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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Revisiting Artifacts of Kohn–Sham Density Functionals for Biosimulation

We revisit the problem of unphysical charge density delocalization/fractionalization induced by the self-interaction error of common approximate Kohn–Sham (KS) density functional theory functionals on simulation of small to medium-sized proteins in a vacuum. Aside from producing unphysical electron densities and total energies, the vanishing of the HOMO–LUMO gap associated with the unphysical charge delocalization leads to an unphysical low-energy spectrum and catastrophic failure of most popular solvers for the KS self-consistent field (SCF) problem. We apply a robust quasi-Newton SCF solver to obtain solutions for some of these difficult cases. The anatomy of the charge delocalization is revealed by the natural deformation orbitals obtained from the density matrix difference between the Hartree–Fock and KS solutions; the charge delocalization not only can occur between charged fragments (such as in zwitterionic polypeptides) but also involves neutral fragments. The vanishing-gap phenomenon and troublesome SCF convergence are both attributed to the unphysical KS Fock operator eigenspectra of molecular fragments (e.g., amino acids or their side chains). Analysis of amino acid pairs suggests that the unphysical charge delocalization can be partially ameliorated by the use of some range-separated hybrid functionals but not by semilocal or standard hybrid functionals. Last, we demonstrate that solutions without the unphysical charge delocalization can be located even for semilocal KS functionals highly prone to such defects, but such solutions have non-Aufbau character and are unstable with respect to mixing of the non-overlapping “frontier” orbitals. Caution should be exercised when unexpectedly small (or vanishing) HOMO–LUMO gaps and atypical SCF convergence patterns (e.g., oscillatory) are observed in KS DFT simulations in any context (bio or otherwise).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Oligoether-Functionalized PEDOT: Combining an EDOT Backbone with Polar Side Chains for Solution Processability and High Electrical Conductivity

Conjugated polymers functionalized with oligoether (OE)-based side chains are a key class of materials for various organic electronic applications, including transparent electrodes, thermoelectrics, electrochromic displays, and electrochemical transistors. Herein, we report a highly soluble OE-functionalized poly(3,4-ethylenedioxythiophene) (PEDOT) homopolymer, prepared by direct (hetero)arylation polymerization, which allows solution processing to yield films with comparable redox properties to oxidatively polymerized PEDOT. This polymer, PEDOT(OE3), when optimally oxidatively doped, reaches among the highest electrical conductivities of any OE-functionalized polymer and is comparable to more synthetically complex OE-functionalized polymers. X-ray scattering and spectroscopy were utilized to rationalize the transport properties resulting from varying the doping level. Comparison of PEDOT(OE3) to a series of OE-functionalized dioxythiophenes with varying amounts of 3,4-ethylenedioxythiophene units allows for a deeper understanding of structure–property relationships through charge-transport models. Ultimately, PEDOT(OE3) is shown to be a material with exceptional charge-transport properties and is promising for various applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

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.

Fiamenghi, Mateus B↗
DOE OSTI2025

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A functional microbiome catalogue crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Copper-dependent halogenase catalyses unactivated C−H bond functionalization

Carbon–hydrogen (C–H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp 3 )−H bond. In recent years, metalloenzymes have been found to perform C(sp 3 )−H bond functionalization. Despite substantial progresses in the past two decades, enzymatic halogenation and pseudohalogenation of unactivated C(sp 3 )−H—providing a functional handle for further modification—have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes. Here, in this work, we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp 3 )−H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp 3 )−H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs—one interchain and two intrachain—of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp 3 )−H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.

biocatalysis↗
DOE OSTI2024

Delocalization error poisons the density-functional many-body expansion

The many-body expansion is a fragment-based approach to large-scale quantum chemistry that partitions a single monolithic calculation into manageable subsystems. This technique is increasingly being used as a basis for fitting classical force fields to electronic structure data, especially for water and aqueous ions, and for machine learning. Here, we show that the many-body expansion based on semilocal density functional theory affords wild oscillations and runaway error accumulation for ion–water interactions, typified by F − (H 2 O) N with N ≳ 15. We attribute these oscillations to self-interaction error in the density-functional approximation. The effect is minor or negligible in small water clusters, explaining why it has not been noticed previously, but grows to catastrophic proportion in clusters that are only moderately larger. This behavior can be counteracted with hybrid functionals but only if the fraction of exact exchange is ≳50%, whereas modern meta-generalized gradient approximations including ωB97X-V, SCAN, and SCAN0 are insufficient to eliminate divergent behavior. Other mitigation strategies including counterpoise correction, density correction (i.e., exchange–correlation functionals evaluated atop Hartree–Fock densities), and dielectric continuum boundary conditions do little to curtail the problematic oscillations. In contrast, energy-based screening to cull unimportant subsystems can successfully forestall divergent behavior. These results suggest that extreme caution is warranted when the many-body expansion is combined with density functional theory.

