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At least 37 records · Page 2

Off-shell Partition Functions in 3d Gravity

We explore three-dimensional gravity with negative cosmological constant via canonical quantization. We focus on chiral gravity which is related to a single copy of PSL(2,R) Chern-Simons theory and is simpler to treat in canonical quantization. Its phase space for an initial value surface Σ is given by the appropriate moduli space of Riemann surfaces. We use geometric quantization to compute partition functions of chiral gravity on three-manifolds of the form Σ×S 1 , where Σ can have asymptotic boundaries. Most of these topologies do not admit a classical solution and are thus not amenable to a direct semiclassical path integral computation. We use an index theorem that expresses the partition function as an integral of characteristic classes over phase space. In the presence of n asymptotic boundaries, we use techniques from equivariant cohomology to localize the integral to a finite-dimensional integral over $\overline{M}$ g,n , which we evaluate in low genus cases. Higher genus partition functions quickly become complicated since they depend in an oscillatory way on Newton's constant. There is a precise sense in which one can isolate the non-oscillatory part which we call the fake partition function. We establish that there is a topological recursion that computes the fake partition functions for arbitrary Riemann surfaces Σ. As a result, there is a scaling limit in which the model reduces to JT gravity and our methods give a novel way to compute JT partition functions via equivariant localization.

Classical and Quantum Gravity↗

Fourier Neural Networks as Function Approximators and Differential Equation Solvers

We present a Fourier neural network (FNN) that can be mapped directly to the Fourier decomposition. The choice of activation and loss function yields results that replicate a Fourier series expansion closely while preserving a straightforward architecture with a single hidden layer. The simplicity of this network architecture facilitates the integration with any other higher-complexity networks, at a data pre- or postprocessing stage. We validate this FNN on naturally periodic smooth functions and on piecewise continuous periodic functions. We showcase the use of this FNN for modeling or solving partial differential equations with periodic boundary conditions. The main advantages of the current approach are the validity of the solution outside the training region, interpretability of the trained model, and simplicity of use.

Fourier decomposition↗

40 Ca transverse response function from coupled-cluster theory

Here, we present calculations of the 40 Ca transverse response function obtained from coupled-cluster theory used in conjunction with the Lorentz integral transform method. We employ nuclear forces derived at next-to-next-to leading order in chiral effective field theory with and without Δ degrees of freedom. We first benchmark this approach on the 4 He nucleus and compare both the transverse sum rule and the response function to earlier calculations based on different methods. As expected from the power counting of the chiral expansion of electromagnetic currents and from previous studies, our results retaining only one-body term underestimate the experimental data for 4 He by about 20%. However, when the method is applied to 40 Ca at the same order of the expansion, response functions do not lack strength and agree well with the world electron scattering data. We discuss various sources of theoretical uncertainties and comment on the comparison of our results with the available experiments.

39 ≤ A ≤ 58↗

Green’s function methods for excited states and x-ray spectra of functional materials

Many interesting properties of functional materials, such as dynamic response and thermodynamic behavior, depend on their excited state properties. These functional properties are often related to excitations in the system, such as phonons and plasmons, which lead to inelastic losses, lifetime, and other dynamic effects. The excitations are pure many-body correlation effects that are missing from independent particle theories. They are revealed in x-ray spectra such as photoemission and absorption, where they show up as satellites beyond the quasi-particle approximation. Our main focus in this work is the use of Green's function methods to describe these effects. In particular, we discuss how the cumulant Green's function provides a unified treatment of such dynamic correlation effects in many contexts. Besides a robust theoretical framework, these methods also yield widely applicable tools for practical calculations of many functional properties of materials. Furthermore, this methodology is illustrated with a number of applications ranging from optical and x-ray spectra to thermodynamic properties, and dynamic response. Some recent extensions for more correlated systems are also briefly discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Solid-State Side-Chain Functionalization of Conjugated Polymers for Expanded Chemical and Functional Versatility

Conjugated polymers that integrate diverse chemical functionalities with high electronic performance are essential for advanced organic electronic, optoelectronic, and biointerfaced technologies. Achieving such multifunctionality typically requires grafting functional units onto polymer side chains. However, conventional solution-phase approaches remain constrained by solubility limitations, side-chain-induced packing disruptions, and challenges in preserving charge transport. Here, we introduce a solid-state side-chain functionalization strategy that exploits a swellable polar side-chain architecture and azide–alkyne click chemistry to enable efficient molecular diffusion and reaction throughout predeposited polymer thin films. This approach substantially broadens the chemical compatibility of graftable units and mitigates the adverse effects on the electrical property. Moreover, the method supports spatially selective functionalization within a continuous film, enabling the patterned incorporation of chemically distinct groups to produce spatially defined optical properties. Here, this solid-state strategy thus provides a versatile platform for constructing conjugated polymers with expanded chemical versatility, preserved electronic performance, and programmable spatial functionality.

