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DOE OSTI2024

40th Eastern Regional Photosynthesis Conference

Photosynthesis has shaped global biochemistry and geochemistry in its production of almost all atmospheric oxygen, and almost every electron that supports the processes of life on Earth was extracted from water by the light-dependent reactions, many of which were then used to fix carbon in the dark reactions. To humans, that fixed carbon is the originator of all fossil fuels and a critical step in conversion of solar photons to human-usable energy. The Eastern Regional Photosynthesis Conference (ERPC) serves as a forum for advancement of science in this field. As a regional-level conference, it specializes in providing developmental opportunities for early-career researchers from undergraduates to pre-tenure professors, as well as broadening the field in terms of participating scholars and research approaches to produce new interdisciplinary collaborations. Funding from the Department of Energy is used to mitigate registration and attendance costs for junior (non-PI) researchers. The ERPC is one of the three regional conferences in the field of photosynthesis research in the United States, alongside the Western Photosynthesis Conference (currently in California) and the Midwestern Photosynthesis Conference (Turkey Run, Indiana). A longstanding incubator for scientific discourse, discovery, and collaborations, this conference has spawned many collaborations which led to Department of Energy-funded projects and brought two full generations of scientists into the field. In 2023 the landmark 40th such conference was held at the Woods Hole Marine Biological Laboratory in Massachusetts. The conference was held April 14th-16th, 2023. The majority of the total attendees are traditionally undergraduates, graduate students, and postdoctoral researchers, whose scientific development greatly benefits from conferences like these. Almost all talks besides the ones given by invited speakers were given by young scientists who benefited from this award. Many posters presented at this conference were also the work of junior scientists. This conference is many young scientists' first exposure to the photosynthesis research community and its primary goal is to provide a positive atmosphere for those attendees, as exemplified by the three poster sessions and dedicated interactions between senior and junior scientists. Additionally, this was the first year of a successful equitable outreach and speaker recruitment plan to provide fair representation at the conference in line with Department of Energy policies and mission. The central focus of the ERPC is the understanding of energy flow from photons to usable chemical products in both natural and artificial photosynthesis. We support the DOE-BES aim of understanding of the biochemical/biophysical processes of photosynthesis to inform new technology development and field applications. This year’s theme, “Photosynthesis Across Scales,” reflected the scope of work being done from the individual exciton to the crop scale. This research encompasses applied biology, chemistry, physics, and materials engineering. The aim of this conference is to present new discoveries, techniques, and questions which can be sourced from any of these disciplines and provide an audience which is broadly qualified to use or respond to these developments.

08 HYDROGEN↗

DOE OSTI2020

Microstructure and diffusion behavior of uranium fuel with minor additives

Fission product lanthanides in metallic fuels are known to cause adverse fuel-cladding chemical interaction (FCCI). Tin (Sn) and palladium (Pd) are being explored as the potential additives to reduce or mitigate lanthanide-induced FCCI by forming stable Sn-Ln and Pd-Ln compounds. The current study is an investigation of the fuel alloys, U–4Sn, U–4Sn-4Ln, U–4Pd, and U–4Pd-4Ln (wt. %), and their diffusion behaviors with Fe. Microstructural analysis was performed using scanning electron microscopy (SEM). Further, the binary phases in the UPd and USn alloys are identified as UPd 3 and suspected U 2 Sn, where U 2 Sn is unknown in the literature. The binary phases in the UPdLn alloy are identified as PdLn and Pd-rich Pd-Ln (Pd 4 Ln 3 and Pd 3 Ln 2 ), and in the USnLn alloy is SnLn. Diffusion of Fe with these binary phases is insignificant compared to the diffusion with U. The Ln-induced FCCI can be mitigated by the additives.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Preliminary Enhanced LAW Glass Formulation Algorithm

