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Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Global properties of nuclei at finite-temperature within the covariant energy density functional theory

In stellar environments nuclei appear at finite temperatures, becoming extremely hot in core-collapse supernovae and neutron-star mergers. However, due to theoretical and computational complexity, most model calculations of nuclear properties are performed at zero temperature, while those existing at finite temperatures are limited only to selected regions of the nuclide chart. In this study we perform the global calculation of nuclear properties for even-even 8 ≤ Z ≤ 104 nuclei at temperatures in range 0 ≤ T ≤ 2 MeV. Calculations are based on the finite-temperature relativistic Hartree-Bogoliubov model supplemented by the Bonche-Levit-Vautherin vapor subtraction procedure. We find that near the neutron-drip line the continuum states have significant contribution already at moderate temperature T ≈ 1 MeV, thus emphasizing the necessity of the vapor subtraction procedure. Results include neutron emission lifetimes, quadrupole deformations, neutron-skin thickness, proton and neutron pairing gaps, entropy and excitation energy. Up to the temperature T ≈ 1 MeV, the nuclear landscape is influenced only moderately by the finite-temperature effects, mainly by reducing the pairing correlations. Here, as the temperature increases further, the effects on nuclear structures become pronounced, reducing both the deformations and the shell effects.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Expanding the Cage of 2D Bromide Perovskites by Large A-Site Cations

Two-dimensional (2D) halide perovskites have outstanding optoelectronic properties, and they feature a variety of organic cation spacers and cage A-site cations that can be incorporated into their structures. It has recently been reported that the Goldschmidt tolerance factor can be relaxed and expanded in iodide 2D perovskites. Bromide 2D perovskites, whose multilayer structures and optical properties are much less studied, provide a great platform for studying structure-property relationships for 2D perovskites with large Asite cations. Herein, we report the synthesis and structure of three new 2D bromide perovskites-(BA)(2)(MHy)(2)Pb3Br10 (BA, butylammonium; MHy, methylhydrazinium), (BA)(2)(EA)(2)Pb3Br10 (EA is ethylammonium), and (BA)(2)(DMA)Pb2Br7 (DMA is dimethylammonium). We compared them with other 2D perovskites with different A-site cations but with the same spacer and layer thickness. Single-crystal structures show that the Pb-Br bonds are elongated to accommodate the large A-site cations. Additionally, the octahedra in (BA)(2)(MHy)(2)Pb3Br10 and (BA)(2)(EA)(2)Pb3Br10 are highly distorted, and their different stacking patterns of the inner and outer layers lead to the formation of the n = 3 phases. Density functional theory calculations show that 2D perovskites with larger A-site cations (e.g., DMA, MHy, and EA) have smaller band dispersions and larger effective masses than those with Cs+ and MA. (BA)(2)(MHy)(2)Pb3Br10 also exhibits one of the largest Rashba splittings in the literature. Structures with large cage cations also exhibit high band gaps within the same n number and short photoluminescence (PL) lifetimes. Temperature- and power-dependent PL measurements reveal that the broad shoulder in the PL peak originates from the trap states.

Emission↗

Solution characterization of the dynamic conjugative entry exclusion protein TraG

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor–donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding–mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.

59 BASIC BIOLOGICAL SCIENCES↗

Material Effects on Electron-Capture Decay in Cryogenic Sensors

Several current searches for physics beyond the standard model are based on measuring the electron-capture (EC) decay of radionuclides implanted into cryogenic high-resolution sensors. The sensitivity of these experiments has already reached the level where systematic effects related to atomic state energy changes from the host material are a limiting factor. One example is a neutrino mass study based on the nuclear EC decay of 7 Be to 7 Li inside cryogenic Ta-based sensors. Here, to understand the material effects at the required level, we use density-functional theory to model the electronic structure of lithium atoms in different atomic environments of the polycrystalline Ta absorber film. The calculations reveal that the Li 1s binding energies can vary by more than 2 eV due to insertion at different lattice sites, at grain boundaries, in disordered Ta, and in the vicinity of various impurities. However, the total range of Li 1s shifts does not exceed 4 eV, even for extreme amorphous disorder. Furthermore, when investigating the effects on the Li 2s levels, we find broadening of more than 5 eV due to hybridization with the Ta band structure. Material effects are shown to contribute significantly to peak broadening in Ta-based sensors that are used to search for physics beyond the standard model in the EC decay of 7 Be, but they do not explain the full extent of observed broadening. Understanding these in-medium effects will be required for current- and future-generation experiments that observe low-energy radiation from the EC decay of implanted isotopes to evaluate potential limitations on the measurement sensitivity.

