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DOE OSTI2023

Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions

Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Measuring Muon Antineutrino Charged-Current Interactions Without Mesons in the Final State, in the NOvA Near Detector

NOvA is a long-baseline neutrino experiment based at Fermilab in the US, with the primary aim of measuring neutrino and antineutrino oscillations. This will enhance our understanding of electroweak interactions by measuring the neutrino mixing angles, CP-violating phase and neutrino mass ordering. To measure these oscillations, we first need to have a deep understanding of how neutrinos and antineutrinos interact with matter. Antineutrino interaction cross sections are, at present, particularly poorly constrained, and processes such as meson exchange currents are not well understood in the antineutrino sector. This analysis will develop a cross-section measurement of muon antineutrino interactions without mesons (e.g. pions or kaons) in the final state, in the NOvA near detector. A high-statistics, high-purity sample is obtained through a cut-based selection process implementing machine learning techniques. The sample is dominated by quasi-elastic and meson exchange current interactions which are sensitive to nuclear effects such as Final-State Interactions. The cross section will be extracted as a function of the incoming neutrino energy and the kinematics of the outgoing particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Continuing Analysis of Charge Current Interactions in ANNIE

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a gadolinium-loaded water Cherenkov detector on the Fermilab Booster Neutrino Beam (BNB).Using νμ in the energy range of 500 to 1000 MeV, ANNIE is designed to measure final-state neutrons.In this poster we will cover the ongoing analysis work exploring Charged-Current neutrino interactions. Charged-Current (CC) νμ interactions in this regime have uncertainties in the relative contributions of quasielastic and res- onance production. Together with intranuclear final-state interactions (FSI) and missing hadronic energy, these interactions drive important biases in neutrino energy reconstruction. ANNIE mit- igates these effects by combining muon kinematics from the downstream Muon Range Detector (MRD) with neutron identification via delayed gamma cascades from thermal captures on gadolin- ium. We characterize CC0π and Δ samples by measuring neutron multiplicity versus event topology and reconstructed kinematics, comparing neutron-tagged data to interaction-model predictions to probe resonance production and pion FSI/absorption

Fleming, Dylon [UC, Davis; Fermilab] (ORCID:000000↗

DOE OSTI2026

Measurement of charged-current quasi elastic-like and inclusive muon (anti-) neutrino interactions using NuMI beam the ICARUS detector

The ICARUS experiment, utilizing Liquid Argon Time Projection Chamber (LArTPC) technology, has been successfully taking physics data at Fermilab since June 2022. The experiment's primary objective is to function as the far detector of the Short Baseline Neutrino program (SBN), searching for hints of physics beyond three-flavour PMNS neutrino oscillations. ICARUS also offers other diverse physics capabilities, including searches beyond the standard model and measurements of cross-sections. In addition to being exposed to the Booster Neutrino (BNB) beamline of the SBN experiment, ICARUS sits 795 m downstream and 5.75 degrees off-axis from the NuMI beam line. Due to the off-axis angle between NuMI and ICARUS, coupled with contributions from both pion and kaon decays to neutrino fluxes, interactions of NuMI neutrinos within ICARUS can be detected over a range of several GeV in energy. Measurements of these interactions present unique opportunities to infer neutrino interaction cross sections on an argon nuclear target within an energy range that overlaps both the SBN oscillation search and a significant portion of the DUNE spectrum. This poster will summarize the current status of muon-neutrino and muon-antineutrino charged current inclusive cross section measurements in ICARUS using the FHC and RHC NuMI sample respectively. Such inclusive measurements provide robust benchmarks for the overall interaction rate and muon kinematics, with reduced dependence on hadronic final-state modeling. The measurement of the muon-antineutrino Argon charged current inclusive cross section is particularly exciting and highly relevant for DUNE, given the scarcity of antineutrino-Argon cross section measurements in the literature. In addition, this poster will highlight ICARUS's first measurement of muon-neutrino Argon charged current mesonless final states using both transverse kinematic imbalance (TKI) variables and muon-proton kinematic variables. These measurements provide sensitivity to nuclear effects, final-state interactions, and nucleon correlations in argon, offering important constraints for improving neutrino interaction modeling for upcoming DUNE.

