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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%–94% of the variance in aneuploid strains’ growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.

genic load↗
DOE OSTI2025

Removal of Homogeneous Broadening from 1 H-Detected Multidimensional Solid-State NMR Spectra

1 H-detected magic-angle spinning (MAS) NMR experiments have revolutionized the NMR studies of biological and inorganic solids by providing unparalleled sensitivity and resolution. Despite these gains, homogeneous broadening, originating from the incomplete removal of homonuclear dipolar interactions under fast MAS, remains highly prevalent and limits the achievable resolution. In direct analogy to super-resolution microscopy methods, we show that resolution beyond that currently achievable by fast MAS alone can be obtained by experiment-driven deconvolution. Following the acquisition of a single 2D NMR spectrum to measure the frequency-dependent homogeneous lineshapes, any number of 1 H-detected spectra can be enhanced in resolution, yielding comparable spectra as obtained with twice the MAS frequency. In conclusion, the versatility of this approach is demonstrated in the enhancement of single- and double-quantum homonuclear correlation spectra, in addition to heteronuclear correlation spectra acquired on a surface organometallic complex and the protein GB1.

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

Synthesis, Stability, and Magnetic Properties of Antiperovskite Co 3 PdN

Experimental synthesis and characterization of theoretically predicted compounds are important steps in the materials discovery pipeline. Here, we report on the synthesis of Co 3 PdN, which was recently predicted to be a stable magnetic antiperovskite. The Co 3 PdN thin films were grown by reactive sputtering and were confirmed to form in an antiperovskite crystal structure. The thermal stability of the compound is demonstrated up to 600 K by in situ X-ray diffraction, though the phase persists at slightly higher temperatures (700 K) in an air-free magnetometer. Both ab initio calculations and magnetization measurements find Co 3 PdN to be ferromagnetic with an experimentally determined Curie temperature of T C = 560 ± 5 K. The saturation magnetization of 1.2 μ B /Co found in the experiment is slightly lower than the 1.7 μ B /Co value expected by theory. A narrow magnetic hysteresis loop with a coercive field of 100 Oe at low temperature suggests that Co 3 PdN might be useful in electronic applications requiring fast switching of the magnetization vector. While prior prediction of Co 3 PdN showed a gapped electronic band structure for each spin channel, we show that this was due to incomplete sampling of Brillouin zone paths and that band crossings exist along R-X|M and X|M-R paths. The metallic nature of Co 3 PdN is further confirmed by temperature-dependent transport measurements, which also show a considerable anomalous Hall effect. Altogether, this work represents an appreciable step toward understanding the synthesis, structure, stability, and properties of a new magnetic material.

14 SOLAR ENERGY↗
DOE OSTI2025

Regioisomer-Specific Crystallization of Diglycidyl Ether of Bisphenol F Epoxy Resin

Diglycidyl ether of bisphenol F (DGEBF) is a common industrial epoxy resin, desired for its possible replacement of the bisphenol A (BPA) analogue DGEBA due to potential health hazards of BPA. During curing, crystallization of the DGEBF resin can cause inaccurate resin-to-hardener ratios, resulting in incomplete crosslinking; therefore, understanding the crystallization of DGEBF is important for proper industrial control of the material. Here, in this work, we utilized a combination of single-crystal x-ray diffraction, Raman spectroscopy, and 1 H-NMR to investigate the crystallization of DGEBF. We observed crystallization of two DGEBF regioisomers: ortho-ortho’-DGEBF and ortho-para’-DGEBF, and report their crystal structures. Notably, para-para’-DGEBF crystallization is not observed, indicating crystallization of this regioisomer does not occur under ambient conditions. Density functional theory calculations were performed to describe the phonon modes of the ortho-ortho’- and ortho-para’-DGEBF structures, corroborating Raman signatures for the respective isomers. Using a phonon mode analysis, we identify the presence of three specific optical vibrational modes at 631.3, 344.1, and 345.6 cm -1 that are unique to the para monomer. This work offers insights into the crystallization behavior of DGEBF resins under ambient conditions and may inform potential industrial application of this material.

