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At least 379 records · Page 21

Excited-State Densities from Time-Dependent Density Functional Response Theory

While the variational principle for excited-state energies leads to a route to obtaining excited-state densities from time-dependent density functional theory, relatively little attention has been paid to the quality of the resulting densities in real space obtained with different exchange-correlation functional approximations or how nonadiabatic approximations developed for energies of states of double-excitation character perform for their densities. Here we derive an expression directly in real space for the excited-state density, which includes the case of nonadiabatic kernels and consequently is able, for the first time, to yield densities of states of double-excitation character. Under some well-defined simplifications, we compare the performance of the local-density approximation and exact-exchange approximation, which are in a sense at the opposite extremes of the fundamental functional approximations, on local and charge-transfer excitations in one-dimensional model systems and show that the dressed Time-Dependent Density Functional Theory (TDDFT) approach gives good densities of double excitations.

approximation↗

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗

Optimization of Dimensions of Smooth and Twisted-Tape-Inserted Tubes for Heat Transfer with NaCl/KCl/MgCl 2 Molten Salts by Principle of Entropy Generation Minimization

The entropy generation minimization principle is used as the criterion to optimize the flow and heat transfer of solar collectors and heat exchangers that use molten salts NaCl–KCl–MgCl 2 and KCl–MgCl 2 . The Gnielinski correlation for the Nusselt number versus Reynolds number, as well as the Moody friction factor given by Petukhov, was used for the calculation of the convective heat transfer coefficient and pressure loss due to friction in smooth tubes. For twisted-tap-inserted tube, equations of Nu and friction factor provided by Manglik and Bergles were used. The objective function, the entropy generation rate of the heat transfer system, was expressed as the function of Reynolds number, Prandtl number, heating flux, tube diameter, etc. As a result of the analysis, the optimum Reynolds number was determined and thereby to determine the optimum Nusselt number, convective heat transfer coefficient, friction factor, and tube diameter, which also allows the calculation of optimum flow velocity. The analysis was conducted in the fluid temperature range of 500–700 °C, which covers the operation temperature for supercritical CO 2 power cycles in concentrated solar power (CSP) system. Here, optimized results from the smooth tube and twisted-tap-inserted tube are compared, which is important to the design of solar receivers for CSP systems.

14 SOLAR ENERGY↗

Au 3 -to-Ag 3 coordinate-covalent bonding and other supramolecular interactions with covalent bonding strength

An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(m-Pz-(i-C 3 H7) 2 )] 3 ∙[Ag(m-Tz-(n-C 3 F 7 ) 2 )] 3 (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction – representing the 1st crystallographically-verified M 3 @M' 3 stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M–M' (Au / Ag), metal–π, π–π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol -1 between the two trimer moieties – a large value for intermolecular interactions between adjacent d 10 centres (nearly doubling the value for a recently claimed Au(I) / Cu(I) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) – which becomes 87 kcal mol -1 with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked M 3 @M' 3 product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M' frontier molecular orbitals in such polar-covalent M–M' bonds in this family of molecules. The Au / Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H 3 N: → Ag in [Ag(NH 3 ) 2 ] + , as demonstrated herein quantitatively. Solidstate and molecular modeling illustrate electron flow from the p-basic gold trimer to the p-acidic silver trimer with augmented contributions from ligand-to-ligand’ (LL'CT) and metal-to-ligand (MLCT) charge transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of geometry on columnar to equiaxed transition during electron beam powder bed fusion of IN718