This report summarizes the Preliminary Enhanced Low-Activity Waste Glass Formulation Algorithm (GFA), its background information, and the calculations it performs. The Preliminary Enhanced Low-Activity Waste GFA is a tool developed in MATLAB to formulate glass for a given waste composition while attempting to maximize waste loading. It is intended for use at the Waste Treatment and Immobilization Plant, where nuclear waste will be vitrified into glass. The formulated glass is required to satisfy several processing and product quality constraints. In addition, calculations must account for associated uncertainties in constraint prediction and measurement. The GFA adheres to Pacific Northwest National Laboratory nuclear quality assurance procedures and has been validated and verified. In this second revision to the report, two constraints: the lithium and zirconia target constraints were amended to Table 3.1 and programmed into the algorithm. Additionally, three sections were added. Section 3.2.1 includes the Enhanced LAW Correlation Rules, an addition to the glass optimality criteria. Section 4.0 discusses a stepped process approach taken to ensure the algorithm can adequately react to differences between its recommended output and the actual measurements and transfers made during plant operation, and calculation of specific radionuclide concentrations. Section 5.2 describes changes to the user interaction with the algorithm program including the addition of a graphical user interface and compilation of the software.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

NuGraph2: A Graph Neural Network for Neutrino Event Reconstruction

Neutrino experiments are set to probe some of the most important open questions in physics, from CP violation and the nature of dark matter. The technology of choice for many of these experiments is the liquid argon time projection chamber (LArTPC). In current LArTPC experiments, reconstruction performance often represents a limiting factor for the sensitivity. New developments are therefore needed to unlock the full potential of LArTPC experiments. NuGraph2 is a state of the art Graph Neural Network for reconstruction of data in LArTPC experiments. NuGraph2 utilizes a heterogeneous graph structure, with separate subgraphs of 2D nodes (hits in each plane) connected across planes via 3D nodes (space points). The model provides a consistent description of the neutrino interaction across all planes. NuGraph2 is a multi-purpose network, with a common message-passing attention engine connected to multiple decoders with different classification or regression tasks. These include the classification of detector hits according to the particle type that produced them (semantic segmentation) and the separation of hits from the neutrino interaction from hits due to noise or cosmic-ray background. Additional decoders are being developed, performing tasks such as the regression of the neutrino interaction vertex position. Performance results will be presented based on publicly available samples from MicroBooNE. These include both physics performance metrics, achieving 95% accuracy for semantic segmentation and 98% classification of neutrino hits, as well as computational metrics for training and for inference on CPU or GPU. The status of the NuGraph integration in the LArSoft software framework will be presented, as well as initial studies about model interpretability and injection of domain knowledge.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

NuGraph2: A Graph Neural Network for Neutrino Event Reconstruction

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

NuGraph2: A Graph Neural Network for Neutrino Event Reconstruction

Neutrino experiments are set to probe some of the most important open questions in physics, from CP violation and the nature of dark matter. The technology of choice for many of these experiments is the liquid argon time projection chamber (LArTPC). In current LArTPC experiments, reconstruction performance often represents a limiting factor for the sensitivity. New developments are therefore needed to unlock the full potential of LArTPC experiments. NuGraph2 is a state of the art Graph Neural Network for reconstruction of data in LArTPC experiments [https://arxiv.org/abs/2403.11872]. NuGraph2 utilizes a heterogeneous graph structure, with separate subgraphs of 2D nodes (hits in each plane) connected across planes via 3D nodes (space points). The model provides a consistent description of the neutrino interaction across all planes. NuGraph2 is a multi-purpose network, with a common message-passing attention engine connected to multiple decoders with different classification or regression tasks. These include the classification of detector hits according to the particle type that produced them (semantic segmentation) and the separation of hits from the neutrino interaction from hits due to noise or cosmic-ray background. Additional decoders are being developed, performing tasks such as the regression of the neutrino interaction vertex position. Performance results will be presented based on publicly available samples from MicroBooNE. These include both physics performance metrics, achieving 95% accuracy for semantic segmentation and 98% classification of neutrino hits, as well as computational metrics for training and for inference on CPU or GPU. The status of the NuGraph integration in the LArSoft software framework will be presented, as well as initial studies about model interpretability and injection of domain knowledge.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2–25

