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At least 757 records · Page 42

Active Learning A Neural Network Model For Gold Clusters & Bulk From Sparse First Principles Training Data

Small metal clusters are of fundamental scientific interest and of tremendous significance in catalysis. These nanoscale clusters display diverse geometries and structural motifs depending on the cluster size; a knowledge of this size-dependent structural motifs and their dynamical evolution has been of longstanding interest. Given the high computational cost of first-principles calculations, molecular modeling and atomistic simulations such as molecular dynamics (MD) has proven to be an important complementary tool to aid this understanding. Classical MD typically employ predefined functional forms which limits their ability to capture such complex size-dependent structural and dynamical transformation. Neural Network (NN) based potentials represent flexible alternatives and in principle, well-trained NN potentials can provide high level of flexibility, transferability and accuracy on-par with the reference model used for training. A major challenge, however, is that NN models are interpolative and requires large quantities (similar to 10 4 or greater) of training data to ensure that the model adequately samples the energy landscape both near and far-from-equilibrium. A highly desirable goal is minimize the number of training data, especially if the underlying reference model is first-principles based and hence expensive. In this work, we introduce an active learning (AL) scheme that trains a NN model on-the-fly with minimal amount of first-principles based training data. Our AL workflow is initiated with a sparse training dataset (similar to 1 to 5 data points) and is updated on-the-fly via a Nested Ensemble Monte Carlo scheme that iteratively queries the energy landscape in regions of failure and updates the training pool to improve the network performance. Using a representative system of gold clusters, we demonstrate that our AL workflow can train a NN with similar to 500 total reference calculations. Using an extensive DFT test set of similar to 1100 configurations, we show that our AL-NN is able to accurately predict both the DFT energies and the forces for clusters of a myriad of different sizes. Our NN predictions are within 30 meV/atom and 40 meV/angstrom of the reference DFT calculations. Moreover, our AL-NN model also adequately captures the various size-dependent structural and dynamical properties of gold clusters in excellent agreement with DFT calculations and available experiments. We finally show that our AL-NN model also captures bulk properties reasonably well, even though they were not included in the training data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Achieving 280 Gbar hot spot pressure in DT-layered CH capsule implosions at the National Ignition Facility

We are reporting on a series of indirect-drive 0.9-scale CH capsule implosions (inner radius = 840 μm) fielded in low gas-fill (0.6 mg/cm 3 ) hohlraums of 6.72 mm diameter at the National Ignition Facility. Thanks to the 11%-reduction of the capsule size at a given hohlraum diameter compared to previously tested full-scale capsules, we achieved good hot spot symmetry control near 33% cone-fraction and without the need to invoke cross beam energy transfer. As a result, we achieved a hot spot pressure of 280 ± 40 Gbar, which is the highest pressure demonstrated in layered DT implosions with CH capsules to date. Pushing this design to higher velocity resulted in a reduction of neutron yield. Highly resolved capsule simulations suggest that higher Au M-shell preheat resulted in an increase in Atwood number at the ablator–ice interface, which leads to increased fuel-ablator instability and mixing. The results reported here provide important scaling information for next-generation CH designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Compact in situ probe for magnetotransport measurements of 2D materials under variable tensile strain

The recent development of freestanding oxide membranes has opened new opportunities for strain engineering of transition metal oxides beyond values accessible in bulk samples. While a number of studies have been performed with fixed strain, the ability to dynamically control the strain state during measurement would be greatly enabling. To this end, we present an in situ uniaxial strain probe optimized for transport measurements of tensile-strained 2D or quasi-2D materials down to 2 K. Utilizing a flexible polyimide substrate as the stress transfer medium, our platform simplifies the sample preparation process and allows precise alignment of strain fields relative to the crystalline axes. An in situ optical microscope monitors the macroscopic strain state operando and makes it possible to complete an entire magnetotransport study at cryogenic temperatures under continuous strain variations. We demonstrate the capabilities of the probe on a freestanding LaNiO 3 membrane, where we induce tensile strain up to 8% and observe a corresponding strong transport anisotropy. In view of the rapid developments in low-dimensional materials synthesis and the plethora of novel quantum phenomena they exhibit, this strain probe provides general instrumentation for examining and controlling these properties via strain.

