Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “INTERACTIONS”

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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Swine Host Protein Coiled-Coil Domain-Containing 115 (CCDC115) Interacts with Classical Swine Fever Virus Structural Glycoprotein E2 during Virus Replication

Interactions between the major structural glycoprotein E2 of classical swine fever virus (CSFV) with host proteins have been identified as important factors affecting virus replication and virulence. Previously, using the yeast two-hybrid system, we identified swine host proteins specifically interacting with CSFV E2. In this report, we use a proximity ligation assay to demonstrate that swine host protein CCDC115 interacts with E2 in CSFV-infected swine cells. Using a randomly mutated E2 library in the context of a yeast two-hybrid methodology, specific amino acid mutations in the CSFV E2 protein responsible for disrupting the interaction with CCDC115 were identified. A recombinant CSFV mutant (E2ΔCCDC115v) harboring amino acid changes disrupting the E2 protein interaction with CCDC115 was produced and used as a tool to assess the role of the E2–CCDC115 interaction in viral replication and virulence in swine. CSFV E2ΔCCDC115v showed a slightly decreased ability to replicate in the SK6 swine cell line and a greater replication defect in primary swine macrophage cultures. A decreased E2–CCDC115 interaction detected by PLA is observed in cells infected with E2ΔCCDC115v. Importantly, animals intranasally infected with 105 TCID50 of E2ΔCCDC115v experienced a significantly longer survival period when compared with those infected with the parental Brescia strain. This result would indicate that the ability of CSFV E2 to bind host CCDC115 protein during infection plays an important role in virus replication in swine macrophages and in virus virulence during the infection in domestic swine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Measurement of Neutron Multiplicity in Charged Current Neutrino Interactions on Oxygen

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a 26-ton gadolinium-doped water Cherenkov detector located 100~meters downstream in the Booster Neutrino Beam (BNB) at the Fermi National Accelerator Laboratory (Fermilab). Its primary goals are to (1) measure the neutron yield from $\nu_\mu$ interactions as a function of momentum transfer $Q^2$ so that neutrino-nucleus interaction models can be better constrained, and (2) demonstrate the power of novel, fast-timing detectors with the first deployment of Large Area Picosecond PhotoDetectors (LAPPDs). Current knowledge of neutrino-nucleus interactions fall short in modeling the topologies of such interactions, leading to inaccurate reconstruction of event kinematics such as particle energy, direction, and vertex. As a consequence, the accuracy of cross section measurements is impacted, which is necessary for precise physics measurements. Neutrons are an indication of inelasticity and affect the determination of the energy of the parent neutrino. Quantifying the neutron yield is a step towards reducing the associated uncertainties, and thus improving our understanding of these complex interactions and benefiting the next generation of long-baseline neutrino experiments. ANNIE will make use of LAPPDs to measure neutron multiplicity of CC-0$\pi$ $\nu_\mu$ interactions on oxygen, making it the first experiment to deploy an array of these photodetectors. Because the LAPPD is a novel photodetection technology, much customization is required to integrate it into existing electronics. The first half of this thesis covers the significant progress made towards the first deployment of the LAPPD system. From its test stand at Fermilab, the LAPPD system was systematically tested and put together until deployment readiness was achieved. I present my contributions to the design, fabrication, and testing of the waterproof housing and cables, and the commissioning of the LVHV board that powers the LAPPD and its readout electronics. These efforts brought the LAPPD system significantly closer to deployment, and eventually first data. The second half of this thesis presents the vertex and energy reconstruction algorithms developed to analysis the beam data with PMT-only information. While much progress has been made towards the deployment of LAPPDs, with several in the detector tank, efforts to integrate the LAPPD datastream are in progress. Thus, I developed a ring edge detection technique using PMT data to fit the muon vertex and determine its energy. The analysis in this thesis finds average neutron yields of $\Bar{n}_{data} = 0.452 \pm 0.039 (\text{stat}) \pm 0.27 (\text{sys})$ for a selection of muon neutrino candidates in the fiducial volume of ANNIE and corrected with an averaged neutron detection efficiency. An equivalent analysis for simulated beam data results in an average neutron yield of $\Bar{n}_{MC} = 0.582 \pm 0.018 (\text{stat}) \pm 0.25 (\text{sys})$. Future work includes application of efficiency corrections at a positional level, quantification of all systematic uncertainties, and neutron multiplicity measurements with other event topologies.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Validation of the NOνA experiment 2023-tuning on simulated neutrino-matter interactions