We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2–11, 16–17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (D e 's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2–25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83–119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (D e 's) throughout the entire cluster range (n = 2–25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ~4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6–3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Commissioning the DIRC Detector and Searching for Axion-like Particles at GlueX

This thesis centers around problems in the study of the strong nuclear force. The GlueX DIRC, a Cherenkov radiation-based detector, was proposed to upgrade the particle identification capability of the GlueX experiment, which aims to perform quantitative tests of Quantum Chromodynamics in the nonperturbative regime by searching for and studying hybrid mesons. This thesis describes the construction, commissioning, reconstruction, and calibration of the GlueX DIRC detector. Originally proposed to solve the strong CP problem, axions and axion-like particles are hypothetical pseudoscalar particles found in many proposed extensions to the Standard Model of particle physics. This thesis presents a search for photoproduction of axion-like particles using data in photon-proton interactions collected by the GlueX experiment at Jefferson Laboratory in the $\gamma\gamma$ and $\pi^+\pi^-\pi^0$ final states of the axion-like particles. In addition, the Monte Carlo modeling of the strong interaction at low energies leads to challenges known as the event generator tuning problem. This thesis presents a novel approach to the Monte Carlo event generator tuning problem using Bayesian optimization.

Yang, Yunjie↗

DOE OSTI2023

Microstructural characterization of U-20Pu-10Zr-4Sb and U-20Pu-10Zr-4Sb-4Ln

Antimony is being investigated as a potential additive to metallic fuel to control fuel-cladding chemical interactions (FCCI). The most detrimental elements involved in FCCI are fission product lanthanides, leading to brittle intermetallics and low melting eutectic phases. Previous investigations of Sb as an additive focused on U-10Zr, in wt. %, as the fuel. The current investigation expands that to include Pu in the fuel. Here, two alloys, U-20Pu-10Zr-4Sb and U-20Pu-10Zr-4Sb-4Ln (wt. %, Ln=53Nd-25Ce-16Pr-6La) have been investigated using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to characterize the fuel as-cast microstructure and the microstructure after introduction of lanthanides. Sb reacts with Zr initially, forming Zr 2 Sb and Zr 5 Sb 3 , with as much as 20 at. % interstitial Pu present. In the presence of lanthanides, Sb forms Ln 4 Sb 3 with the lanthanides, containing ~14 at. % Pu. The Pu is substitutional for the lanthanides in the crystal lattice.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗

DOE OSTI2026

Time-dependent signals of new physics at the LHC

The Large Hadron Collider (LHC) is sensitive to signals of beyond the Standard Model physics through a variety of channels including missing energy and resonance searches. In most searches, the new physics and the Standard Model backgrounds are assumed to be invariant in time, up to systematic effects from the experiment. However, new physics with a time variation would provide an additional handle to separate signal from background. Such a time variation may come from ultralight dark matter coupling to an oscillating background field. In this paper, we consider an interaction of dark matter with quarks and an additional heavy particle, and show that the sensitivity of a search that uses timing information at the LHC can be up to a factor of two stronger compared to one that does not use time information.

Fieg, Max H. [Fermilab] (ORCID:0000000270276921)↗

DOE OSTI2024

Non-Electricity Based Renewable Fuels: Theory and Computation for Solar Thermochemical Hydrogen