Correlation between spot-melt scan parameters (linear spot-density aka areal energy density), build geometry, and solidification microstructure evolution (columnar vs equiaxed) in a powder bed fusion technology is investigated. It is shown that to maintain the equiaxed solidification microstructure evolution in electron beam powder bed additive manufacturing (AM), the areal energy density per layer needs to be scaled with respect to the 2D cross-sectional area of the layer being melted. Samples with two different cross-sectional areas (40 × 40 mm and 20 × 20 mm) have been fabricated with varying areal energy densities. For a given square cross-section (20 × 20 mm), increasing the areal energy density (4.8 MJ/sq.m to 14.7 MJ/sq.m) transitioned the solidification microstructure from columnar to equiaxed. The observed microstructure data (Electron Back Scattered Diffraction - EBSD) is quantified by calculating the principal component (PC) score using a spatial statistics methodology. The sample with equiaxed grains is found to have a low PC score while the sample with columnar grain had a high PC score. A semi-analytical model is used to simulate the heat transfer and the local solidification conditions as a function of processing parameters (linear spot-density). The result from the heat transfer model is correlated with previously quantified microstructure data. Space-Time analysis of the melt pattern is done and correlated with the observed microstructure. In addition, from the findings, appropriate parameters have been used to additively manufacture a turbine blade with site-specific or hybrid solidification microstructure (traditional fabrication possible via a patented method of localized cold working and heat treatment).

36 MATERIALS SCIENCE↗

Functionalization of Electrodes with Tunable [EMIM] x [Cl] x +1 – Ionic Liquid Clusters for Electrochemical Separations

Functionalization of electrodes with clusters of hydrophobic molecules may improve the energy efficiency and selectivity of electrochemical separations by modulating the desolvation process occurring at the interface. Ionic liquids (IL), which have a broad range of compositions and properties, are potential candidates for controlling the transport, desolvation, and adsorption of target ions at electrochemical interfaces. We report a joint experimental and theoretical investigation of the structure, stability, and selective adsorption properties of the IL clusters 1-ethyl-3-methylimidazolium chloride [EMIM] x [Cl] x+1 - (x = 1 – 10) and demonstrate their ability to adsorb and separate ions from solution. The structure and stability of the IL clusters are determined experimentally using high-mass-resolution electrospray ionization mass spectrometry, collision-induced dissociation, and negative ion photoelectron spectroscopy. Global optimization theory and ab initio molecular dynamics simulations provide molecular-level insight into the bonding and structural fluxionality of these species. Ion soft landing is used to selectively functionalize the surface of highly oriented pyrolytic graphite (HOPG) working electrodes with [EMIM] 1 [Cl] 2 - , [EMIM] 3 [Cl] 4 - , and [EMIM] 5 [Cl] 6 - clusters. Kelvin probe microscopy provides insight into the relative stability of the clusters on HOPG and their effect on the work function of IL-functionalized electrodes. Cyclic voltammetry measurements reveal irreversible adsorption of Fe(CN) 6 4-/3- anions during redox cycling, while electrochemical impedance spectroscopy indicates a substantial decrease in the electron transfer resistance of the IL-functionalized electrodes due to adsorption of Fe(CN) 6 4-/3- . Overall, our findings demonstrate that IL clusters with different size and stoichiometry may be used to increase the efficiency of electrochemical separations, opening new horizons in selective electrode functionalization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temperature-dependent Battery Performance of a Na 3 V 2 (PO 4 ) 2 F 3 @MWCNT Cathode and In-situ Heat Generation on Cycling

Excellent structural stability, high operating voltage, and high capacity have made Na 3 V 2 (PO 4 ) 2 F 3 a promising cathode material for sodium-ion batteries. However, high-temperature battery performances and heat generation measurements have not been systematically reported yet. Carbon-coated Na 3 V 2 (PO 4 ) 2 F 3 @MWCNT (multi-walled carbon nanotube) samples are fabricated by a hydrothermal-assisted sol-gel method and the electrochemical performances are evaluated at three different temperatures (25, 45, and 55 °C). Furthermore, the well-crystallized Na 3 V 2 (PO 4 ) 2 F 3 @MWCNT samples exhibit good cycling stability at both low and high temperatures; they deliver an initial discharge capacity of 120–125 mAhg -1 at a 1 C rate with a retention of 53 % capacity after 1,400 cycles with 99 % columbic efficiency. The half-cell delivers a capacity of 100 mAhg -1 even at a high rate of 10 C at room temperature. Furthermore, the Na 3 V 2 (PO 4 ) 2 F 3 @MWCNT samples show good long-term durability; the capacity loss is an average of 0.05 % per cycle at a 1 C rate at 55 °C. Additionally, ionic diffusivity and charge transfer resistance are evaluated as functions of state of charge, and they explain the high electrochemical performance of the Na 3 V 2 (PO 4 ) 2 F 3 @MWCNT samples. In-situ heat generation measurements reveal reversible results upon cycling owing to the high structural stability of the material. Excellent electrochemical performances are also demonstrated in the full-cell configuration with hard carbon as well as antimony Sb/C anodes.

