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At least 271 records · Page 15

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DOE OSTI2025

Global optimization of harmonic oscillator basis in covariant density functional theory

The present investigation focuses on the improvement of the accuracy of the description of binding energies within moderately sized fermionic basis. Using the solutions corresponding to infinite fermionic basis it was shown that in the case of meson exchange (ME) covariant energy density functionals (CEDFs) the global accuracy of the description of binding energies in the finite $N_F$ = 16 - 20 bases can be drastically (by a factor ranging from ~3 up to ~9 dependent on the functional and $N_F$) improved by a global optimization of oscillator frequency of the basis. This is a consequence of the unique feature of the ME functionals in which with increasing fermionic basis size fermionic and mesonic energies approach the exact (infinite basis) solution from above and below, respectively. As a consequence, an optimal oscillator frequency $\hbar\omega_0$ of the basis can be defined which provides an accurate reproduction of exact total binding energies by the ones calculated in truncated basis. This leads to a very high accuracy of the calculations in moderately sized $N_F=20$ basis when mass dependent oscillator frequency is used: global rms differences $\delta B_{rms}$ between the binding energies calculated in infinite and truncated bases are only 0.025 MeV and 0.031 MeV for the NL5(Z) and DD-MEZ functionals, respectively. Optimized values of the oscillator frequency $\hbar\omega_0$ are provided for three major classes of CEDFs, i.e. for density dependent meson exchange functionals, nonlinear meson exchange ones and point coupling functionals.

Binding energy & masses↗

DOE OSTI2026

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2014

Modified Displacement Transfer Functions for Deformed Shape Predictions of Slender Curved Structures with Varying Curvatives

To eliminate the need to use finite-element modeling for structure shape predictions, a new method was invented. This method is to use the Displacement Transfer Functions to transform the measured surface strains into deflections for mapping out overall structural deformed shapes. The Displacement Transfer Functions are expressed in terms of rectilinearly distributed surface strains, and contain no material properties. This report is to apply the patented method to the shape predictions of non-symmetrically loaded slender curved structures with different curvatures up to a full circle. Because the measured surface strains are not available, finite-element analysis had to be used to analytically generate the surface strains. Previously formulated straight-beam Displacement Transfer Functions were modified by introducing the curvature-effect correction terms. Through single-point or dual-point collocations with finite-elementgenerated deflection curves, functional forms of the curvature-effect correction terms were empirically established. The resulting modified Displacement Transfer Functions can then provide quite accurate shape predictions. Also, the uniform straight-beam Displacement Transfer Function was applied to the shape predictions of a section-cut of a generic capsule (GC) outer curved sandwich wall. The resulting GC shape predictions are quite accurate in partial regions where the radius of curvature does not change sharply.

displacement transfer functions↗

NASA NTRS2015

Variable-Domain Displacement Transfer Functions for Converting Surface Strains into Deflections for Structural Deformed Shape Predictions

Variable-Domain Displacement Transfer Functions were formulated for shape predictions of complex wing structures, for which surface strain-sensing stations must be properly distributed to avoid jointed junctures, and must be increased in the high strain gradient region. Each embedded beam (depth-wise cross section of structure along a surface strain-sensing line) was discretized into small variable domains. Thus, the surface strain distribution can be described with a piecewise linear or a piecewise nonlinear function. Through discretization, the embedded beam curvature equation can be piece-wisely integrated to obtain the Variable-Domain Displacement Transfer Functions (for each embedded beam), which are expressed in terms of geometrical parameters of the embedded beam and the surface strains along the strain-sensing line. By inputting the surface strain data into the Displacement Transfer Functions, slopes and deflections along each embedded beam can be calculated for mapping out overall structural deformed shapes. A long tapered cantilever tubular beam was chosen for shape prediction analysis. The input surface strains were analytically generated from finite-element analysis. The shape prediction accuracies of the Variable- Domain Displacement Transfer Functions were then determined in light of the finite-element generated slopes and deflections, and were fofound to be comparable to the accuracies of the constant-domain Displacement Transfer Functions