Roy, Promita [Fermilab; Virginia Tech.]↗

DOE OSTI2024

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗

DOE OSTI2021

The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status

RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA–protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA–protein interactions in plants thus far and highlight the understanding of plant RNA–protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA–protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA–protein interactions for the study of gene regulation and RNA biology in plants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Effects of Dark Matter Self-interactions on Sagittarius and its Stream

This work explores how assumptions regarding the particle-physics nature of dark matter can alter the evolution of the Sagittarius (Sgr) dwarf spheroidal galaxy and its expansive stellar stream. We run a large suite of N-body simulations to model the infall of a spherically symmetric Sgr-like dwarf, exploring how the presence of dark matter self-interactions impacts its evolution. For a scattering cross section of σ/m χ = 30 cm 2 g −1 (at orbital velocity scales), these interactions result in significantly less stellar mass and little to no dark matter bound to the progenitor at the present day. To isolate the cause of this mass loss, we introduce a novel technique for controlling which pairs of dark matter simulation particles can interact. This enables us to identify ram-pressure evaporation—the scattering of satellite and host dark matter particles—as the primary source of the enhanced mass loss. The rapid disintegration of the Sgr progenitor when self-interactions are allowed alters some key properties of the resulting stellar stream, most dramatically suppressing the presence of a “spur” on the apocenter of the trailing stream arm that correlates with the mass of the satellite at last pericenter. We demonstrate how the effects on the Sgr system scale with the particular choice of self-interaction cross section, which affects the degree of ram-pressure evaporation. These findings generalize beyond the Sgr system, underscoring that dwarf stellar streams and dwarf galaxies with close passages may serve as sensitive probes for dark matter self-interactions.

Milky Way dark matter halo↗

DOE OSTI2024

Quantum Scales of Galaxies from Self-interacting Ultralight Dark Matter

We derive the characteristic scales for physical quantities of dwarf galaxies, such as mass, size, acceleration, and angular momentum, within the self-interacting ultralight dark matter (ULDM) model. Due to the small mass of ULDM, even minor self-interactions can drastically alter these scales in the Thomas-Fermi limit. We suggest that these characteristic scales are connected to mysteries of observed galaxies. Oscillation of ULDM field can explain the current cosmological density of dark matter. Many cosmological constraints suggest that the energy scale $\tilde{m}$ for self-interacting ULDM is typically of the order $10~eV$, whereas the mass $m$ for the non-interacting case is around $10^{-21}~eV$. Self-interacting ULDM provides the better explanation for cosmological observations than the non-interacting case.

Astrophysics of Galaxies (astro-ph.GA)↗

DOE OSTI2020

Using CESM-RESFire to understand climate–fire–ecosystem interactions and the implications for decadal climate variability

Large wildfires exert strong disturbance on regional and global climate systems and ecosystems by perturbing radiative forcing as well as the carbon and water balance between the atmosphere and land surface, while short- and long-term variations in fire weather, terrestrial ecosystems, and human activity modulate fire intensity and reshape fire regimes. The complex climate–fire–ecosystem interactions were not fully integrated in previous climate model studies, and the resulting effects on the projections of future climate change are not well understood. Here we use the fully interactive REgion-Specific ecosystem feedback Fire model (RESFire) that was developed in the Community Earth System Model (CESM) to investigate these interactions and their impacts on climate systems and fire activity. We designed two sets of decadal simulations using CESM-RESFire for present-day (2001–2010) and future (2051–2060) scenarios, respectively, and conducted a series of sensitivity experiments to assess the effects of individual feedback pathways among climate, fire, and ecosystems. Our implementation of RESFire, which includes online land–atmosphere coupling of fire emissions and fire-induced land cover change (LCC), reproduces the observed aerosol optical depth (AOD) from space-based Moderate Resolution Imaging Spectroradiometer (MODIS) satellite products and ground-based AErosol RObotic NETwork (AERONET) data; it agrees well with carbon budget benchmarks from previous studies. We estimate the global averaged net radiative effect of both fire aerosols and fire-induced LCC at –0.59±0.52 W m –2 , which is dominated by fire aerosol–cloud interactions (–0.82±0.19 W m –2 ), in the present-day scenario under climatological conditions of the 2000s. The fire-related net cooling effect increases by ~170 % to –1.60±0.27 W m –2 in the 2050s under the conditions of the Representative Concentration Pathway 4.5 (RCP4.5) scenario. Such considerably enhanced radiative effect is attributed to the largely increased global burned area (+19 %) and fire carbon emissions (+100 %) from the 2000s to the 2050s driven by climate change. The net ecosystem exchange (NEE) of carbon between the land and atmosphere components in the simulations increases by 33 % accordingly, implying that biomass burning is an increasing carbon source at short-term timescales in the future. High-latitude regions with prevalent peatlands would be more vulnerable to increased fire threats due to climate change, and the increase in fire aerosols could counter the projected decrease in anthropogenic aerosols due to air pollution control policies in many regions. We also evaluate two distinct feedback mechanisms that are associated with fire aerosols and fire-induced LCC, respectively. On a global scale, the first mechanism imposes positive feedbacks to fire activity through enhanced droughts with suppressed precipitation by fire aerosol–cloud interactions, while the second one manifests as negative feedbacks due to reduced fuel loads by fire consumption and post-fire tree mortality and recovery processes. These two feedback pathways with opposite effects compete at regional to global scales and increase the complexity of climate–fire–ecosystem interactions and their climatic impacts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Microphysics regimes due to haze–cloud interactions: cloud oscillation and cloud collapse