2D materials↗

Enabling accurate chemical modeling of shocked energetic materials using a machine learning interatomic potential

Understanding the complex chemistry of organic materials under dynamic compression is important for many applications, but it is challenging due to the large number of reactions occurring at various time scales. Here, in this study, we develop a machine learning potential based on Chebyshev polynomials to study the insensitive energetic material 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under detonation. We discuss a strategy for constructing diverse training data needed to capture the complex chemistry of TATB. Our potential demonstrates strong transferability across a wide range of thermodynamic conditions and other explosives, enabling accurate and reliable chemical modeling of organic materials under extreme conditions. The efficiency of our approach allows for simulations over several nanoseconds and for large system sizes, providing detailed insights into the chemistry of shocked TATB. The model accurately reproduces experimental Hugoniot equation of state data, and our simulations reveal the rapid formation of nitrogen-rich carbon clusters following shock. The methods and datasets developed here offer a robust framework for accurate chemical modeling of other shocked organic energetic materials.

Chemistry↗

A line-binned treatment of opacities for the spectra and light curves from neutron star mergers

ABSTRACT The electromagnetic observations of GW170817 were able to dramatically increase our understanding of neutron star mergers beyond what we learned from gravitational waves alone. These observations provided insight on all aspects of the merger from the nature of the gamma-ray burst to the characteristics of the ejected material. The ejecta of neutron star mergers are expected to produce such electromagnetic transients, called kilonovae or macronovae. Characteristics of the ejecta include large velocity gradients, relative to supernovae, and the presence of heavy r-process elements, which pose significant challenges to the accurate calculation of radiative opacities and radiation transport. For example, these opacities include a dense forest of bound–bound features arising from near-neutral lanthanide and actinide elements. Here we investigate the use of fine-structure, line-binned opacities that preserve the integral of the opacity over frequency. Advantages of this area-preserving approach over the traditional expansion–opacity formalism include the ability to pre-calculate opacity tables that are independent of the type of hydrodynamic expansion and thus eliminate the computational expense of calculating opacities within radiation-transport simulations. Tabular opacities are generated for all 14 lanthanides as well as a representative actinide element, uranium. We demonstrate that spectral simulations produced with the line-binned opacities agree well with results produced with the more accurate continuous Monte Carlo Sobolev approach, as well as with the commonly used expansion–opacity formalism. The agreement between the line-binned and expansion–opacity results is explained as arising from the similarity in their opacities in the limit of low optical depth, where radiation transport is important in the ejecta. Additional investigations illustrate the convergence of opacity with respect to the number of included lines, and elucidate sensitivities to different atomic physics approximations, such as fully and semirelativistic approaches.

79 ASTRONOMY AND ASTROPHYSICS↗

Development of Modified Perturbation Solutions to the One-Phase Stefan Problems With a Convective Boundary

The classical Stefan problem is used to track the moving solid-liquid interface during the freezing process. Perturbation theory has often been applied to find an approximate analytical solution due to the nonlinearity of the moving interface. However, the Stefan number (i.e., the sensible over latent heat) must be small and usually less than 0.01 to assume the perturbation expansion, which in turn limits the thermal engineering applications. In this study, a modified perturbation solution is developed by adding a correction term after the leading-order solution to be valid for a much wider range of Stefan numbers (i.e., 0.01 less than or equal to Ste less than or equal to 1). Specifically, a one-phase Stefan problem is first formulated subjected to a convective boundary in the Cartesian, cylindrical, and spherical coordinate systems for inward solidification. The leading-order solution is calculated based on the regular perturbation theory, while the correction term is obtained using the Monte-Carlo method and a multi-variant regression. Results show that the correction term has a linear relationship with the Stefan number and is not significantly influenced by the Biot number. The proposed modified perturbation solution can accurately and rapidly predict the nonlinear moving interface motion for the freezing process.

