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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning↗
DOE OSTI2021

Elevating density functional theory to chemical accuracy for water simulations through a density-corrected many-body formalism

Abstract Density functional theory (DFT) has been extensively used to model the properties of water. Albeit maintaining a good balance between accuracy and efficiency, no density functional has so far achieved the degree of accuracy necessary to correctly predict the properties of water across the entire phase diagram. Here, we present density-corrected SCAN (DC-SCAN) calculations for water which, minimizing density-driven errors, elevate the accuracy of the SCAN functional to that of “gold standard” coupled-cluster theory. Building upon the accuracy of DC-SCAN within a many-body formalism, we introduce a data-driven many-body potential energy function, MB-SCAN(DC), that quantitatively reproduces coupled cluster reference values for interaction, binding, and individual many-body energies of water clusters. Importantly, molecular dynamics simulations carried out with MB-SCAN(DC) also reproduce the properties of liquid water, which thus demonstrates that MB-SCAN(DC) is effectively the first DFT-based model that correctly describes water from the gas to the liquid phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Hole–hole Tamm–Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation

The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole–hole Tamm–Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole–hole counterpart to the more established particle–particle TDA (pp-TDA) method, both of which are derived from the particle–particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. Furthermore, the treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. Additionally, we show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states—particularly those with both low-lying ππ* and nπ* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Exact-two-component block-localized wave function: A simple scheme for the automatic computation of relativistic ΔSCF

Block-localized wave function is a useful method for optimizing constrained determinants. In this article, we extend the generalized block-localized wave function technique to relativistic two-component framework. Optimization of excited state determinants for two-component wave functions presents a unique challenge because the excited state manifold is often quite dense with degenerate states. Furthermore, we test the degree to which certain symmetries result naturally from the ΔSCF optimization such as time reversal symmetry and symmetry with respect to the total angular momentum operator on a series of atomic systems. Variational optimizations may often break symmetry in order to lower the overall energy, just as unrestricted Hartree-Fock breaks spin symmetry. Overall, we demonstrate that time reversal symmetry is roughly maintained when using Hartree-Fock, but less so when using Kohn-Sham density functional theory. Additionally, maintaining total angular momentum symmetry appears to be system dependent and not guaranteed. Finally, we were able to trace the breaking of total angular momentum symmetry to the relaxation of core electrons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Dynamic density functional theory of polymers with salt in electric fields

Here we present a dynamic density functional theory for modeling the effects of applied electric fields on the local structure of polymers with added salt (polymer electrolytes). Time-dependent equations for the local electrostatic potential and volume fractions of polymer, cation, and anion of added salt are developed using the principles of linear irreversible thermodynamics. For such a development, a field theoretic description of the free energy of polymer melts doped with salts is used, which captures the effects of local variations in the dielectric function. Connections of the dynamic density functional theory with experiments are established by relating the three phenomenological Onsager’s transport coefficients of the theory to the mutual diffusion of electrolyte, ionic conductivity, and transference number of one of the ions. The theory is connected with a statistical mechanical model developed by Bearman and Kirkwood [J. Chem. Phys. 28, 136 (1958)] after relating the three transport coefficients to friction coefficients. The steady-state limit of the dynamic density functional theory is used to understand the effects of dielectric inhomogeneity on the phase separation in polymer electrolytes. The theory developed here provides not only a way to connect with experiments but also to develop multi-scale models for studying connections between local structure and ion transport in polymer electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

On the functional dependence of transition-potential coupled cluster

Orbital relaxation of the core region is a primary source of error in the computation of core ionization and core excitation energies. Recently, Transition-Potential Coupled Cluster (TP-CC) methods have been used to explicitly treat orbital relaxation using non-variational molecular orbitals determined by reoccupation of orbitals optimized for a fractional core occupation. The amount of fractional occupation is governed by parameter λ, and recommended values for accurate TP-CCSD and XTP-CCSD computations of carbon, nitrogen, oxygen, and fluorine K edges were previously determined. Herein, we explore the performance of several density functionals for generating the fractionally occupied orbitals used in TP-CCSD. These functionals include HF, BP86, BH&HLYP, B3LYP, M06-2X, and ωB97m-V. The fractionally occupied orbitals computed across the various functionals were subsequently employed as the initial orbitals for our TP-CCSD calculations of organic K-edge x-ray absorption and photoelectron spectra. Regardless of the functional used to generate the fractionally occupied orbitals, the TP-CCSD calculations yield accurate and comparable core ionization energies, core excitation energies, and oscillator strengths.