Conjugated polymers↗

Construction of meta-GGA functionals through restoration of exact constraint adherence to regularized SCAN functionals

The strongly constrained and appropriately normed (SCAN) meta-GGA exchange–correlation functional is constructed as a chemical environment-determined interpolation between two separate energy densities: one describes single-orbital electron densities accurately and another describes slowly varying densities accurately. To conserve constraints known for the exact exchange–correlation functional, the derivatives of this interpolation vanish in the slowly varying limit. While theoretically convenient, this choice introduces numerical challenges that degrade the functional’s efficiency. We have recently reported a modification to the SCAN meta-GGA, termed restored-regularized-SCAN (r 2 SCAN) , that introduces two regularizations into SCAN, which improve its numerical performance at the expense of not recovering the fourth order term of the slowly varying density gradient expansion for exchange. Here, we show the derivation of a progression of density functional approximations [regularized SCAN (rSCAN), r++SCAN, r 2 SCAN, and r 4 SCAN] with increasing adherence to exact conditions while maintaining a smooth interpolation. The greater smoothness of r 2 SCAN seems to lead to better general accuracy than the additional exact constraint of SCAN or r 4 SCAN does.

, correlation energy↗

Functional equations and separation of variables for exact g -function

The g-function is a measure of degrees of freedom associated to a boundary of two-dimensional quantum field theories. In integrable theories, it can be computed exactly in a form of the Fredholm determinant, but it is often hard to evaluate numerically. In this paper, we derive functional equations — or equivalently integral equations of the thermodynamic Bethe ansatz (TBA) type — which directly compute the g-function in the simplest integrable theory; the sinh-Gordon theory at the self-dual point. The derivation is based on the classic result by Tracy and Widom on the relation between Fredholm determinants and TBA, which was used also in the context of topological string. We demonstrate the efficiency of our formulation through the numerical computation and compare the results in the UV limit with the Liouville CFT. As a side result, we present multiple integrals of Q-functions which we conjecture to describe a universal part of the g-function, and discuss its implication to integrable spin chains.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.

59 BASIC BIOLOGICAL SCIENCES↗

Source function from two-particle correlation function through entropy-regularized Richardson-Lucy deblurring

Source functions are obtained from p – p and d – α correlation functions by applying the Richardson-Lucy (RL) deblurring to the Koonin-Pratt (KP) equation. To prevent fitting of noise in the correlation function, total-variation (TV) regularization is employed that has been effective in ordinary image restoration. TV alone cannot ensure normalization of the source functions. To ensure the latter, we propose a maximum-entropy regularized RL algorithm (MEM-RL). We outline the MEM-RL formalism and optimization strategy for the KP equation, demonstrating its effectiveness on both simulated and experimental data, including the p – p and d – α correlation functions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

QuantImPy: Minkowski functionals and functions with Python

The Minkowski functionals and functions are a family of morphological measures and can be used to describe both the morphology (shape) and topology (connectedness) of a system. This paper presents the QuantImPy Python package which can compute both the Minkowski functionals and functions. In addition, this package can efficiently perform basic morphological operations and compute their distance maps. QuantImPy is easy to install, well documented, integrated with existing Python packages, and open source.

97 MATHEMATICS AND COMPUTING↗

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗

Response Functions of Correlated Systems within Green's Function Theory

Why use Green's functions as the fundamental variable? Wave-function (Psi) methods are king for high-fidelity and Density-functional (Rho) methods are very efficient (Kohn-Sham). Goldilocks principle: Green's function (G) methods straddle the Rho and Psi methods, intermediate in both accuracy and efficiency. Also, when interest lies in excitations & 2-particle properties: G-methods are natural - intrinsic to the theory.

DMFT↗

Modeling Pb(II) Adsorption on Mineral Surfaces: Bridging Density Functional Theory and Experiment with Thermodynamic Insights

Despite decades of work on aqueous lead (Pb) adsorption on a-Fe2O3 (hematite) and a-Al2O3 (alumina), gaps between measurements and modeling obscure molecular-level understanding. Achieving well-matched geometries between theory and experimental for mineral-water interfaces is a hurdle, as surface functional group type and distribution must be accounted for in determining mechanisms. Additionally, computational methods that can describe the substrate are often not appropriate to capture aqueous effects. Progress requires focusing on well-studied and relevant systems, such as key facets (001),(012), and (110) of hematite and alumina, and ubiquitous contaminants such as aqueous Pb. In the past, bulk-parametrized bond-valence principles were used to rationalize Pb(II) adsorption trends. These approaches can break down at surfaces, where flexible bonding environments and adsorption-induced surface relaxations play a critical role. Here, we adapt and apply a density functional theory (DFT) and thermodynamics framework, integrating DFT-calculated energies with experimental data and electrochemical principles, to predict Pb(II) adsorption. Our model results capture trends across the full set of surfaces and predict that inner-sphere Pb(II) sorption on (001) alumina varies from unfavorable to weakly favorable across a range of pH conditions. This aligns with experiment insights that Pb(II) interacts at that surface through outer-sphere interactions. Extending to Fe(II) adsorption, we demonstrate a coverage-dependent site preference, potentially explaining disorder in overlayers grown by the oxidative adsorption of Fe(II) on hematite (001).