NOνA is a long-baseline neutrino oscillation experiment that utilizes a two-detector design to study the oscillations of muon neutrinos into electron neutrinos over a baseline of 810 km. The Near Detector (ND) measures the neutrino beam spectrum and composition before oscillation, which is then compared to the oscillated neutrino energy spectrum observed in the Far Detector (FD). In the ND, the neutrinos are detected through their interactions with the heavy target nuclei within the detector. NOνA employs the GENIE neutrino event generator for simulating these neutrino-nucleus interactions. However, the default GENIE prediction does not adequately reproduce the ND data. To address this, NOνA developed a tune of the neutrino interaction models within GENIE version 3:0:6 to minimize discrepancies between the simulated predictions and the observed data in the ND. This dissertation tests the NOνA’s 2023 tune of the GENIE neutrino cross-section simulations by performing a data/simulations comparison for the ND. The analysis employed datasets comprising $2.55\times10^{21}$ protons-on-target (POT) in neutrino beam mode and $1.14\times10^{21}$ POT in antineutrino beam mode. The NOνA tuning of neutrino-matter interaction simulations matches with ND data within the $1\sigma$ error band, overestimating muon neutrino and antineutrino charged current interactions by approximately 6 % and 9 %, respectively. Discrepancies were observed in the energy region dominated by Quasi-Elastic-like interactions. Systematic uncertainties associated with the modeling of the neutrino cross-section, particularly those pertaining Quasi-Elastic like interactions, contributed considerably to the overall error in the simulations. Furthermore, the reconstruction algorithm used in NOνA for particle classification demonstrated significant misidentifications between charged pions and protons, as well as a tendency to overlook additional pions or protons in multi-particle simulated events.

Cortés Parra, Camilo Andrés↗
DOE OSTI2023

Understanding hadronic interactions using advanced reconstruction techniques

ProtoDUNE-SP served as the prototype of the future Deep Underground Neutrino Experiment (DUNE). With a total liquid argon mass of 0.77 kt, it stood as the most extensive monolithic single-phase Liquid Argon Time Projection Chamber (LArTPC) ever constructed. Strategically located and operated at CERN, ProtoDUNE-SP benefited from a specialized charged-particle test beam, offering a momentum range of 0.3 - 7 GeV/c. This setup provided a unique opportunity to conduct in-depth studies on hadronic interactions within argon. Hadronic interactions play a fundamental role in neutrino physics, particularly in the intricacies of neutrino detection. We depend on analyzing the outcomes of these interactions to accurately determine both the flavor and energy of the interacting neutrinos. Pions, as one of the primary byproducts of neutrino interactions, are crucial for understanding the overall dynamics and kinematics of these processes. Accurately characterizing and understanding the interaction of pions with argon can significantly enhance the precision of neutrino simulations and measurements.Being a Liquid Argon Time Projection Chamber (LArTPC), ProtoDUNE-SP is distinguished by its ability to produce high-definition images of charged particles as they traverse through the detector's active volume. Yet, accurately reconstructing these particle interactions and determining their kinematic attributes remains a challenging task. The successes of deep learning in diverse domains, especially in image recognition, provide a promising approach for addressing this challenge in ProtoDUNE. This thesis discusses a measurement of the Piplus - argon inelastic cross section in the energy range of 2400 to 3000 MeV, using data taken by protoDUNE during the fall of 2018. Additionally, panoptic segmentation, a machine learning technique, is introduced and validated through its application in the reconstruction of the neutral pion rest mass. The aim is to showcase how these advanced methods can enhance the quality of event reconstruction.