Neu, Jennifer [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2025

Reactive Transport Modeling of Hydrogen Production from Serpentinization of Olivine

Hydrogen production from serpentinization of ultramafic rocks represents a promising natural pathway for generating carbon-free energy, yet its kinetics and controlling factors remain incompletely understood. A key challenge in advancing serpentinization research lies in the heterogeneity of porosity and permeability in rocks, which leads to nonuniform fluid velocity fields, as well as uncertainties in estimating reactive surface area and identifying appropriate mineral reaction equilibria. Additional complexities arise from the role of dissolved SiO 2 , Fe 2+ /Fe 3+ partitioning, and the limited effect of pH variations within the strongly alkaline regime on hydrogen yields. These challenges hinder straightforward extrapolation from laboratory tests to practical applications of hydrogen production from natural rocks. Here, in this work, we address these questions using a simulation-based reactive transport modeling framework calibrated against controlled laboratory experiments reported elsewhere. The model couples geochemical kinetics, multiphase flow, and mineralogical feedbacks, enabling systematic evaluation of how surface area, dissolved silica concentration, Fe redox state, temperature, and pressure govern serpentinization and H2 generation. We find that surface area exerts the strongest control on reaction rates and hydrogen yields, while Fe 2+ /Fe 3+ ratios act as secondary modulators. Elevated dissolved silica concentrations suppress hydrogen production but accelerate serpentine precipitation, whereas increasing pH beyond 12 within the strongly alkaline regime produces only marginal gains. Finally, we demonstrate that integrating targeted experiments with calibrated simulations offers a powerful and efficient approach for predicting hydrogen yields and assessing parameter trade-offs in industrial-scale applications. This integration can substantially reduce the experimental burden while improving predictive capability, thereby enhancing both the mechanistic understanding and the practical feasibility of hydrogen production from serpentinization.

08 HYDROGEN↗
DOE OSTI2025

Interactions between Per- and Polyfluoroalkyl Substances (PFAS) at the Water–Air Interface

Per- and polyfluoroalkyl substances (PFAS)--so-called “forever chemicals”--contaminate the drinking water of about 100 million people in the U.S. alone and are inefficiently removed by standard treatment techniques. A key property of these compounds that underlies their fate and transport and the efficacy of several promising remediation approaches is that they accumulate at the water−air interface. This phenomenon remains incompletely understood, particularly under conditions relevant to natural and treatment systems where water−air interfaces often carry significant loads of other organic contaminants or natural organic matter. To understand the impact of organic loading on PFAS adsorption, we carried out molecular dynamics simulations of PFAS at varying interfacial densities. We find that adsorbed PFAS form strong mutual interactions (attraction between perfluoroalkyl chains and electrostatic interactions among charged head groups) that give rise to ordered interfacial coatings. Furthermore, these interactions often involve near-cancellation of hydrophobic attraction and Coulomb repulsion. Our findings explain an apparent paradox whereby PFAS adsorption isotherms often suggest minimal mutual interactions while simultaneously displaying a high sensitivity to the composition and density of interfacial coatings. Consideration of the compounds present with PFAS at the interface has the potential to allow for more accurate predictions of fate and transport and the design of more efficient remediation approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Imprint of Anthropogenic Sources and Soil Removal on the Surface Concentration of H2 in the Contiguous US

Hydrogen (H2) is experiencing renewed interest throughout the world as a low carbon fuel alternative or complement to fossil fuels. Significant uncertainties remain regarding the environmental impact of increasing H2 usage, in part due to gaps in our understanding of the H2 atmospheric budget, including the H2 release from industrial activities and the H2 soil removal, the most important sink of H2. This study focuses on H2 dry air mole fractions measured by the NOAA Global Monitoring Laboratory in discrete ambient air samples collected every few days at sites located in the contiguous United States between 2010 and 2022. We take advantage of the long-term observations from this network to study the regional distribution of H2 sources using the potential source contribution function (PSCF). We find that H2 PSCF is consistent with a large anthropogenic source of atmospheric H2 from the incomplete combustion of fossil fuel. However, episodic air masses with high H2 dry air mole fractions (>700 ppb) recorded at some sampling locations in the Western and Southeastern US are not associated with elevated CO, suggesting significant noncombustion anthropogenic or geological sources of H2. Air masses depleted in H2 are recorded in rural or remote continental sites. Our analysis of observations from a tall tower in NE Colorado suggests that the degree of H2 depletion not only reflects differences in soil exposure but also the regional inhibition of the soil sink under arid conditions.