Coupled-cluster methods↗
DOE OSTI2020

M06-SX screened-exchange density functional for chemistry and solid-state physics

Significance Density functionals with Hartree–Fock exchange have been widely used for a wide range of chemical applications, but the nonlocal character of exchange makes long-range exchange computationally expensive for solid-state calculations with periodic boundary conditions, and full exchange is nonphysical for condensed-phase systems. Here, we present a screened-exchange (SX) density functional, M06-SX, that is especially designed to have good accuracy for both solid-state physics and chemical applications with less computational cost than full Hartree–Fock exchange. The M06-SX functional gives accuracy comparable to functionals with full Hartree–Fock exchange for predicting chemical properties of molecules, while also being practical with good accuracy for plane wave calculations on band gaps and lattice constants of solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Elastic depths for detecting shape anomalies in functional data

This this paper, we propose a new family of depth measures called the elastic depths that can be used to greatly improve shape anomaly detection in functional data. Shape anomalies are functions that have considerably different geometric forms or features from the rest of the data. Identifying them is generally more difficult than identifying magnitude anomalies because shape anomalies are often not distinguishable from the bulk of the data with visualization methods. The proposed elastic depths use the recently developed elastic distances to directly measure the centrality of functions in the amplitude and phase spaces. Measuring shape outlyingness in these spaces provides a rigorous quantification of shape which, in turn, gives the elastic depths a strong theoretical and practical advantage over other methods in detecting shape anomalies. A simple boxplot and thresholding method are introduced to identify shape anomalies using the elastic depths. We assess the elastic depth's detection skill on simulated shape outlier scenarios and compare them against popular shape anomaly detectors. Finally, bond yields, image outlines, and hurricane trajectories are used to demonstrate our method's applicability to functional data observed on three different manifolds.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition

Abstract Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Tensor-polarized parton density in the 𝑁 → Δ transition from the large-𝑁 𝑐 light-cone wave function

The tensor-polarized parton density is defined by the forward matrix element of a partonic operator in the 𝑁 → Δ transition. In this work, we investigate it by employing the large-𝑁 𝑐 light-cone wave function derived from the mean-field approach. The mean-field picture is based on low-energy effective dynamics in the large-𝑁 𝑐 limit, where the baryon wave function is formulated in the rest frame. By exploiting the covariance of the mean-field solution, we derive the corresponding large-𝑁 𝑐 light-cone wave function—decomposed unambiguously into 3⁢𝑄 , 5⁢𝑄 , 7⁢𝑄 , and higher Fock components—in the infinite momentum frame. Evaluating the overlap of these wave functions, we derive an overlap representation of the tensor-polarized parton density in the 𝑁 → Δ transition and find that the leading contribution arises from the 5⁢𝑄 Fock sector. This indicates that the tensor-polarized parton density directly probes the genuine 5⁢𝑄 component and is governed by chiral dynamics. Our numerical analysis shows that the 𝑁 → Δ tensor-polarized parton density is suppressed, consistent with standard large-𝑁 𝑐 expectations. Finally, we establish connections among the tensor-polarized parton density, the generalized parton distribution 𝐻 𝑋 , and the energy-momentum tensor form factor 𝐹 4 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Shortcomings of meta-GGA functionals when describing magnetism

Several recent studies have shown that SCAN, a functional belonging to the meta-generalized gradient approximation (MGGA) family, leads to significantly overestimated magnetic moments in itinerant ferromagnetic metals. However, this behavior is not inherent to the MGGA level of approximation since TPSS, for instance, does not lead to such severe overestimations. In order to provide a broader view of the accuracy of MGGAfunctionals for magnetism, we extend the assessment to more functionals but also to antiferromagnetic solids. The results show that to describe magnetism there is overall no real advantage in using a MGGA functional compared to GGAs. For both types of approximation, an improvement in ferromagnetic metals is necessarily accompanied by a deterioration (underestimation) in antiferromagnetic insulators, and vice versa. Furthermore, we also provide some analysis in order to understand in more detail the relation between the mathematical form of the functionals and the results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Analytical continuation of matrix-valued functions: Carathéodory formalism