Sarasty Segura, Carlos Eduardo↗
DOE OSTI2023

A centralized resource for bacterial–fungal interactions research

Research on bacterial-fungal interactions (BFIs) has revealed that fungi and bacteria frequently interact with one another within diverse ecosystems and microbiomes. Assessing the current state of knowledge within the field of BFI research, particularly with respect to what interactions between bacteria and fungi have been previously described, is very challenging and time consuming. This is largely due to a lack of any centralized resource, with reports of BFIs being spread across publications in numerous journals using non-standardized text to describe the relationships. To address this issue, we have developed the BFI Research Portal, a publicly accessible database of previously reported interactions between bacterial and fungal taxa to serve as a centralized resource for the field. Users can query bacterial or fungal taxa to see what members from the other kingdom have been observed as interaction partners. Search results are accompanied by interactive and intuitive visual outputs, and the database is a dynamic resource that will be updated as new BFIs are reported.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Controlling Dzyaloshinskii-Moriya interaction in a centrosymmetric nonsymmorphic crystal

Presence of the Dzyaloshinskii-Moriya (DM) interaction in limited noncentrosymmet ric materials leads to novel spin textures and exotic chiral physics. Emergence of DM interaction in centrosymmetric crystals could greatly enrich material realization. Here we show that an itinerant centrosymmetric crystal respecting a nonsymmorphic space group is a new platform for the DM interaction. Taking P4/nmm space group as an example, we demonstrate that the Ruderman-Kittel-Kasuya-Yosida (RKKY) in teraction induces the DM interactions, in addition to the Heisenberg exchange and the Kaplan-Shekhtman-Entin-wohlman-Aharony (KSEA) interaction. Here, the direction of DM vector depends on the positions of magnetic atoms in the real space, and the amplitude depends on the location of the Fermi surface in the reciprocal space. The diversity stems from the position-dependent site groups and the momentum-dependent electronic structures guaranteed by the nonsymmorphic symmetries. Our study unveils the role of the nonsymmorphic symmetries in affecting magnetism, and suggests that the nonsymmorphic crystals can be promising platforms to design magnetic interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Hyperfine and quadrupole interactions for Dy isotopes in DyPc 2 molecules

Nuclear spin levels play a vital role in understanding magnetization dynamics and implementation and control of quantum bits in lanthanide-based single-molecule magnets. We investigate the hyperfine and nuclear quadrupole interactions for 161 Dy and 163 Dy nuclei in anionic DyPc 2 (Pc=phthalocyanine) single-molecule magnets, using multiconfigurational ab initio methods (beyond density-functional theory) including spin–orbit interaction. The two isotopes of Dy are chosen because the others have zero nuclear spin. Both isotopes have the nuclear spin I =5/2, although the magnitude and sign of the nuclear magnetic moment differ from each other. The large energy gap between the electronic ground and first-excited Kramers doublets, allows us to map the microscopic hyperfine and quadrupole interaction Hamiltonian onto an effective Hamiltonian with an electronic pseudo-spin that corresponds to the ground Kramers doublet. Our ab initio calculations illustrate that the coupling between the nuclear spin and electronic orbital angular momentum contributes the most to the hyperfine interaction and that both the hyperfine and nuclear quadrupole interactions for 161 Dy and 163 Dy nuclei are much smaller than those for the 159 Tb nucleus in TbPc 2 single-molecule magnets. The calculated separations of the electronic-nuclear levels are comparable to experimental data reported for 163 DyPc 2 . We demonstrate that hyperfine interaction for the Dy Kramers ion leads to tunnel splitting (or quantum tunneling of magnetization) at zero field. This effect does not occur for TbPc 2 single-molecule magnets. The magnetic field values of the avoided level crossings for 161 DyPc 2 and 163 DyPc 2 are found to be noticeably different, which can be observed from the experiment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Density Functional Theory Guided Investigation of Ligand‐Induced Neptunyl‐Neptunyl Interactions

Abstract Actinyl‐actinyl interactions are particularly prevalent for the pentavalent neptunyl cation (Np(V)O 2 ) + where these interactions appear either as a T ‐ or D ‐shape (diamond‐shape). T ‐shaped interactions have been previously identified in high concentration Np(V) solutions containing simple anions (NO 3 − , ClO 4 − , Cl − ) whereas D ‐shaped have only been isolated in the solid‐state in the presence of carboxylate ligands. In this study, Density Functional Theory (DFT) calculations were paired with Raman spectroscopy to evaluate the formation of D ‐shaped interactions in the presence of aliphatic (R=H (formate), CH 3 (acetate), CH 2 CH 3 (propionate)) and aromatic (R=C 6 H 5 (benzoate), C 6 H 4 OH (4‐hydroxybenzoate), C 5 H 4 N (isonicotinate)) carboxylate ligands. DFT studies indicate that the Δ G to form hydrated T ‐ and D ‐shaped forms are not spontaneous but become so with the addition of the carboxylate ligands. Raman spectra of the Np(V) carboxylate solutions contained vibrational modes associated with the D ‐shaped interactions, but spectral changes observed over time indicate a dynamic system. Crystallization experiments from the Np(V) carboxylate systems confirmed the presence of D‐ shaped dimers for the aromatic carboxylates, suggesting that the choice of the anion in solution favors actinyl‐actinyl interactions even at low concentrations (≤20 mM) of Np(V).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