Paulot, Fabien↗
DOE OSTI2026

Excitation Wavelength-Dependent Emission from Americium(III) in Mineral Acid Solutions

The photoluminescence behavior of trivalent americium, Am(III), in mineral acid solutions is reported under direct-metal excitation at seven high-energy wavelengths in the ultraviolet and visible regions (378-512 nm). This study revealed a dependence of the Am(III)-based visible emission profile on the chosen excitation wavelength. For example, excitation at the more common wavelength of 504 nm produces the two expected emission bands: one at approximately 600 nm (5D1' to 7F0') and another at 690 nm (5D1' to 7F1'). When the excitation wavelength is shifted to 398 nm (targeting the 5D3', 5H7' from 7F0' transitions), the emission occurs almost exclusively at 600 nm. This behavior is unexpected and potentially highlights fundamental knowledge gaps in the current understanding of the intraconfigurational 5f-5f electronic transitions that give rise to Am(III) photoluminescence. Although a full interpretation of these results is limited by the incomplete understanding of Am(III) speciation in mineral acid systems, this study explores several potential explanations for the observed behavior and challenges the widely held assumption of a single emissive Am(III) species.

Americium↗
DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

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

Slimmer Geminals For Accurate F12 Electronic Structure Models

The Slater-type F12 geminal length scales originally tuned for the second-order Mo̷ller-Plesset F12 method are too large for higher-order F12 methods formulated using the SP (diagonal fixed-coefficient spin-adapted) F12 ansatz. The new geminal parameters reported herein reduce the basis set incompleteness errors (BSIEs) of absolute coupled-cluster singles and doubles F12 correlation energies by a significant─and increase with the cardinal number of the basis─margin. The effect of geminal reoptimization is especially pronounced for the cc-pVXZ-F12 basis sets (specifically designed for use with F12 methods) relative to their conventional aug-cc-pVXZ counterparts. The BSIEs of relative energies are less affected, but substantial reductions can be obtained, especially for atomization energies and ionization potentials with the cc-pVXZ-F12 basis sets. The new geminal parameters are therefore recommended for all applications of high-order F12 methods, such as coupled-cluster F12 methods and transcorrelated F12 methods.

Powell, Samuel R. [Virginia Polytechnic Inst. and ↗
DOE OSTI2025

Bond Dissociation Energies and Electronic Calculations on the Actinide Halides ThX and UX (X = Cl, Br, I)

Resonant two-photon ionization spectroscopy has been used to locate predissociation thresholds in the spectra of the actinide halides ThX and UX, where X = Cl, Br, and I. These predissociation thresholds are identified as the bond dissociation energies (BDEs) of the molecules. The resulting values show very similar BDEs for the corresponding ThX and UX species, with the thorium molecules being slightly more strongly bound: D 0 (ThCl) = 5.077(6) eV, D 0 (ThBr) = 4.391(4) eV, D 0 (ThI) = 3.537(8) eV, D 0 (UCl) = 4.989(3) eV, D 0 (UBr) = 4.313(3) eV, and D 0 (UI) = 3.449(8) eV. Here, the estimated error limit is given in parentheses in units of the last reported digit. Spinor-based coupled cluster calculations have also been carried out on the halides of this work, including also ThF and UF. Here, the final D 0 values after including contributions due to basis set incompleteness, outer-core-correlation, picture-change, and QED effects are within 0.04 eV of the present experimental values in each case.

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

New Perspectives on Vibrational Energy Transfer in Energetic Materials: Insights from Pressure-Tuned Ultrafast Spectroscopy

Understanding the manner in which vibrational energy flows between molecular and lattice vibrations is of great interest in physical chemistry due to its central role in reactivity and energy dissipation in molecular materials. Here, in this feature article, we highlight our recent efforts employing ultrafast broadband infrared spectroscopy toward understanding the interplay between molecular and lattice vibrations in energetic materials, motivated by the open questions surrounding the role of vibrational energy transfer (VET) in reaction initiation in these materials. Our work addresses the ongoing debate on the participation of doorway modes in VET. We further present new results from high-pressure ultrafast experiments on RDX, a hydrogen-bonded material, and BNFF, a hydrogen-free material, to explore how intermolecular interaction strength governs VET pathways and time scales. Collectively, our findings reveal that vibrational dynamics in these systems occurs across three distinct time regimes, with VET being incomplete out to hundreds of picoseconds, suggesting the importance of considering nonstatistical reactions in the modeling of these materials. These time scales vary as intermolecular interaction strength is indirectly modified by application of static pressure, indicating dramatic changes to the vibrational structure of these materials under shock-relevant conditions. Our results thus shed light on how intermolecular interactions shape vibrational energy redistribution in molecular materials, and highlight the need for further theoretical and experimental investigation.