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

Efficient real space formalism for hybrid density functionals

We present an efficient real space formalism for hybrid exchange-correlation functionals in generalized Kohn–Sham density functional theory (DFT). In particular, we develop an efficient representation for any function of the real space finite-difference Laplacian matrix by leveraging its Kronecker product structure, thereby enabling the time to solution of associated linear systems to be highly competitive with the fast Fourier transform scheme while not imposing any restrictions on the boundary conditions. We implement this formalism for both the unscreened and range-separated variants of hybrid functionals. We verify its accuracy and efficiency through comparisons with established planewave codes for isolated as well as bulk systems. In particular, we demonstrate up to an order-of-magnitude speedup in time to solution for the real space method. We also apply the framework to study the structure of liquid water using ab initio molecular dynamics, where we find good agreement with the literature. Overall, the current formalism provides an avenue for efficient real-space DFT calculations with hybrid density functionals.

Chemistry↗
DOE OSTI2024

Functional role of myosin-binding protein H in thick filaments of developing vertebrate fast-twitch skeletal muscle

Myosin-binding protein H (MyBP-H) is a component of the vertebrate skeletal muscle sarcomere with sequence and domain homology to myosin-binding protein C (MyBP-C). Whereas skeletal muscle isoforms of MyBP-C (fMyBP-C, sMyBP-C) modulate muscle contractility via interactions with actin thin filaments and myosin motors within the muscle sarcomere “C-zone,” MyBP-H has no known function. This is in part due to MyBP-H having limited expression in adult fast-twitch muscle and no known involvement in muscle disease. Quantitative proteomics reported here reveal that MyBP-H is highly expressed in prenatal rat fast-twitch muscles and larval zebrafish, suggesting a conserved role in muscle development and prompting studies to define its function. We take advantage of the genetic control of the zebrafish model and a combination of structural, functional, and biophysical techniques to interrogate the role of MyBP-H. Transgenic, FLAG-tagged MyBP-H or fMyBP-C both localize to the C-zones in larval myofibers, whereas genetic depletion of endogenous MyBP-H or fMyBP-C leads to increased accumulation of the other, suggesting competition for C-zone binding sites. Does MyBP-H modulate contractility in the C-zone? Globular domains critical to MyBP-C’s modulatory functions are absent from MyBP-H, suggesting that MyBP-H may be functionally silent. However, our results suggest an active role. In vitro motility experiments indicate MyBP-H shares MyBP-C’s capacity as a molecular “brake.” These results provide new insights and raise questions about the role of the C-zone during muscle development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Empirical investigation of nuclear correlation function distributions in lattice QCD

Two-point correlation functions of systems with baryon number 𝐵 ∈ {1,2,3,4} are investigated using lattice quantum chromodynamics (QCD). In particular, the empirical distributions of importance-sampling Monte-Carlo samples of these correlation functions are examined as a function of the spacetime separation between the two points and the baryon number. While the exact forms of these distributions are not known for QCD, recent work has determined asymptotic expressions for analogous correlation function distributions in simpler theories such as scalar field theory and the disordered phase of the 𝑂⁡(𝑁) model. The theoretical 𝑂⁡(𝑁) model distributions are found to provide an accurate description of the empirical QCD distributions at zero momentum over a wide range of temporal separations for each baryon number when assessed with a range of different statistical tests. In particular, the behavior of the baryon number 𝐵 QCD correlation function at large temporal separation is well reproduced by the 𝑂⁡(𝑁 ∼ 2/𝐵) model distribution.

Lattice field theory↗
DOE OSTI2024

Universal function for heavy-ion fusion cross sections

A universal function for heavy-ion fusion cross sections, Y = $\sqrt{π}$ Xerfc (- X ) + exp(- X 2 ) is proposed. By scaling both the cross section σ(E) and the energy E, heavy-ion fusion cross section data are found to follow closely a universal function over the whole energy range. The scaling is developed from either a simple, empirical single-Gaussian barrier distribution model for the representation d 2 (σE)/dE 2 , or the modified Siwek-Wilczynski model. The cross section expressions of these models are analytical, and can be easily used for all heavy-ion fusion excitation functions. Thus a bench marking of heavy-ion fusion excitation functions has been achieved. Finally, a general discussion regarding the universal function is given.

