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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding the interactions and regulatory relationships among biomolecules is essential for deciphering complex biological systems and elucidating the mechanisms behind diverse biological functions. Traditionally, the collection of such molecular interaction data has relied on expert curation, a process that is both time-consuming and labor-intensive. To address these limitations, this study explores the use of large language models (LLMs) to automate the genome-scale extraction of molecular interaction knowledge. Here, we evaluate the performance of various LLMs on key biological tasks, including the identification of protein-protein interactions, detection of genes associated with pathways influenced by low-dose radiation, and inference of gene regulatory relationships. Our findings demonstrate that larger LLMs tend to perform better, particularly in extracting intricate gene and protein interactions. Despite their strengths, these models face challenges in recognizing functionally diverse gene groups and highly correlated regulatory relationships. Through a comprehensive analysis using established molecular interaction and pathway databases, we show that LLMs possess the potential to identify relevant biomolecules and predict their interactions, offering valuable insights and marking a significant step toward AI-driven biological knowledge discovery.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2026

Long-Range Fit: A Software Package for the Representation and Study of Long-Range Molecular Interactions

Describing intermolecular forces is fundamental to modeling and predicting the behavior of molecular systems. In particular, long-range molecular interactions─with electrostatic, induction, and dispersion as the main components─play a critical role, especially for low-temperature and low-density regimes. Long-range interactions are often described through perturbation theory, representing the electronic charge distribution via a multipolar series of the moments and polarizability tensors corresponding to each molecule. However, while the theory is well established, obtaining the resulting analytical expressions (and their practical implementation) constitutes a highly complex and system-dependent task. To address this challenge, we developed long-range-fit (LRF), an interactive and user-friendly software package designed to automate the generation and fitting of long-range interaction terms for arbitrary molecules in nondegenerate (ground or excited) electronic states. We have derived and implemented all terms up to 15th order, without approximations, via a spherical tensor representation, with symmetry adaptation to all molecular point-group symmetries. The resulting potential energy surface is compatible with most representations of the close interaction region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2000

Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth unit dimensions to be measured as they were being incorporated into the crystal. These measurements showed that growth on the (110) face proceeded by the formation of new 4(sub 3) helices from the addition of many growth units of at least tetramer size. This is the first time that a time-resolved AFM technique has been used to observe individual molecular events during crystal growth.

Nadarajah, Arunan↗
DOE OSTI2024

Roles of kaolinite-oil-gas molecular interactions in hydrogen storage within depleted reservoirs

Hydrogen is a clean alternative to fossil fuels, emitting only water vapor during combustion. In a future hydrogen economy, large-scale storage will be an important component of the supply chain. Due to its low volumetric density, conventional surface storage methods are inadequate. Underground hydrogen storage (UHS) offers a viable solution, enabling the storage of millions of cubic meters. Among potential geological sites, including salt caverns, aquifers, and depleted gas reservoirs, depleted oil reservoirs show promise. Studying hydrogen interactions with residual oil and reservoir minerals is vital for understanding the properties of hydrogen and the reservoir post-injection. In this work, we employed molecular dynamics simulations to gain molecular-level insights into these interactions. We investigated hydrogen dissolution in oil, adsorption at kaolinite/oil interfaces, the role of CO 2 as a cushion gas, and the influence of kaolinite’s hydrophobicity on H 2 behavior. The main findings include: (1) hydrogen dissolves more in oil than in water, (2) the introduction of CO 2 suppresses hydrogen dissolution in oil and reduces the interfacial tension (IFT) between oil and gas, (3) CO 2 decreases H 2 partitioning near kaolinite surfaces due to its strong affinity for the hydrophilic gibbsite surface of kaolinite, and (4) CO 2 is more effective than H 2 in reducing IFT between kaolinite and the oil–gas mixture. These findings emphasize the effectiveness of CO 2 as a cushion gas and the important role of clay hydrophobicity in UHS, providing insights that are challenging to obtain experimentally.

08 HYDROGEN↗
NASA NTRS1978

Ames interactive molecular model building system - A 3-D computer modelling system applied to the study of the origin of life

The investigation of specific interactions among biological molecules must take into consideration the stereochemistry of the structures. Thus, models of the molecules are essential for describing the spatial organization of potentially interacting groups, and estimations of conformation are required for a description of spatial organization. Both the function of visualizing molecules, and that of estimating conformation through calculations of energy, are part of the molecular modeling system described in the present paper. The potential uses of the system in investigating some aspects of the origin of life rest on the assumption that translation of conformation from genetic elements to catalytic elements would have been required for the development of the first replicating systems subject to the process of biological evolution.