displacement transfer functions↗

NASA NTRS2022

Earth System Model Parameter Adjustment Using a Green's Functions Approach

We demonstrate the practicality and effectiveness of using a Green's functions estimation approach for adjusting uncertain parameters in an Earth system model (ESM). This estimation approach has previously been applied to an intermediate-complexity climate model and to individual ESM components, e.g., ocean, sea ice, or carbon cycle components. Here, the Green's functions approach is applied to a state-of-the-art ESM that comprises a global atmosphere/land configuration of the Goddard Earth Observing System (GEOS) coupled to an ocean and sea ice configuration of the Massachusetts Institute of Technology general circulation model (MITgcm). Horizontal grid spacing is approximately 110 km for GEOS and 37–110 km for MITgcm. In addition to the reference GEOS-MITgcm simulation, we carried out a series of model sensitivity experiments, in which 20 uncertain parameters are perturbed. These “control” parameters can be used to adjust sea ice, microphysics, turbulence, radiation, and surface schemes in the coupled simulation. We defined eight observational targets: sea ice fraction, net surface shortwave radiation, downward longwave radiation, near-surface temperature, sea surface temperature, sea surface salinity, and ocean temperature and salinity at 300 m. We applied the Green's functions approach to optimize the values of the 20 control parameters so as to minimize a weighted least-squares distance between the model and the eight observational targets. The new experiment with the optimized parameters resulted in a total cost reduction of 9 % relative to a simulation that had already been adjusted using other methods. The optimized experiment attained a balanced cost reduction over most of the observational targets. We also report on results from a set of sensitivity experiments that are not used in the final optimized simulation but helped explore options and guided the optimization process. These experiments include an assessment of sensitivity to the number of control parameters and to the selection of observational targets and weights in the cost function. Based on these sensitivity experiments, we selected a specific definition for the cost function. The sensitivity experiments also revealed a decreasing overall cost as the number of control variables was increased. In summary, we recommend using the Green's functions estimation approach as an additional fine-tuning step in the model development process. The method is not a replacement for modelers' experience in choosing and adjusting sensitive model parameters. Instead, it is an additional practical and effective tool for carrying out final adjustments of uncertain ESM parameters.

Green's Function↗

NASA NTRS2022

A Conceptual Framework to Integrate Biodiversity, Ecosystem Function, and Ecosystem Service Models

Global biodiversity and ecosystem service models typically operate independently. Ecosystem service projections may therefore be overly optimistic because they do not always account for the role of biodiversity in maintaining ecological functions. We review models used in recent global model intercomparison projects and develop a novel model integration framework to more fully account for the role of biodiversity in ecosystem function, a key gap for linking biodiversity changes to ecosystem services. We propose two integration pathways. The first uses empirical data on biodiversity–ecosystem function relationships to bridge biodiversity and ecosystem function models and could currently be implemented globally for systems and taxa with sufficient data. We also propose a trait-based approach involving greater incorporation of biodiversity into ecosystem function models. Pursuing both approaches will provide greater insight into biodiversity and ecosystem services projections. Integrating biodiversity, ecosystem function, and ecosystem service modeling will enhance policy development to meet global sustainability goals.

biodiversity models↗

DOE OSTI2025

Green’s Function Perspective on the Nonlinear Density Response of Quantum Many-Body Systems

We derive equations of motion for higher order density response functions using the theory of thermodynamic Green’s functions. We also derive expressions for the higher order generalized dielectric functions and polarization functions. Moreover, we relate higher order response functions and higher order collision integrals within the Martin–Schwinger hierarchy. We expect our results to be highly relevant to the study of a variety of quantum many-body systems such as matter under extreme temperatures, densities, and pressures.

Density Functional Theory↗

DOE OSTI2024

Hierarchical Self‐Assembly of Multidimensional Functional Materials from Sequence‐Defined Peptoids

Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.

Shao, Li↗

DOE OSTI2025

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Anti-symmetric barron functions and their approximation with sums of determinants

A fundamental problem in quantum physics is to encode functions that are completely anti-symmetric under permutations of identical particles. The architecture of neural network models for the electron wave function typically comprises an equivariant component followed by a summation of determinants. The recently introduced Generic Antisymmetric (GA) block is designed to enhance the expressivity of such neural wave functions, and it was found that the 2-layer GA block achieved more accurate energies than the corresponding single-determinant FermiNet architecure, suggesting its promise as a way to improve the expressivity of neural wave functions. In this paper we show how the function expressed by the 2-layer GA block can be decomposed into a sum of determinants. We formalize this result by defining the antisymmetric Barron space as a generalized version of the 2-layer GA block and providing an appromation theorem for this function class. This result can be viewed as a negative result showing that the 2-layer GA block is not more expressive than using multiple determinants.

Abrahamsen, Nilin↗

DOE OSTI2026

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↗

DOE OSTI2024

A Theoretical Benchmark of the Geometric and Optical Properties for 3d Transition Metal Nanoclusters via Density Functional Theory

Understanding structure–property relationships in atomically precise metal nanoclusters is vital in finding selective and tunable catalysts. Here, in this study, density functional theory (DFT) was used to benchmark seven exchange correlation functionals at different basis sets for 17 atomically precise nanoclusters against experimentally determined geometries, band gaps, and optical gaps. The set contains both monometallic and bimetallic clusters that possess at least two types of 3d transition metals (specifically, Cu, Ni, Fe, or Co). The benchmark highlights that PBE0 is a good functional to use regardless of the basis set, and Minnesota functionals do well with respect to specific metals. Further, while long-range corrected functionals overestimate band and optical gaps, they model absorption features better than the other considered functionals. The study additionally looks at the photoinduced hydrogen evolution reaction (HER) and the CO 2 reduction mechanism on nanoclusters reported from the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Increasing Branching and Functionalization Decreases Crystallinity and Crystallization Rate in Linear EVOH

