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DOE OSTI2023

Controlling Molecular Structure and Spin with Multiconfigurational Quantum Chemistry (Final Technical Report)

For many first-row transition metal complexes, structure-property relationships can be obtained from high-level molecular geometry optimizations and subsequent electronic structure studies. The project funded under this award utilized newly implemented fully internally contracted (FIC) nuclear gradients for extended multi-state (XMS) complete active space second-order multireference perturbation theory (CASPT2) to explore geometry changes in first-row transition metal coordination complexes. At the start of the project, only one full geometry optimization using FIC-CASPT2 analytical gradients had been reported (J. Chem. Theory Comput., 2016, 12 (8), 3781), and many open-questions regarding the performance and achievable accuracy in applying such computations to larger complexes persisted. Key deliverables in the report include the implementation of the numerical Hessian and subsequent vibrational analysis in the BAGEL program package. This includes both full Hessian vibrational analysis (FHVA) and a partial Hessian vibrational analysis (PHVA). The latter of which allows us to reduce the significant cost of computing the vibrational frequencies in a large molecule by focusing on the modes of highest interest. The gradient code also proved useful in the development of an approach to improve the Hubbard-U correction by removing bias in predicting spin-splitting in Fe(II) complexes via plane-wave density functional theory (DFT). Finally, we showed for three families of complexes (spin-crossover (SCO) complexes, metallocorroles complexes, and those with metal-metal bonds) that CASPT2 can result in good molecular geometries and established best practices in undertaking this work. We are now using this approach in collaborative projects with experimental groups, which would not have been possible at the start of this project. A common theme also arose through this work that static and dynamic correlation must be recovered in a balanced way to yield quantitative results. By systematically varying how both effects were included, we were able to make key chemical insights. This work supported the training of two postdoctoral scholars, one graduate student, and one undergraduate student in applying high-level wavefunction based methods to challenging systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Experimental validation of universal plasma blob formation mechanism

Anomalous plasma transport in the boundary region of a tokamak plasma is commonly associated with the formation and evolution of coherent density structures known as blobs. Recently, a theory for a universal mechanism of plasma blob formation has been put forward. It is based on a breaking process of a radially elongated streamer due to poloidal and radial velocity shears. The theory is well supported by two-dimensional and three-dimensional numerical simulation results but lacks experimental validation. Here, we report the first ever experimental validation of this universal criterion by testing it against NSTX data on blobs obtained using the gas-puff imaging diagnostic. It is found that the criterion is widely satisfied in most L-mode discharges and may explain the significantly larger number of blob events. We also validate the theoretical criterion against ADITYA Langmuir probe data taken in the scrape-off layer region.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Gigahertz-frequency acousto-optic phase modulation of visible light in a CMOS-fabricated photonic circuit

Optical phase modulators operating at visible wavelengths are essential components for photonic technologies such as those for quantum control, communications, and laser ranging. However, they remain challenging to implement in scalable, integrated platforms capable of handling high optical powers. Here we present a visible-light, gigahertz-frequency acousto-optic phase modulator, fabricated on a 200-mm wafer in a volume CMOS foundry, that supports greater than 500 mW of optical power at 730 nm. The device combines a piezoelectric transducer and a photonic waveguide within a single, wavelength-scale structure that confines both a propagating optical mode and an electrically excitable breathing-mode mechanical resonance. By tuning the device’s geometry to optimize the optomechanical interaction, we achieve modulation depths up to 4.85 rad with 80 mW of applied microwave power at 2.31 GHz in a 2-mm-long device. This corresponds to resonant modulation figures of merit of V π = 1.32V and V π ⋅ L = 0.26V cm. To our knowledge, this is the lowest V π ever demonstrated in any acousto-optic phase modulator and represents a 15-fold reduction in V π and a 100-fold reduction in required microwave power relative to state-of-the-art modulators with high visible-wavelength power handling commonly employed in quantum control systems.