36 MATERIALS SCIENCE↗

Promoting electrochemical rates by concurrent ionic-electronic conductivity enhancement in high mass loading cathode electrode

Enhancing the fast charging capacity of thick electrodes with high mass loading is imperative in expediting the widespread adoption of electric vehicles. Nonetheless, the insufficient charge transfer kinetics of thick electrodes hinder the movement of effective electrons and ions, hence diminishing capacity at high current rates. In this work, we applied sustainable and biodegradable cellulose nanocrystals (CNCs) as electrode additives. It is the first time to simultaneously improve the electronic conductivity by optimizing the carbon dispersion and establishing electron transfer networks, as well as boosting the ionic conductivity of electrodes by shortening the ion transfer pathway. Specifically, the LiNi 0.6 Mn 0.2 Co 0.2 O 2 electrodes incorporating 1% dual functional CNCs additive exhibit improved effective electrical conductivity from 0.11 to 0.16 S/m and risen effective ionic conductivity from 0.36 to 0.62 S/m, in comparison to counterpart electrodes without CNCs. Therefore, the 1% CNC electrode with a high mass loading of 27.0 mg/cm 2 delivers a discharge capacity of 128 mAh/g at 1 C, which is superior to that of the CNC-free electrodes (95 mAh/g). In short, this study presents a novel environmentally friendly, economically viable, and dual-functional electrode additive that enhances both electronic and ionic conductivities with the aim of facilitating the widespread adoption of fast-charging high mass loading electrodes.

25 ENERGY STORAGE↗

First measurement of prompt and non-prompt D* + vector meson spin alignment in pp collisions at $\sqrt{s}$ = 13 TeV

This letter reports the first measurement of spin alignment, with respect to the helicity axis, for D* + vector mesons and their charge conjugates from charm-quark hadronisation (prompt) and from beauty meson decays (non-prompt) in hadron collisions. The measurements were performed at midrapidity (|y| < 0.8) as a function of transverse momentum (p T ) in proton–proton (pp) collisions collected by ALICE at the centre-of-mass energy $\sqrt{s}$ = 13 TeV. The diagonal spin density matrix element $ρ$00 of D* + mesons was measured from the angular distribution of the D* + → D 0 (→ K - π + )π + decay products, in the D* + rest frame, with respect to the D* + momentum direction in the pp centre of mass frame. The $ρ$00 value for prompt D* + mesons is consistent with 1/3, which implies no spin alignment. However, for non prompt D* + mesons an evidence of $ρ$00 larger than 1/3 is found. The measured value of the spin density element is $ρ$00 = 0.455±0.022(stat.)±0.035(syst.) in the 5 < p T < 20 GeV/c interval, which is consistent with a Pythia 8 Monte Carlo simulation coupled with the EvtGen package, which implements the helicity conservation in the decay of D* + meson from beauty mesons. In non-central heavy-ion collisions, the spin of the D* + mesons may be globally aligned with the direction of the initial angular momentum and magnetic field. Based on the results for pp collisions reported in this letter it is shown that alignment of non-prompt D* + mesons due to the helicity conservation coupled to the collective anisotropic expansion may mimic the signal of global spin alignment in heavy-ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets

Thousands of chemical properties can be calculated for small molecules, which can be used to place the molecules within the context of a broader “chemical space.” These definitions vary based on compounds of interest and the goals for the given chemical space definition. Here, we introduce a customizable (i.e., modular) Python module, chespa, built to easily assess different chemical space definitions through cluster-ing of compounds in these spaces and visualize trends of these clusters. To demonstrate this, chespa currently streamlines prediction of vari-ous molecule descriptors (predicted chemical properties, molecular substructures, AI-based chemical space, and chemical class ontology) in order to test 6 different chemical space definitions. Furthermore, we investigated how these varying definitions trend with mass spectrometry (MS)-based observability, i.e., the ability of a molecule to be observed with MS (e.g., as a function of the molecule ionizability), using an example data set from the U.S. EPA's Non-Targeted Analysis Collaborative Trial (ENTACT), where blinded samples had been analyzed previously, providing 1,398 data points. Improved understanding of observability would offer many advantages in small molecule identifica-tion, such as (i) a priori selection of experimental conditions based on suspected sample composition, (ii) the ability to reduce the number of candidate structures during compound identification by removing those less likely to ionize, and, in turn, (iii) a reduced false discovery rate and increased confidence in identifications. Factors controlling observability are not fully understood, making prediction of this property non-trivial and a prime candidate for chemical space analysis. Chespa is available at github.com/pnnl/chespa.

