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At least 145 records · Page 8

Assessing density functionals for describing methane dissociative chemisorption on Pt(110)-(2×1) surface

In this work, we explore the suitability of several density functionals with the generalized gradient approximation (GGA) and beyond for describing the dissociative chemisorption of methane on the reconstructed Pt(110)-(2×1) surface. The bulk and surface structures of the metal, methane adsorption energy, and dissociation barrier are used to assess the functionals. A van der Waals corrected GGA functional (optPBE-vdW) and a metaGGA functional with van der Waals correction (MS PBEl-rVV10) are selected for ab initio molecular dynamics calculations of the sticking probability. Our results suggest that the use of these two functionals may lead to a better agreement with existing experimental results, thus serving as a good starting point for future development of reliable machine-learned potential energy surfaces for the dissociation of methane on the Pt(110)-(2×1) surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Measurement-based quantum simulation of Abelian lattice gauge theories

Numerical simulation of lattice gauge theories is an indispensable tool in high energy physics, and their quantum simulation is expected to become a major application of quantum computers in the future. In this work, for an Abelian lattice gauge theory in d d spacetime dimensions, we define an entangled resource state (generalized cluster state) that reflects the spacetime structure of the gauge theory. We show that sequential single-qubit measurements with the bases adapted according to the former measurement outcomes induce a deterministic Hamiltonian quantum simulation of the gauge theory on the boundary. Our construction includes the (2+1) ( 2 + 1 ) -dimensional Abelian lattice gauge theory simulated on three-dimensional cluster state as an example, and generalizes to the simulation of Wegner’s lattice models M_{(d,n)} M ( d , n ) that involve higher-form Abelian gauge fields. We demonstrate that the generalized cluster state has a symmetry-protected topological order with respect to generalized global symmetries that are related to the symmetries of the simulated gauge theories on the boundary.Our procedure can be generalized to the simulation of Kitaev’s Majorana chain on a fermionic resource state. We also study the imaginary-time quantum simulation with two-qubit measurements and post-selections, and a classical-quantum correspondence, where the statistical partition function of the model M_{(d,n)} M ( d , n ) is written as the overlap between the product of two-qubit measurement bases and the wave function of the generalized cluster state.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Computation and illustration of the generalized order restricted criterion (GORIC) for shape constrained spline functions

The selection of a model among alternative models that include inequality constraints is a complex task. The generalized order restricted criterion (GORIC) is a suitable approach to do so. However, the GORIC proves challenging to compute in the general case. This report discusses a number of methods to compute the GORIC and illustrates its use with a didactic example.

97 MATHEMATICS AND COMPUTING↗

Transient work function gating: A new photoemission regime

We present the theoretical basis for a new photoemission regime, transient work function gating (TWFG), which temporally and energetically gates photoemission and produces near-threshold photoelectrons with thermally limited emittance, percent-level quantum efficiency, and control over temporal coherence. The technique consists of actively gating the work function of a generalized photocathode using a non-ionizing long-wavelength optical field to produce an adiabatic modulation of the carrier density at their surface. We examine TWFG as a means to circumvent the long-standing trade-off between low emittance and high quantum efficiency, untethered to particle source or photocathode specifics. TWFG promises new opportunities in photoemission physics for next generation electron and accelerator-based x-ray photon sources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Superintegrable systems from block separation of variables and unified derivation of their quadratic algebras

Highlights: • A new method for constructing D-dimensional minimally superintegrable systems. • Superintegrable systems from block coordinate separation of variables. • Unified derivation of quadratic symmetry algebras via gauge transformations. - Abstract: We present a new method for constructing D-dimensional minimally superintegrable systems based on block coordinate separation of variables. We give two new families of superintegrable systems with N (N≤D) singular terms of the partitioned coordinates and involving arbitrary functions. These Hamiltonians generalize the singular oscillator and Coulomb systems. We derive their exact energy spectra via separation of variables. We also obtain the quadratic algebras satisfied by the integrals of motion of these models. We show how the quadratic symmetry algebras can be constructed by novel application of the gauge transformations from those of the non-partitioned cases. We demonstrate that these quadratic algebraic structures display a universal nature to the extent that their forms are independent of the functions in the singular potentials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Global study of separable pairing interaction in covariant density functional theory

A systematic global investigation of pairing properties based on all available experimental data on pairing indicators has been performed for the first time in the framework of covariant density functional theory. It is based on the separable pairing interaction. The optimization of the scaling factors of this interaction to experimental data clearly reveals its isospin dependence in the neutron subsystem. However, the situation is less certain in the proton subsystem since similar accuracy of the description of pairing indicators can be achieved both with isospin-dependent and mass-dependent scaling factors. The differences in the functional dependencies of scaling factors lead to uncertainties in the prediction of proton and neutron pairing properties which are especially pronounced at high isospin and could have a significant impact on some physical observables. For a given part of the nuclear chart the scaling factors for spherical nuclei are smaller than those for deformed ones; this feature exists also in nonrelativistic density functional theories. Furthermore, its origin is traced back to particle-vibration coupling in odd-A nuclei which is missing in all existing global studies of pairing. Although the present investigation is based on the NL5(E) covariant energy density functional (CEDF), its general conclusions are expected to be valid also for other CEDFs built at the Hartree level.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome

In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.