25 ENERGY STORAGE↗

Differing behavioral changes in crayfish and bluegill under short- and long-chain PFAS exposures: Field study in Northern Michigan, USA

The emergent contaminant family, per- and poly-fluorinated alkyl substances (PFAS) has gained research attention due to their widespread detection and stability within the environment. Despite the growing amount of research on perfluorooctanesulfonic acid (PFOS) and perfluoro-n-octanoic acid (PFOA) in aquatic organisms, investigations detailing behavioral and physiological effects of aquatic organisms exposed to a mixture of PFAS analytes in the wild have been limited. The objective of this study was to evaluate the potential behavioral and histological effects of environmental exposure to PFAS compounds within multiple trophic levels of aquatic ecosystems. The current study investigates effects of environmentally relevant PFAS concentration exposures in crayfish (Faxonius immunis, F. rusticus, F. virilis) and bluegill (Lepomis macrochirus) sourced from four water bodies in Northern Michigan. Antipredator response and foraging behavioral assays were used to investigate potential effects on crayfish; a swimming speed behavioral assay and liver and gill histology analysis were used to investigate potential effects on fish. Linear mixed model and multiple regression analyses resulted in significant relationships between tissue accumulation levels of long chain PFAS compounds and crayfish foraging and fish critical swimming speed responses. Crayfish foraging decreased and fish critical swim speeds increased with PFAS exposure which may lead to energetic and population concerns. Antipredator response in crayfish and liver and gill histology in fish were not significantly related to PFAS tissue or water concentrations. The sensitivity of crayfish and bluegill behavior contributes to the growing body of research regarding the differential toxicity of short-chain and long-chain PFAS compounds. The sensitivity of some aquatic organism behaviors to PFAS accumulated in tissue may have implications for PFAS transfer and alterations to ecosystem functioning; based on the results of this field study, further laboratory research is recommended to further evaluate these relationships.

59 BASIC BIOLOGICAL SCIENCES↗

Functional roles of the [2Fe-2S] clusters in Synechocystis PCC 6803 Hox [NiFe]-hydrogenase reactivity with ferredoxins

The HoxEFUYH complex of Synechocystis PCC 6803 (S. 6803) consists of a HoxEFU ferredoxin:NAD(P)H oxidoreductase subcomplex and a HoxYH [NiFe]-hydrogenase subcomplex that catalyzes reversible H2 oxidation. Prior studies have suggested that the presence of HoxE is required for reactivity with ferredoxin; however, it is unknown how HoxE is functionally integrated into the electron transfer network of the HoxEFU:ferredoxin complex. Deciphering electron transfer pathways is challenged by the rich iron-sulfur cluster content of HoxEFU, which includes a [2Fe-2S] cluster in each subunit, along with multiple [4Fe-4S] clusters and a flavin cofactor. To resolve the role of HoxE, we determined the biophysical and thermodynamic properties of each [2Fe-2S] cluster in HoxEFU using steady-state and potentiometric EPR analysis in combination with square wave voltammetry (SWV). The temperature-dependence of the EPR signal for HoxE confirmed the coordination of a single [2Fe-2S] cluster that was shown by SWV to have an E m = -424 mV (versus SHE). Strikingly, when the E m of the HoxE [2Fe-2S] cluster was analyzed in HoxEFU titrations, it was shifted by >100 mV to an E m < -525 mV (versus SHE). EPR titrations of HoxEFU gave an E m value for the [2Fe-2S] cluster of HoxF, E m = -419 mV and HoxU, E m = -349 mV. These values were used to re-analyze the diaphorase kinetics in reactions performed with ferredoxins with varying E m 's. The results are formulated into a model of HoxEFU:ferredoxin reactivity and the role of HoxE in mediating electron transfer within the HoxEFU:ferredoxin complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Functional group activation and coupling agent migration induced by plasma treatment in adhesive for enhanced toughness of metal-composite joints

