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At least 73 records · Page 4

Analysis and design of fast flow liquid Li divertor for fusion nuclear science facility (FNSF) using coupled plasma boundary and LM MHD/heat transfer codes *

The SOLPS-ITER code is utilized to analyze the boundary plasma associated with a fast-flow lithium (Li) divertor configuration in the fusion nuclear science facility (FNSF) tokamak and identify operational regimes with acceptable divertor and core conditions. Plasma transport from the SOLPS-ITER code has been coupled with a liquid metal (LM) MHD/heat transfer code to model a Li open-surface divertor design and assess its impact on the scrape-off-layer (SOL) and core plasma performance. Simulations with only Neon (Ne) impurity seeding have been conducted to evaluate its impact on meeting FNSF design demands for the divertor and upstream plasma parameters. Simulation results indicate that Ne seeding significantly mitigates divertor heat flux but potentially reduces both upstream electron and main ion density due to fuel dilution. The combined application of Ne seeding and deuterium (D 2 ) puffing is required to satisfy the FNSF design requirements on upstream density ($n^{OMP}_{e,sep}$~1× 10 20 m -3 ) and divertor energy flux ($q^{Odiv}_{\bot,max}$<10 MW m -2 ). D 2 puffing plays a role in counteracting upstream density drops and augmenting energy and momentum losses through atomic and molecular processes. The inlet Li flow velocity is systematically varied across a wide range to identify acceptable flows and corresponding LM surface temperatures. This comprehensive analysis identifies the acceptable Li flow parameters, LM surface temperature, and emitted Li fluxes necessary to meet the major design constraints. The emitted Li fluxes exhibit minimal impact on the main plasma at surface temperatures up to approximately ~525 °C, corresponding emitted Li fluxes of up to φ Li ~2X10 23 atoms s -1 . Uncertainties in the Li emission processes from the surface are also investigated, primarily influencing Li loss in the lower surface temperature range (<525 °C), with simulation results indicating a minor impact on the divertor and upstream plasma. Conversely, evaporation predominantly drives the Li loss processes at higher surface temperature ranges (>525 °C), contaminating both the divertor and upstream plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Diagnostics: Chapter 8 of the special issue: on the path to tokamak burning plasma operation

