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DOE OSTI2025

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Ribavirin targets sugar transporter 6 to suppress acquisition and transmission of rice stripe tenuivirus by its vector Laodelphax striatellus

Abstract BACKGROUND Rice stripe tenuivirus (RSV) is one of the most destructive pathogens of rice and other cereal crops. The virus is transmitted by the small brown planthopper (SBPH, Laodelphax striatellus ) in a circulative‐propagative manner. Thus, blocking transmission by the insect vector would provide an effective strategy to prevent epidemic outbreaks of the disease. RESULTS In this study, we explored the effect of ribavirin on acquisition and transmission of the virus by specifically inhibiting the expression of sugar transporter 6 (LsSt‐6), which was recently reported as a key vector component for RSV transmission. Ribavirin at the highest concentration tested (250 μmol L ‐1 ) significantly reduced RSV acquisition and transmission efficiency by SBPHs through inhibiting LsSt‐6 messenger RNA (mRNA) level. Survival of the model insect Spodoptera frugiperda cell line (Sf9) was 95.0 ± 2.2 and 85.6 ± 2.1% after exposure to 250 μmol L ‐1 ribavirin or 8‐azaguanine, respectively. Further study confirmed that 250 μmol L ‐1 ribavirin also significantly reduced LsSt‐6 mRNA and protein levels in Sf9 cells. However, 8‐azaguanine did not significantly inhibit viral infectivity and LsSt‐6 mRNA levels in SBPH or the Sf9 cell line. CONCLUSION This result provides evidence that ribavirin has the potential to disrupt LsSt‐6 expression but not others like viral RNAs to prevent acquiring RSV, which leads to less viral accumulation in SBPH tissues and thereby lower transmission efficiency. © 2020 Society of Chemical Industry

Hajano, Jamal‐U‐Ddin↗

DOE OSTI2022

Gravity as a portal to reheating, leptogenesis and dark matter

We show that a minimal scenario, utilizing only the graviton as an intermediate messenger between the inflaton, the dark sector and the Standard Model (SM), is able to generate simultaneously the observed relic density of dark matter (DM), the baryon asymmetry through leptogenesis, as well as a sufficiently hot thermal bath after inflation. We assume an inflaton potential of the form V(Φ) ∝ Φ k about the minimum at the end of inflation. The possibility of reheating via minimal gravitational interactions has been excluded by constraints on dark radiation for excessive gravitational waves produced from inflation. We thus extend the minimal model in several ways: i) we consider non-minimal gravitational couplings — this points to the parameter range of DM masses M N 1 ≃ 2–10 PeV, and right-handed neutrino masses M N 2 ≃ (5–20) × 10 11 GeV, and T RH ≲ 3 × 10 5 GeV (for k ≤ 20); ii) we propose an explanation for the PeV excess observed by IceCube when the DM has a direct but small Yukawa coupling to the SM; and iii) we also propose a novel scenario, where the gravitational production of DM is a two-step process, first through the production of two scalars, which then decay to fermionic DM final states. In this case, the absence of a helicity suppression enhances the production of DM and baryon asymmetry, and allows a great range for the parameters including a dark matter mass below an MeV where dark matter warmness can be observable by cosmic 21-cm lines, even when gravitational interactions are responsible for reheating. We also show that detectable primordial gravitational wave signals provide the opportunity to probe this scenario for T RH ≲ 5 × 10 6 GeV in future experiments, such as BBO, DECIGO, CE and ET.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Investigating Mercury’s Environment with the Two-Spacecraft BepiColombo Mission