Dominated by photovoltaics and wind, current renewable energy sources generate mostly electricity, but 80% of the global final energy consumption occurs in form of fuels. Therefore, direct solar fuel generation would be a major breakthrough for the energy transition. Solar thermochemical hydrogen (STCH) is one of the very few potential routes towards scalable renewable fuels, but currently suffers from lack of an oxide working material that could optimally perform energy conversion within the thermodynamic boundary conditions. Theory and computation can contribute in two distinct ways, through materials search and discovery, but also by providing detailed mechanistic models for specific systems so to advance our understanding of possible design strategies. To enable high-throughput materials screening, we developed a defect graph neural network (dGNN) machine learning approach,[1] which accelerates the prediction of defect formation energies by replacing the tedious density functional theory (DFT) supercell calculations for all possible defect sites. This approach enables high-throughput database screening of oxides, which was integrated with thermodynamic modeling to extract the reduction entropies as additional selection criterion for STCH. Once potential candidate materials are identified, detailed models can guide materials design by predicting performance characteristics. One challenge is to quantitatively predict thermochemical equilibria at high concentrations when the redox active defects start to interact with each other, thereby impeding the formation of additional defects. Introducing a model for the free energy of defect interaction, parametrized on the basis of DFT data, we simulated the complete STCH redox cycle for (Sr,Ce)MnO3 alloys, achieving near-quantitative agreement with experimental data.[2] The analysis of these simulations reveals how defect interactions diminish the reduction entropy and H2 yield, suggesting to include these interactions in design considerations. Finally, we revisit the popular van't Hoff method for analyzing reduction enthalpies and entropies. This method is not ideal, as it involves a temperature-dependent convolution of gas-phase and solid-state entropies, causing uncertainties in the same order of magnitude as the physical quantities of interest. To avoid this problem, we suggest a simple alternative approach which can be applied to experimental and simulated data alike.

first-principles calculations↗

DOE OSTI2023

Dramatic relativistic effects on the ns dipole angular distribution asymmetry parameter, β ns , of heavy and superheavy elements

A theoretical study of the dipole photoelectron angular distribution asymmetry parameter, β, of the 6s, 5s and 4s subshells has been conducted for a range of closed-shell heavy, Hg (Z = 80), Rn (Z = 86), Ra (Z = 88) and superheavy, No (Z = 102), Cn (Z = 112), Og (Z = 118), Ubn (Z = 120) elements to understand the deviation of β from the nonrelativistic value of 2 owing to relativistic effects. It was found that the deviation, strongest in Cooper minimum regions, persists over all energy for all ns subshells, and the deviations increase with Z. Furthermore, three levels of relativistic calculations were performed in order to pinpoint the particular interactions responsible for the details of the behavior of the ns β's as functions of energy, n, and Z and, in addition to the effects of the (relativistic) spin–orbit interaction, interchannel coupling was found to be of crucial importance in the determination of the β parameter in most of the situations studied.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Elucidating the factors controlling the methanol synthesis from CO 2 on ZnPd-ZnO/TiO 2 catalysts prepared by direct/inverse impregnation

The direct hydrogenation of CO 2 to methanol over supported ZnPd intermetallic catalysts remains a challenge due to the complex nature of the active sites, which are highly dependent on both the dispersion of ZnPd intermetallics and their proximity to ZnO. This study investigates the effect of the Pd and Zn incorporation order on methanol synthesis over TiO 2 -supported ZnPd catalysts. Catalysts were prepared via direct (Pd/Zn), inverse (Zn/Pd), and co-impregnation (Pd+Zn) methods using anatase TiO 2 as the support. Comprehensive characterization by XRD, HRTEM, CO-DRIFTS and XPS revealed that the formation of small and crystalline intermetallic β-ZnPd particles and their interaction with ZnO/ZnO x depends on the sequence of Pd and Zn incorporation. It was found that, under the reaction conditions, the ZnO x species plays a critical role in facilitating the formation of the intermetallic ZnPd through the interactions between Pd and ZnO x . In addition, ZnO x species have also been shown to modulate key catalytic properties, such as CO 2 activation and methanol selectivity. Specifically, the ZnPd/Pd surface ratio, determined by Pd dispersion and proximity to ZnO/ZnO x , was shown to determine the methanol production from CO 2 directly or via a CO intermediate. The Pd/Zn catalyst showed superior selectivity due to the in-situ formation of intermetallic species facilitated by Pd-ZnO x interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Not all platinum surfaces are the same: Effect of the support on fundamental properties of platinum adlayer and its implications for the activity toward hydrogen evolution reaction