This chapter presents the activity conducted by the ITPA topical group (TG) on Diagnostics over about the last 15 years. Following a general introduction of the ITER Diagnostics led by their measurement roles, the document is organized in several subchapters detailing the design support, research and development activity conducted by each of the specialist working groups (WGs) of the TG. Please note that the magnetic diagnostics were supported at the TG without a specific WG. Their status is included in the general introduction. In the following some highlights of the subchapter’s contents are provided. Recent advances in ITER first wall (FW) diagnostics for the measurements of plasma-metallic wall interaction in support of the ITER research plan are reported. An InfraRed imaging Video Bolometer for ITER has been developed and tested on several tokamaks to measure the radiated power loss. A laser-induced breakdown spectroscopy (LIBS) technique which utilizes a pulsed laser beam to ablate locally by forming a crater, will measure local tritium inventory in the FW material. Real-time Residual Gas Analyzers will measure the neutral gas composition in a divertor port and an equatorial port during plasma operation. Due to the full metallic FW environment, the plasma-wall interaction in ITER will face several challenges such as the compromised radiated power and divertor heat flux measurements by reflection. Ray tracing and analysis codes have been developed to eliminate and correct the effects of reflection in the measurements. The characteristics of the reflecting surfaces depending on the roughness and angle of the incidence have been measured by dedicated experiments, and the results were applied to the reflection elimination. For the measurement of the metallic impurity radiation induced by eroded metallic atoms, a vacuum ultraviolet spectrometer has been developed and tested. An extensive thermonuclear diagnostic suite will be required to support the operation of ITER and the planned experimental program for future burning plasma experiments. Due to the harsh environmental conditions, the implementation of diagnostic systems in ITER is a major challenge. These conditions include high levels of neutron and gamma fluxes, neutron heating, particle bombardment. Therefore, the selection and design of diagnostic systems must take into account a number of phenomena previously unseen in diagnostic design. For this reason, the measurement of neutrons and confined or lost fast ions, with particular emphasis on alpha particles, is critical to ITER. The diagnostics associated with these measurements will be important for future plasma-burning experiments at ITER. The high neutron emission and very large plasma size in ITER make neutron diagnostics the main diagnostic method used to measure plasma parameters such as fusion power, fusion power density, ion temperature, energy of fast ions and their spatial distributions in the plasma core. Active spectroscopy techniques are methods where a neutral particle beam is injected into the plasma and information on plasma parameters is extracted from the measurement of line emission resulting from the beam-plasma interaction, either by plasma ions or by beam atoms. Spatial localization is achieved by crossing the beamline and multiple observation lines. The ITER plasma will be a high temperature, moderately dense, fully ionized collisional plasma. The plasma facing surfaces are principally metallic being fashioned from beryllium or tungsten but many other elements, arising from either structural or from operational needs, may enter this plasma. The energy range of the emitted photons range from meV (infra-red) to multi keV (x-rays) and originate from all areas of the plasma volume. The primary role of passive emission diagnostics is to identify what is in the plasma from spectral signatures. Extracting quantitative information from these measurements such as impurity content, ion temperature, rotation, degree of detachment and radiated power depends on calibrated instruments, a physics model of the atomic and molecular processes and plasma transport and an analysis workflow that takes into account environmental effects such as reflections. The particular needs for ITER have prompted a multi-machine, many-year effort to address all these aspects and this chapter reviews the work on diagnostic design, experiments and new analysis techniques. An overview of the laser diagnostics to be implemented on ITER is also provided in this paper. This includes descriptions of the Thomson scattering in the core, edge and divertor regions, polarimetry and interferometry diagnostics used for measuring plasma density and also measurements of helium density in the divertor using Laser Induced Flourescence. Techniques which can allow improvements on current measurements are also addressed in particular expanding poloidal polarimetry measurements to measure field fluctuations and proposed use of dispersion interferometery which has a number of advantages over existing methods. This paper identifies particular areas where further research and testing on existing tokamaks is useful even at this advanced stage to inform the design of diagnostics for ITER. Outstanding areas of concern for the implementation of laser diagnostics, in particular with a view to reliable operation are identified. An overview of the latest developments of microwave diagnostic systems and techniques is given. The primary focus is the contributions for ITER—the next step burning plasma experiment—which is supplemented by describing recent progress of techniques applicable for fusion experiments beyond ITER. The contributions are intentionally kept concise, and are being supplemented by a rich list of references for further studies. Radiation induced effects are receiving continuous and well-deserved attention of the ITER diagnostic community and they are in many cases one of the primary design drivers of the ITER diagnostic systems. The paper summarizes recent progress in this area focusing primarily on the ITER diagnostics but in some cases provides also outlook for the possible solutions for even more demanding radiation environment of fusion reactors beyond ITER. Despite advancements in the area of modeling and simulation of various radiation induced effects, experimental testing in a nuclear environment as close as possible to the target one is still seen as unavoidable for proper qualification of particular diagnostic functional elements. Recent advancement within three diagnostic areas: optical diagnostics, magnetics and bolometers is covered. Encouraging results on qualification of silica glass vacuum window assemblies are presented. In the area of magnetic sensors, progress of irradiation tests performed on ITER in-vessel LTCC inductive sensors is presented with outlook for novel technological approaches to inductive sensors utilizing thick printing and photolithography technologies being highlighted. Summary of advancements in the area of steady state magnetic field sensors based on Hall effect is given. New results of neutron irradiation test of the ITER borosilicate glass inserts for vacuum electrical feedthroughs are summarized finding negligible swelling at target level of neutron fluence. Off-line irradiation tests of fiber optic current sensors for plasma current measurement demonstrated that both for gamma doses up to 5 MGy and a total neutron fluence up to 10 15 cm −2 , radiation induced changes are still compatible with required measurement accuracy on ITER. The ITER bolometers are given as an example how considering radiation effects may influence the diagnostic design. Finally, outlook for future main R&D directions is outlined. All optical and laser-based diagnostics in ITER will be using mirrors to guide plasma radiation toward detectors, cameras and sensors. In the hostile plasma, radiation and particle environment the optical characteristics of diagnostic mirrors will degrade directly affecting the entire performance of involved diagnostic systems. An assessment of factors affecting mirror performance is provided. Among the prime adverse factors are deposition of plasma impurities, sputtering of mirror surface and steam ingress in the vicinity of mirrors. Within the International Tokamak Physics Activity with active support by ITER central team and domestic agencies, the structured research and development (R&D) program on mitigation of risks for diagnostic mirrors is underway. Within this program the mirror material development, the passive mitigation of mirror degradation by using diagnostic ducts and shutters along with an active mirror recovery program comprising the in-situ mirror cleaning and calibration is underway. Recent developments in diagnostic mirror R&D are described in this Chapter along with an example of their implementation of R&D solutions in ITER Infrared Thermography diagnostic. An assessment of still open engineering and physics questions, considerations on mirror risks during an early phase of ITER operation are given along with an overview of diagnostic mirror evolution in the late ITER operation stage toward the demonstration fusion power plant. Several crucial areas of diagnostic R&D outlined in ITER Research Plan are addressed. The basic control groups in a fusion reactor can be broken-down in five categories: (1) plasma position, magnetic configuration, and plasma current control, (2) profile control and confinement optimization, (3) MHD control and suppression, (4) edge dissipation control, radiation and plasma exhaust control and (5) break-down optimization. These categories are coupled via the physics (a control action in one domain will affect the other domains) and via shared actuators (e.g. ECRH for impurity accumulation avoidance, current density distribution control and MHD suppression). Consequently, a supervisory control system should determine the priority of the various control tasks, their couplings, and the interfaces with the safety and interlock system. For the systematic development of the various controllers taking the complexity of the plasma and the control system into account, a model-based approach is required. A short historical overview is given of the developments in systems and control theory and control engineering with special emphasis on those developments that are most relevant for Nuclear Fusion research and operation. An overview is given of the state of the field of fusion plasma control for the control categories. It will be shown how synthetic diagnostics are being developed in ITER and how they are used in diagnostic design and design validation and how they can be in model-based controller synthesis using relatively simple models. In modern control methods, multiple diagnostics are used to constrain relatively simple models. The constrained models provide an estimate for the state. This opens the route to state controllers, such as model predictive control. A major challenge in nuclear fusion research is the coherent combination of data from heterogeneous diagnostics and modeling codes for machine control and safety as well as physics studies. Measured data from different diagnostics often provide information about the same subset of physical parameters. Additionally, information provided by some diagnostics might be needed for the analysis of other diagnostics. A joint analysis of complementary and redundant data allows, e.g. to improve the reliability of parameter estimation, to increase the spatial and temporal resolution of profiles, to obtain synergistic effects, to consider diagnostics interdependencies and to find and resolve data inconsistencies. Physics-based modeling and parameter relationships provide additional information improving the treatment of ill-posed inversion problems. A coherent combination of all kind of available information within a probabilistic framework allows for improved data analysis results. The concept of integrated data analysis (IDA) in the framework of Bayesian probability theory is outlined and contrasted with conventional data analysis. Components of the probabilistic approach are summarized and specific ingredients beneficial for data analysis at fusion devices are discussed.