River–aquifer interactions enhancing evapotranspiration in a semiarid riparian zone: A modelling study

The hydrologic flows across the river–aquifer interface play an important role in groundwater dynamics and biogeochemical reactions within the subsurface; however, little is known about the effects of river–aquifer interactions on land surface processes. In this study, we developed a fully coupled three-dimensional (3D) land surface and subsurface model at a high resolution (~1 km) that accounts for high-frequency hydrologic exchange flow conditions to investigate how river–aquifer interactions modulate surface water budgets in the Upper Columbia-Priest Rapids watershed, a typical semiarid watershed located in the northwestern United States where river stage fluctuates in response to reservoir releases changing. Our results show that the spatiotemporal dynamics of river–aquifer interactions are highly heterogeneous, driven mainly by river-stage fluctuations. Adding 6.64 × 10 6 m 3 year –1 of water over the watershed from the river to groundwater owing to the lateral flow, river–aquifer interactions led to an increase in soil evaporation and transpiration supplied by higher soil moisture content, particularly in deeper subsurface. In a hypothetic future scenarios where a 5-m rise in river stage was assumed, the hydrologic flow exchange rates were intensified, resulting in higher surface water over the entire watershed. Overall, lateral flow induced by river–aquifer exchanges leads to an increase in evapotranspiration of ~75% in the historical period and of ~83% in the hypothetical future scenario. Finally, our study demonstrates the potential of coupled model as an effective tool for understanding river–aquifer–land surface interactions, and indicates that river–aquifer interactions fundamentally alter the water balance of the riparian zone for the semiarid watershed and will likely become more frequent and intense in the future under the effects of climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Utilizing plant synthetic biology to accelerate plant-microbe interactions research

Plant-microbe interactions are critical to ecosystem resilience and substantially influence crop production. From the perspective of plant science, two important focus areas concerning plant-microbe interactions include: 1) understanding plant molecular mechanisms involved in plant-microbe interfaces and 2) engineering plants for increasing plant disease resistance or enhancing beneficial interactions with microbes to increase their resilience to biotic and abiotic stress conditions. Molecular biology and genetics approaches have been used to investigate the molecular mechanisms underlying plant responses to various beneficial and pathogenic microbes. While these approaches are valuable for elucidating the functions of individual genes and pathways, they fall short of unraveling the complex cross-talk across pathways or systems that plants employ to respond and adapt to environmental stresses. Also, genetic engineering of plants to increase disease resistance or enhance symbiosis with microbes has mainly been attempted or conducted through targeted manipulation of single genes/pathways of plants. Recent advancements in synthetic biology tool development are paving the way for multi-gene characterization and engineering in plants in relation to plant-microbe interactions. Here, we briefly summarize the current understanding of plant molecular pathways involved in plant interactions with beneficial and pathogenic microorganisms. Then, we highlight the progress in applying plant synthetic biology to elucidate the molecular basis of plant responses to microbes, enhance plant disease resistance, engineer synthetic symbiosis, and conduct in situ microbiome engineering. Lastly, we discuss the challenges, opportunities, and future directions for advancing plant-microbe interactions research using the capabilities of plant synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bridging cognitive gaps between user and model in interactive dimension reduction

Interactive machine learning (ML) systems are difficult to design because of the "Two Black Boxes" problem that exists at the interface between human and machine. Many algorithms that are used in interactive ML systems are black boxes that are presented to users, while the human cognition represents a second black box that can be difficult for the algorithm to interpret. These two black boxes create cognitive gaps between the user and the interactive ML model when a user interacts with the system. In this paper, we identify several cognitive gaps that exist in a previously-developed interactive visual analytics (VA) system, Andromeda. These cognitive gaps that we are addressing in Andromeda are representative of common problems in other VA systems. Our goal with this work is to open both black boxes and bridge these cognitive gaps by making improvements to the original Andromeda system, including designing new visual features to help people better understand how Andromeda processes and interacts with data and improving the underlying algorithm so that the Andromeda system can better understand the intent of the user during the data exploration process. We evaluate our designs through both qualitative and quantitative analysis (i.e., user study and simulation analysis), and the results confirm that the improved Andromeda system outperforms the original version significantly in a series of high-dimensional data understanding tasks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Predicting and Understanding Non-Covalent Interactions Using Novel Forms of Symmetry-Adapted Perturbation Theory