low & intermediate energy heavy-ion reactions↗
DOE OSTI2024

Electronic structure and optical properties of halide double perovskites from a Wannier-localized optimally-tuned screened range-separated hybrid functional

Halide double perovskites are a chemically diverse and growing class of compound semiconductors that are promising for optoelectronic applications. However, the prediction of their fundamental gaps and optical properties with density functional theory (DFT) and ab initio many-body perturbation theory has been a significant challenge. Recently, a nonempirical Wannier-localized optimally tuned screened range-separated hybrid (WOT-SRSH) functional has been shown to accurately produce the fundamental band gaps of a wide set of semiconductors and insulators, including lead halide perovskites. Here, in this study, we apply the WOT-SRSH functional to five halide double perovskites and compare the results with those obtained from other known functionals and previous GW calculations. We also use the approach as a starting point for GW calculations and we compute the band structures and optical absorption spectrum for Cs 2 AgBiBr 6 , using both time-dependent DFT and the GW-Bethe-Salpeter equation approach. We show that the WOT-SRSH functional leads to accurate fundamental and optical band gaps, as well as optical absorption spectra, consistent with spectroscopic measurements, thereby establishing WOT-SRSH as a viable method for the accurate prediction of optoelectronic properties of halide double perovskites.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Investigating late-stage particle production in pp collisions with balance functions

Balance functions have been regarded in the past as a method of investigating the late-stage hadronization found in the presence of a strongly-coupled medium. They are also used to constrain mechanisms of particle production in large and small collision systems. Charge balance functions for inclusive and identified particle pairs are reported as a function of charged particle multiplicity in proton–proton collisions simulated with the PYTHIA8 and the EPOS4 models. The charge balance functions of inclusive, pion, kaon, and proton pairs exhibit amplitudes and shapes that depend on particle species and differ significantly in the two models due to the different particle production mechanisms implemented in PYTHIA and EPOS. The shapes and amplitudes also evolve with multiplicity in both models. In addition, the evolution of the longitudinal rms width and that of balance functions integrals with multiplicity (and average transverse momentum) feature significant differences in the two models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Insights into posttranslational regulation of skeletal muscle contractile function by the acetyltransferases, p300 and CBP

Here, mice with skeletal muscle-specific and inducible double knockout of the lysine acetyltransferases, p300 (E1A binding protein p300) and CBP (cAMP-response element-binding protein binding protein), referred to as i-mPCKO, demonstrate a dramatic loss of contractile function in skeletal muscle and ultimately die within 7 days. Given that many proteins involved in ATP generation and cross-bridge cycling are acetylated, we investigated whether these processes are dysregulated in skeletal muscle from i-mPCKO mice and, thus, whether they could underlie the rapid loss of muscle contractile function. Just 4–5 days after inducing knockout of p300 and CBP in skeletal muscle from adult i-mPCKO mice, there was ~90% reduction in ex vivo contractile function in the extensor digitorum longus (EDL) and a ~65% reduction in in vivo ankle dorsiflexion torque, as compared with wild type (WT; i.e., Cre negative) littermates. Despite this profound loss of contractile force in i-mPCKO mice, there were no genotype-driven differences in fatigability during repeated contractions, nor were there genotype differences in mitochondrial-specific pathway enrichment of the proteome, intermyofibrillar mitochondrial volume, or mitochondrial respiratory function. As it relates to cross-bridge cycling, remarkably, the overt loss of contractile function in i-mPCKO muscle was reversed in permeabilized fibers supplied with exogenous Ca 2+ and ATP, with active tension being similar between i-mPCKO and WT mice, regardless of Ca 2+ concentration. Actin-myosin motility was also similar in skeletal muscle from i-mPCKO and WT mice. In conclusion, neither mitochondrial abundance/function, nor actomyosin cross-bridge cycling, are the underlying driver of contractile dysfunction in i-mPCKO mice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and functional characterization of IgG- and non-IgG-based T-cell-engaging bispecific antibodies