Abstract. It is known that aqueous haze particles can be activated into cloud droplets in a supersaturated environment. However, haze–cloud interactions have not been fully explored, partly because haze particles are not represented in most cloud-resolving models. Here, we conduct a series of large-eddy simulations (LESs) of a cloud in a convection chamber using a haze-capable Eulerian-based bin microphysics scheme to explore haze–cloud interactions over a wide range of aerosol injection rates. Results show that the cloud is in a slow microphysics regime at low aerosol injection rates, where the cloud responds slowly to an environmental change and droplet deactivation is negligible. The cloud is in a fast microphysics regime at moderate aerosol injection rates, where the cloud responds quickly to an environmental change and haze–cloud interactions are important. More interestingly, two more microphysics regimes are observed at high aerosol injection rates due to haze–cloud interactions. Cloud oscillation is driven by the oscillation of the mean supersaturation around the critical supersaturation of aerosol due to haze–cloud interactions. Cloud collapse happens under weaker forcing of supersaturation where the chamber transfers cloud droplets to haze particles efficiently, leading to a significant decrease (collapse) in cloud droplet number concentration. One special case of cloud collapse is the haze-only regime. It occurs at extremely high aerosol injection rates, where droplet activation is inhibited, and the sedimentation of haze particles is balanced by the aerosol injection rate. Our results suggest that haze particles and their interactions with cloud droplets should be considered, especially in polluted conditions.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1972

The interaction lengths of energetic pions and protons in iron

The interaction lengths of pions and protons in iron have been measured using an ionization spectrometer composed of alternating layers of iron and plastic scintillator. These measurements cover an energy range from 9.3 to 18 GeV. The interaction lengths were determined by accurate statistical analyses of the experimental data using the maximum likelihood method. The dependence of the interaction length on the parameters used to define an interaction was studied, and the results reported employ parameters chosen to minimize the percentage uncertainty in the interaction length. The mean interaction length of pions was found to be approximately 20% greater than that of protons.

Crannell, H.↗

NASA NTRS1973

Flowfield analysis for successive oblique shock wave interactions with a turbulent boundary layer

A computation procedure is described for predicting flow fields which develop when successive interactions between oblique shock waves and a turbulent boundary layer occur. Computations were carried out for axisymmetric internal flows at free stream Mach numbers = 3.82 and 2.82. The effect of boundary layer bleed was considered for the free stream Mach number = 2.82 flow. A control volume analysis is used to predict changes in the flow field across the interactions. Two bleed flow models were considered. A turbulent boundary layer program was used to compute changes in the boundary layer between the interactions. The results given are for flows with two shock wave interactions and for bleed at the second interaction site. In principle the method described may be extended to account for additional interactions. The predicted results are compared with measured results and are shown to be in good agreement when the bleed flow rate is low (on the order of 3 percent of the boundary layer mass flow), or when there is no bleed. As the bleed flow rate is increased, differences between the predicted and measured results become larger. Shortcomings of the bleed flow models at higher bleed flow rates are discussed.