DIRECT ENERGY CONVERSION,MATHEMATICS AND COMPUTING↗

Kinetics and Mechanism of Tetravalent Cerium Extraction by Di-2-Ethylhexyl Isobutyramide (DEHiBA)

DEHiBA is a fully-incinerable, CHON extractant with a high selectivity for hexavalent actinides. However, as a recently-developed ligand, much remains unknown about its physical and chemical properties, including its extraction and phase disengagement rates. Here, we present data on the phase transfer kinetics of Ce(IV) extraction and stripping by both DEHiBA and TBP collected using microfluidic devices. Ce(IV) was selected as a surrogate for Pu(IV) and Np(IV) in the initial tests of the microfluidics system prior to testing with the actinides. Pseudo first-order reaction rate constants are determined for both systems, and the corresponding Damköhler numbers (Da) are calculated to establish whether the extraction and stripping processes are kinetically or diffusion controlled. The stoichiometry of the extracted Ce(IV)-DEHiBA complex is determined, and the phase disengagement properties under extraction conditions are assessed using the dimensionless dispersion number. A possible explanation for the favorable extraction of Ce(IV) by DEHiBA, which is known to poorly extract many tetravalent cations, is presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗

First-principles modeling of conductivity at the (001), (110), and (111) SrTiO 3 /LaAlO 3 heterointerfaces

Here, the complex polar oxide heterojunction of SrTiO 3 /LaAlO 3 (STO/LAO) is of great interest due to the emergent physical phenomena observed at the interface. STO and LAO separately are wide band-gap insulators. However, upon joining them at the 001, 110, and 111 crystallographic planes, the interface undergoes a transition to a conductive state. Although first-principles modeling of the 001 plane interface has been widely studied, there is a lack of reports regarding the 110 and 111. This paper expands the theoretical model of the STO/LAO heterointerface to the three crystallographic planes (001, 110, and 111) where the conductivity has been experimentally reported. The calculations showed that whereas at the 001 interface the conductivity appears at a critical thickness of 4 monolayers of LAO, the 110 and 111 planes have no clear critical thickness; these two interfaces were always conductive. Nevertheless, the number of conductive electrons per unit cell increases with the thickness of the LAO layer in the 110 and 111 interfaces. This is related to the energy levels downshifting due to the electrostatic potential buildup (which was in the opposite direction respect to the 001 interface), increasing the number of conductive sates below the Fermi level. Given the absence of a critical thickness and the fact that chemical intermixing and oxygen vacancies at the interface were not considered, the main mechanism responsible for the conductivity in the 110 and 111 planes was attributed to the large structure reconstruction that locally changes the energy levels at the interface causing charge transfer and accumulation at the layers close to the interface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Toward Mixed Analog-Digital Quantum Signal Processing: Quantum AD/DA Conversion and the Fourier Transform

Signal processing stands as a pillar of classical computation and modern information technology, applicable to both analog and digital signals. Recently, advancements in quantum information science have suggested that quantum signal processing (QSP) can enable more powerful signal processing capabilities. However, the developments in QSP have primarily leveraged digital quantum resources, such as discrete-variable (DV) systems like qubits, rather than analog quantum resources, such as continuous-variable (CV) systems like quantum oscillators. Consequently, there remains a gap in understanding how signal processing can be performed on hybrid CV-DV quantum computers. Here we address this gap by developing a new paradigm of mixed analog-digital QSP. We demonstrate the utility of this paradigm by showcasing how it naturally enables analog-digital conversion of quantum signals—specifically, the transfer of states between DV and CV quantum systems. We then show that such quantum analog-digital conversion enables new implementations of quantum algorithms on CV-DV hardware. This is exemplified by realizing the quantum Fourier transform of a state encoded on qubits via the free-evolution of a quantum oscillator, albeit with a runtime exponential in the number of qubits due to information theoretic arguments. Collectively, this work marks a significant step forward in hybrid CV-DV quantum computation, providing a foundation for scalable analog-digital signal processing on quantum processors.

42 ENGINEERING↗

Characterizing Heat Transfer in sCO 2 Cycle Coolers Utilizing the Wilson Plot Technique

Effective design of coolers can decrease the capital expense of supercritical carbon dioxide (sCO 2 ) power plants. Improved datasets reporting heat transfer from the CO 2 in the cycle cooler allow design engineers to calculate the required length of heat exchanger streams more accurately, thus reducing cooler material and heat exchanger cost. This study considered a shell-and-tube heat exchanger with non-condensing CO 2 on the tube side and water flow on the shell side. The average Nusselt number on the tube side was measured employing the Wilson plot technique for a flow at a Reynolds number, Re, equal to 1×10 5 and for a heat flux to mass flux ratio, Q"/G, ranging from 50 to 350 J/kg. The results indicate that the Nusselt number, Nu, increases as the CO 2 pressure decreases towards the critical point. The results also indicate that Nu increases to maximum at Q"/G = 215 J/kg and then decreases with further increases in Q"/G. The difference in Nu measured between the horizontal and vertical heat exchanger with downward flowing CO 2 is less than the experimental error.