The adsorption of atomic hydrogen on a platinum monolayer supported on orthorhombic Mo 2 C(100) surface has been investigated, considering different hydrogen surface coverages. Calculations have been performed using density functional theory with the Perdew-Burke-Ernzerhof exchange correlation functional and a D3 Van der Waals corrections. The theoretical insight has been gained into atomic hydrogen interaction with Pt monolayer, supported on both molybdenum and well-studied tungsten carbide, and considering hydrogen surface coverage. Fundamental properties of Pt adlayer depend on the support, affecting hydrogen evolution activity of the resulting systems. At low hydrogen coverage all systems, with the exception of Pt supported on the molybdenum-terminated Mo 2 C, adsorb H comparably to a pristine Pt(111) surface and their high activity for the hydrogen evolution reaction is predicted. Additionally, at higher coverages supported Pt monolayers interact with atomic hydrogen unlike the Pt(111), suggesting that the activity of the supported and unsupported platinum toward hydrogen evolution reaction have different origins. Furthermore, the position of the supported platinum monolayers on the volcano curve is a function of the surface coverage, more so than for extended metal surfaces. Therefore, hydrogen surface coverage is a key variable to understand the catalytic potential, approaching towards an improved model for screening of electrocatalytic systems.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Disulfonated Poly(arylene ether sulfone) Random Copolymers Containing Hierarchical Iptycene Units for Proton Exchange Membranes

Two series of disulfonated iptycene-based poly(arylene ether sulfone) random copolymers, i.e., TRP-BP (triptycene-based) and PENT-BP (pentiptycene-based), were synthesized via condensation polymerization from disulfonated monomer and comonomers to prepare proton exchange membranes (PEMs) for potential applications in electrochemical devices such as fuel cell. To investigate the effect of iptycene units on membrane performance, these copolymers were systematically varied in composition (i.e., iptycene content) and the degree of sulfonation (i.e., 30–50%), which were characterized comprehensively in terms of water uptake, swelling ratio, oxidative stability, thermal and mechanical properties, and proton conductivity at various temperatures. Comparing to copolymers without iptycene units, TRP-BP and PENT-BP ionomers showed greatly enhanced thermal and oxidative stabilities due to strong intra- and inter-molecular supramolecular interactions induced by hierarchical iptycene units. In addition, the introduction of iptycene units in general provides PEMs with exceptional dimensional stability of low volume swelling ratio at high water uptakes, which is ascribed to the supramolecularly interlocked structure as well as high fractional free volume of iptycene-based polymers. It is demonstrated that the combination of high proton conductivity and good membrane dimension stability is the result of the synergistic effects of multiple factors including free volume (iptycene content), sulfonation degree, hydrophobicity, and swelling behavior (supramolecular interactions).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Identification of recG genetic interactions in Escherichia coli by transposon sequencing

ABSTRACT Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli , the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing to identify recG genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the dam , uvrD , rnhA , radA , and rep genes. The conditional importance of these five genes in cells lacking recG was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with uvrD, rep, and radA , but not rnhA or dam ) were suppressed by deletion of recF or recO , indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a recG deletion when combined with dam , uvrD , radA , or rnhA deletions but not with rep . The results reinforce the idea of RecG as a general genome guardian. RecG has at least two functions. It plays an important role in the resolution of joint molecules behind the fork, formed during post-replication gap repair. RecG is also required to suppress genome over-replication caused by unscheduled replication initiation at R-loops, at double-strand breaks caused by dam inactivation, and during replication termination. IMPORTANCE DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the recG gene, which renders Escherichia coli cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported recG genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Robust resonator-assisted ZZ cancellation in superconducting quantum processors

Strong qubit interactions are essential for faster two-qubit gates, but they often come with undesirable ZZ interactions that limit gate fidelity. Existing methods to mitigate these interactions, such as flux-tunable couplers, can introduce additional noise and complexity. In contrast, our work presents a simpler, more robust approach using a driven resonator to cancel the static ZZ interaction between qubits [1]. The experiment was performed on a revised 9-qubit quantum processing unit from Rigetti, developed in collaboration with SQMS scientists. We validate the resonator-induced-phase (RIP) interaction, where an off-resonant drive on the resonator dynamically cancels ZZ coupling. This marks an important step toward high gate fidelities. We also explore the entangling gates enabled by this coupling scheme, focusing on minimizing gate duration and qubit decoherence while maintaining effective ZZ cancellation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