Freedman, Jacob M. [Univ. of Arizona, Tucson, AZ (↗

DOE OSTI2025

Mean-field dynamo as a quantum-like modulational instability

Presented here is a novel formulation of the mean-field dynamo as a modulational instability of magnetohydrodynamic (MHD) turbulence. This formulation, termed mean-field wave kinetics (MFWK), is based on the Weyl symbol calculus and allows describing the interaction between the mean fields (magnetic field and fluid velocity) and turbulence without requiring scale separation that is commonly assumed in the literature. The turbulence is described by the Wigner–Moyal equation for the spectrum of the two-point correlation matrix (Wigner matrix) of magnetic-field and velocity fluctuations and depicts the turbulence as an effective plasma of quantum-like particles that interact via the mean fields. Eddy–eddy interactions, which serve as ‘collisions’ in this effective plasma, are modelled within the standard minimal tau approximation to aid comparison with existing theories. Using MFWK, the non-local electromotive force is calculated for generic turbulence from first principles, modulo the limitations of MFWK. This result is then used to study, both analytically and numerically, the modulational modes of MHD turbulence, which appear as linear instabilities of the said effective quantum-like plasma of fluctuations. The standard α 2 -dynamo and other known results are reproduced as special cases. A new dynamo effect is predicted that is driven by correlations between the turbulent flow velocity and the turbulent current.

astrophysical plasmas↗

DOE OSTI2020

Bimetallics in a Nutshell: Complexes Supported by Chelating Naphthyridine-Based Ligands

Bimetallic motifs are a structural feature common to some of the most effective and synthetically useful catalysts known, including in the active sites of many metalloenzymes and on the surfaces of industrially relevant heterogeneous materials. However, the complexity of these systems often hampers detailed studies of their fundamental properties. To glean valuable mechanistic insight into how these catalysts function, this research group has prepared a family of dinucleating 1,8-naphthyridine ligands that bind two first-row transition metals in close proximity, originally designed to help mimic the proposed active site of metal oxide surfaces. Of the various bimetallic combinations examined, dicopper(I) is particularly versatile, as neutral bridging ligands adopt a variety of different binding modes depending on the configuration of frontier orbitals available to interact with the Cu centers. Organodicopper complexes are readily accessible, either through the traditional route of salt metathesis or via the activation of tetraarylborate anions through aryl group abstraction by a dicopper(I) unit. The resulting bridging aryl complexes engage in C-H bond activations, notably with terminal alkynes to afford bridging alkynyl species. In this work, the μ-hydrocarbyl complexes are surprisingly tolerant of water and elevated temperatures. This stability was leveraged to isolate a species that typically represents a fleeting intermediate in Cu-catalyzed azide-alkyne coupling (CuAAC); reaction of a bridging alkynyl complex with an organic azide afforded the first example of a well-defined, symmetrically bridged dicopper triazolide. This complex was shown to be an intermediate during CuAAC, providing support for a proposed bimetallic mechanism. These platforms are not limited to formally low oxidation states; chemical oxidation of the hydrocarbyl complexes cleanly results in formation of mixed valence Cu I Cu II complexes with varying degrees of distortion in both the bridging moiety and the dicopper core. Higher oxidation states, e.g. , dicopper(II), are easily accessed via oxidation of a dicopper(I) compound with air to give a Cu II 2 (μ-OH) 2 complex. Reduction of this compound with silanes resulted in the unexpected formation of pentametallic copper(I) dihydride clusters or trimetallic monohydride complexes, depending on the nature of the silane. Finally, development of an unsymmetrical naphthyridine ligand with mixed donor side-arms enables selective synthesis of an isostructural series of six heterobimetallic complexes, demonstrating the power of ligand design in the preparation of heterometallic assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Pb dimerization greatly accelerates charge losses in MAPbI 3 : Time-domain ab initio analysis

