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At least 181 records · Page 10

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Radiation of the plant pyridoxal 5'-phosphate (PLP)-dependent aromatic L -amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L -amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. In this paper, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

59 BASIC BIOLOGICAL SCIENCES↗

Application of molecular convergent close-coupling cross sections in a collisional radiative model for the triplet system of molecular hydrogen

Collisional radiative (CR) models for molecular hydrogen are of high relevance for performing qualitative and quantitative analysis of excited-state population densities measured in plasmas or predicting the dependence of plasma emission on parameter variations. Although the development of such models for H 2 started decades ago, major uncertainties still exist regarding the most important set of input parameters, namely the cross sections for electron-impact excitation. The deviations between cross sections from different datasets are particularly pronounced in the energy region close to the threshold energy, strongly increasing the uncertainty of CR models applied to low-temperature plasmas. This paper presents experimental validation of a set of newly calculated non ro-vibrationally resolved electron-impact cross sections calculated for the triplet system of H 2 using the molecular convergent close-coupling method in the adiabatic-nuclei formulation. These cross sections are implemented into a CR model based on the flexible solver Yacora. A first comparison of CR calculations with the different datasets to experimentally-determined population densities is performed at a planar ICP discharge for varying pressure (between 1 and 10 Pa) and RF power (between 700 and 1100 W). For the experimentally-accessible electron temperature and density range (2.5–10 eV and 1.8–3.3 × 10 16 m –3 , respectively), very good agreement between the model and experiment is obtained using the new data set, in contrast to previously used cross sections.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Rapidly-convergent flux-surface shape parameterization

We propose a novel flux-surface parameterization suitable for local MHD equilibrium calculations with strongly-shaped flux surfaces. The method is based on a systematic expansion in a small number of intuitive shape parameters, and reduces to the well-known Miller D-shaped parameterization in the limit where some of the coefficients are set to zero. Here, the new parameterization is valid for up-down asymmetric plasmas and provides an improvement to the Miller form. Simultaneously, the method is rapidly convergent and requires only about half the number of shape parameters as a general Fourier representation in the pedestal.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Polarized photoelectrons from converging vector waves

Abstract This paper investigates the spin characteristics of photoelectrons when hydrogen-like ions are centro-symmetrically irradiated with converging vector waves—a non-paraxial form of structured light. For a photon with given total angular momentum and third component thereof, photoelectrons with both helicities are obtained—in contrast to the fixed helicities produced by left- or right-circularly polarized light. The angular distribution of photoelectrons is broadly tunable through the radiation mode numbers, and opposite helicities can be extracted in synchronism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Non-invasive imaging reveals convergence in root and stem vulnerability to cavitation across five tree species

Root vulnerability to cavitation is challenging to measure and under-represented in current datasets. This gap limits the precision of models used to predict plant responses to drought because roots comprise the critical interface between plant and soil. In this study, we measured vulnerability to drought-induced cavitation in woody roots and stems of five tree species (Acacia aneura, Cedrus deodara, Eucalyptus crebra, Eucalytus saligna, and Quercus palustris) with a wide range of xylem anatomies. X-ray microtomography was used to visualize the accumulation of xylem embolism in stems and roots of intact plants that were naturally dehydrated to varying levels of water stress. Vulnerability to cavitation, defined as the water potential causing a 50% loss of hydraulic function (P 50 ), varied broadly among the species (–4.51 MPa to –11.93 MPa in stems and –3.13 MPa to –9.64 MPa in roots). The P 50 of roots and stems was significantly related across species, with species that had more vulnerable stems also having more vulnerable roots. While there was strong convergence in root and stem vulnerability to cavitation, the P 50 of roots was significantly higher than the P 50 of stems in three species. However, the difference in root and stem vulnerability for these species was small; between 1% and 31% of stem P 50 . Thus, while some differences existed between organs, roots were not dramatically more vulnerable to embolism than stems, and the differences observed were less than those reported in previous studies. Further study is required to evaluate the vulnerability across root orders and to extend these conclusions to a greater number of species and xylem functional types.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Tolerance of Zirconium Diboride under Electron Irradiation through in-situ Convergent Beam Electron Diffraction and Energy-dispersive X-ray Spectroscopy

Zirconium diboride (ZrB 2 ) is a ultra-high temperature ceramic with high melting temperature (>3000 K), super strength and hardness, good thermal conductivity, and excellent resistance to plasma erosion and chemical erosion, being widely applied in hypersonic flight, arc-electrodes, refractory materials, and plasma-facing materials in fusion reactors. Therefore, the structural stability of the material is essential for the applications. Up to now, the material was investigated under neutron irradiation and high-energy ion irradiations. It was reported that the neutron irradiation caused swelling and catastrophic cracking. High-energy ions (30 keV He + ) changed the surface morphology and caused the bright blue and brown colors on ZrB 2 surfaces between 920 K and 1120 K. The electron irradiation tolerance of the material has not been reported yet. Here we used convergent beam electron diffraction (CBED) and energy-dispersive X-ray spectroscopy (EDS) to investigate structural tolerances of ZrB 2 crystals under high-energy electrons at room temperature under vacuum. Finally, the investigation would benefit the understanding of its structural tolerance at microscales.