20 FOSSIL-FUELED POWER PLANTS↗

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M.↗

Cooperative Lanthanide Solvation in an Ionic Liquid for Critical Materials Separations

Effectively separating critical materials, including intra-lanthanide separations, is crucial for meeting growing application demands. Liquid–liquid extraction (LLE) is the industry standard for lanthanide separations, where the selectivity can depend on small changes in metal coordination. In this work, we investigate representative lanthanide Eu coordination with a neutral malonamide extractant in an imidazolium bistriflimide ionic liquid (IL) solvent. Through systematic titrations of the water and extractant and under extraction conditions, we observe surprising cooperative Eu solvation with the IL anion and extractant. Time-resolved fluorescence spectroscopy measurements show strong extractant coordination in water-saturated IL. Lifetime measurements show no water coordination, and extended X-ray fine structure spectroscopy data provide a coordination number of 10. Molecular dynamics simulations confirm this coordination number and reveal IL anion coordination in the final Eu complex, even though it is ordinarily a significantly weaker ligand compared to water. The lack of water in the final extracted complex and IL anion coordination potentially explain the increased extraction in LLE systems using ILs, as evidenced by higher distribution ratios for cation exchange extraction, despite the energetic cost of cation transfer to the aqueous phase. These results highlight the opportunities for tuning metal coordination to drive extraction in unique solvent systems.

Carr, Amanda J.↗

Enhancing X-ray Sensitivity via the Antenna Effect in Quantum Shells with Multiexciton Emission

Quantum shells (QSs) with efficient multiexciton emission can generate multiple excitons per particle under high-energy excitation, thereby improving exciton utilization under intense X-ray exposure and offering strong potential for X-ray-based scintillation applications. However, these QSs are typically composed of low-atomic-number (Z) elements, which substantially limits their X-ray absorption efficiency and leads to poor X-ray sensitivity. Here, we overcome this fundamental limitation by introducing a high-Z antenna-sensitization strategy that couples QSs to heavy-element molecular absorbers, which act as X-ray harvesting centers and funnel energy into the QSs via efficient interfacial transfer. By combining enhanced X-ray absorption with efficient interfacial energy transfer and improved exciton utilization, we achieve more than an order-of-magnitude increase in multiexciton-driven QS radioluminescence (RL) relative to pristine shells. Additionally, a high X-ray imaging resolution of 25.2 lp mm –1 was achieved, exceeding the performance of most previously reported X-ray imaging scintillators. These findings offer a promising design strategy for advancing QS-based materials toward high-performance X-ray imaging applications.

antenna effect↗

Vibronic exciton model for low bandgap donor–acceptor polymers

In this study, a vibronic exciton model is introduced to describe the excited state band structure and associated absorption spectra of low bandgap donor–acceptor conjugated polymers. The Hamiltonian is represented in a diabatic basis consisting of Frenkel-like donor and acceptor fragment excitations as well as charge-transfer (CT) excitations between neighboring fragments. States are coupled to each other through electron and hole transfer as well as Coulombically, through interacting fragment transition dipole moments. Local vibronic coupling involving the prominent aromatic-quinoidal vibrational mode, which is responsible for pronounced vibronic progressions in most conjugated oligomers and polymers, is also included. The DAD repeat unit is shown to behave like a J-aggregate trimer, driven by both the sizable in-phase electron and hole transfer integrals between donor and acceptor fragments as well as negative Coulomb coupling between donor and acceptor fragment excitations. The J-aggregate behavior is enhanced in the polymer limit through inter-repeat unit coupling, with the 0–0 vibronic peak significantly enhanced in the lowest-energy near-IR band. In addition, the radiative rate is enhanced by the number of coherently connected repeat units. The near-IR band is shown to possess roughly equal admixtures of CT and Frenkel-like excitations. Applications are made to the polymer PffBT4T-2DT, with the simulated absorption spectrum quantitatively capturing the salient features of the measured spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multidimensional Coherent Spectroscopy of Molecular Polaritons: Langevin Approach