Although sometimes derided as “weak” interactions, non-covalent forces play a critical role in ligand binding and crystal packing and in determining the conformational landscape of flexible molecules. Symmetry-adapted perturbation theory (SAPT) provides a framework for accurate ab initio calculation of intermolecular interactions and furnishes a natural decomposition of the interaction energy into physically meaningful components: semiclassical electrostatics (rigorously obtained from monomer charge densities), Pauli or steric repulsion, induction (including both polarization and charge transfer), and dispersion. This decomposition helps to foster deeper understanding of non-covalent interactions and can be used to construct transferable, physics-based force fields. Separability of the SAPT interaction energy also provides the flexibility to construct composite methods, a feature that we exploit to improve the description of dispersion interactions. Furthermore, these are challenging to describe accurately because they arise from nonlocal electron correlation effects that appear for the first time at second order in perturbation theory but are not quantitatively described at that level.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Process Interactions Can Change Process Ranking in a Coupled Complex System Under Process Model and Parametric Uncertainty

For a complex hydrologic system with multiple processes and process interactions, global sensitivity analysis is often used to identify important or influential parameters for model development and improvement. The identification is complicated by process model uncertainty, when a system process can be represented by multiple process models. This study develops a new total-effect process sensitivity index to identify influential processes under model uncertainty. This is done by extending Sobol's total-effect parameter sensitivity index for one system model to total-effect process sensitivity index for multiple system models to account for uncertainty in process models and model parameters. The total-effect process sensitivity index includes not only the first-order process sensitivity index for measuring the importance of individual processes but also higher-order indices that account for process interactions. The total-effect process sensitivity index can identify an influential process that itself and its interactions with other processes influence a model output. Here, the total-effect process sensitivity index is applied to two numerical examples: (a) Sobol's G*-functions with analytical solutions of first-order and total-effect process sensitivity indices, and (b) groundwater flow models with interactions between recharge, geology, and snowmelt processes. The second evaluation shows that, due to second-order and higher-order process interactions, the first-order and total-effect process sensitivity indices give different process ranking. It is thus necessary to estimate both first-order and total-effect process sensitivity indices to appreciate the difference between the first-order impact of a process alone and the overall total-effect impact of the process itself and its interactions with other processes on a model output.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The many-body electronic interactions of Fe(II)–porphyrin

Fe(II)–porphyrin complexes exhibit a diverse range of electronic interactions between the metal and macrocycle. Herein, the incremental full configuration interaction method is applied to the entire space of valence orbitals of a Fe(II)–porphyrin model using a modest basis set. A novel visualization framework is proposed to analyze individual many-body contributions to the correlation energy, providing detailed maps of this complex’s highly correlated electronic structure. Furthermore, this technique is used to parse the numerous interactions of two low-lying triplet states ( 3 A 2 g and 3 E g ) and to show that strong metal d–d and macrocycle π–π orbital interactions preferentially stabilize the 3 A 2 g state. d–π interactions, on the other hand, preferentially stabilize the 3 E g state and primarily appear when correlating six electrons at a time. Ultimately, the Fe(II)–porphyrin model’s full set of 88 valence electrons are correlated in 275 orbitals, showing the interactions up to the 4-body level, which covers the great majority of correlations in this system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Climate change–induced stress disrupts ectomycorrhizal interaction networks at the boreal–temperate ecotone