42 ENGINEERING↗

A transmission hologram for slitless spectrophotometry on a convergent telescope beam. 1. Focus and resolution

We report in this paper the test of a plane holographic optical element to be used as an aberration-corrected grating for a slitless spectrograph, inserted in a convergent telescope beam. Our long-term objective is the optimization of a specific hologram to switch the auxiliary telescope imager of the Vera Rubin Observatory into an accurate slitless spectrograph, dedicated to the atmospheric transmission measurement. We present and discuss here the promising results of tests performed with prototype holograms at the CTIO $0.9\,$m telescope during a run of 17 nights in 2017 May–June. After their on-sky geometrical characterization, the performances of the holograms as aberration-balanced dispersive optical elements have been established by analysing spectra obtained from spectrophotometric standard stars and narrow-band emitter planetary nebulae. Thanks to their additional optical function, our holographic disperser prototypes allow us to produce significantly better focused spectra within the full visible wavelength domain $[370,1050]\,$nm than a regular grating, which suffers from strong defocusing and aberrations when used in similar conditions. We show that the resolution of our slitless on-axis spectrograph equipped with the hologram approaches its theoretical performance. While estimating the benefits of a hologram for the spectrum resolution, the roadmap to produce a competitive holographic element for the Vera Rubin Observatory auxiliary telescope has been established.

79 ASTRONOMY AND ASTROPHYSICS↗

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Evolutionary Biology↗

Convergent close-coupling calculations of electrons scattering on electronically excited molecular hydrogen

We use the adiabatic-nuclei molecular convergent close-coupling method to perform calculations of 0.01–1000 eV electrons scattering on the c 3 Π u , a 3 $Σ$$^{+}_{g}$, B 1 $Σ$$^{+}_{u}$, C 1 Π u , and EF 1 $Σ$$^{+}_{g}$ states of H 2 in the v=0 vibrational level. Elastic, superelastic, ionization, and grand-total cross sections are presented, as well as cross sections for excitation of the n=2–3 singlet and triplet states of H 2 (where n is the atomic-limit principle quantum number). Comparison with available theoretical results is made. Good agreement is found with the recent R-matrix results [J. Phys. B 53, 245203 (2020)] for most of the exchange and dipole-forbidden transitions, but not for the dipole-allowed transitions. Here, the sources of disagreement were found to be an unconverged partial-wave expansion and the utilization of the fixed-nuclei approximation (as opposed to adiabatic-nuclei) in the R-matrix calculations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Convergent close-coupling calculations of electron scattering on HeH +

Here, we use the molecular convergent close-coupling (MCCC) method to perform calculations of 10–1000 eV electron scattering on the ground state of HeH + . Cross sections are presented for excitation of the n = 2 – 3 singlet and triplet states (where n is the united-atoms-limit principle quantum number), as well as ionization. We also present cross sections for He + and H + ion production following dissociative excitation and ionization. The He + production cross section is compared with the measurements of Lecointre, Jureta, Urbain, and Defrance [J. Lecointre, J. J. Jureta, X. Urbain, and P. Defrance, J. Phys. B At. Mol. Opt. Phys. 47, 015203 (2014)]. We find that the MCCC results are up to 30% higher than experiment.

74 ATOMIC AND MOLECULAR PHYSICS↗

Elastic scattering and rotational excitation of H 2 by electron impact: Convergent close-coupling calculations

We apply the adiabatic-nuclei molecular convergent close-coupling (MCCC) method to the study of elastic scattering and rotational excitation of H 2 by 0.01–20-eV electrons. Integral cross sections are presented for all rotational transitions with |Δ⁢N| ≤ 2 and N i = 0–31 within the v = 0 vibrational level and differential cross sections for a selection of transitions. Agreement with the available measurements and previous calculations is mostly excellent, depending on the transition and incident energy. Finally, we suggest possible reasons, and argue for the accuracy of the MCCC data.

74 ATOMIC AND MOLECULAR PHYSICS↗

Convergent close-coupling calculations of electron scattering on LiH

Cross sections for electron scattering on the ground state of LiH are calculated using the molecular convergent close-coupling method. The fixed-nuclei approximation is utilized, and calculations are performed at the mean internuclear separation of 3.06 𝑎 0 for projectile energies ranging from 0.1 to 500 eV. Here, a model-potential approach is utilized to treat the LiH molecule as a two-electron system, and good agreement is found with the literature for various properties of the structure model. Cross sections are presented for elastic scattering, excitation to several electronic states, and ionization. Comparison is made with existing results, and qualitative agreement is found with small close-coupling calculations at low projectile energies. Good agreement is found with first-order results at high projectile energies.