60 APPLIED LIFE SCIENCES↗

Perturbative quantum evolution of the gravitational state and dressing in general backgrounds

This paper sets up a perturbative treatment of the evolving quantum state of a gravitational system, in a Schrödinger-like picture, working about a general background. This connects gauge symmetry, the constraints, gravitational dressing, and evolution. Starting with a general time slicing, we give a simple derivation of the relation between the constraints, the Hamiltonian, and its well-known boundary term. Among different approaches to quantization with constraints, we focus on a “gauge-invariant canonical quantization,” which is developed perturbatively in the gravitational coupling. The leading-order solution of the constraints (including the Wheeler-DeWitt equation) for perturbations about the background is given in terms of an explicit construction of gravitational dressings built using certain generalized Green’s functions; different such dressings corresponding to adding propagating gravitational waves to a particular solution of the constraints. Dressed operators commute with the constraints, expressing their gauge invariance, and have an algebraic structure differing significantly from the undressed operators of the underlying field theory. These operators can act on the vacuum to create dressed states, and evolution of general such states is then generated by the boundary Hamiltonian, and alternately may be characterized using other relational observables. This provides a concrete approach to studying perturbative time evolution, including the leading gravitational backreaction, of quantum states of black holes with flat or anti–de-Sitter asymptotics, for example on horizon-crossing slices. This description of evolution in turn provides a starting point for investigating possibly important corrections to quantum evolution, that go beyond quantized general relativity. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

r 2 SCAN-D4: Dispersion corrected meta-generalized gradient approximation for general chemical applications

We combine a regularized variant of the strongly constrained and appropriately normed semilocal density functional with the latest generation semi-classical London dispersion correction. The resulting density functional approximation r 2 SCAN-D4 has the speed of generalized gradient approximations while approaching the accuracy of hybrid functionals for general chemical applications. We demonstrate its numerical robustness in real-life settings and benchmark molecular geometries, general main group and organo-metallic thermochemistry, and non-covalent interactions in supramolecular complexes and molecular crystals. Main group and transition metal bond lengths have errors of just 0.8%, which is competitive with hybrid functionals for main group molecules and outperforms them for transition metal complexes. The weighted mean absolute deviation (WTMAD2) on the large GMTKN55 database of chemical properties is exceptionally small at 7.5 kcal/mol. This also holds for metal organic reactions with an MAD of 3.3 kcal/mol. The versatile applicability to organic and metal–organic systems transfers to condensed systems, where lattice energies of molecular crystals are within the chemical accuracy (errors <1 kcal/mol).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Perspectives on van der Waals Density Functionals: The Case of TiS 2

The van der Waals interaction is of foundational importance for a wide variety of physical systems. In particular, van der Waals forces lie at the heart of potential device technologies that may be realized from the functional organization of layered two-dimensional (2D) nanomaterials. Furthermore, for intermediate to large-scale applications modeling, van der Waals density functionals have become the de facto choice for first-principles calculations. In particular, the vdW-DF family of functionals have provided a systematic approach to this theoretically challenging problem. While much progress has been made, there remains room for improvement in the microscopic description of vdW forces from these density functionals. In this work, we compute benchmark results for the binding energy and the electronic density response to binding in TiS2 via accurate diffusion quantum Monte Carlo calculations. We compare these benchmark data to results obtained from local, semilocal, and van der Waals functionals. In particular, we gauge the quality of the original vdW-DF/vdW-DF2 functionals, as well as updated variants such as vdW-DF-C09, vdW-DF-optB88, vdW-DF-optB86b, and vdW-DF2-B86R. We find a close relationship between the accuracy of predicted interlayer separation distances and binding energies for TiS 2 , with the vdW-DF-optB88 functional performing very well in terms of both quantities. In general, the more recently developed functionals are systematic improvements over older ones. However, when considering the response of the electron density to binding, we find that local-density approximation (LDA) and PBEsol generally outperform the vdW-DF functionals in describing the interlayer charge accumulation with vdW-DF-C09 variants performing the best overall.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Horizon constraints on holographic Green’s functions

