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Ab initio self-energy embedding for the photoemission spectra of NiO and MnO
The accurate ab initio simulation of periodic solids with strong correlations is one of the grand challenges of condensed matter. While mature methods exist for weakly correlated solids, the ab initio description of strongly correlated systems is an active field of research. In this work, we show results for the single-particle spectral function of the two correlated $\textit{d}$-electron solids NiO and MnO from self-energy embedding theory. Unlike earlier work, the theory does not use any adjustable parameters and is fully ab initio, while being able to treat both the strong correlation and the nonlocal screening physics of these materials. Here, we derive the method, discuss aspects of the embedding and choices of physically important orbitals, and compare our results to x-ray and angle-resolved photoemission spectroscopy as well as bremsstrahlung-isochromat spectroscopy.
Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora
Abstract The oomycete Phytophthora palmivora infects the fruit of cacao trees ( Theobroma cacao ) causing black pod rot and reducing yields. Cacao genotypes vary in their resistance levels to P. palmivora , yet our understanding of how cacao fruit respond to the pathogen at the molecular level during disease establishment is limited. To address this issue, disease development and RNA-Seq studies were conducted on pods of seven cacao genotypes (ICS1, WFT, Gu133, Spa9, CCN51, Sca6 and Pound7) to better understand their reactions to the post-penetration stage of P. palmivora infection. The pod tissue- P. palmivora pathogen assay resulted in the genotypes being classified as susceptible (ICS1, WFT, Gu133 and Spa9) or resistant (CCN51, Sca6 and Pound7). The number of differentially expressed genes (DEGs) ranged from 1625 to 6957 depending on genotype. A custom gene correlation approach identified 34 correlation groups. De novo motif analysis was conducted on upstream promoter sequences of differentially expressed genes, identifying 76 novel motifs, 31 of which were over-represented in the upstream sequences of correlation groups and associated with gene ontology terms related to oxidative stress response, defense against fungal pathogens, general metabolism and cell function. Genes in one correlation group (Group 6) were strongly induced in all genotypes and enriched in genes annotated with defense-responsive terms. Expression pattern profiling revealed that genes in Group 6 were induced to higher levels in the resistant genotypes. An additional analysis allowed the identification of 17 candidate cis -regulatory modules likely to be involved in cacao defense against P. palmivora . This study is a comprehensive exploration of the cacao pod transcriptional response to P. palmivora spread after infection. We identified cacao genes, promoter motifs, and promoter motif combinations associated with post-penetration resistance to P. palmivora in cacao pods and provide this information as a resource to support future and ongoing efforts to breed P. palmivora -resistant cacao.
Correlation energy of the uniform electron gas determined by ground-state conditional probability density functional theory
Conditional-probability density functional theory (CP-DFT) is a formally exact method for finding correlation energies from Kohn-Sham DFT without evaluating an explicit energy functional. We present details on how to generate accurate exchange-correlation energies for the ground-state uniform gas. We also use the exchange hole in a CP antiparallel spin calculation to extract the high-density limit. We give a highly accurate analytic solution to the Thomas-Fermi model for this problem, showing its performance relative to Kohn-Sham and may be useful at high temperatures. We explore several approximations to the CP potential. Furthermore, results are compared to accurate parameterizations for both exchange-correlation energies and holes.
Multi-matrix correlators and localization
Abstract We study generating functions of$$ \frac{1}{4} $$ 1 4 -BPS states in$$ \mathcal{N} $$ N = 4 super Yang-Mills at finiteNby attempting to generalize the Harish-Chandra-Itzykson-Zuber integral to multiple commuting matrices. This allows us to compute the overlaps of two or more generating functions; such calculations arise in the computation of two-point correlators in the free-field limit. We discuss the four-matrix HCIZ integral in the U(2) context and lay out a prescription for finding a more general formula forN> 2. We then discuss its connections with the restricted Schur polynomial operator basis. Our results generalize readily to arbitrary numbers of matrices, opening up the opportunity to study more generic BPS operators.