The interaction networks formed by ectomycorrhizal fungi (EMF) and their tree hosts, which are important to both forest recruitment and ecosystem carbon and nutrient retention, may be particularly susceptible to climate change at the boreal–temperate forest ecotone where environmental conditions are changing rapidly. Here, we quantified the compositional and functional trait responses of EMF communities and their interaction networks with two boreal ( Pinus banksiana and Betula papyrifera ) and two temperate ( Pinus strobus and Quercus macrocarpa ) hosts to a factorial combination of experimentally elevated temperatures and reduced rainfall in a long-term open-air field experiment. The study was conducted at the B4WarmED (Boreal Forest Warming at an Ecotone in Danger) experiment in Minnesota, USA, where infrared lamps and buried heating cables elevate temperatures (ambient, +3.1 °C) and rain-out shelters reduce growing season precipitation (ambient, ~30% reduction). EMF communities were characterized and interaction networks inferred from metabarcoding of fungal-colonized root tips. Warming and rainfall reduction significantly altered EMF community composition, leading to an increase in the relative abundance of EMF with contact-short distance exploration types. These compositional changes, which likely limited the capacity for mycelial connections between trees, corresponded with shifts from highly redundant EMF interaction networks under ambient conditions to less redundant (more specialized) networks. Further, the observed changes in EMF communities and interaction networks were correlated with changes in soil moisture and host photosynthesis. Collectively, these results indicate that the projected changes in climate will likely lead to significant shifts in the traits, structure, and integrity of EMF communities as well as their interaction networks in forest ecosystems at the boreal–temperate ecotone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Investigation of N 2 /O 2 plasma interaction with Pt-catalyst: effect of metastable adsorbates on product hysteresis

The coupling of catalysts and atmospheric-pressure plasma has the potential to improve the efficiency of certain catalytic reactions. Understanding the changes that the catalyst surface undergoes during exposure to plasma is key to improving plasma–catalytic performance. In this work, long term exposure of Pt–Al 2 O 3 powder catalyst to an Ar/N 2 /O 2 non-equilibrium atmospheric-pressure plasma-jet was investigated. Products produced by the interaction were analyzed downstream with Fourier-transform infrared spectroscopy while surface species were analyzed operandi with diffuse reflectance infrared Fourier transform spectroscopy. During exposure, the catalyst temperature was ramped cyclically between 100 °C and 350 °C to understand how substrate temperature affects the plasma–catalyst interaction. Long-lasting changes were revealed to take place on the catalyst surface during plasma exposure. At low temperatures, Pt–O and Pt–NO accumulate on the surface which react at elevated temperatures to form NO 2 . NO 2 initially appears to spill on to the Al 2 O 3 support as nitrites and nitrates instead of desorbing. Stable surface conditions are only achieved after prolonged plasma exposure, when nitrate sites on the Al 2 O 3 support are filled. By changing the catalyst temperature at various rates, the impact of total plasma species flux to the surface was analyzed. It was found that decreasing the heating rate increased the hysteresis in the pattern of NO 2 formation during thermal cycling. The variation with temperature demonstrates that plasma exposure results in a buildup of surface NO x and oxygen species which react or desorb at high temperatures. The observed changes are discussed from the generic viewpoint that a non-equilibrium plasma interacting with a catalyst at low temperature introduces metastable steady-state surface conditions. Upon heating above a threshold temperature, the introduced surface modifications can change either due to thermal effects, or, for a plasma environment, by additional interaction with the incident plasma species flux. The surface/material changes take place in a highly predictable fashion and after sufficient time above the threshold temperature reach a steady-state condition that is different from the transient behavior that is observed during initial heating. During cooling the plasma-surface interaction exhibits a different behavior than during heating, and this results in hysteresis of diverse observables. The metastability/hysteresis description appears quite generic and analogous to hysteresis behavior seen for different systems. Furthermore, it is expected to be useful for understanding the consequences of plasma–catalyst surface interactions for various systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform

Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Plasma Wall Interaction with 3-D Plasma Boundaries