We explore a new class of general properties of thermal holographic Green’s functions that can be deduced from the near-horizon behaviour of classical perturbations in asymptotically anti-de Sitter spacetimes. We show that at negative imaginary Matsubara frequencies and appropriate complex values of the wavenumber the retarded Green’s functions of generic operators are not uniquely defined, due to the lack of a unique ingoing solution for the bulk perturbations. From a boundary perspective these ‘pole-skipping’ points correspond to locations in the complex frequency and momentum planes at which a line of poles of the retarded Green’s function intersects with a line of zeroes. As a consequence the dispersion relations of collective modes in the boundary theory at energy scales ω ~ T are directly constrained by the bulk dynamics near the black-brane horizon. For the case of conserved U(1) current and energy-momentum tensor operators we give examples where the dispersion relations of hydrodynamic modes pass through a succession of poleskipping points as real wavenumber is increased. We discuss implications of our results for transport, hydrodynamics and quantum chaos in holographic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Merging of the superbanana plateau and $\sqrt{v}$ transport regimes in nearly quasisymmetric stellarators

We report alpha particle confinement is one of the most demanding issues for stellarators. It now seems clear that it is possible to design optimized stellarators that confine the background plasma at near tokamak radial transport levels. Moreover, adequate collisionless alpha particle confinement is possible in the core of a highly optimized stellarator. Here, the collisional confinement of barely trapped alphas in an optimized stellarator is considered by accounting for the resonance due to the reversal in direction of the drift within a flux surface and investigating the sensitive role of magnetic shear in keeping this resonance close to the passing boundary in some nearly quasisymmetric stellarator configurations. The treatment relies on a narrow collisional boundary layer formulation that combines the responses of both these resonant pitch angle alphas and the remaining barely trapped alphas. A novel merged regime treatment leads to explicit expressions for the energy diffusivity for both superbanana plateau (or resonant plateau) and $\sqrt{v}$ transport in the large aspect ratio limit for a slowing down tail alpha distribution function, where v is the effective pitch angle scattering collision frequency of the trapped alphas off the background ions. Depending on the details of the optimization scheme and the sign of the magnetic shear, modest magnetic shear can be used to reduce superbanana (or resonant) plateau transport to below the $\sqrt{v}$ transport level. In addition, a quasilinear equation retaining spatial diffusion is derived for a general alpha distribution function that allows the radial alpha transport to modify the distribution so it is no longer isotropic in velocity space.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Forward and Off-Forward Parton Distributions from Lattice QCD

The interpretation of (semi-)inclusive and certain exclusive scattering processes relies on the factorization of hard parton level cross sections from long-range and non-perturbative parton correlations. The familiar Parton Distribution Functions (PDFs) and Generalized Parton Distributions quantify the non-perturbative dynamics in these situations and address a number of key questions surrounding the structure of hadrons. A certain class of matrix elements accessible in lattice QCD, so called Lattice Cross Sections, have been shown to factorize into these collinear distributions in a manner akin to the factorization of hadronic cross sections. In the short-distance regime, matrix elements of space-like separated two-current operators and parton bilinears can be expressed as the convolution of perturbative coefficient functions and the PDFs. Matrix elements of this type are isolated in the pion and nucleon, each offering a glimpse of the unpolarized valence quark content of these phenomenologically important hadronic states. The calculations within the nucleon represent the first application of the distillation spatial smearing paradigm to the collinear structure of hadrons, and is found to offer higher precision data compared to similar calculations in the literature. A novel method to obtain PDFs from these lattice data, while simultaneously controlling systematic effects, is developed and applied to the nucleon dataset. The coordinate space factorization of space-like separated parton bilinears has also recently been extended to include Generalized Parton Distributions. Preliminary results in off-forward nucleon matrix elements using distillation are explored.

Egerer, Colin↗

Synthetic and Mechanistic Implications of Chlorine Photoelimination in Nickel/Photoredox C(sp 3 )–H Cross-Coupling