The ESA-JAXA BepiColombo mission will provide simultaneous measurements from two spacecraft, offering an unprecedented opportunity to investigate magnetospheric and exospheric dynamics at Mercury as well as their interactions with the solar wind, radiation, and interplanetary dust. Many scientific instruments onboard the two spacecraft will be completely, or partially devoted to study the near-space environment of Mercury as well as the complex processes that govern it. Many issues remain unsolved even after the MESSENGER mission that ended in 2015. The specific orbits of the two spacecraft, MPO and Mio, and the comprehensive scientific payload allow a wider range of scientific questions to be addressed than those that could be achieved by the individual instruments acting alone, or by previous missions. These joint observations are of key importance because many phenomena in Mercury’s environment are highly temporally and spatially variable. Finally, examples of possible coordinated observations are described in this article, analysing the required geometrical conditions, pointing, resolutions and operation timing of different BepiColombo instruments sensors.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Development of a cosmic ray oriented trigger for the fluorescence telescope on EUSO-SPB2

The Extreme Universe Space Observatory on a Super Pressure Balloon 2 (EUSO-SPB2), in preparation, aims to make the first observations of Ultra-High Energy Cosmic Rays (UHECRs) from near space using optical techniques. EUSO-SPB2 will prototype instrumentation for future satellite-based missions, including the Probe of Extreme Multi-Messenger Astrophysics (POEMMA) and K-EUSO. The payload will consist of two telescopes. The first is a Cherenkov telescope (CT) being developed to quantify the background for future below-the-limb very high energy (E 10 PeV) astrophysical neutrino observations, and the second is a fluorescence telescope (FT) being developed for detection of UHECRs. The FT will consist of a Schmidt telescope, and a 6192 pixel ultraviolet camera with an integration time of 1.05 s. The first step in the data acquisition process for the FT is a hardware level trigger in order to decide which data to record. In order to maximize the number of UHECR induced extensive air showers (EASs) which can be detected, a novel trigger algorithm has been developed based on the intricacies and limitations of the detector. Finally, the expected performance of the trigger has been characterized by simulations and, pending hardware verification, shows that EUSO-SPB2 is well positioned to attempt the first near-space observation of UHECRs via optical techniques.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Activity model for 36 elements in Fe-Ni-Si-S-C liquids with application to terrestrial planet accretion and mantle geochemistry: New data for Ru, Re, Pt, Os, Ti, Nb, and Ta

Understanding siderophile element partitioning between metal and silicate melts under diverse conditions can be used to place important constraints on the materials and conditions of planetary accretion and core formation, as well as post core formation processes. However, the effects of Si on the partitioning and activity coefficients for these elements are not well known, despite Si likely being one of the dominant light elements in Earth’s core. To address this gap in understanding, we have undertaken a systematic study of the highly siderophile elements Re, Pt, Os, and Ru, and the refractory lithophile elements Nb, Ta and Ti at 1600 °C and 1 GPa, to derive epsilon interaction parameters for these elements in FeSi metallic liquids. Positive epsilon interaction parameters were measured for Nb, Ta, Ti, Ru, Re, Pt, and Os, indicating that dissolved Si in Fe liquids causes a decrease in their metal/silicate partition coefficients (or ‘silicophobic’ behavior). Furthermore, ε$_{Re, Os, or Ru}^{Si}$ > ε$_{Re, Os, or Ru}^{S}$ which means Si causes a larger decrease in D(metal/silicate) than S, and the chalcophile behavior expected from some elements will be completely masked by the presence of Si in a metallic liquid. The new parameters are used to update an activity model that now includes 36 siderophile elements in Fe-Ni-Si-S-C liquids (27 trace elements considered here). Systematic assessment of these 27 elements shows which have the strongest affinity for Si, C, and S, and also how activity coefficients for these elements would vary during accretion and core formation in Earth, Mars, and Mercury of widely differing fO 2 and core compositional conditions. The activity model is combined with new partitioning expressions for Mo, W, Cr, Re Ru, Pt, and Os and applied to aspects of post core formation mantle geochemistry of Earth, Mars, and Mercury. Our updated expressions show that the BSE Mo/W ratio can easily be achieved with metal/silicate partitioning during growth of the Earth, whereas Re, Os and Ru become lower than and highly fractionated compared with BSE values during core formation and accretion, and thus nearly 99% of their BSE abundances are likely contributed by late accretion. Ru isotopes should be a very good indicator of the source material for the late accretion. The high Pt/Os and Re/Os developed in a deepening magma ocean during the growth of the Earth, indicates 186 Os and 187 Os isotopes could be coupled if this ancient material remained isolated and subsequently became entrained in mantle plumes and measured in surficial lavas. The extent to which this occurred will be limited by the low Os content of this ancient material, thus requiring mixing as a major component in plume sources. Martian mantle Hf/W ratio stays low during accretion and core formation modelling, suggesting that W isotope anomalies are more likely due to solid/liquid silicate fractionation than to core formation. Finally, Ti contents measured by MESSENGER at Mercury’s surface can be explained by segregation of either a metallic core (IW-6 to -8) or metallic core + sulfide (IW-4 to -7.5) followed by mantle melting.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2025