Finite-temperature quantum field theories are formulated in terms of Green's functions and self-energies on the Matsubara axis. In multiorbital systems, these quantities are related to positive semidefinite matrix-valued functions of the Carathéodory and Schur class. Analysis, interpretation, and evaluation of derived quantities such as real-frequency response functions requires analytic continuation of the off-diagonal elements to the real axis. Here we derive the criteria under which such functions exist for given Matsubara data and present an interpolation algorithm that intrinsically respects their mathematical properties. For small systems with precise Matsubara data, we find that the continuation exactly recovers all off-diagonal and diagonal elements. In real-materials systems, we show that the precision of the continuation is sufficient for the analytic continuation to commute with the Dyson equation, and we show that the truncation of the off-diagonal self-energy elements leads to considerable approximation artifacts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nonlocal and nonadiabatic Pauli potential for time-dependent orbital-free density functional theory

Time-dependent orbital-free density functional theory is an efficient ab initio method for calculating the electronic dynamics of large systems. In comparison to standard time-dependent density functional theory, it computes only a single electronic state regardless of system size, but it requires an additional time-dependent Pauli potential term. Herein we propose a nonadiabatic and nonlocal Pauli potential whose main ingredients are the time-dependent particle and current densities. Our calculations of the optical spectra of metallic and semiconductor clusters indicate that nonlocal and nonadiabatic time-dependent orbital-free density functional theory performs accurately for metallic systems and semiquantitatively for semiconductors. This paper opens the door to wide applicability of time-dependent orbital-free density functional theory for nonequilibrium electron and electron-nuclear dynamics of complex materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

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↗
DOE OSTI2021

Nuclear energy density functionals grounded in ab initio calculations

Here, we discuss the construction of a nuclear energy density functional (EDF) from ab initio computations and advocate the need for a methodical approach that is free from ad hoc assumptions. The equations of state (EoSs) of symmetric nuclear and pure neutron matter are computed using the chiral NNLO sat and the phenomenological AV4' + UIX c Hamiltonians as inputs to self-consistent Green's function (SCGF) and auxiliary field diffusion Monte Carlo (AFDMC) methods. We propose a convenient parametrization of the EoS as a function of the Fermi momentum and fit it on the SCGF and AFDMC calculations. We apply the ab initio based EDF to carry out an analysis of the binding energies and charge radii of different nuclei in the local density approximation. The NNLO sat -based EDF produces encouraging results, whereas the AV4' + UIX c -based one is farther from experiment. Possible explanations of these different behaviors are suggested, and the importance of gradient and spin-orbit terms is analyzed. Our paper paves the way for a practical and systematic way to merge ab initio nuclear theory and density functional theory, while shedding light on some critical aspects of this procedure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Cluster model of C 12 in the density functional theory framework

We employ the constrained density functional theory to investigate cluster phenomena for the 12 C nucleus. The proton and neutron densities are generated from the placement of three 4 He nuclei (α particles) geometrically. These densities are then used in a density constrained Hartree-Fock calculation that produces an antisymmetrized state with the same densities through energy minimization. In the calculations no a priori analytic form for the single-particle states is assumed and the full energy density functional is utilized. The geometrical scan of the energy landscape provides the ground state of 12 C as an equilateral triangular configuration of three αs with molecular bond like structures. The use of the nucleon localization function provides further insight to these configurations. One can conclude that these configurations are a hybrid between a pure mean-field and a pure α particle condensate. Furthermore, this development could facilitate density functional theory based fusion calculations with a more realistic 12 C ground state.

6 ≤ A ≤ 19↗
DOE OSTI2024

Quark counting, Drell-Yan West, and the pion wave function

The relation between the pion's quark distribution function, 𝑞⁡(𝑥), its light-front wave function, and the elastic charge form factor, 𝐹⁡(Δ 2 ), is explored. The square of the leading-twist pion wave function at a special probe scale, 𝜁 𝐻 , is determined using models and Poincaré covariance from realistic results for 𝑞⁡(𝑥). This wave function is then used to compute form factors with the result that the Drell-Yan-West and quark counting relationships are not satisfied. A new relationship between 𝑞⁡(𝑥) and 𝐹⁡(Δ 2 ) is proposed.

Form factors↗
DOE OSTI2023

X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula

Here, we study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