Coeckelenbergh, Y.↗
DOE OSTI2025

Tuning Molecular Interactions between Peptoids and Substrates to Achieve Surface-Agnostic Coating

Achieving programmable and robust coatings that maintain functionality while adhering to various surface types with molecular-level tunability and programmable features remains challenging. In this study, we develop adaptable and stable surface-agnostic coatings (SACs) based on crystalline peptoid membranes by tuning interpeptoid and peptoid-substrate interactions. We utilize two complementary methods: (1) surfaceinduced assembly, where peptoid membranes form directly on substrates, and (2) depositing preformed peptoid crystalline membranes via an aqueous layer-by-layer (LbL) assembly technique. These strategies are applied to substrates with diverse surface chemistries and topographies, including mica, highly ordered pyrolytic graphite (HOPG), MoS 2 , sapphire, and porous membranes like porous alumina and polysulfide. Atomic force microscopy confirms the formation of peptoid coatings and reveals differences in assembly behavior across surfaces. Moisture vapor transport measurements serve as a proof-of-concept test for membrane continuity and tunable permeance. Together, these findings demonstrate the adaptability and programmability of peptoid-based SACs, enabling rational coating design on surfaces with diverse chemical and topographical features. Furthermore, this work opens pathways for using peptoid membranes as programmable surface modifiers in functional interfaces, protective coatings, and membrane platforms.

biomimetic polymers↗
DOE OSTI2026

Selectivity in gas–liquid interactions: Molecular beam scattering of CD 4 and ND 3 from an aqueous flat liquid jet

The dynamics of polar and nonpolar molecules colliding with an aqueous surface are characterized by scattering molecular beams of deuterated methane and ammonia, CD 4 and ND 3 (E i = 28.9 and 30.3 kJ mol −1 , respectively), from a flat liquid jet of cold salty water (8 m LiBr, 230 K). Translational energy distributions of scattered species collected as a function of collision geometry probe both impulsive scattering (IS) and thermal desorption (TD) mechanisms. Here, we find that CD 4 scattering is dominated by IS and exhibits a super-specular angular distribution. The fraction of TD scattering events is notably smaller for cold salty water than for dodecane, consistent with a higher free energy of solvation for CD 4 in the water jet. In contrast, no scattering signal is seen for ND 3 from the water jet, a result attributed to the high solubility and efficient protonation of ND 3 in liquid water. The IS channel for CD 4 was analyzed using a soft-sphere model, yielding a higher internal energy (E int ) and lower effective surface mass (m eff ) than was seen for Ne/water; the higher value of E int is attributed to rotational excitation of the scattered CD 4 . These findings demonstrate that the outcomes of a gas–liquid collision—scattering trajectory, surface adherence, and energy transfer—are directed at the molecular level by both the gaseous scatterer and liquid surface.

Foreman, Madison M. [University of California, Ber↗
NASA NTRS1987

Tunable ultraviolet laser studies of photon-molecular interactions of cometary interest

Most of the cometary radicals are thought to be formed in the coma by photodissociation processes. Successful modeling of the coma requires a detailed knowledge of the products that are formed from the various parent molecules and the energy partitioning among these products. This information has to be obtained as a function of wavelength, because the sun is not a monochromatic source. In this review, the status of the experimental knowledge of some key molecules is discussed, along with the prospects of some new laboratory techniques that can fill in the gaps in the present knowledge.

Jackson, William M.↗
NASA NTRS1989

Semiclassical approach to atomic and molecular interactions

A general approach, combining quantum and classical mechanics, is used to determine the electron position and velocity distributions in atoms and atomic ions (positive and negative). The Hartree-Fock electronic wave functions and the classical central field approximation are used for evaluation of the dynamic properties of the localized electrons. The distributions, which are of fundamental importance in applications of the binary encounter approximation to description of atomic and ionic collissions, are obtained in the form of simple analytical expressions. The quantum-classical distributions of this work are compared with several other distributions in Ne, Ar, and Al atoms in the ground state.