Nunez, Jamie↗

Ice Supersaturation Variability in Cirrus Clouds: Role of Vertical Wind Speeds and Deposition Coefficients

Abstract Aircraft measurements reveal ice supersaturation statistics in cirrus (ISSs) with broad maxima around ice saturation and pronounced variance. In this study, processes shaping ISSs in midlatitude and tropical upper tropospheric conditions are systematically investigated. Water vapor deposition and sublimation of size‐resolved ice crystal populations are simulated in an air parcel framework. Mesoscale temperature fluctuations (MTFs) due to gravity waves force the temporal evolution of supersaturation. Various levels of background wave forcing and cirrus thickness are distinguished in stochastic ensemble simulations. Kinetic limitations to ice mass growth are brought about by supersaturation‐dependent deposition coefficients that represent efficient and inefficient growth modes as a function of ice crystal size. The simulations identify a wide range of deposition coefficients in cirrus, but most values stay above 0.01 such that kinetic limitations to water uptake remain moderate. Supersaturation quenching times are long, typically 0.5–2 hr. The wave forcing thus causes a remarkably large variability in ISSs and cirrus microphysical properties except in the thickest cirrus, producing ensemble‐mean ISSs in line with in‐situ measurements. ISS variance is controlled by MTFs and increases with decreasing cirrus integral radii. In comparison, the impact of ice crystal growth rates on ISSs is small. These results contribute to efforts directed at identifying and solving issues associated with ice‐supersaturated areas and non‐equilibrium cirrus physics in global models.

Meteorology & Atmospheric Sciences↗

Extrinsic n-type doping of Cd 3 As 2 thin films

Cd 3 As 2 provides an excellent platform for studying the physics of three-dimensional Dirac semimetals due to its stability as well as its compatibility with thin film growth. Crystals made using both bulk and thin film synthesis are unintentionally doped n-type, and other than introducing Zn to reduce the carrier concentration, no efforts have been reported to alter this intrinsic doping without major changes to the band structure. Here, group VI elements Te and Se are introduced during epitaxy to increase the electron concentration of the films. Starting from an unintentionally doped electron concentration of 1–2 × 10 17 cm -3 , concentrations of up to 3 × 10 18 cm -3 are achieved. Analysis of Shubnikov–de Haas oscillations reveals good agreement in calculated effective mass and Fermi velocity of highly doped films with unintentionally doped single crystals with similar electron concentrations. The density functional theory is also performed to study the effects of group VI substitutions and confirms no strong perturbations in the electronic structure. This work ultimately demonstrates tunability in the carrier concentration using extrinsic dopants without substantial changes in the band structure, allowing for intentional design of Fermi-level position for device applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman’s path integral formalism of quantum mechanics. Here, the flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

36 MATERIALS SCIENCE↗

A transient site balance model for atomic layer etching

We present a transient site balance model of plasma-assisted atomic layer etching of silicon (Si) with alternating exposure to chlorine gas (Cl 2 ) and argon ions (Ar + ). Molecular dynamics (MD) simulation results are used to provide parameters for the model. The model couples the dynamics of a top monolayer surface region ('top layer') and a perfectly mixed subsurface region ('mixed layer'). The differential equations describing the rates of change of the Cl coverage in the two layers are transient mass balances. Model predictions include Cl coverages and rates of etching of various species from the surface as a function of Cl 2 or Ar + fluence. The simplified phenomenological model reproduces the MD simulation results well over a range of conditions. Comparing model predictions directly to experimental optical emission spectroscopy data, as reported in a previous paper, provides further evidence of the accuracy of the model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Constraining neutrino-nucleon form factors with charged-current scattering at the Electron-Ion Collider