In recent years, the development of light-driven reactions has contributed numerous advances in synthetic organic chemistry. A particularly active research area combines photoredox catalysis with nickel catalysis to accomplish otherwise inaccessible cross-coupling reactions. In these reactions, the photoredox catalyst absorbs light to generate an electronically excited charge-transfer state that can engage in electron or energy transfer with a substrate and the nickel catalyst. Our group questioned whether photoinduced activation of the nickel catalyst itself could also contribute new approaches to cross-coupling. Over the past 5 years, we have sought to advance this hypothesis for the development of a suite of mild and site-selective C(sp 3 )–H cross-coupling reactions with chloride-containing coupling partners via photoelimination of a Ni–Cl bond. On the basis of a report from the Nocera laboratory, we reasoned that photolysis of a Ni(III) aryl chloride species, generated by single-electron oxidation of a typical Ni(II) intermediate in cross-coupling, might allow for the catalytic generation of chlorine atoms. Combining this with the ability of Ni(II) to accept alkyl radicals, we hypothesized that photocatalytically generated chlorine atoms could mediate hydrogen atom transfer (HAT) with C(sp 3 )–H bonds to generate a substrate-derived alkyl radical that is captured by the Ni center in cross-coupling. A photoredox catalyst was envisioned to promote the necessary single-electron oxidation and reduction of the Ni catalyst to facilitate an overall redox-neutral process. Overall, this strategy would offer a visible-light-driven mechanism for chlorine radical formation enabled by the sequential capture of two photons. As an initial demonstration, we developed a Ni/photoredox-catalyzed α-oxy C(sp 3 )–H arylation of cyclic and acyclic ethers. This method was extended to a mild formylation of abundant and complex aryl chlorides through selective 2-functionalization of 1,3-dioxolane. Seeking to develop a suite of reactions that introduce carbon at all different oxidation states, we explored C(sp 3 )–H cross-coupling with trimethyl orthoformate, a common laboratory solvent. We found that trimethyl orthoformate serves as a source of methyl radical for a methylation reaction via β-scission from a tertiary radical generated upon chlorine-mediated HAT. Since chlorine radical is capable of abstracting unactivated C(sp 3 )–H bonds, our efforts have also been directed at cross-coupling with a range of feedstock chemicals, such as alkanes and toluenes, along with late-stage intermediates, using chloroformates as coupling partners. Overall, this platform enables access to valuable synthetic transformations with (hetero)aryl chlorides, which despite being the most ubiquitous and inexpensive aryl halide coupling partners, are rarely reactive in Ni/photoredox catalysis. Little is known about the photophysics and photochemistry of organometallic Ni complexes relevant to cross-coupling. We have conducted mechanistic investigations, including computational, spectroscopic, emission quenching, and stoichiometric oxidation studies, of Ni(II) aryl halide complexes common to Ni/photoredox reactions. These studies indicate that chlorine radical generation from excited Ni(III) is operative in the described C(sp 3 )–H functionalization methods. More generally, the studies illustrate that the photochemistry of cross-coupling catalysts cannot be ignored in metallaphotoredox reactions. We anticipate that further mechanistic understanding should facilitate catalyst design and lead to the development of new synthetic methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing the Limitations of Self-Interaction-Corrected Functionals for Describing the Hydrated Electron

Simulating the hydrated electron using density functional theory is challenging due to the prevalence of self-interaction error in standard functionals. Hybrid functionals like PBEh(40) can reasonably describe the chemistry of an excess electron in water and partially mitigate self-interaction error by incorporating exact Hartree–Fock exchange, but they are computationally expensive making them impractical for large-scale and long-time ab initio molecular dynamics simulations. Explicit self-interaction correction schemes that are applied on an orbital-by-orbital basis offer a potential alternative when the correction is limited to the singly occupied molecular orbital obtained with a generalized gradient approximation functional. Here, we examine whether the Perdew–Zunger self-interaction correction scheme applied to the revPBE functional can provide a computationally efficient and physically sensible alternative to PBEh(40) for the hydrated electron. We find that functionals incorporating a self-interaction correction scheme should be viewed with caution when applied to the hydrated electron and its reactivity. Furthermore, we show that it is critical to consider extensive sampling and diverse chemical environments when validating their performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity

How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes, resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements, and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic (press) disturbance of the magnitude of organic carbon inputs with acute (pulse) effects of physical disturbance by tillage and chemical disturbance due to inorganic fertilization and pesticide application. We show that because of the variety of ways it can be assessed, biodiversity—here based on microbial small subunit rRNA gene phylotypes—does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with rRNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea, and fungi do not share a common response to land management change, and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately.

59 BASIC BIOLOGICAL SCIENCES↗

RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori

Abstract Ribonucleases are central players in post-transcriptional regulation, a major level of gene expression regulation in all cells. Here, we characterized the 3′-5′ exoribonuclease RNase R from the bacterial pathogen Helicobacter pylori. The ‘prototypical’ Escherichia coli RNase R displays both exoribonuclease and helicase activities, but whether this latter RNA unwinding function is a general feature of bacterial RNase R had not been addressed. We observed that H. pylori HpRNase R protein does not carry the domains responsible for helicase activity and accordingly the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The lack of RNase R helicase domains is widespread among the Campylobacterota, which include Helicobacter and Campylobacter genera, and this loss occurred gradually during their evolution. An in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori was discovered. Purified RhpA facilitates the degradation of double stranded RNA by HpRNase R, showing that this complex is functional. HpRNase R has a minor role in 5S rRNA maturation and few targets in H. pylori, all included in the RhpA regulon. We concluded that during evolution, HpRNase R has co-opted the RhpA helicase to compensate for its lack of helicase activity.

Tejada-Arranz, Alejandro↗