ITER↗

Permissiveness and competition within and between Neurospora crassa syncytia

A multinucleate syncytium is a common growth form in filamentous fungi. Comprehensive functions of the syncytial state remain unknown, but it likely allows for a wide range of adaptations to enable filamentous fungi to coordinate growth, reproduction, responses to the environment, and to distribute nuclear and cytoplasmic elements across a colony. Indeed, the underlying mechanistic details of how syncytia regulate cellular and molecular processes spatiotemporally across a colony are largely unexplored. Here, we implemented a strategy to analyze the relative fitness of different nuclear populations in syncytia of Neurospora crassa , including nuclei with loss-of-function mutations in essential genes, based on production of multinucleate asexual spores using flow cytometry of pairings between strains with differentially fluorescently tagged nuclear histones. The distribution of homokaryotic and heterokaryotic asexual spores in pairings was assessed between different auxotrophic and morphological mutants, as well as with strains that were defective in somatic cell fusion or were heterokaryon incompatible. Mutant nuclei were compartmentalized into both homokaryotic and heterokaryotic asexual spores, a type of bet hedging for maintenance and evolution of mutational events, despite disadvantages to the syncytium. However, in pairings between strains that were blocked in somatic cell fusion or were heterokaryon incompatible, we observed a “winner-takes-all” phenotype, where asexual spores originating from paired strains were predominantly one genotype. These data indicate that syncytial fungal cells are permissive and tolerate a wide array of nuclear functionality, but that cells/colonies that are unable to cooperate via syncytia formation actively compete for resources.

59 BASIC BIOLOGICAL SCIENCES↗

Direct Monitoring of Conical Intersection Passage via Electronic Coherences in Twisted X-Ray Diffraction

Quantum coherences in electronic motions play a critical role in determining the pathways and outcomes of virtually all photophysical and photochemical molecular processes. However, the direct observation of electronic coherences in the vicinity of conical intersections remains a formidable challenge. Here we propose a novel time-resolved twisted x-ray diffraction technique that can directly monitor the electronic coherences created as the molecule passes through a conical intersection. We show that the contribution of electronic populations to this signal is canceled out when using twisted x-ray beams that carry a light orbital angular momentum, providing a direct measurement of transient electronic coherences in gas-phase molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding and Controlling the Formation of Nonradiative Defects in Blue Organic Triplet Emitters