Next-generation neutrino oscillation experiments such as the Deep Underground Neutrino Experiment require percent-level knowledge of neutrino-nucleon interaction cross sections. The nucleon axial form factor 𝐹 𝐴 ⁡(𝑄 2 ), parametrized by the axial mass 𝑀 𝐴 , is the dominant source of uncertainty in the quasielastic channel, and the parity-violating structure function 𝑥⁢𝐹 3 is poorly constrained on free nucleons. We propose using charged-current (CC) electron-proton scattering at the Electron-Ion Collider (EIC) to address both problems simultaneously. The measurement exploits three key features of the EIC: (1) helicity-selective electron bunches provide in situ electromagnetic background rejection; (2) a longitudinally polarized proton target enables extraction of 𝐹 𝐴 ⁡(𝑄 2 ) through the target-spin asymmetry 𝐴 𝑈⁢𝐿 ; and (3) the 𝑦-distribution leverage in CC deep inelastic scattering (DIS) separates 𝐹 2 and 𝑥⁢𝐹 3 on a free proton, without nuclear corrections. Using a Fisher information analysis at $\sqrt{𝑠}$ =141 GeV with 500 fb −1 of integrated luminosity, we project the Cramér-Rao statistical floor of 𝛿⁢𝑀 𝐴 ≈0.03 GeV (3%). Incorporating first-order realistic detector effects, such as zero-degree calorimeter acceptance, 𝑄 2 smearing (5%), and background noise from helicity subtraction, the projected sensitivity is severely background-limited due to the small signal-to-background ratio (𝑆/𝐵 ≈ 3 ×10 −4 ) in the elastic channel. Achieving competitive sensitivity (𝛿⁢𝑀 𝐴 ≈ 0.14 GeV) would require ∼10 −7 background suppression, 3 orders of magnitude beyond current projections. The CC DIS 𝑦 distribution provides subpercent extraction of 𝑥⁢𝐹$^{𝑊^{−}}_{3}$ over 0.05 < 𝑥 < 0.5, representing the most robust electroweak measurement in the near term.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Spectral properties and enhanced superconductivity in renormalized Migdal-Eliashberg theory

Migdal-Eliashberg theory describes the properties of the normal and superconducting states of electron-phonon-mediated superconductors based on a perturbative treatment of the electron-phonon interactions. It is necessary to include both electron and phonon self-energies self-consistently in Migdal-Eliashberg theory in order to match numerically exact results from determinantal quantum Monte Carlo in the adiabatic limit. Here in this work we provide a method to obtain the real-axis solutions of the Migdal-Eliashberg equations with electron and phonon self-energies calculated self-consistently. Our method avoids the typical challenge of computing cumbersome singular integrals on the real axis and is numerically stable and exhibits fast convergence. Analyzing the resulting real-frequency spectra and self-energies of the two-dimensional Holstein model, we find that self-consistently including the lowest-order correction to the phonon self-energy significantly affects the solution of the Migdal-Eliashberg equations. The calculation captures the broadness of the spectral function, renormalization of the phonon dispersion, enhanced effective electron-phonon coupling strength, minimal increase in the electron effective mass, and the enhancement of superconductivity which manifests as a superconducting ground state despite strong competition with charge-density-wave order. We discuss surprising differences in two common definitions of the electron-phonon coupling strength derived from the electron mass and the density of states, quantities which are accessible through experiments such as angle-resolved photoemission spectroscopy and electron tunneling. An approximate upper bound on 2Δ/T c for conventional superconductors mediated by retarded electron-phonon interactions is proposed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum oscillations in the field-induced ferromagnetic state of MnBi 2-x Sb x Te 4