Here, we report the crystallization behavior of a linear poly(ethylene-co-vinyl alcohol) (LEVOH) under isothermal crystallization as a function of both OH incorporation and undercooling, and compare the results to conventional branched EVOH. This LEVOH is synthesized by post-polymerization functionalization of polycyclooctene, and it exhibits a half-crystallization time and primary crystallization rate nearly an order of magnitude faster than branched EVOH at ~ 6 mol% OH incorporation. While the LEVOH obtains approximately twice the extent of crystallization compared to the branched equivalent, as OH incorporation increases, the crystallization kinetics and crystallinity of LEVOH decrease. The crystal structure of LEVOH is orthorhombic at low functionalization (≤ 11 mol% OH), a mixture of orthorhombic and hexagonal at moderate functionalization (17 - 21 mol%), and hexagonal at high functionalization (23 %). The LEVOH crystallizes into plates, with crystallite widths ~ 20 - 60 times the crystallite thickness. Ultimately, we show LEVOH crystallizes faster and to a greater extent than commercial branched EVOH, a potential advantage of post-polymerization functionalization as part of polymer-to-polymer upcycling.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Informing Robust Functional Relationship Benchmarks: An Evaluation of the Temperature Sensitivity of Ecosystem Respiration Across the Arctic-Boreal Region

During land model development, simulated carbon dynamics are often benchmarked against observational data sets to evaluate model performance. Functional relationship benchmarks are the relationship between a driving variable (e.g., temperature) and a response variable (e.g., ecosystem respiration) and are a promising tool for assessing model performance by evaluating modeled sensitivities to changing environmental conditions. However, observed functional relationships can be influenced by choices made during data collection and throughout the benchmarking process, impacting the inferred skill of land models. To avoid misrepresenting a model's true performance, it is necessary to systematically evaluate best practices when constructing functional relationship benchmarks. We developed a set of guidelines for constructing functional relationship benchmarks, considering the choice of data set, number of daily observations, temporal extent, and temporal resolution across Alaska and Canada over a 20-year period from 2001 to 2020. The temperature sensitivity of ecosystem respiration from observations, evaluated through an apparent Q 10 , is highly variable both spatially and as a result of the data processing approach applied in the benchmark formation. When benchmarking 13 models from the Warming Permafrost Model Intercomparison Project (WrPMIP), the range in inferred model skill is substantially impacted by the choices applied in constructing functional relationship benchmarks. The inferred performance of a given model is most sensitive to the number of daily observations and temporal extent, followed by choice of benchmark data set and temporal averaging. Results from this analysis can guide the development of consistent and robust functional relationships for future model evaluation studies.

Poe, Jeralyn [Northern Arizona University, Flagsta↗

DOE OSTI2024

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.

Chemistry↗

DOE OSTI2024

Interactive tools for functional annotation of bacterial genomes

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein’s function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein’s function. Ideally, accurate annotations would allow us to predict a bacterium’s capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Cosmological constraints using Minkowski functionals from the first year data of the Hyper Suprime-Cam

We use Minkowski functionals to analyse weak lensing convergence maps from the first-year data release of the Subaru Hyper Suprime-Cam (HSC-Y1) survey. Minkowski functionals provide a description of the morphological properties of a field, capturing the non-Gaussian features of the Universe matter-density distribution. Using simulated catalogues that reproduce survey conditions and encode cosmological information, we emulate Minkowski functionals predictions across a range of cosmological parameters to derive the best-fit from the data. By applying multiple scales cuts, we rigorously mitigate systematic effects, including baryonic feedback and intrinsic alignments. From the analysis, combining constraints of the angular power spectrum and Minkowski functionals, we obtain S8≡σ8Ωm/0.3=0.808−0.046+0.033 and Ωm=0.293−0.043+0.157⁠. These results represent a 40 per cent improvement on the S8 constraints compared to using power spectrum only. Minkowski functionals results are consistent with other two-point, and higher order statistics constraints using the same data, being in agreement with CMB results from the Planck S8 measurements. Our study demonstrates the power of Minkowski functionals beyond two-point statistics to constrain and break the degeneracy between Ωm and σ8⁠.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Multiparticle integral and differential correlation functions

This paper formalizes the use of integral and differential cumulants for measurements of multiparticle event-by-event transverse momentum fluctuations, rapidity fluctuations, as well as net-charge fluctuations. This enables the introduction of multiparticle balance functions, defined based on differential correlation functions (factorial cumulants), that suppress two- and three-prong resonance decays effects and enable measurements of underlying long-range correlations obeying quantum number conservation constraints. These multiparticle balance functions satisfy simple sum rules determined by quantum number conservation. It is additionally shown that these multiparticle balance functions arise as an intrinsic component of high-order net-charge cumulants. This implies that the magnitude of these cumulants, measured in a specific experimental acceptance, is strictly constrained by charge conservation and primarily determined by the rapidity and momentum width of these balance functions. The paper also presents techniques to reduce the computation time of differential correlation functions up to order n = 10 based on the methods of moments. Published by the American Physical Society 2024

Physics↗