Commercial adhesive paste was additionally activated using low-power oxygen plasma with different plasma exposure durations to investigate its interfacial bonding contribution in adhesively-bonded Aural-5/CFRP-PA6 double cantilever beam (DCB) joints with plasma-treated adherends. The plasma-treated adhesive showed enhanced functional peak intensities in Fourier transfer infrared spectroscopy (FTIR) as plasma exposure time was increased, and some degree of oxidation was also detected via X-ray photoelectron spectroscopy (XPS). A small molecule, dicyandiamde (coupling agent) in adhesive was migrated to adhesive layer, where double concentration of coupling agent was detected after 10 minutes of plasma treatment. As a result, characterization of the adhesive/CFRP-PA6 interface after DCB fracture showed additional chemical bonds formed through amine-initiated epoxy ring opening polymerization, as well as amide bonds and ester bonds. In conclusion, these additional bonds at the adhesive/CFRP-PA6 interfaces led to significantly increased failure extensions and fracture energies of the joints as the plasma exposure time on the adhesive increased, compared to the joints with plasma-treated adherends but non-plasma-treated adhesive as commonly seen in the literature.

36 MATERIALS SCIENCE↗

How the Size and Density of Charge-Transfer Excitons Depend on Heterojunction’s Architecture

We have characterized the size, intensity, density, and distribution of charge-transfer (CT) excitons as a function of the acceptor–donor architecture of prototypical organic interfaces. This characterization was done by computational analysis of 17 models of varying numbers, positions, and orientations of the donor and acceptor molecules. The models’ building blocks were phenyl-C61-butyric acid methyl ester (PCBM) fullerene acceptors and dual-band donor polymers composed of thiophene, benzothiadiazole, and benzotriazole subunits. The electronic structure of the donor–acceptor complexes was computed with the time-dependent long-range-corrected density-functional tight-binding method and analyzed with the fragment-based one-electron transition density matrix. In all models, the complexes with edge-on orientation have denser spectra of low-energy CT states lying below the absorption bands compared to the complexes with face-on orientation. This CT-state distribution in edge-on complexes provides a gate to efficiently populate cold CT excitons. Moreover, the cold CT excitons have a higher degree of charge separation in the edge-on than in the face-on complexes. The CT amount and the CT exciton size generally increase with the energy of the CT states, although the electron remains localized on a single molecule in cold CT states. Delocalization over two PCBM molecules was observed for high-energy CT states. The exciton size also depends on the orientation. Larger excitons are produced by the delocalization of the electrons perpendicularly to the interface. When the delocalization is parallel, the smaller electron–hole distances yield moderately sized CT excitons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Group-Additivity–Embedded Multiscale Modeling for Electric Field-Enhanced Nanocatalysis

Elucidating structure-performance relationships remains a central challenge in field-enhanced catalysis, where nanoparticles exhibit nonuniform surface sites with site-dependent responses to electric fields. Low-coordination sites (edges, corners, and tips) are particularly electric field-sensitive (EF), leading to nonuniform charge distribution, adsorption energies, and catalytic activity. Here, using ammonia decomposition on a ruthenium cluster as a model system, we develop a transferable multiscale framework integrating density functional theory, group additivity (GA), Brønsted-Evans-Polanyi scaling, and microkinetic modeling to predict EF-dependent activity across nonuniform cluster sites. Across sites and fields, the nitrogen adsorption energy (E N ) emerges as the governing descriptor, yielding robust volcano relationships whose optimum shifts systematically with field: negative fields strengthen N binding via electron accumulation, while positive fields weaken N binding via charge depletion, moving the optimal E N toward weaker binding. Microkinetic analysis shows that N≡N bond formation remains the key kinetic bottleneck over most conditions; positive fields lower the effective barrier and, critically, increase the fraction of near-optimal active sites, leading to a net enhancement in overall activity relative to zero-field and negative-field cases. By capturing EF- and site-dependent energetics with high accuracy and low computational cost, this GA-embedded multi-scale simulation workflow provides a physically interpretable route to predict and design field-enhanced nanocatalysis.