Sun, C. C.↗

NASA NTRS1979

Space environmental interactions with spacecraft surfaces

Environmental interactions are defined as the response of spacecraft surfaces to the charged-particle environment. These interactions are divided into two broad categories: spacecraft passive, in which the environment acts on the surfaces and spacecraft active, in which the spacecraft or a system on the spacecraft causes the interaction. The principal spacecraft passive interaction of concern is the spacecraft charging phenomenon. The spacecraft active category introduces the concept of interactions with the thermal plasma environment and Earth's magnetic fields, which are important at all altitudes and must be considered the designs of proposed large space structures and space power systems. The status of the spacecraft charging investigations is reviewed along with the spacecraft active interactions.

Stevens, J. N.↗

NASA NTRS1979

Nonlinear interaction of waves in boundary-layer flows

First-order nonlinear interactions of Tollmien-Schlichting waves of different frequencies and initial amplitudes in boundary-layer flows are analyzed by using the method of multiple scales. For the case of two waves, a strong nonlinear interaction exists if one of the frequencies w2 is twice the other frequency w1. Numerical results for flow past a flat plate show that this interaction mechanism is strongly destabilizing even in regions where either the fundamental or its harmonic is damped in the absence of the interaction. For the case of three waves, a strong nonlinear interaction exists when w3 = w2- w1. This combination resonance causes the amplitude of the wave with the difference frequency w3 to multiply many times in magnitude in a short distance even if it is damped in the absence of the interaction. The initial amplitudes play a dominant role in determining the changes in the amplitudes of the waves in both of these mechanisms.

Nayfeh, A. H.↗

NASA NTRS1979

Space environmental interactions with spacecraft surfaces

The employment of large structures in space, which would be necessary in connection with a number of space missions and space activities currently being contemplated, might involve special problems as a result of the interactions of the structures with the charged particle environment. Such interactions would be particularly significant in the case of high operational voltages. A review is presented of possible interactions between spacecraft surfaces and charged-particle environments. The categories of spacecraft-environmental interactions are examined and a description of spacecraft charging interactions is presented. The status of charging investigation is considered, taking into account the environment, aspects of analytical modeling, materials characterization, materials development, space flight experiments, and design guidelines. High voltage surface-plasma interactions are also investigated.

Stevens, N. J.↗

NASA NTRS1979

Concepts leading to the IMAGE-100 hybrid interactive system

As LACIE Procedure 1 evolved from the Classification and Mensuration Subsystem smallfields procedures, it became evident that two computational systems would have merit-the LACIE/Earth Resources Interactive Processing System based on a large IBM-360 computer oriented for operational use with high computational throughput, and a smaller, highly interactive system based on a PDP 11-45 minicomputer and its display system, the IMAGE-100. The latter had advantages for certain phases; notably, interactive spectral aids could be implemented quite rapidly. This would allow testing and development of Procedure 1 before its implementation on the LACIE/Earth Resources Interactive Processing System. The resulting minicomputer system, called the Classification and Mensuration Subsystem IMAGE-100 Hybrid System, allowed Procedure-1 operations to be performed interactively, except for clustering, classification, and automatic selection of best acquisitions, which were offloaded to the LACIE/Earth Resources Interactive Processing System.

Mackin, T. F.↗

NASA NTRS1980

Viscous theory of surface noise interaction phenomena

A viscous linear surface noise interaction problem is formulated that includes noise production by an oscillating surface, turbulent or vortical interaction with a surface, and scattering of sound by a surface. The importance of viscosity in establishing uniqueness of solution and partitioning of energy into acoustic and vortical modes is discussed. The results of inviscid two dimensional airfoil theory are used to examine the interactive noise problem in the limit of high reduced frequency and small Helmholtz number. It is shown that in the case of vortex interaction with a surface, the noise produced with the full Kutta condition is 3 dB less than the no Kutta condition result. The results of a study of an airfoil oscillating in a medium at rest are discussed. It is concluded that viscosity can be a controlling factor in analyses and experiments of surface noise interaction phenomena and that the effect of edge bluntness as well as viscosity must be included in the problem formulation to correctly calculate the interactive noise.

Yates, J. E.↗