Three-step colloidal gelation revealed by time-resolved x-ray photon correlation spectroscopy
The gelation of PEGylated gold nanoparticles dispersed in a glycerol–water mixture is probed in situ by x-ray photon correlation spectroscopy. Following the evolution of structure and dynamics over 10 4 s, a three-step gelation process is found. First, a simultaneous increase of the Ornstein–Zernike length ξ and slowdown of dynamics is characterized by an anomalous q-dependence of the relaxation times of τ ∝q -6 and strongly stretched intermediate scattering functions. After the structure of the gel network has been established, evidenced by a constant ξ, the dynamics show aging during the second gelation step accompanied by a change toward ballistic dynamics with τ ∝ q -1 and compressed correlation functions. In the third step, aging continues after the arrest of particle motion. Our observations further suggest that gelation is characterized by stress release as evidenced by anisotropic dynamics once gelation sets in.
Understanding the effect of density functional choice and van der Waals treatment on predicting the binding configuration, loading, and stability of amine-grafted metal organic frameworks
Metal organic frameworks (MOFs) are crystalline, three-dimensional structures with high surface areas and tunable porosities. Made from metal nodes connected by organic linkers, the exact properties of a given MOF are determined by node and linker choice. MOFs hold promise for numerous applications, including gas capture and storage. M2(4,4′-dioxidobiphenyl-3,3′-dicarboxylate)—henceforth simply M2(dobpdc), with M = Mg, Mn, Fe, Co, Ni, Cu, or Zn—is regarded as one of the most promising structures for CO2 capture applications. Further modification of the MOF with diamines or tetramines can significantly boost gas species selectivity, a necessity for the ultra-dilute CO2 concentrations in the direct-air capture of CO2. There are countless potential diamines and tetramines, paving the way for a vast number of potential sorbents to be probed for CO2 adsorption properties. The number of amines and their configuration in the MOF pore are key drivers of CO2 adsorption capacity and kinetics, and so a validation of computational prediction of these quantities is required to suitably use computational methods in the discovery and screening of amine-functionalized sorbents. In this work, we study the predictive accuracy of density functional theory and related calculations on amine loading and configuration for one diamine and two tetramines. In particular, we explore the Perdew–Burke–Ernzerhof (PBE) functional and its formulation for solids (PBEsol) with and without the Grimme-D2 and Grimme-D3 pairwise corrections (PBE+D2/3 and PBEsol+D2/3), two revised PBE functionals with the Grimme-D2 and Grimme-D3 pairwise corrections (RPBE+D2/3 and revPBE+D2/3), and the nonlocal van der Waals correlation (vdW-DF2) functional. We also investigate a universal graph deep learning interatomic potential’s (M3GNet) predictive accuracy for loading and configuration. These results allow us to identify a useful screening procedure for configuration prediction that has a coarse component for quick evaluation and a higher accuracy component for detailed analysis. Our general observation is that the neural network-based potential can be used as a high-level and rapid screening tool, whereas PBEsol+D3 gives a completely qualitatively predictive picture across all systems studied, and can thus be used for high accuracy motif predictions. We close by briefly exploring the predictions of relative thermal stability for the different functionals and dispersion corrections.
Constructing the Mechanism of Dinoflagellate Luciferin Bioluminescence Using Computation
Dinoflagellate luciferin bioluminescence is unique since it does not rely on decarboxylation but is poorly understood compared to that of firefly, bacteria, and coelenterata luciferins. Here, in this work, we computationally investigate possible protonation states, stereoisomers, a chemical mechanism, and the dynamics of the bioluminescence intermediate that is responsible for chemiexcitation. Using semiempirical dynamics, time-dependent density functional theory static calculations, and a correlation diagram, we find that the intermediate’s functional group that is likely responsible for chemiexcitation is a 4-member ring, a dioxetanol, that undergoes [2π + 2π] cycloreversion and the biolumiphore is the cleaved structure. The simulated emission spectra and luciferase-dependent absorbance spectra agree with the experimental data, giving support to our proposed mechanism and biolumiphore. We also compute circular dichroism spectra of the intermediate’s four stereoisomers to guide future experiments in differentiating them.
A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes
Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition. By contrasting plasmids from cultivated and uncultivated organisms, we identify important functions that expand existing knowledge of plasmid roles in these habitats. This study represents a notable step forward in elucidating plasmid diversity and function within soil microbiomes and establishes a foundational framework for exploring their roles in natural environments.