Carlson, Daniel Ryan [Sandia National Laboratories↗
DOE OSTI2024

Time-Resolved X-ray Emission Spectroscopy and Resonant Inelastic X-ray Scattering Spectroscopy of Laser Irradiated Carbon

The existence of liquid carbon as an intermediate phase preceding the formation of novel carbon materials has been a point of contention for several decades. Experimental observation of such a liquid state requires nonthermal melting of solid carbon materials at various laser fluences and pulse properties. Reflectivity experiments performed in the mid-1980s reached opposing conclusions regarding the metallic or insulating properties of the purported liquid state. Time-resolved X-ray absorption studies showed shortening of C–C bonds and increasing diffraction densities, thought to evidence a liquid or glassy carbon state, respectively. Nevertheless, none of these experiments provided information on the electronic structure of the proposed liquid state. Herein, we report the results of time-resolved resonant inelastic X-ray scattering (RIXS) and time-resolved X-ray emission spectroscopy (XES) studies on amorphous carbon (a-C) and ultrananocrystalline diamond (UNCD) as a function of delay time between the irradiating pulse and X-ray probe. For both a-C and UNCD, we attribute decreases in RIXS or XES signals to transition blocking, relaxation, and finally, ablation. Increased signal at 20 ps following the irradiation of the UNCD is attributed to the probable formation of nanoscale structures in the ablation plume. Further, differences in the amount of signal observed between a-C and UNCD are explained by the difference in sample thickness and, specifically, incomplete melting of the UNCD film. Comparisons to spectral simulations based on MD trajectories at extreme conditions indicate that the carbon state in our experiments is crystalline. Normal mode analysis confirmed that symmetrical bending or stretching of the C–C bonds in the diamond lattice results in XES spectra with small intensity differences. Overall, we observed no evidence of melting to a liquid state, as determined by the lack of changes in the spectral properties for up to 100 ps delays following the melting pulses.

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

Monte Carlo Explicitly Correlated Second-Order Many-Body Green’s Function Calculations of Semiconductor Band Gaps

A systematically converging series of ab initio, post-density-functional, size-consistent, electron-correlated approximations is desired for predictive computing of felectronic band structures of insulating, semiconducting, and metallic solids. A series that meets all of these desiderata (except the applicability to metals) is ab initio many-body Green's function theory based on Gaussian-type-orbital (GTO) basis sets. Here, its leading-order approximation, the second-order Green's function (GF2) method in the diagonal and frequency-independent approximations with the aug-cc-pVDZ basis set, is applied to the fundamental band gaps of three semiconductors (diamond, silicon, and silicon carbide in the zincblende structure) using cluster models. Corrections are made to the basis-set-incompleteness errors by the explicit-correlation (F12) ansatz (GF2-F12) for the valence band edges. The crystals are modeled as surface-passivated clusters of increasing sizes, whose wave functions are expanded by up to 2709 GTO basis functions. Immense computational costs of these calculations are overcome by the highly scalable stochastic algorithm of the Monte Carlo GF2-F12 method, whose operation cost per state increases only as a cubic power of system size, which has a tiny memory footprint and easily achieves near-perfect parallel efficiency on thousands of CPUs or on hundreds of GPUs. The correlated, F12-corrected highest-occupied and lowest-unoccupied molecular-orbital energy (HOMO-LUMO) gap is 5.78 ± 0.07 eV for C 87 H 76 as compared with the experimental value of the fundamental (indirect) band gap of bulk diamond at 5.48 eV. The correlated, F12-corrected HOMO-LUMO gaps for Si 75 H 76 and Si 32 C 43 H 76 are 2.56 ± 0.15 eV and 3.50 ± 0.12 eV, respectively, which are expected to decrease further with increasing cluster sizes. As a result, the experimental fundamental (indirect) band gaps of bulk silicon and silicon carbide are 1.17 eV and 2.42 eV, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Challenges in Pulsed-Field Gradient Nuclear Magnetic Resonance on Magnetically Heterogeneous Interfaces: Sequence and Field-Dependent Apparent Diffusion Coefficients