Kunc, Joseph A.↗
NASA NTRS1976

Molecular contamination study by interaction of a molecular beam with a platinum surface

The capability of molecular beam scattering from a solid surface is analyzed for identification of molecular contamination of the surface. The design and setup of the molecular beam source and the measuring setup for the application of a phase sensitive measuring technique for the determination of the scattered beam intensity are described. The scattering distributions of helium and nitrogen molecular beams interacting with a platinum surface were measured for different amounts of contamination from diffusion pump oil for surface temperatures ranging from 30 to 400 C. The results indicate the scattering of molecular beams from a platinum surface is a very sensitive method for detecting surface contamination.

Nuss, H. E.↗
DOE OSTI2025

Polyethylene Glycol Surface Modification and Polythiophene Side-Chain Chemistry: A Combined Strategy toward High-Capacity Lithium-Ion Battery Anodes

In the development of high-capacity lithium-ion batteries (LIBs), the combined optimization of active material interfaces and polymer binder chemistry plays a critical role in improving electrode performance and longevity. This work explores a dual design strategy incorporating polyethylene glycol (PEG) surface modification and carboxylated polythiophene side-chain tailoring to enhance the electrochemical behavior of magnetite (Fe 3 O 4 )-based anodes. PEG is employed to improve interfacial stability, while carboxylated polythiophene binders with varying alkyl side-chain lengths─poly[3-(potassium-4-butanoate)thiophene-2,5-diyl] (P3KBT), poly[3-(potassium-5-pentanoate)thiophene-2,5-diyl] (P3KPT), and poly[3-(potassium-6-hexanoate)thiophene-2,5-diyl] (P3KHT)─are used to modulate molecular interactions and ion transport. Among these three analogs, the PEG–Fe 3 O 4 –P3KHT electrode exhibits superior ion-transfer kinetics, the highest capacity retention, and the lowest charge-transfer resistance after extended cycling. Compared to their non-PEG analogs, PEG-coated electrodes demonstrate enhanced structural integrity and electrochemical behavior, emphasizing the synergistic effects of surface modification and side-chain chemistry. These findings highlight the importance of interfacial interactions and molecular design in achieving robust and high-performance composite anodes for next-generation LIBs.

Fe3O4↗
DOE OSTI2026

Primary biomolecular adsorption energetics of core–shell nanocomplexes: Implications for biological interactions

Molecular organization at the nano-bio interface governing the colloidal stability, reactivity, immune recognition, and drug delivery performance of nanoparticles remains difficult to predict. Quantifying the primary hydration energetics of biomolecule-coated nanomaterials can determine those interactions and provide a basis for engineered nanocarriers with tailored behavior in biological systems. Here, we measured the thermodynamics of water adsorption on patchy dry magnetite (Fe 3 O 4 ) nanoparticles coated with three model biomolecules, bovine serum albumin, potato starch, and lauric acid and compared these properties to the hydration energetics of the corresponding free dry biomolecules. The results demonstrate how the surface functionalization alters the hydrophilicity, the accessible hydrophilic surface, and the interaction potential of the nanocomplex surface with biological media. The protein coating increases the interaction potential of the surface of the nanocomplex. The weaker interaction potential of the polysaccharide coating and the relatively large hydrophilic surface area allow dynamic and reversible binding, while the fatty acid rearranges into a partial bilayer with very strong hydrophilicity. The findings establish the hydration enthalpy as a quantitative basis to determine and interpret nanoparticle interactions with proteins, membranes, and biological fluids, and provide a thermodynamic foundation for designing nanocarriers with predictable biological reactivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2001

Contamination Effects Due to Space Environmental Interactions

Molecular and particulate contaminants are commonly generated from the orbital spacecraft operations that are under the influence of the space environment. Once generated, these contaminants may attach to the surfaces of the spacecraft or may remain in the vicinity of the spacecraft. In the event these contaminants come to rest on the surfaces of the spacecraft or situated in the line-of-sight of the observation path, they will create various degrees of contamination effect which may cause undesirable effects for normal spacecraft operations, There will be circumstances in which the spacecraft may be subjected to special space environment due to operational conditions. Interactions between contaminants and special space environment may alter or greatly increase the contamination effect due to the synergistic effect. This paper will address the various types of contamination generation on orbit, the general effects of the contamination on spacecraft systems, and the typical impacts on the spacecraft operations due to the contamination effect. In addition, this paper will explain the contamination effect induced by the space environment and will discuss the intensified contamination effect resulting from the synergistic effect with the special space environment.

Chen, Philip T.↗
DOE OSTI2024

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