Measurements of dihadron correlations relative to the event plane in Au+Au collisions at $\sqrt{s_{NN}} =200$ GeV*
Dihadron azimuthal correlations containing a high transverse momentum ($ p_{T} $) trigger particle are sensitive to the properties of the nuclear medium created at RHIC through the strong interactions occurring between the traversing parton and the medium, i.e. jet-quenching. Previous measurements revealed a strong modification to dihadron azimuthal correlations in Au+Au collisions with respect to p+p and d+Au collisions. The modification increases with the collision centrality, suggesting a path-length or energy density dependence to the jet-quenching effect. This paper reports STAR measurements of dihadron azimuthal correlations in mid-central (20%-60%) Au+Au collisions at $ \sqrt{s_{\rm{NN}}} = 200 $ GeV as a function of the trigger particle's azimuthal angle relative to the event plane, $ \phi_{s} = | \phi_{t}- \psi_{{\rm{EP}}}| $. The azimuthal correlation is studied as a function of both the trigger and associated particle $ p_{T} $. The subtractions of the combinatorial background and anisotropic flow, assuming Zero Yield At Minimum (ZYAM), are described. The correlation results are first discussed with subtraction of the even harmonic (elliptic and quadrangular) flow backgrounds. The away-side correlation is strongly modified, and the modification varies with $ \phi_{s} $, with a double-peak structure for out-of-plane trigger particles. The near-side ridge (long range pseudo-rapidity $ \Delta\eta $ correlation) appears to drop with increasing $ \phi_{s} $ while the jet-like component remains approximately constant. The correlation functions are further studied with the subtraction of odd harmonic triangular flow background arising from fluctuations. It is found that the triangular flow, while responsible for the majority of the amplitudes, is not sufficient to explain the $ \phi_{s} $-dependence of the ridge or the away-side double-peak structure. The dropping ridge with $ \phi_{s} $ could be attributed to a $ \phi_{s} $-dependent elliptic anisotropy; however, the physics mechanism of the ridge remains an open question. Even with a $ \phi_{s} $-dependent elliptic flow, the away-side correlation structure is robust. These results, with extensive systematic studies of the dihadron correlations as a function of $ \phi_{s} $, trigger and associated particle $ p_{T} $, and the pseudo-rapidity range $ \Delta\eta $, should provide stringent inputs to help understand the underlying physics mechanisms of jet-medium interactions in high energy nuclear collisions.
Fault Network Geometry Modulates Earthquake Source Spectra Across Scales
Earthquake source spectra provide unique insights into the earthquake rupture process. Motivated by previous research suggesting that complex fault geometries enhance high‐frequency seismic radiation, we study the influence of fault network geometry on earthquake source spectra using multiple independent observations. At regional scales, we examine correlations of stress drop measurements with surface fault trace misalignment in Southern California, Japan, and Central Italy. At a global scale, we examine correlations of moment‐rate function complexity of large earthquakes with focal mechanism variability, a proxy for local fault complexity. Despite significant scatter in the observations, we find overall consistent positive correlations. The concept that elastic interactions of discrete fault structures during the earthquake rupture process generates high‐frequency ground motions offers a coherent framework for interpreting our observations. These findings suggest that variations in fault complexity explain why some earthquakes produce stronger high‐frequency ground motions than others.
A selection function toolbox for subsets of astronomical catalogues
ABSTRACT Large catalogues are ubiquitous throughout astronomy, but most scientific analyses are carried out on smaller samples selected from these catalogues by chosen cuts on catalogued quantities. The selection function of that scientific sample – the probability that a star in the catalogue will satisfy these cuts and so make it into the sample – is thus unique to each scientific analysis. We have created a general framework that can flexibly estimate the selection function of a sample drawn from a catalogue in terms of position, magnitude and colour. Our method is unique in using the binomial likelihood and accounting for correlations in the selection function across position, magnitude, and colour using Gaussian processes and spherical harmonics. We have created a new open-source python package selectionfunctiontoolbox that implements this framework and used it to make three different estimates of the APOGEE DR16 red giant sample selection function, as a subset of 2MASS, with each estimate using an increasing amount of technical knowledge of the APOGEE targeting. In a companion paper, we applied our methodology to derive estimates of the astrometric and spectroscopic selection functions of Gaia EDR3. Our framework will make it trivial for astrophysicists to estimate the selection function that they should be using with the custom sample of stars that they have chosen to answer their scientific question.