Metal halide perovskites constitute a new type of semiconducting materials with long charge carrier lifetimes and efficient light-harvesting. The performance of perovskite solar cells and related devices is limited by nonradiative charge and energy losses, facilitated by defects. Combining nonadiabatic molecular dynamics and time-domain density functional theory, we demonstrate that charge losses depend strongly on the defect chemical state. By considering an extra Pb atom in CH 3 NH 3 PbI 3 , which is a common defect in lead halide perovskites, we investigate its influence on charge trapping and recombination. In a chemically inert form as a Pb interstitial, the extra Pb atom has only a mild influence on charge recombination. However, if the extra Pb atom binds to a native Pb atom to form a dimer, the charge trapping and recombination are greatly accelerated because the Pb-dimer creates a localized midgap trap state that couples strongly to the perovskite valence band edge. Holes disappear from the valence band two orders of magnitude faster than in the pristine perovskite and recombine with conduction band electrons one order of magnitude faster. The simulations identify the phonon modes involved in the nonradiative charge trapping and recombination and highlight the importance of rapid decoherence within the electronic subsystem for long carrier lifetimes. The detailed atomistic analysis of the charge trapping and recombination mechanisms enriches the understanding of defect properties and provides theoretical guidance for improving perovskite performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Atomistic Materials Modeling of High-Pressure Hydrogen Interactions in Ethylene Propylene Diene Monomer (EPDM) Rubber

Elastomeric rubbers serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose-liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. Cyclic (de)pressurization is known to degrade these materials through the process of cavitation. This readily visible failure mode occurs as a fracture or rupture of the material and is due to the oversaturated gas localizing to form gas bubbles. Computational modeling in the Hydrogen Materials Compatibility Program (H-Mat), co-led by Sandia National Laboratories and Pacific Northwest National Laboratory, employs multi-scale simulation efforts to build a predictive understanding of hydrogen-induced damage in materials. Modeling efforts within the project aim to provide insight into how to formulate materials that are less sensitive to high-pressure hydrogen-induced failure. In this document, we summarize results from atomistic molecular dynamics simulations, which make predictive assessments of the effects of compositional variations in the commonly used elastomer, ethylene propylene diene monomer (EPDM).

08 HYDROGEN↗

DOE OSTI2021

Heat pulse propagation and anomalous electron heat transport measurements on the optimized stellarator W7-X

The optimized stellarator Wendelstein 7-X (W7-X) is designed to have an approximately quasi-isodynamic magnetic configuration with reduced neoclassical transport in comparison to a classical stellarator, and turbulent transport is expected to be a significant source of anomalous heat transport across the plasma minor radius. The ion temperature gradient driven mode and the trapped electron mode (TEM) are thought to be responsible for the ion-scale turbulence in W7-X plasmas with volume averaged pressure below 1%. In this work, the electron temperature gradient driven turbulence is shown to be a good candidate for the explanation of the observed electron heat flux, in the inner plasma region where the density gradient is weak (in the outer region, a relatively stronger density gradient would drive additional TEM turbulence). Further, the experimental electron heat transport measured during electron cyclotron resonant heating power and plasma density scans is compared to neoclassical predictions, and the stiffness in the electron heat transport measured during transient transport experiments is presented in three common magnetic configurations of W7-X. In low-(β) plasma discharges, the stiffness in the electron heat flux, quantified by the ratio of the heat pulse to power balance diffusivity, ${\chi }_{\mathrm{e}}^{\mathrm{H}\mathrm{P}}/{\chi }_{\mathrm{e}}^{\mathrm{P}\mathrm{B}}$, is measured to be less than 2, and trend downwards with increasing collisionality.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Sensitivity of surface temperature to oceanic forcing via q-Flux Green’s function experiments. Part III: asymmetric response to warming and cooling