ammonia decomposition↗

Sizing and Location Selection of Medium‐Voltage Back‐to‐Back Converters for DER‐Dominated Distribution Systems

Medium‐voltage back‐to‐back (MVB2B) converters can connect two distribution systems and quantifiably transfer power between them. This function can enable the MVB2B converter to exchange distributed energy resource (DER)‐generated power between two systems and bring significant value to enhancing distribution system DER adoption. Our previous work analysed and demonstrated the value MVB2B converter can bring to DER integration. As continuous work, this paper presents a methodology that helps address the MVB2B converter sizing and location selection problem in distribution systems with high DER penetrations. The proposed methodology aims to address three critical problems for MVB2B converter implementation in the real world: (1) which distribution systems are better to be connected, (2) what converter size is appropriate for connecting the distribution systems, and (3) where the optimal connection points are in the systems for connecting the MVB2B converter. The proposed methodology has been demonstrated by case studies that include various scenarios involving distribution systems with different dominated load types and high photovoltaic penetrations. The results demonstrate that selecting the optimal converter size based on net revenue and time of return considerations leads to a balance between maximizing energy savings and minimizing financial payback periods. Furthermore, feeder pair selection based on load profile standard deviation effectively identifies systems that derive the greatest value from MVB2B integration. Finally, an optimized connection point selection approach using a voltage load sensitivity matrix ensures minimal system impact while facilitating efficient power exchange. These findings provide practical insights for the real‐world deployment of MVB2B converters to enhance DER hosting capacity and improve grid resilience.

14 SOLAR ENERGY↗

Local models of two-temperature accretion disc coronae – II. Ion thermal conduction and the absence of disc evaporation

We use local stratified shearing-box simulations with magnetic field-aligned thermal conduction to study an idealized model of the coupling between a cold, radiatively efficient accretion disc, and an overlying, hot, two-temperature corona. Evaporation of a cold disc by conduction from the hot corona has been proposed as a means of mediating the soft-to-hard state transitions observed in X-ray binary systems. We model the coronal plasma in our local disc patch as an MHD fluid subject to both free-streaming ion conduction and a parametrized cooling function that captures the collisional transfer of energy from hot ions to colder, rapidly cooling leptons. In all of our models, independent of the initial net vertical magnetic flux (NF) threading the disc, we find no evidence of disc evaporation. The ion heat flux into the disc is radiated away before conduction can heat the disc’s surface layers. When an initial NF is present, steady-state temperature, density, and outflow velocities in our model coronae are unaffected by conduction. Instead of facilitating disc evaporation, thermal conduction is more likely to feed the disc with plasma condensing out of the corona, particularly in flows without NF. Our work indicates that uncertainties in the amount of NF threading the disc hold far greater influence over whether or not the disc will evaporate into a radiatively inefficient accretion flow compared to thermal conduction. We speculate that a change in net flux mediates disc truncation/evaporation.