Image Distinguishability Analysis Testing Through Principal Components and Its Application to Hot Spot Scale Invariance
Hot spots are spatial regions of intense energy localization that govern initiation of secondary high explosives. Studies that characterize or compare simulated hot spots are frequently either qualitatively descriptive or resort to quantitative distribution functions that neglect stochastic variations and spatial correlations—effects that are also neglected in common comparison tests like the Kolmogorov–Smirnov test. To this end, we develop an image distinguishability analysis (IDA) test based on principal component (PC) analysis that makes pixel-by-pixel comparisons between small, for example, O(<10), image data sets. The IDA test makes comparisons through a generalized distance metric in the PC space and a test statistic that is derived to calculate mathematical equation-values. Here, we derive a statistical distribution and criticality criterion to determine whether images are distinguishable from established baselines. We apply the IDA test on images generated from molecular dynamics simulations of hot spots from pore collapse in TATB to assess scale invariance in the complex patterns of hot spots that form in a representative high explosive crystal. The IDA test shows that TATB hot spot spatial temperature fields and their derived temperature histograms exhibit scale-invariant features over specific intervals of shock orientation, strength, and initial pore diameter. However, the IDA test also shows that qualitatively different conclusions regarding invariance can be reached depending on whether the hot spot is treated as a spatially correlated field as opposed to a distribution function that lacks spatial information.
Progress towards understanding ultranonlocality through the wave-vector and frequency dependence of approximate exchange-correlation kernels
In the framework of time-dependent density functional theory (TDDFT), the exact exchange-correlation (xc) kernel f xc (n, q, ω) determines the ground-state energy, excited-state energies, lifetimes, and the time-dependent linear density response of any many-electron system. The recently developed MCP07 xc kernel f xc (n, q, ω) of A. Ruzsinszky et al. [Phys. Rev. B 101, 245135 (2020)] yields excellent uniform electron gas (UEG) ground-state energies and plausible plasmon lifetimes. As MCP07 is constructed to describe f xc of the UEG, it cannot capture optical properties of real materials. To verify this claim, we follow Nazarov et al. [Phys. Rev. Lett. 102, 113001 (2009)] to construct the long-range, dynamic xc kernel, lim q→0 f xc (n, q, ω) = -α(ω)e 2 /q 2 , of a weakly inhomogeneous electron gas, using MCP07 and other common xc kernels. The strong wavevector and frequency dependence of the “ultranonlocality” coefficient α(ω) is demonstrated for a variety of simple metals and semiconductors. We examine how imposing exact constraints on an approximate kernel shapes α(ω). Comparisons to kernels derived from correlated-wavefunction calculations are drawn.
On the statistical theory of self-gravitating collisionless dark matter flow
Dark matter, if it exists, accounts for five times as much as the ordinary baryonic matter. Compared to hydrodynamic turbulence, the flow of dark matter might possess the widest presence in our universe. This paper presents a statistical theory for the flow of dark matter that is compared with N-body simulations. By contrast to hydrodynamics of normal fluids, dark matter flow is self-gravitating, long-range, and collisionless with a scale-dependent flow behavior. The peculiar velocity field is of constant divergence nature on small scale and irrotational on large scale. The statistical measures, i.e., correlation, structure, dispersion, and spectrum functions, are modeled on both small and large scales, respectively. Kinematic relations between statistical measures are fully developed for incompressible, constant divergence, and irrotational flow. Incompressible and constant divergence flow share the same kinematic relations for even order correlations. The limiting correlation of velocity $\mathrm{ρ_{L}=1/2}$ on the smallest scale ( r = 0) is a unique feature of collisionless flow ($\mathrm{ρ_{L}=1}$ for incompressible flow). On large scale, transverse velocity correlation has an exponential form $T_{2}∝e^{–r/r_2}$ with a constant comoving scale r 2 =21.3 Mpc/h that may be related to the horizon size at matter–radiation equality. All other correlation, structure, dispersion, and spectrum functions for velocity, density, and potential fields are derived analytically from kinematic relations for irrotational flow. On small scale, longitudinal structure function follows one-fourth law of ${S}_{2}^{1}∝r^{1/4}$. All other statistical measures can be obtained from kinematic relations for constant divergence flow. Vorticity is negatively correlated for scale r between 1 and 7 Mpc/h. Divergence is negatively correlated for r > 30 Mpc/h that leads to a negative density correlation.
