defined in cooperation with two companies from Belgium (Belgoprocess and Leniko) and a Croatian company Ekoteh as well as with the support of the IAEA experts. The generic safety assessment and operational procedures for the mobile systems are developed. Based on safety assessment the acceptance criteria and operational limits and conditions are established. Operational procedures include: (a) equipment and material requirements, (b) assembling procedure of the mobile unit, (c) procedure for acceptance of devices for dismantling and conditioning, (d) dismantling procedure for devices to recover the DSRS, (e) characterization of DSRS, (f) encapsulation procedure of DSRS, (g) disassembling procedure of the mobile unit, and (h) keeping records, identification and traceability. In addition, radiation safety, health safety, security and emergency preparedness plans are prepared. The generic safety assessment and operational procedures could be updated with site specific requirements, DSRS inventory, and different needs for future customers. Developed mobile systems could be used in all situations when it is feasible to perform conditioning of DSRS on the spot in the county and worldwide. Development of these mobile units was just the first step to create the Reference Center for Radioactive Waste Treatment and Disused Radioactive Sources Conditioning for Small Facilities which can become a regional training center in the future, and/or as a tool for comprehensive national search and secure programmes. In the next phases development of e-learning platforms and blended learning packages as well as application for the IAEA Qualified Technical Centre (QTC) for the management of DSRS is foreseen. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Emulating Variable Uranium Enrichments With Radiation Signature Training Devices (RSTD)

Radiological signature training devices (RSTDs) are sealed sources (or assemblies of sources) that emulate the radiation signature of larger masses of special nuclear material for passive detection while maintaining a minimal logistical footprint in security, radiological safety, criticality safety, and transportation requirements. Previous work focused on emulation of large quantities of highly enriched uranium for search and field identification with radioisotope identification detectors and mobile systems. New work has expanded into investigating use of the RSTDs with laboratory safeguards tools, such as MGAU and FRAM, and emulating uranium spectra of multiple enrichments over more energy regions (particularly the x-ray region).

Blessinger, Christopher S.↗
DOE OSTI2021

Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase

Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification of a carbonic anhydrase–Rubisco complex within the alpha-carboxysome

Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO 2 fixation—Rubisco and carbonic anhydrase—and are the centerpiece of the bacterial CO 2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO 2 by carbonic anhydrase, producing a high CO 2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus . We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data

The dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D fast Fourier transforms, correlation, and pair distribution functions are explored using the unsupervised linear unmixing, demonstrating the presence of static ordered and dynamic disordered phases and establishing their time dynamics. Here, the deep learning (DL)-based workflow is developed to analyze detailed particle dynamics and explore the evolution of local geometries. Finally, we use a combination of DL feature extraction and mixture modeling to define particle neighborhoods free of physics constraints, allowing for a separation of possible classes of particle behavior and identification of the associated transitions. Overall, this work establishes the workflow for the analysis of the self-organization processes in complex systems from observational data and provides insight into the fundamental mechanisms.

36 MATERIALS SCIENCE↗