79 ASTRONOMY AND ASTROPHYSICS↗

Molecular tail chemistry controls thermal transport in fullerene films

Herein we report on the thermal conductivities of alkyl- and indene-group functionalized fullerene derivative thin films as measured via time domain thermoreflectance and steady state thermoreflectance. The thermal conductivities vary from 0.064 ± 0.007 W m – 1 K – 1 for [6,6]-phenyl C 61 -butyric acid methyl ester (PCBM) to 0.15 ± 0.017 W m – 1 K – 1 for indene- C 60 bisadduct at room temperature and do not exhibit significant temperature dependence from 300 to 375 K. In comparison to the thermal conductivity of PCBM, increasing the length of the alkyl chain, as in the case of [6,6]-phenyl C 61 -butyric acid butyl ester, and [6,6]-phenyl C 61 -butyric acid octyl ester leads to higher thermal conductivities. Likewise, increasing the number of alkyl chains attached to the fullerenes as in the case of bisadduct PCBM leads to a higher thermal conductivity compared to that of PCBM. We present atomistic insights into the role of chemical functionalization on the overall heat transfer in these fullerene derivatives by conducting molecular dynamics simulations and lattice dynamics calculations. The thermal conductivities predicted via our atomistic simulations qualitatively agree with the experimental trends for our fullerene derivatives. Lattice dynamics calculations reveal that one of the main factors dictating the ultralow thermal conductivities in fullerene derivatives is the large reduction in modal diffusivities in the molecular crystals as calculated from the Allen-Feldman model, thus providing an explanation for their largely reduced thermal conductivities as compared to that of C 60 crystals. The low diffusivities result from high degrees of localization of Einstein-like vibrations in fullerene derivatives due to the molecular side chains, providing the ability to dial-in the properties of these low thermal conductivity solids via molecular engineering.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Software-Defined Virtual Synchronous Condenser

Synchronous condensers (SCs) play important roles in integrating wind energy into relatively weak power grids. However, the design of SCs usually depends on specific application requirements and may not be adaptive enough to the frequently-changing grid conditions caused by the transition from conventional to renewable power generation. This paper devises a software-defined virtual synchronous condenser (SDViSC) method to address the challenges. Our contributions are fourfold: 1) design of a virtual synchronous condenser (ViSC) to enable full converter wind turbines to provide built-in SC functionalities; 2) engineering SDViSCs to transfer hardware-based ViSC controllers into software services, where a Tustin transformation-based software-defined control algorithm guarantees accurate tracking of fast dynamics under limited communication bandwidth; 3) a software-defined networking-enhanced SDViSC communication scheme to allow enhanced communication reliability and reduced communication bandwidth occupation; and 4) Prototype of SDViSC on our real-time, cyber-in-the-loop digital twin of large-wind-farm in an RTDS environment. Furthermore, extensive test results validate the excellent performance of SDViSC to support reliable and resilient operations of wind farms under various physical and cyber conditions.

17 WIND ENERGY↗

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↗

Measurement of $d^2 \sigma/d|\vec{q}|d E_{avail}$ and 2p2h contribution using charged current $\nu_\mu$ interactions in the NOvA Near Detector

This Thesis presents the analysis methods and measurement of the $d^2 \sigma/d|\vec{q}|d E_{avail}$-CC inclusive cross section that describes neutrino scattering in a predominantly hydrocarbon medium. Studies that are prerequisite for the analysis including, variable determinations, event selections, efficiency, purity determinations, and systematic uncertainty estimations, are summarized. Tests of the analysis are also detailed, and shown to reproduce the input distributions. The double-differential cross-section measurement provides the foundation for determination of the inclusive rate for the excess induced by 2p2h processes together with nuclear medium effects that are not described by the Fermi gas model. The methodology for the extraction of this rate, defined as the excess observed relative to the rate estimated for known single-nucleon interactions, is described in detail. The following new measurements are reported in this Thesis: (1) The $\nu_\mu-$CC inclusive double-differential cross section as a function of three-momentum transfer and available hadronic energy, for an average $E_\nu$ of 1.8 GeV, is obtained. The double-differential cross section value that obtains when the bin widths are taken to be the dimensions of the entire analysis domain, e.g. $0.2 \le |\vec{q}| \le 2.0 GeV/c$ and $0.0 \le E_{avail} \le 2.0$ GeV, is inclusive cross section is $(6.05 \pm 0.75)\times10^{-39}$ cm$^2$/GeV/GeV/$c$/nucleon. An event excess attributed to 2p2h-MEC processes is observed; most of the rate occurs in a contiguous phase space region $0.3 \le |\vec{q}| \le 1.0$ GeV$/c$ $0.0 \le E_{avail} \le 0.35$ GeV. This rate represents $12.0\pm 6.5\%$ of the observed CC inclusive cross section; its cross section ratio relative to CCQE scattering is estimated to be $44.3 \pm 23.9\%$.

Olson, Travis Grant↗