lead contamination↗

Lattice-QCD Computable Quark Correlation Functions at Three-Loop Order and Extraction of Splitting Functions

We present the first complete next-to-next-to-next-to-leading-order calculation of the matching coefficients that link unpolarized flavor nonsinglet parton distribution functions with lattice QCD computable correlation functions. By using this high-order result, we notice a reduction in theoretical uncertainties compared to relying solely on previously known lower-order matching coefficients. Furthermore, based on this result we have extracted the three-loop unpolarized flavor nonsinglet splitting function, which is in agreement with the state-of-the-art result. Because of the simplicity of our method, it has the potential to advance the calculation of splitting functions to the desired four-loop order.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Time‐Dependent Density Functional Theory of Narrow Band Gap Semiconductors Using a Screened Range‐Separated Hybrid Functional

Abstract Predicting the band structure and optical absorption spectra of narrow band gap semiconductors is challenging for electronic structure methods. Here, it is shown shown that density functional theory can yield accurate band structures and time‐dependent density functional theory (TDDFT) can yield accurate optical absorption spectra for these systems. This is achieved by using a screened range‐separated hybrid (SRSH) functional with a single empirical parameter, fit to reproduce the experimental band gap. By comparing TDDFT results based on the SRSH approach with those obtained based on the Heyd–Scuseria–Ernzerhof functional it is shown that screened long‐range exact exchange improves the accuracy of the TDDFT spectra for these systems.

Wing, Dahvyd↗

Optimized Auxiliary Functions for Robust Mitigation of Finite-Size Errors in Periodic Hybrid Density Functional Theory

When calculating properties of periodic systems at the thermodynamic limit (TDL), the dominant source of finite size error (FSE) arises from the long-range Coulomb interaction, and can manifest as a slowly converging quadrature error when approximating an integral in the reciprocal space by a finite sum. The singularity subtraction (SS) method offers a systematic approach for reducing this quadrature error and thus the FSE. Here, in this work, we first investigate the performance of the SS method in the simplest setting, aiming at reducing the FSE in exact exchange calculations by subtracting the Coulomb contribution with a single, adjustable Gaussian auxiliary function. We demonstrate that a simple fitting method can robustly estimate the optimal Gaussian width and leads to rapid convergence toward the TDL. Furthermore, we suggest new forms of the auxiliary function, whose optimal parameters could also be determined through least-squares fitting. For a range of semiconductors and insulators, the proposed auxiliary functions achieve robust, millihartree-level accuracy in hybrid density functional theory calculations, including cases with sparse k-meshes and large basis sets.

Quiton, Stephen Jon [University of California, Ber↗

Synthesis and Surface Attachment of Molecular Re(I) Hydride Species with Silatrane Functionalized Bipyridyl Ligands

Three molecular Re hydrides of the form ( R bpy)Re(CO) 3 H with 2,2′-bipyridine (bpy) ligands containing silatrane functional groups for surface attachment on metal oxide surfaces were synthesized. IR spectroscopy and cyclic voltammetry (CV) demonstrated that the complexes containing the silatrane functional groups have electronic properties similar to those of a control compound, which did not contain functional groups for attachment. Additionally, in a similar fashion to the control compound, the silatrane containing Re hydrides are electrocatalysts for the reduction of CO 2 to CO in solution. The silatrane containing complexes were immobilized on a thin layer of TiO 2 on Si, and the resulting composites were characterized using X-ray photoelectron and IR spectroscopy as well as cyclic voltammetry in the dark and under illumination. Control experiments indicated that the hydride complexes are not stable on the surface and degrade to species which contain a bpy ligand, three CO ligands, and an unknown ligand in the sixth site. Similarly, when one of the silatrane containing Re hydride complexes was immobilized on Si nanoparticles with a thin layer of SiO 2 or silica nanoparticles, the hydride ligand was lost. Density functional theory calculations were used to corroborate the observed behavior of hydride species on a surface. Altogether, this work demonstrates the difficulties associated with attaching well-defined molecular hydride complexes to metal oxide surfaces.

Anions↗