Bispecific T-cell-engaging antibodies are a growing class of therapeutics with numerous molecules being tested in clinical trials and, currently, seven of them have received market approval. They are structurally complex and function as adaptors to redirect the cytotoxicity of T cells to kill tumor cells. T-cell-engaging bispecific antibodies can be generally divided into two categories: IgG/IgG-like and non-IgG-like formats. Different formats may have different intrinsic potencies and physiochemical properties, and comprehensive studies are needed to gain a better understanding of how the differences in formats impact on structural and functional characteristics. In this study, we designed and generated bispecific T-cell-engaging antibodies with IgG-like (DVD-Ig) and non-IgG (BiTE) formats. Both target the same pair of antigens (EGFR and CD3) to minimize the possible influence of targets on functional characterization. We performed a side-by-side comparison to assess differences in the physiochemical and biological properties of these two bispecific T-cell-engaging antibodies using a variety of breast and ovarian cancer cell-based functional assays to delineate the structural–functional relationships and anti-tumor activities/potency. We found that the Fc portion of T-cell-engaging bispecific antibodies can significantly impact antigen binding activity, potency, and stability in addition to eliciting different mechanisms of action that contribute the killing of cancer cells.

cluster of differentiation 3 (CD3)↗
DOE OSTI2025

On the Stability Analysis of Astrophysical Cooling Functions

To model the temperature evolution of optically thin astrophysical environments at MHD scales, radiative and collisional cooling rates are typically either pretabulated or fit into a functional form and then input into MHD codes as a radiative loss function. Thermal balance requires estimates of the analogous heating rates, which are harder to calculate, and due to uncertainties in the underlying dissipative heating processes these rates are often simply parameterized. The resulting net cooling function defines an equilibrium curve that varies with density and temperature. Such cooling functions can make the gas prone to thermal instability (TI), which will cause departures from equilibrium. There has been no systematic study of thermally unstable parameter space for nonequilibrium states. Motivated by our recent finding that there is a related linear instability, catastrophic cooling instability, that can dominate over TI, here we carry out such a study. We show that Balbus instability criteria for TI can be used to define a critical cooling rate, Λ c , that permits a nonequilibrium analysis of cooling functions through the mapping of TI zones. We furthermore illustrate how thermal conduction modifies the shape of TI zones. Upon applying a Λ c -based stability analysis to coronal loop simulations, we find that loops undergoing periodic episodes of coronal rain formation are linearly unstable to catastrophic cooling instability, while TI is stabilized by thermal conduction.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Weak Form Scientific Machine Learning: Test Function Construction for System Identification

Weak form Scientific Machine Learning (WSciML) is a recently developed framework for data-driven modeling and scientific discovery. It leverages the weak form of equation error residuals to provide enhanced noise robustness in system identification via convolving model equations with test functions, reformulating the problem to avoid direct differentiation of data. The performance, however, relies on wisely choosing a set of compactly supported test functions. In this work, we mathematically motivate a novel data-driven method for constructing Single-scale-Local reference functions for creating the set of test functions. Our approach numerically approximates the integration error introduced by the quadrature and identifies the support size for which the error is minimal, without requiring access to the model parameter values. Through numerical experiments across various models, noise levels, and temporal resolutions, we demonstrate that the selected supports consistently align with regions of minimal parameter estimation error. We also compare the proposed method against the strategy for constructing Multi-scale-Global (and orthogonal) test functions introduced in our prior work, demonstrating the improved computational efficiency.

FOS: Computer and information sciences↗
DOE OSTI2024

Power Analysis of an ePump Applied to the Linear Functions of an Agricultural Planter

Like many other industries, the agricultural industry has recently ex-perienced pressure to reduce vehicle emissions while improving productivity. Electric actuation is perceived as a viable solution to replace or augment hydrau-lic and mechanical actuation. However, electrification presents challenges with regards to linear functions, where hydraulic actuators have advantages in terms of compactness, tolerance to contamination and resistance to shocks. A combined electro-hydraulic actuation architecture can leverage the benefits of both electric and hydraulic actuation, while reducing the drawbacks of both approaches. This work investigates the potential of a centralized electric driven pump (ePump) system powering the pressure-controlled linear functions of an agricul-tural planter, with the goal of improving the operating point of the main supply pump. In this application, the rotary functions are hydraulically actuated, alt-hough such a solution could be applied also to electric rotary actuation. This is accomplished by setting the ePump to boost the pressure supplied by the tractor to the level required by the linear functions. An accumulator is used to stabilize the flow requirements of the linear functions, and control the pressure supplied to the actuators. Two control schemes are proposed for the regulation of the ac-cumulator pressure, one favoring an efficient operating point for the ePump, the other favoring stable steady state operation. A simulation model of the baseline system and proposed system is developed and validated using experimental data from a full-scale machine. Using the vali-dated simulation, both control architectures are then evaluated for improvement in system power consumption and dynamic requirements on the ePump to assess their effectiveness. Both systems demonstrate significant improvement in power consumption over the baseline system, with the best solution improving effi-ciency by 64%.

24 POWER TRANSMISSION AND DISTRIBUTION↗