Phosphorescent organic light-emitting devices (PHOLEDs) suffer from destructive molecular processes due to triplet-polaron and triplet-triplet annihilation. These processes are energetically driven and hence are particularly active in decreasing the lifetime of blue PHOLEDs. It has recently been shown that increasing triplet radiative rates via the Purcell effect effectively extends the device operational lifetime by reducing the triplet radiative lifetime, thus decreasing their density and the probability of triplet-annihilation reactions. We provide an analytical framework using Marcus theory to explain the observed, approximately exponential relationship between exciton energy and device lifetime. From transient drift-diffusion dynamics, we show that the Purcell effect reduces the exciton density in the steady state and increases the photoluminescent yield, thereby reducing defect generation rates and extending the device lifetime. We control the radiative rate of excitons in microcavities, thereby connecting the exciton energy and decay rates with the observed device lifetime. The device lifetime is shown to follow a power-law dependence on the Purcell factor ( PF m ) with m = 1.5 to 2.5, dependent on the TTA-to-TPA ratio and photoluminescence quantum yield. From our analysis, a fivefold increase in PF has the potential to extend the blue PHOLED lifetime by up to 2 orders of magnitude, making the blue PHOLED lifetime comparable to that of state-of-the-art green PHOLEDs. Published by the American Physical Society 2024

Zhao, Haonan (ORCID:0000000190584422)↗

Hsa_circ_0000515 is a novel circular RNA implicated in the development of breast cancer through its regulation of the microRNA‐296‐5p/CXCL10 axis

Cancer metastasis is a major cause of death among women afflicted with breast cancer (BC) and understanding the molecular processes involved is a major focus in BC research. Circular RNAs (circRNAs) have emerged as genomic regulatory molecules in carcinogenesis and metastasis; however, their role in BC is unclear. We characterized a novel circRNA, hsa_circ_0000515, in context of BC. We collected 340 cancerous tissues surgically resected from BC patients and found hsa_circ_0000515 was upregulated in BC tissues and associated with poor prognosis of BC. Silencing of hsa_circ_0000515 impaired cell cycle progression, cell proliferation, and invasion, attenuated inflammatory response, and reduced the proangiogenetic potential of BC cells. RNA pull‐down and dual‐luciferase reporter gene assays showed that hsa_circ_0000515 binds miR‐296‐5p, preventing it from repressing CXCL10 expression. We also observed that miR‐296‐5p inhibition or CXCL10 overexpression promoted cell cycle progression, restored proliferative, invasive and proangiogenetic abilities, and increased inflammatory response in MCF‐7 cells in the absence of hsa_circ_0000515. In vivo analyses showed that partial loss of hsa_circ_0000515 reduced the tumor growth of MCF‐7 cells in nude mice. The key findings from this study revealed that targeting hsa_circ_0000515 might be an effective strategy to combat BC.

Cai, Fenglin↗

Pre–T cell receptors topologically sample self-ligands during thymocyte β-selection

Self-discrimination, a critical but ill-defined molecular process programmed during thymocyte development, requires myriad pre–T cell receptors (preTCRs) and αβTCRs. Using x-ray crystallography, we show how a preTCR applies the concave β-sheet surface of its single variable domain (Vβ) to “horizontally” grab the protruding MHC α2-helix. By contrast, αβTCRs purpose all six complementarity-determining region (CDR) loops of their paired VαVβ module to recognize peptides bound to major histocompatibility complex molecules (pMHCs) in “vertical” head-to-head binding. Additionally, the preTCR topological fit ensures that CDR3β reaches the peptide’s featured C-terminal segment for pMHC sampling, establishing the subsequent αβTCR canonical docking mode. “Horizontal” docking precludes germline CDR1β- and CDR2β-MHC binding to broaden β-chain repertoire diversification before αβTCR-mediated selection refinement. Thus, one subunit successively attunes the recognition logic of related multicomponent receptors.

59 BASIC BIOLOGICAL SCIENCES↗

Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Visualizing microbial community dynamics within soil environments remains challenging. Here, we developed a custom-built SoilBox system that facilitates probing various changes occurring in microbial community development and molecular processes when exposed to environmental perturbations (e.g., temperature changes, drought, nutrient availability). Using confocal microscopy along with mass spectrometry imaging, we demonstrate the power of this system by correlating microbial growth and spatial metabolic information from soil communities under different moisture regimes.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular 9 Be + $p$ fusion reaction

Here, we study (nuclear) fusion reactions in beryllium. We argue that some are nuclear long-distance molecular processes of interest for low-energy nuclear reactions. For these, we develop a novel reaction model. We note a chain of reactions that can naturally arise in beryllium target created by nonequilibrium proton reactions.