We present a microscopic theory for nonlinear optical spectroscopy of N molecules in an optical cavity. Using the Heisenberg-Langevin equation, an analytical expression is derived for the time- and frequency-resolved signals accounting for arbitrary numbers of vibrational excitations. We identify clear signatures of the polariton-polaron interaction from multidimensional projections of the signal, e.g., pathways and timescales. Cooperative dynamics of cavity polaritons against intramolecular vibrations is revealed, along with a crosstalk between long-range coherence and vibronic coupling that may lead to localization effects. Our results further characterize the polaritonic coherence and the population transfer that is slower.

74 ATOMIC AND MOLECULAR PHYSICS↗

Hydrodynamic instabilities and heat transfer characteristics in the duct flow of a fluid in the supercritical thermodynamic regime

The behavior of fluids at supercritical thermodynamic conditions is inherently complex due to large variations in thermodynamic and transport properties. Recent numerical and experimental investigations illustrate ongoing interest for these fluids, especially supercritical CO 2 and supercritical water, for a variety of applications. For example, supercritical water reactors (SCWR) operate in this extreme condition of high-pressure and temperature, resulting in highly dynamic flow fields and unexpected heat transfer regimes. The potential heat transfer benefits in this regime are directly associated with the extreme variations in thermodynamic and transport properties, which occur at, and above, the critical point. This work characterizes the hydrodynamic instabilities that arise for fluids at supercritical thermodynamic conditions when buoyancy forces are significant. Two specific configurations are considered, a natural convection cavity flow, and a mixed convection, heated, horizontal channel flow. Natural convection flow in a cavity is a classical configuration with expected behavior below the critical point. This configuration aids in characterizing the effect of the variable properties in the supercritical thermodynamic regime. Further, limited studies in the existing literature have been conducted for low-Reynolds and intermediate-Rayleigh numbers, mixed-convection channel flows for supercritical water, which is the focus of the channel flow configuration. To investigate the thermally driven hydrodynamic instabilities in this regime, a high-order fully-implicit numerical method is used. Such strong variations in thermophysical properties (in particular, density) are difficult to simulate and an altogether compressible framework is needed. Therefore, the compressible Navier-Stokes equations are solved without any additional assumptions. The fully implicit, high-order in space and time, reconstructed discontinuous Galerkin method as implemented within the multi-physics code called ALE3D (Arbitrary Lagrangian and Eulerian in 2D and 3D), developed at Lawrence Livermore National Laboratory (LLNL), is used. This fully implicit, L-stable method accurately captures the compressible nature of the ow in the limit of very low Mach number. It has been widely accepted that above the critical point, only one phase is observed. However, recent research has indicated the existence of the distinct gas-like and liquid-like regions separated by the Widom line, the locus of the maxima of the specific heat. Along the Widom line, density decreases 6-fold, viscosity drops by a factor of 2, while specific heat spikes by an order of magnitude. These variations, specifically in density and viscosity, produce a thick pseudo-interface and flow dynamics behavior akin to film boiling. A pseudo-film at the heated wall of the cavity and the horizontal channel is observed where buoyancy forces induce mixing through the specific configurations. Further the local Rayleigh and Richardson numbers provide maps of the flow field and the buoyancy forces driving the microscopic mixing. In the first chapter, I describe a background of supercritical fluid and the various applications. The second chapter focuses on the mathematical model and numerical method used for simulations, where a description of the equation of state for supercritical water is described. The third chapter focuses on the natural convection cavity with a heated bottom wall. In this cavity a gas-like and a liquid-like flow within the supercritical thermodynamic regime are observed. The fourth chapter focuses on a forced convection, horizontal channel, distinguishing between the gas-like, liquid-like, and mixed flow regimes. Mixed convection flow, with the addition of gravitational forces in the horizontal channel show the influence of variable properties on the hydrodynamic development, heat transfer, and rising instabilities. The last chapter of this research focuses on characterizing the unstable hydrodynamics through time-averaging processes and analysis of the movement of energy through the developing plumes.

42 ENGINEERING↗

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