Antibacterial ADP-ribosyl cyclase toxins inhibit bacterial growth by rapidly depleting NAD(P) +

In metazoans, enzymes belonging to the bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose (cADPr) hydrolase family regulate diverse cellular processes by synthesizing and hydrolyzing the intracellular second messenger cADPr, derived from the electron carrier NAD+. However, bacterial enzymes belonging to this family have not been characterized. Here, we identify a bacterial ADP-ribosyl cyclase that is associated with the type VII secretion system and functions as an antibacterial toxin. This enzyme, which we name Tac1, inhibits bacterial growth by rapidly hydrolyzing NAD+ and NADP+. We determine the X-ray crystal structure of Tac1 to a resolution of 1.4 Å, which reveals that this protein adopts the core catalytic fold of metazoan ADP-ribosyl cyclase enzymes such as CD38. Using a combination of biochemical and mutagenesis approaches, we identify catalytic residues within the active site of Tac1, which are responsible for the formation of a cADPr catalytic intermediate and subsequent hydrolysis of this intermediate into linear ADP-ribose. A bioinformatic analysis reveals that Tac1 is the founding member of a widespread family of bacterial ADP-ribosyl cyclase enzymes, many of which are associated with interbacterial conflict systems. We also identify enzymes in this family that are not associated with biological conflict systems and demonstrate that they produce cADPr as their major product rather than linear ADP-ribose, suggesting that these enzymes serve a biological function distinct from interbacterial antagonism. Together, these findings demonstrate that ADP-ribosyl cyclase/cADPr hydrolase enzymes function as toxins in diverse bacterial conflict systems and suggest that cADPr may play a previously overlooked role in bacterial physiology.

Colautti, Jake↗

DOE OSTI2020

Electromagnetic & Weak Probes: Experimental Overview

Electromagnetic and electroweak probes are the most versatile probes in the study of heavy-ion collisions. Produced at every stage in the evolution of QCD matter, its messengers are practically inert to the strongly interacting medium they travel through. In this contribution, I will discuss a selection of new results from experiments at the LHC, RHIC, and SIS facilities, spanning almost four orders of magnitude in beam energy. Finally, I will conclude with a brief overview of the experimental landscape in the near future.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Dense nuclear matter equation of state from heavy-ion collisions

The nuclear equation of state (EOS) is at the center of numerous theoretical and experimental efforts in nuclear physics. With advances in microscopic theories for nuclear interactions, the availability of experiments probing nuclear matter under conditions not reached before, endeavors to develop sophisticated and reliable transport simulations to interpret these experiments, and the advent of multi-messenger astronomy, the next decade will bring new opportunities for determining the nuclear matter EOS, elucidating its dependence on density, temperature, and isospin asymmetry. Among controlled terrestrial experiments, collisions of heavy nuclei at intermediate beam energies (from a few tens of MeV/nucleon to about 25 GeV/nucleon in the fixed-target frame) probe the widest ranges of baryon density and temperature, enabling studies of nuclear matter from a few tenths to about 5 times the nuclear saturation density and for temperatures from a few to well above a hundred MeV, respectively. Collisions of neutron-rich isotopes further bring the opportunity to probe effects due to the isospin asymmetry. However, capitalizing on the enormous scientific effort aimed at uncovering the dense nuclear matter EOS, both at RHIC and at FRIB as well as at other international facilities, depends on the continued development of state-of-the-art hadronic transport simulations. Furthermore, this white paper highlights the essential role that heavy-ion collision experiments and hadronic transport simulations play in understanding strong interactions in dense nuclear matter, with an emphasis on how these efforts can be used together with microscopic approaches and neutron star studies to uncover the nuclear EOS.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