Climate response is often assumed to be linear in climate sensitivity studies. However, by examining the surface temperature (TS) response to pairs of oceanic forcings of equal amplitude but opposite sign in a large set of local q-flux perturbation experiments with CAM5 coupled to a slab, we find strong asymmetry in TS responses to the heating and cooling forcings, indicating a strong nonlinearity intrinsic to the climate system examined. Regardless of where the symmetric forcing is placed, the cooling response to the negative forcing always exceeds the warming to the positive forcing, implying an intrinsic inclination towards cooling of our current climate. Thus, the ongoing global warming induced by increasing greenhouse gases may have already been alleviated by the asymmetric component of the response. The common asymmetry in TS response peaks in high latitudes, especially along sea ice edges, with notable seasonal dependence. Decomposition into different radiative feedbacks through a radiative kernel indicates that the asymmetry in the TS response is realized largely through lapse rate and albedo feedbacks. Further process interference experiments disabling the seasonal cycle and/or sea ice reveal that the asymmetry originates ultimately from the presence of the sea ice component and is further amplified by the seasonal cycle. The fact that a pair of opposite tropical q-flux forcings can excite very similar asymmetric response as a pair placed at 55°S strongly suggests the asymmetric response is a manifestation of an internal mode of the climate model system.

Liu, Fukai↗

DOE OSTI2023

Dirichlet-type absorbing boundary conditions for peridynamic scalar waves in two-dimensional viscous media

Construction of absorbing boundary conditions (ABCs) for nonlocal models is generally challenging, primarily due to the fact that nonlocal operators are commonly associated with volume constrained boundary conditions. Moreover, application of Fourier and Laplace transforms, which are essential for the majority of available methods for ABCs, to nonlocal models is complicated. In this paper, we propose a simple method to construct accurate ABCs for peridynamic scalar wave-type problems in viscous media. The proposed ABCs are constructed in the time and space domains and are of Dirichlet type. Consequently, their implementation is relatively simple, since no derivatives of the wave field are required. The proposed ABCs are derived at the continuum level, from a semi-analytical solution of the exterior domain using harmonic exponential basis functions in space and time (plane-wave modes). The numerical implementation is done using a meshfree collocation approach employed within a boundary layer adjacent to the interior domain boundary. The modes satisfy the peridynamic numerical dispersion relation, resulting in a compatible solution of the interior region (near-field) with that of the exterior region (far-field). The accuracy and stability of the proposed ABCs are demonstrated with several numerical examples in two-dimensional unbounded domains.

42 ENGINEERING↗

DOE OSTI2024

DEVELOPMENT OF PLASMA SIMULATION TOOL FOR THE ACCEL-ERATING CAVITIES

Plasma processing of superconducting radio frequency (SRF) cavities has shown an improvement in accelerating gradient by reducing the radiation due to field emission and multipacting. Plasma processing is a common tech-nique where the free oxygen produced by the plasma breaks down and removes hydrocarbons from surfaces. This increases the work function and reduces the second-ary emission coefficient. The hydrocarbon fragments of H2, CO, CO2, and H2O are removed from the system with the process gas which is flowing through the system. Here, we present COMSOL for the first time to simulate the plasma processing of an SRF cavity. In this work, we use Jefferson Lab's C75 SRF cavities design as our case study. Using simulation, we predict the condition of plasma ignition inside the SRF cavity. The simulation provides information about the optimal rf coupling to the cavity, mode for plasma ignition, choice of gas concen-tration, power, and pressure.

Senevirathne, I.↗

DOE OSTI2020

Formulation and solution approach for calibrating activity-based travel demand model-system via microsimulation

This study addresses the problem of calibrating utility-maximizing nested logit activity-based travel demand model-systems. After estimation, it is common practice to use aggregate measurements to calibrate the estimated model-system’s parameters prior to their application in transportation planning, policy making, and operations. However, calibration of activity-based model-systems has received much less attention. Existing calibration approaches are myopic heuristics in the sense that they do not consider the fundamental inter-dependencies among choice-models and do not have a systematic way to adjust model parameters. Also, other purely simulation-based approaches do not perform well in large-scale applications. In this study, we focus on utility-maximizing nested logit activity-based model-systems and calibrating aggregate statistics such as activity shares, mode shares, time-dependent & mode-specific OD flows, and time-dependent & mode-specific sensor counts. We formulate the calibration problem as a simulation-based optimization problem and propose a stochastic gradient-based solution procedure to solve it. The solution procedure relies on microsimulation to calculate expectations of the aggregate statistics of interest to the calibration problem. Additionally, we derive approximate analytical expressions for the gradient of the objective function —that are evaluated through microsimulation on mini-batches of the population. The proposed solution procedure is sensitive to the fundamental structure of the activity-based model-system and is non-myopic in considering the dependencies across its model components. The formulated optimization problem is non-convex, highly nonlinear, and potentially has multiple-minima. Lastly, we show —through a real-world application— that the proposed solution procedure outperforms other state-of-the-art purely simulation-based optimization approaches in terms of computational efficiency, stability, and convergence. We also compare various gradient-based solution algorithms to determine the best algorithm to update the parameters. This work has the potential to facilitate wider and easier application of activity-based model-systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Evidence for ground-state electron capture of K 40