Analytical harmonic vibrational frequencies with VV10-containing density functionals: Theory, efficient implementation, and benchmark assessments
VV10 is a powerful nonlocal density functional for long-range correlation that is used to include dispersion effects in many modern density functionals, such as the meta-generalized gradient approximation (mGGA), B97M-V, the hybrid GGA, ωB97X-V, and the hybrid mGGA, ωB97M-V. While energies and analytical gradients for VV10 are already widely available, this study reports the first derivation and efficient implementation of the analytical second derivatives of the VV10 energy. The additional compute cost of the VV10 contributions to analytical frequencies is shown to be small in all but the smallest basis sets for recommended grid sizes. Here, this study also reports the assessment of VV10-containing functionals for predicting harmonic frequencies using the analytical second derivative code. The contribution of VV10 to simulating harmonic frequencies is shown to be small for small molecules but important for systems where weak interactions are important, such as water clusters. In the latter cases, B97M-V, ωB97M-V, and ωB97X-V perform very well. The convergence of frequencies with respect to the grid size and atomic orbital basis set size is studied, and recommendations are reported. Finally, scaling factors to allow comparison of scaled harmonic frequencies with experimental fundamental frequencies and to predict zero-point vibrational energy are presented for some recently developed functionals (including r2SCAN, B97M-V, ωB97X-V, M06-SX, and ωB97M-V).
A composite likelihood approach for inference under photometric redshift uncertainty
ABSTRACT Obtaining accurately calibrated redshift distributions of photometric samples is one of the great challenges in photometric surveys like LSST, Euclid, HSC, KiDS, and DES. We present an inference methodology that combines the redshift information from the galaxy photometry with constraints from two-point functions, utilizing cross-correlations with spatially overlapping spectroscopic samples, and illustrate the approach on CosmoDC2 simulations. Our likelihood framework is designed to integrate directly into a typical large-scale structure and weak lensing analysis based on two-point functions. We discuss efficient and accurate inference techniques that allow us to scale the method to the large samples of galaxies to be expected in LSST. We consider statistical challenges like the parametrization of redshift systematics, discuss and evaluate techniques to regularize the sample redshift distributions, and investigate techniques that can help to detect and calibrate sources of systematic error using posterior predictive checks. We evaluate and forecast photometric redshift performance using data from the CosmoDC2 simulations, within which we mimic a DESI-like spectroscopic calibration sample for cross-correlations. Using a combination of spatial cross-correlations and photometry, we show that we can provide calibration of the mean of the sample redshift distribution to an accuracy of at least 0.002(1 + z), consistent with the LSST-Y1 science requirements for weak lensing and large-scale structure probes.
Introducing the embedded random phase approximation: H 2 dissociative adsorption on Cu(111) as an exemplar
The random phase approximation (RPA) as a means of treating electron correlation recently has been shown to outperform standard density functional theory (DFT) approximations in a variety of cases. However, the computational cost of the RPA is substantially more than DFT, especially when aiming to study extended surfaces. Properly accounting for sufficient surface ensemble size, Brillouin zone sampling, and vacuum separation of periodic images in standard periodic-planewave-based DFT code raises the cost to achieve converged results. Here, we show that sub-system embedding schemes enable use of the RPA for modeling heterogeneous reactions at reduced computational cost. Further, we explore two different embedded RPA (emb-RPA) approaches, periodic emb-RPA and cluster emb-RPA. We use the (experimentally and theoretically) well-studied H 2 dissociative adsorption on Cu(111) as our exemplar, and first perform full periodic RPA calculations as a benchmark. The full RPA results match well the semi-empirical barrier fit to experimental observables and others derived from high-level computations, e.g., from recent embedded n-electron valence second order perturbation theory [Zhao et al., J. Chem. Theory Comput. 16(11), 7078–7088 (2020)] and quantum Monte Carlo [Doblhoff-Dier et al., J. Chem. Theory Comput. 13(7), 3208–3219 (2017)] simulations. Among the two emb-RPA approaches tested, the cluster emb-RPA accurately reproduces the energy profile (maximum error of 50 meV along the reaction pathway) while reducing the computational cost by approximately two orders of magnitude. We therefore expect that the embedded cluster approach will enable wider RPA implementation in heterogeneous catalysis.