Rafelski, Johann [Univ. of Arizona, Tucson, AZ (Un↗

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

Background: Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. Results: We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the “Reactome,” we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling. Conclusions: Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services.

59 BASIC BIOLOGICAL SCIENCES↗

SARS-CoV2 Docking Dataset for MLMol Language Model (50M)

This is a processed molecular dataset from this https://doi.ccs.ornl.gov/ui/doi/348 adding up to 50M molecules for the training and 486K molecules for the validation. Instructions on how to use/run/train this dataset can be found here: https://code.ornl.gov/candle/mlmol

Tsaris, Aristeidis↗

Retrospective Analysis of Geothermal Mineral Recovery and Domestic Resource Assessment - References

This reference database in RIS format contains all of the references that were collected as part of our retrospective analysis of geothermal mineral recovery (REE and Li) activities and domestic resource assessment. The outputs detail the chemistry and molecular processes used in lithium recovery from geothermal brines. The articles included include information about the study including more information on geothermal brines and the technologies used for recovering lithium from geothermal brines.

15 GEOTHERMAL ENERGY↗

Plasmonics-Enhanced Optical Imaging Systems for Bioenergy Research

This final report summarizes the key accomplishments of the project entitled “Plasmonics-Enhanced Optical Imaging Systems for Bioenergy Research”. The goal of this project is aimed at developing innovative and improved imaging instrumentation for visualization and quantitative characterization of biomarkers related to molecular processes and cellular function in living plants. This project focused on three specific aims: 1) Development of Advanced Multimodal Optical Sensing And Imaging Combinatory (MOSAIC) System for SERS biosensing and bioimaging. 2) Evaluation of MOSAIC technologies for sensing and imaging gene expression in plant systems using plasmonic nanoprobes. 3) Application of MOSAIC techniques to bioenergy research.

47 OTHER INSTRUMENTATION↗

Path Sampling for Rare Events Boosted by Machine Learning

The study by Jung et al. introduced Artificial Intelligence for Molecular Mechanism Discovery (AIMMD), a novel sampling algorithm that integrates machine learning to enhance the efficiency of transition path sampling (TPS). By enabling on-the-fly estimation of the committor probability and simultaneously deriving a human-interpretable reaction coordinate, AIMMD offers a robust framework for elucidating the mechanistic pathways of complex molecular processes. Here, this commentary provides a discussion and critical analysis of the core AIMMD framework, explores its recent extensions, and offers an assessment of the method’s potential impact and limitations.

Minh, Porhouy [Univ. of Minnesota, Minneapolis, MN↗

Fragmentation Dynamics of Fluorene Explored Using Ultrafast XUV-Vis Pump-Probe Spectroscopy

We report on the use of extreme ultraviolet (XUV, 30.3 nm) radiation from the Free-electron LASer in Hamburg (FLASH) and visible (Vis, 405 nm) photons from an optical laser to investigate the relaxation and fragmentation dynamics of fluorene ions. The ultrashort laser pulses allow to resolve the molecular processes occurring on the femtosecond timescales. Fluorene is a prototypical small polycyclic aromatic hydrocarbon (PAH). Through their infrared emission signature, PAHs have been shown to be ubiquitous in the universe, and they are assumed to play an important role in the chemistry of the interstellar medium. Our experiments track the ionization and dissociative ionization products of fluorene through time-of-flight mass spectrometry and velocity-map imaging. Multiple processes involved in the formation of each of the fragment ions are disentangled through analysis of the ion images. The relaxation lifetimes of the excited fluorene monocation and dication obtained through the fragment formation channels are reported to be in the range of a few tens of femtoseconds to a few picoseconds.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Syncytia in Fungi

Filamentous fungi typically grow as interconnected multinucleate syncytia that can be microscopic to many hectares in size. Mechanistic details and rules that govern the formation and function of these multinucleate syncytia are largely unexplored, including details on syncytial morphology and the regulatory controls of cellular and molecular processes. Recent discoveries have revealed various adaptations that enable fungal syncytia to accomplish coordinated behaviors, including cell growth, nuclear division, secretion, communication, and adaptation of the hyphal network for mixing nuclear and cytoplasmic organelles. In this review, we highlight recent studies using advanced technologies to define rules that govern organizing principles of hyphal and colony differentiation, including various aspects of nuclear and mitochondrial cooperation versus competition. We place these findings into context with previous foundational literature and present still unanswered questions on mechanistic aspects, function, and morphological diversity of fungal syncytia across the fungal kingdom.

59 BASIC BIOLOGICAL SCIENCES↗