The radioactive nuclei 26 Al and 60 Fe in the Cosmos and in the solar system

The cosmic evolution of the chemical elements from the Big Bang to the present time is driven by nuclear fusion reactions inside stars and stellar explosions. A cycle of matter recurrently re-processes metal-enriched stellar ejecta into the next generation of stars. The study of cosmic nucleosynthesis and this matter cycle requires the understanding of the physics of nuclear reactions, of the conditions at which the nuclear reactions are activated inside the stars and stellar explosions, of the stellar ejection mechanisms through winds and explosions, and of the transport of the ejecta towards the next cycle, from hot plasma to cold, star-forming gas. Due to the long timescales of stellar evolution, and because of the infrequent occurrence of stellar explosions, observational studies are challenging, as they have biases in time and space as well as different sensitivities related to the various astronomical methods. Here, we describe in detail the astrophysical and nuclear-physical processes involved in creating two radioactive isotopes useful in such studies, 26 Al and 60 Fe. Due to their radioactive lifetime of the order of a million years, these isotopes are suitable to characterise simultaneously the processes of nuclear fusion reactions and of interstellar transport. We describe and discuss the nuclear reactions involved in the production and destruction of 26 Al and 60 Fe, the key characteristics of the stellar sites of their nucleosynthesis and their interstellar journey after ejection from the nucleosynthesis sites. This allows us to connect the theoretical astrophysical aspects to the variety of astronomical messengers presented here, from stardust and cosmic-ray composition measurements, through observation of γ rays produced by radioactivity, to material deposited in deep-sea ocean crusts and to the inferred composition of the first solids that have formed in the Solar System. We show that considering measurements of the isotopic ratio of 26 Al to 60 Fe eliminate some of the unknowns when interpreting astronomical results, and discuss the lessons learned from these two isotopes on cosmic chemical evolution. This review paper has emerged from an ISSI-BJ Team project in 2017–2019, bringing together nuclear physicists, astronomers, and astrophysicists in this inter-disciplinary discussion.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Infrared Spectrum of the Pyrene Anion in the CH Stretching Region

In this work, we report the infrared spectrum of pyrene anion, measured using messenger tagging with up to three Ar atoms. We assign the spectrum using density functional theory and vibrational perturbation theory. Additionally, we discuss our results in the context of computed and experimental spectra from the literature as well as recent observations from astronomical sources, addressing the question whether PAH anions could contribute to the strong infrared emission bands at 3.29 μm from carbon- rich regions of space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Competition between Water–Water Hydrogen Bonds and Water–π Bonds in Pyrene–Water Cluster Anions

We present infrared spectra and density functional theory calculations of hydrated pyrene anion clusters with up to four water molecules. The experimental spectra were acquired using infrared Ar messenger photodissociation spectroscopy. Water molecules form clusters on the surface of the pyrene, forming hydrogen bonds with the pi-system. The structures of the water clusters and their interaction with the π-system are encoded in the OH stretching vibrational modes. Here, we find that the interactions between water molecules are stronger than they are between water molecules and the π-system. While all clusters show multiple conformers, three- and four-membered rings are the lowest energy structures in the larger hydrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Cryogenic “Iodide-Tagging” Photoelectron Spectroscopy: A Sensitive Probe for Specific Binding Sites of Amino Acids