Potassium-40 is a widespread, naturally occurring isotope whose radioactivity impacts estimated geological ages spanning billions of years, nuclear structure theory, and subatomic rare-event searches—including those for dark matter and neutrinoless double-beta decay. The decays of this long-lived isotope must be precisely known for its use as a geochronometer, and to account for its presence in low-background experiments. There are several known decay modes for potassium-40, but a predicted electron-capture decay directly to the ground state of argon-40 has never been observed. The existence of this decay mode impacts several fields, while theoretical predictions span an order of magnitude. Here we report on the first, successful observation of this rare decay mode, obtained by the KDK (potassium decay) Collaboration using a novel combination of a low-threshold x-ray detector surrounded by a tonne-scale, high-efficiency γ -ray tagger at Oak Ridge National Laboratory. A blinded analysis reveals a distinctly nonzero ratio of intensities of ground-state electron-captures ( I EC 0 ) over excited-state ones ( I EC * ) of I EC 0 / I EC * = 0.0095 ± stat 0.0022 ± sys 0.0010 (68% CL), with the null hypothesis rejected at 4 σ [Stukel et al. , Phys. Rev. Lett. 131 , 052503 (2023) ]. In terms of branching ratio, this unambiguous signal yields I EC 0 = 0.098 % ± stat 0.023 % ± sys 0.010 % , roughly half of the commonly used prediction. This first observation of a third-forbidden unique electron capture improves our understanding of low-energy backgrounds in dark-matter searches and has implications for nuclear-structure calculations. For example, a shell-model based theoretical estimate for the neutrinoless double-beta decay half-life of calcium-48 is increased by a factor of 7 - 2 + 3 . Our nonzero measurement shifts geochronological ages by up to a percent; implications are illustrated for Earth and solar system chronologies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Evaluation of Corrosion and Its Impact on the Mechanical Performance of Al–Steel Joints

Aluminum–steel joints are increasingly used in the automotive industry to meet the requirements for energy saving and emission reduction. Among various joining technologies, self-pierce riveting (SPR) and resistance spot welding (RSW) are two well-established technologies for fabricating dissimilar joints with stable and high mechanical performance. However, corrosion will occur in these joints inevitably due to different electrochemical properties, which can degrade the surface quality and the mechanical performance, such as strength. This paper presents a method of understanding the corrosion mechanisms in joining aluminum and steel. For this understanding, a hybrid method combining experimental observations, mechanical properties identification, and analytical approaches was used to assess the evolution of the impact of corrosion on the joining performance, such as traction separation curves. The study was conducted on common combinations used in the vehicles, e.g., a 1.2 mm thickness aluminum alloy (AA 6022) and 2.0 mm thickness hot deep galvanized steel (HDG HSLA 340) joined by SPR and RSW. After the fabrication of these joints, accelerated cyclic corrosion tests of up to 104 cycles were performed, which reproduced the environmental conditions to which a vehicle was exposed. By investigating the microstructural evolution within the joints, the corrosion mechanisms of SPR and RSW joints were revealed, including the initiation and propagation. Moreover, the intrinsic impact of the corrosion on the mechanical performance, including the strength, axial stiffness, and crashworthiness, was analyzed by performing a lap-shear test. It showed that as corrosion proceeds, the fracture modes and mechanical performance are affected significantly.