It is well known that the internal gradient (gi) that exists within pores haunts the diffusion coefficient (D) as measured by the pulsed-field gradient (PFG) nuclear magnetic resonance (NMR). Several PFG-NMR methods developed to determine an accurate D were not successful. Then, the steady-state diffusion coefficient (Dapp,8) for the cation [C4mim]+ of [C4mim][Tf2N]; [1-butyl-3-methylimidazolium][bis(trifluoromethylsulfonyl)imde] ionic liquid confined in ordered mesoporous carbon (OMC) were determined by comparing Dapp,8 obtained from 1H PFG-NMR performed with three different stimulated echo sequences: STE, APFG, and MPFG under the two external magnetic field strength, B0 = 9.4 and 14.1 Tesla. The measured Dapp,8 which is an order of magnitude smaller than D of bulk [C4mim][Tf2N], is in good agreement between APFG and MPFG both in B0 = 9.4 and 14.1 Tesla. However, the strong gi artifact, which caused apparent diffusion coefficient (Dapp) depending strongly and weakly on B0 and temperature, respectively, in diffusion-time dependent Dapp, Dapp(?) obtained from a sequence with monopolar gradients (STE) was suppressed by using sequences employing bipolar gradients (APFG and MPFG) in the region of steady-state diffusion. But incompletely suppressed gi artifact resulting in the different behaviors of the early part of Dapp(?) between the sequences leads a ˜ 0.6 and 0.9 in MPFG and APFG, respectively, in the relationship between mean squared displacement and diffusion time: = 2Dta, where a = 0.5 and 1 for 1-dimensional single file diffusion and 3-dimensional bulk diffusion, respectively. The above observations clearly show that the diffusion behavior of ions/molecules within the pores and pore structure, such as the surface-to-volume ratio? (D?_app (?)=D_0 [1-4/(9vp) S/V v(D_0 ?)]) and tortuosity (T = D0/Dapp,8), are possible to be misunderstood, especially in the systems with a non-negligible gi. This work demonstrates that it may be necessary to test several PFG sequences under multiple external magnetic fields for the correct determination of the diffusion behavior of ions/molecules in the pores with a larger internal gradient, gi.

Han, Kee Sung↗
DOE OSTI2025

Expanded View of NMR Spin–Lattice Relaxation in Fluorine-Containing Ionic Liquids

Fluorine-containing anions are widely used in ionic liquids due to their unique physicochemical properties. However, the local dynamics of both cations and anions and their associated relaxation mechanisms remain incompletely understood. Here, we present a 1 H and 19 F spin–lattice relaxation rate (R1) study as a function of frequency over a broad frequency range from 30 kHz to 800 MHz for ionic liquids containing BF 4 – , PF 6 – , TFSI – , and FSI – anions and EMIM + cation. By combining experimental R 1 H and R 1 F NMR dispersion (NMRD) profiles with relaxation models for both dipolar spin interactions and chemical shift anisotropy (CSA) contributions, we demonstrate that CSA is needed to accurately describe the R 1 F relaxation behavior above ∼300 MHz, the extent of which depends on the anion structure. These findings challenge the long-standing assumption that dipolar contribution is the main source of 19 F relaxation in these systems and highlight the importance of including CSA to accurately interpret 19 F relaxation in ionic liquids, particularly at high frequencies. This work provides new insights into the molecular dynamics of fluorine-containing species.

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

Is the Matrix Completion of Reduced Density Matrices Unique?

Reduced density matrices are central to describing observables in many-body quantum systems. In electronic structure theory, the two-particle reduced density matrix (2-RDM) suffices to determine the energy and other key properties. Recent work has used matrix completion, leveraging the low-rank structure of RDMs and approximate theoretical models, to reconstruct the 2-RDM from partial data and thus reduce the computational cost. However, matrix completion is, in general, an under-determined problem. Revisiting Rosina’s theorem (Rosina, M. Queen’s Papers on Pure and Applied Mathematics , 1968, No. 11, 369), we here show that the matrix completion is unique under certain conditions, identifying the subset of 2-RDM elements that enables its exact reconstruction from incomplete information. Building on this, we introduce a hybrid quantum–stochastic algorithm that achieves exact matrix completion, demonstrated through applications to the Fermi–Hubbard model.

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

Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools

The study of protein-protein interactions (PPIs) provides insight into various biological mechanisms, including the binding of antibodies to antigens, enzymes to inhibitors or promoters, and receptors to ligands. Recent studies of PPIs have led to significant biological breakthroughs. For example, the study of PPIs involved in the human:SARS-CoV-2 viral infection mechanism aided in the development of the SARS-CoV-2 vaccines. Though several databases exist for the manual curation of PPI networks, text mining methods have been routinely demonstrated as useful alternatives for newly studied or understudied species where databases are incomplete. Here, the relationship extraction (RE) performance of several open-source classical text processing, machine learning (ML)-based natural language processing (NLP), and large language model (LLM)-based NLP tools were compared. Overall, our results indicated that networks derived from classical methods tend to have high true positive rates at the expense of having overconnected-networks, ML-based NLP methods have lower true positive rates but networks with the closest structures to the target network, and LLM-based NLP methods tend to exist in-between the two other approaches, with variable performances. Finally, the selection of a specific NLP approach should be tied to the needs of a study and text availability, as models varied in performance due to the amount of text provided.

59 BASIC BIOLOGICAL SCIENCES↗