This work showcases cryogenic and temperature-dependent “iodide-tagging” photoelectron spectroscopy to probe specific binding sites of amino acids using the glycine-iodide complex (Gly?I-) as a case study. Multiple Gly?I- isomers were generated from ambient electrospray ionization and kinetically isolated in a cryogenic ion trap. These structures were characterized with temperature-dependent “iodide-tagging” negative ion photoelectron spectroscopy (NIPES) where iodide was used as the “messenger” to interpret electronic energetics and structural information of various Gly?I- isomers. Accompanied by theoretical computations and Franck-Condon simulations, a total of five cluster structures have been identified along with their various binding motifs. This work demonstrates that “iodide-tagging” NIPES is a powerful general means for probing specific binding interactions in biological molecules of interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria

Synechococcus elongatus PCC 7942 is a model cyanobacterium for study of the circadian clock, photosynthesis, and bioproduction of chemicals, yet nearly 40% of its gene identities and functions remain unknown, in part due to limitations of the existing genetic toolkit. While classical techniques for the study of genes (e.g., deletion or mutagenesis) can yield valuable information about the absence of a gene and its associated protein, there are limits to these approaches, particularly in the study of essential genes. In this research, we developed a tool for inducible degradation of target proteins in S. elongatus by adapting a method using degron tags from the Mesoplasma florum transfer-messenger RNA (tmRNA) system. We observed that M. florum lon protease can rapidly degrade exogenous and native proteins tagged with the cognate sequence within hours of induction. We used this system to inducibly degrade the essential cell division factor, FtsZ, as well as shell protein components of the carboxysome. Our results have implications for carboxysome biogenesis and the rate of carboxysome turnover during cell growth. Lon protease control of proteins offers an alternative approach for the study of essential proteins and protein dynamics in cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Directing Nanoparticle Organization in Response to Diverse Chemical Inputs

Signaling cascades are crucial for transducing stimuli in biological systems, enabling multiple stimuli to regulate a downstream target with precisely controlled timing and amplifying signals through a series of intermediary reactions. Developing a robust signaling system with such capabilities would be pivotal for programming complex behaviors in synthetic DNA-based molecular devices. However, although “software” such as nucleic acid circuits could potentially be harnessed to relay signals to DNA-based nanostructure hardware, such explorations have been limited. Here, in this study, we develop a platform for transducing a variety of stimuli via messenger-mediated reactions to regulate the release and reloading of gold nanoparticles (AuNPs) in a 3D DNA framework. In the first step, an in vitro transcription circuit is engineered to sense and amplify chemical stimuli, including arbitrary DNA sequences and proteins, producing RNA. In the second step, the RNA releases the DNA-coated AuNPs from the DNA framework via a strand displacement reaction. AuNP reloading is controlled by a separate step driven by degradation of the RNA. Our platform holds promise for applications requiring dynamic multiagent control over DNA-based devices, offering a versatile tool for advanced molecular device engineering.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Spectral Properties and Energy Injection in Mercury's Magnetotail Current Sheet

Mercury's magnetotail hosts a thin and highly dynamic current sheet (CS), where magnetic reconnection and strong fluctuations frequently occur. Here, we statistically analyze magnetic field power spectra across 370 magnetotail CSs observed by MESSENGER. About 20% of the events are quasi-laminar, showing single power-law spectra, whereas ∼80% are turbulent, exhibiting a spectral break separating inertial and kinetic ranges. A dawn–dusk asymmetry is identified: inertial-range slopes are systematically shallower on the dawnside, whereas kinetic-range slopes are steeper, indicating more developed turbulence there, consistent with the higher occurrence of reconnection-related processes on the dawnside. Component analysis shows that the transverse components, orthogonal to the tail-aligned principal field ( B X ), display shallow slopes near −1 in the inertial range, suggesting energy injection at ion scales rather than a classical inertial range. These results demonstrate that Mercury's unique plasma environment fundamentally reshapes the initiation of turbulence and the redistribution of energy in the magnetotail.

Mercury↗

DOE OSTI2022

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ 1 -sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ 1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

59 BASIC BIOLOGICAL SCIENCES↗