74 ATOMIC AND MOLECULAR PHYSICS↗

Exact matrix product state representation and convergence of a fully correlated electronic wavefunction in the infinite-basis limit

Here In this paper we present the exact representation of a fully correlated electronic wavefunction as the single-particle basis approaches completeness. It consists of a half-infinite chain of matrices of exponentially increasing size. The complete basis limit is illustrated numerically using the density-matrix renormalization-group method by computing the core-valence entanglement in the C 2 ground state in increasing subsets of cc-pVTZ and pVQZ bases until convergence is reached.

36 MATERIALS SCIENCE↗

Constraining cosmology with the CMB × line intensity mapping-nulling convergence

Lensing reconstruction maps from the cosmic microwave background (CMB) provide direct observations of the matter distribution of the universe without the use of a biased tracer. Such maps, however, constitute projected observables along the line of sight that are dominated by their low-redshift contributions. To cleanly access high-redshift information, Maniyar et al., [Phys. Rev. D 105, 083509 (2022)] showed that a linear combination of lensing maps from both CMB and line intensity mapping (LIM) observations can exactly null the low-redshift contribution to CMB lensing convergence. In this paper we explore the scientific returns of this nulling technique. Here, we show that LIM-nulling estimators can place constraints on standard Λ⁢CDM plus neutrino mass parameters that are competitive with traditional CMB lensing. Additionally, we demonstrate that as a clean probe of the high-redshift universe, LIM nulling can be used for model-independent tests of cosmology beyond Λ⁢CDM and as a probe of the high-redshift matter power spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗

New Probe of the High- z Baryon Acoustic Oscillation Scale: BAO Tomography with CMB × LIM -Nulling Convergence

Standard rulers such as the baryon acoustic oscillation (BAO) scale serve as workhorses for precision tests of cosmology, enabling distance measurements that probe the geometry and expansion history of our Universe. Aside from BAO measurements from the cosmic microwave background (CMB), most standard ruler techniques operate at relatively low redshifts and depend on biased tracers of the matter density field. In a companion paper, we explored the scientific reach of nulling estimators, where CMB lensing convergence maps are cross-correlated with linear combinations of similar maps from line intensity mapping (LIM) to precisely null out the low-redshift contributions to CMB lensing. We showed that nulling estimators can be used to constrain the high redshift matter power spectrum and showed that this spectrum exhibits discernible BAO features. Here we propose using these features as a standard ruler at high redshifts that does not rely on biased tracers. Forecasting such a measurement at z ~ 5, we find that next-generation instruments will be able to constrain the BAO scale to 7.2% precision, while our futuristic observing scenario can constrain the BAO scale to 4% precision. In conclusion, this constitutes a fundamentally new kind of BAO measurement during early epochs in our cosmic history.

79 ASTRONOMY AND ASTROPHYSICS↗

Conditional diffusion machine-learning framework for mapping valence electron distribution from convergent beam electron diffraction

Quantitative convergent beam electron diffraction (CBED) enables determination of aspherical valence electron distributions through refinement of low-order structure factors, which are highly sensitive to chemical bonding and charge density variations. However, conventional quantitative CBED (QCBED) requires solving a highly nonlinear inverse problem with many coupled parameters, and computationally intensive dynamical diffraction calculations, making it time-consuming and difficult to apply to complex systems. More broadly, reconstructing charge density and orbital electron distribution from diffraction data has long been a central challenge in both x-ray and electron crystallography. Here, in this study, we introduce an artificial-intelligence (AI)-based framework that replaces traditional refinement with a data-driven inverse solver. Using a large synthetic CBED dataset generated by Bloch-wave simulations, we train a conditional diffusion model to directly infer crystal structural parameters and multipole density formalism parameters, and hence valence electron distributions, from CBED patterns alone. By learning from forward simulations across realistic parameter space, the model effectively solves the inverse problem. Compared with direct regression approaches, the diffusion-based framework provides posterior parameter distributions for rigorous uncertainty quantification while preserving quantitative fidelity and reducing analysis time by orders of magnitude. By eliminating the need for external single-crystal x-ray diffraction data and complex nonlinear refinement, this approach enables practical, high-throughput, and in situ quantitative CBED, enabling real-time mapping of valence electron distributions and their correlation with functional responses in quantum and energy materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

HPC and Cloud Convergence Beyond Technical Boundaries: Strategies for Economic Sustainability, Standardization, and Data Accessibility

At the IEEE/ACM International Conference for High-Performance Computing, Networking, Storage, and Analysis (SC23), held in Denver, experts discussed the convergence of high-performance computing and cloud computing. Experts explored how this integration could address current scientific computing limitations, enhance computational capabilities, and foster global collaboration while focusing on economic, security, technical, and community challenges and opportunities.

97 MATHEMATICS AND COMPUTING↗

Convergence of Energy and IT Sectors

Today there has never been a more profound codependence and synergetic convergence, such as the one between the energy and IT sectors, and the industries will need to work together more closely to meet today’s growing data center power demands.

AI↗