Chemistry↗

DOE OSTI2020

2020 IEEE PES Innovative Smart Grid Technologies Europe (ISGT-Europe)

Recent proliferation of distributed energy sources in distribution or sub-transmission systems necessitates close monitoring of these three-phase power grids which typically operate under unbalanced loading conditions. Unlike the transmission systems where the network equations are commonly based on the positive sequence component models, a detailed three phase model will have to be used in implementing network applications for these systems. In the specific case of the state estimator, where measurement and parameter errors may bias the solution, bad data and parameter error detection algorithms should also be incorporated. Implementing the state estimator and error detection algorithms for three-phase systems impose additional computational burden and modifications to the state estimation code. This paper proposes a practical solution to avoid these issues by using synchronized phasor measurements and modal decoupling. The previously developed parameter error detection algorithm based on the normalized Lagrange multipliers (NLM) test is applied to the measurements independently in each mode in parallel, not only saving CPU time but also avoiding new code development for a three-phase estimator. Different parameter error scenarios are created and tested to verify the effectiveness of the proposed error detection approach.

Khalili, Ramtin↗

DOE OSTI2024

Thermochemical Data for Furan-based Monomer Candidates for Frontal Ring-Opening Metathesis Polymerization (FROMP)

This dataset includes 471 furan-based monomer candidates for frontal ring-opening metathesis polymerization (FROMP) and relevant thermochemistry as calculated with density functional theory (DFT). The monomer candidates were combinatorically enumerated using Diels-Alder reactions of furan derivatives as dienes and four types of dienophiles (alkenes, alkynes, allenes, and benzynes). Common substituents were enumerated for the dienophile classes, and methyl substitution on the diene was explored. We used the SMILES arbitrary target specification (SMARTS) language to produce monomers and ring-opened structures from diene and dienophile precursor SMILES, and we studied the ring-opening reaction using a homodesmotic equation with ethene. RDKit conformers were initially generated from SMILES, then optimized with GFN2-xTB. The two conformers lowest in energy were then optimized with DFT using the wb97x-D3 functional, def2-TZVP basis set, and def2/J auxiliary basis set. Gibbs free energy corrections were obtained through frequency calculations. Structures with imaginary frequencies below -50 cm^{-1} were excluded from this work, and smaller imaginary modes were flipped to be positive for free energy calculations. Modes below 50 cm^{-1} were treated with the modified rigid rotor approximation, and all thermochemical values were calculated at T=200C. The CSV file contains the monomer SMILES, the free energy of reaction for Diels-Alder addition (G_DA_200), and the enthalpy of the ring-opening reaction (H_RO_200). All energies are given in kcal/mol. An interactive HTML is also included to visualize the monomers in this dataset.

Chua, Lauren↗

DOE OSTI2025

Measurements of differential charged-current cross sections on argon for electron neutrinos with final-state protons in MicroBooNE

This work presents single-differential electron-neutrino charged-current cross sections on argon measured using the MicroBooNE detector at the Fermi National Accelerator Laboratory. The analysis uses data recorded when the Neutrinos at the Main Injector beam was operating in both neutrino and antineutrino modes, with exposures of $2 \times 10^{20}$ and $5 \times 10^{20}$ protons on target, respectively. A selection algorithm targeting electron-neutrino charged-current interactions with at least one proton, one electron, and no pions in the final topology is used to measure differential cross sections as a function of outgoing electron energy, total visible energy, and opening angle between the electron and the most energetic proton. The interaction rate as a function of proton multiplicity is also reported. The total cross section is measured as [4.1 $\pm$ 0.4 (stat.) $\pm$ 1.2 (syst.)]$ $$\times 10^{-39} \mathrm{cm}^{2}/ \mathrm{nucleon}$. The unfolded cross-section measurements are compared to predictions from neutrino event generators commonly employed in the field. Good agreement is seen across all variables within uncertainties.

Abratenko, P. [Tufts U. (main)]↗

DOE OSTI2020

Bacterial Origin and Reductive Evolution of the CPR Group

The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. Here, these features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.

59 BASIC BIOLOGICAL SCIENCES↗