The intrinsic antiferromagnetic topological insulator MnBi2Te4 undergoes a metamagnetic transition in a c-axis magnetic field. It has been predicted that ferromagnetic MnBi2Te4 is an ideal Weyl semimetal with a single pair of Weyl nodes. Here we report measurements of quantum oscillations detected in the field-induced ferromagnetic phase of MnBi 2-x Sb x Te 4 , where Sb substitution tunes the majority carriers from electrons to holes. Single-frequency Shubnikov–de Haas oscillations were observed in a wide range of Sb concentrations (0.54≤x≤1.21). The evolution of the oscillation frequency and the effective mass shows reasonable agreement with the Weyl semimetal band structure of ferromagnetic MnBi 2 Te 4 predicted by density functional calculations. Intriguingly, the quantum oscillation frequency shows a strong temperature dependence, indicating that the electronic structure depends sensitively on magnetism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exclusive π 0 p electroproduction off protons in the resonance region at photon virtualities 0.4 GeV 2 ≤ Q 2 ≤ 1 GeV 2

The limited electroproduction process e p → e ' p ' π 0 was measured in the range of photon virtualities Q 2 = 0.4 – 1.0 GeV 2 and the invariant mass range of the p π 0 system of W = 1.1 – 1.8 GeV. These kinematics are covered in exclusive π 0 electroproduction off the proton with nearly complete angular coverage in the p π 0 center-of-mass system and with high statistical accuracy. Nearly 36 000 cross-section points were measured, and the structure functions σ T + ε σ L , σ L T , and σ T T , were extracted via fitting the φ π 0 dependence of the cross section. A Legendre polynomial expansion analysis demonstrates the sensitivity of our data to high-lying N * and Δ * resonances with M > 1.6 GeV. As part of a broad effort to determine the electrocouplings of the N * and Δ * resonances using both single- and double-pion electroproduction, this dataset is key for the reliable extraction of the high-lying resonance electrocouplings from the combined isospin analysis of the N π and π + π - p channels.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Constraint of pionless EFT using two-nucleon spectra from lattice QCD

Finite-volume pionless effective field theory (FVEFT π/ ) at next-to-leading order (NLO) is used to analyze the two-nucleon lattice QCD spectrum of Ref. [1], performed at quark masses corresponding to a pion mass of approximately 800 MeV. Specifically, the effective theory is formulated in finite volume, and variational sets of wave functions are optimized using differential programming. Using these wave functions projected to the appropriate finite-volume symmetry group, variational bounds from FVEFT π/ are obtained for the ground state, as well as excited states. By comparison with the lattice QCD GEVP spectrum, different low energy constants (LECs) are constrained. Furthermore, relativistic corrections are incorporated, allowing for the s-d-wave mixing term in the deuteron channel.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Scaling hyporheic nitrogen cycling in large river alluvial aquifers

Research Element 1: Denitrification is a difficult flux to measure when fluxes are low and when the ecosystem is difficult to sample. These attributes describe Nyack floodplain, a large gravel-bedded aquifer adjacent to the Middle Fork Flathead River. Given that denitrification is simply respiration with nitrate as a terminal electron acceptor, we reasoned that N 2 production should negatively covary with oxygen respiration so long that oxygen is available. We sampled 16 wells 8 times throughout a year and analyzed these water samples on a membrane-inlet mass spectrometer for N 2 :Ar and O 2 . We fit multilevel models to N 2 :Ar as a function of dissolved oxygen. Within wells, there was no relationship between O 2 and N 2 :Ar. Among wells N 2 :Ar increased as O 2 declined. Based on the slope of this relationship, ~ -0.07, and estimated oxygen respiration in Nyack derived from prior studies, a possible range for denitrification is 0-8 mmol m -2 d -1 corresponding to a turnover rate for nitrate of 0-0.2/d. This estimated turnover rate is in the lower 20% of rates measured in the LINX 2 study, yet shows that even in a low nitrate (0.005 mmol/L) aquifer denitrification can be a substantial sink for dissolved N. Research Element 3 and 4: We developed a new theoretical approach to describe the relationship between water inflow, water outflow, and water age in porous media control volumes under dynamic flow conditions. Our approach had three distinct steps. First we described the application of well-established equations borrowed from Chemical Engineering to describe water age distributions in the hyporheic zone under steady state conditions. We published the associated results in the scientific journal PLOS ONE. Second, we developed a new theory ("flow spans") to describe how predicted steady-state water age distributions will respond to time varying imbalances in hyporheic discharge and recharge. Finally, we developed a proof-of-concept simulation model based on the new theory and used the model to examine the effects of flow regulation on a simulated river with characteristics representative of western U.S. montane rivers with expansive hyporheic zones.

54 ENVIRONMENTAL SCIENCES↗