The interaction of the edge plasma and the material surfaces is one of the most critical challenges on the path to harness fusion power as new, fundamental energy source. This challenge typically combines the thrust to reach high density, low temperature (detached) plasmas in front of the divertor target plates as well as understanding the plasma material interaction (PMI) in particular in this regime. The combination of both research thrusts represents an extraordinarily challenging subject encompassing spatial scales spanning nanometers to meters in all states of matter and across a broad energy range. Modeling capabilities, which help to interpret data from nowadays experiments and enable extrapolation to future devices are urgently required. This is in particular true for toroidal magnetic confinement devices with three-dimensional (3D) plasma boundaries. Such plasma boundary geometries occur in tokamaks, when small amplitude magnetic perturbations are used to stabilize the unruly edge plasma or in stellarators, that are inherently 3D plasma confinement devices. In this project, the impact of 3D plasma boundaries on the plasma material interaction (PMI) was assessed. This work focused on plasma boundary conditions, in which high-density conditions at the material surfaces yield mitigation of the otherwise immense heat and particle loads that these materials would see. These so-called high recycling and eventually detached plasma regimes are of great interest for future reactor operation. In the project, key features that are unique to 3D boundaries were explored in comparison to canonically assumed axisymmetric plasma edge situations in tokamaks. In particular, the relevance of the 3D boundary situation in the extrapolation to the plasma boundary solution at ITER, the next step fusion energy experiment under construction as a multi-national, world-wide large-science experiment in southern France, has been explored. The EMC3-EIRENE plasma edge fluid and kinetic neutral transport code has been advanced to cope with the challenging and unprecedented conditions in the ITER boundary plasma including 3D fields that are planned to be used to suppress harmful edge instabilities, the so-called edge localized modes. This is a vital integration challenge for ITER and the results from this grant have provide a leading capability for this assessment. It was shown that the detachment process in a 3D edge solution for ITER follows the recycling regimes that are known from axisymmetric solutions, but that multiple plasma exhaust channels connected to the material surfaces are established which feature individual recycling characteristics. Because these channels touch the material surfaces in the divertor in a 3D geometry, the compatibility with the plasma material interaction (PMI), including erosion and impurity generation has been found to be an important part of the integration challenge. To address this, the fully 3D plasma material interaction code ERO2 has been adapted to these ITER specific geometries and a homogeneous mixing model was implemented, that allows to consider the mixing of Be and Was used at ITER in the PMI modeling. This model enhancement has been used to study non-local migration of Be in the JET ITER like wall configuration and it has been shown that with this model such complex migration processes in ITER relevant plasma shapes and with ITER relevant plasma boundary conditions can be addressed. The combined modeling approach using EMC3-EIRENE as a plasma boundary transport code and the ERO2 specialized PMI model will be an asset for the continued preparations of ITER operation as well as for Fusion Pilot Plant efforts that have emerged in the U.S. during the evolution of this grant. The predictive capability of this numerical tool has been validated at the DIII-D US national fusion facility. Here, dedicated plasma edge diagnostics were implemented to measure the impurity household around a 3D edge plasma during ELM suppression by 3D fields. Dedicated experiments with local material probes using these diagnostics and the state-of-the-art suite of boundary measurements at DIII-D have shown that the 3D perturbation of the plasma edge that is excreted by such 3D control fields yield a perturbation of the plasma boundary flux structure and hence also of the resulting PMI. The 3D boundary plasma is composed out of helical magnetic flux channels that intersect the divertor targets at an angle relative to the main guiding field, i.e., the toroidal magnetic field component of the tokamak. A similar effect has been measured as well on limiter surfaces during the startup campaign at the new stellarator experiment Wendelstein 7-X. These experiments ad initial analysis with the ERO plasma material interaction model, suggested that the place of erosion for a given particle from the surface and its re-deposition can be different in such 3D field geometries yielding potentially a significant level of net-erosion. This is not the case for axisymmetric solutions, where it was shown in the past that the eroded particles are effectively re-deposited into gaps produced by erosion at the same position and hence the net-erosion levels are small. For ITER, the quest to suppress the ELMs and at the same time maintain the integrity of the divertor is an issue, which these fundamental findings will help to resolve. The coupling of this work to the extrapolation in the ITER program has been addressed by both the PI and the lead numerical scientist being ITER Science Fellows in the duration of the contract and forward. A second focus in the exploration of 3D boundary effects on tokamaks and stellarators has been set on the measurement of helium exhaust features with such 3D fields. This is important because He represents the ash of the fusion process and needs to be exhausted. It was shown that 3D field application compatible with suppression of ELMs yields an increase of the helium exhaust performance. The ratio of the effective helium confinement time over the energy confinement time was reduced by almost 50% which demonstrated that the impact of helium accumulation in the plasma core with respect to the confinement of energy to sustain the fusion reaction is significantly improved with such 3D control fields. It was shown that this is the case for tokamaks as well as stellarators. At the Large helical Device in Japan, a similar enhancement of the helium exhaust features when small amplitude additional 3D fields were applied was measured. This is an important additional function of 3D field application and its impact on ITER is presently being studied in combination with investigations of helium exhaust in 3D field geometries of stellarator devices.

3D plasma edge transport↗