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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗
DOE OSTI2026

From molecular to macroscopic: predicting liquid–liquid phase equilibria and small-angle scattering of mixtures of organic liquids from atomistic simulation using Kirkwood–Buff theory

Macroscopic phase equilibria between solutions define the functionality of many biological and industrial processes, yet they are challenging to predict due to the inherent complexity of liquids containing large molecules. This work introduces an approach for the purely predictive calculation of such phase equilibria in temperature-composition space from molecular dynamics (MD) simulations at one temperature in the single-phase region. We use an approach developed previously to obtain the entropic and enthalpic contributions to the free energy of mixing from the atomic-scale information given by MD simulations via Kirkwood–Buff theory. This allows us to accurately estimate the free energy of mixing as a function of temperature, and thus obtain liquid–liquid phase equilibria, including liquid–liquid critical points, associated binodal and spinodal lines, and composition fluctuations across a region of temperature and composition. Results for binary malonamide–alkane systems are validated by comparison to a direct experimental probe of the fluctuations: the small angle X-ray scattering intensity near zero wavenumber. The MDKB → Phase method demonstrated here provides a significant improvement in predicting liquid–liquid equilibria and free energy as a function of temperature for our systems of interest compared to conventional thermodynamic models. The accurate performance of this purely predictive approach lies in its preservation of atomistic details when determining thermodynamic properties. Furthermore, its inherent extensibility to multi-component systems will likely make the MDKB → Phase approach a valuable general tool for connecting molecular interactions to macroscopic phase equilibria and for the computational screening of materials for targeted thermodynamic behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Computationally Guided Design of Polymer-Coated Microparticles as Reusable Materials

Long-duration space exploration missions and sustained lunar or Martian surface operations present greater demands for multifunctional and reusable materials. By scaling down the amount of material to be launched from Earth, both mission cost and risk can be reduced. In this regard, leveraging in-space manufacturing capabilities with reusable feedstock materials is an attractive option, as it will allow for articles to be generated on demand, utilized, and then recycled for additional use. NASA’s Enabling Sustained Presence Using Recyclables (ESPUR) project aims to develop reusable materials using polymer-coated microparticles that are bonded via reversible Diels-Alder reactions, where only modest heat is needed to trigger the reverse reaction and enable reuse. For proof-of-concept demonstration, research is currently focused on the fabrication of epoxy microparticles that contain a copoly(carbonate urethane) coating with maleimide and furan functionalities. Here, we discuss the integration of computational materials modeling approaches to help navigate the large design space in this development effort. We perform molecular dynamics (MD) simulations with atomistic and coarse-grained models of the copolymer, which allow us to evaluate the effects of design parameters like the molecular weight and composition on the molecular interactions and chain dynamics. We show how the properties change with the reversible bonds. We also leverage discrete element method (DEM) simulations to assess how microparticle design parameters like the size ratio and volume fraction can be tuned to increase the packing density and number of microparticle contacts to improve the mechanical properties. Our results demonstrate how computational tools can be used in close collaboration with experimental efforts to accelerate material design.

reusable materials↗
DOE OSTI2025

Structural insights into transcriptional regulation by the helicase RECQL5

Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.

Biochemistry & Molecular Biology↗
NASA NTRS2003

Twinning, Epitaxy and Domain Switching in Ferroelastic Inclusion Compounds

Our research is in the area of solid-state organic chemistry, which lies at the interface between physical organic chemistry and materials science. We use crystalline solids as models to probe fundamental issues about physical processes, molecular interactions and chemical reactions that are important for fabrication, stabilization and application of technological materials. Much of our most recent work has focused on the phenomena of ferroelastic and ferroelectric domain switching, in which application of an external force or electric field to a crystal causes the molecules inside the crystal to reorient, in tandem, to a new orientational state. To better understand and control the domain switching process, we have designed and synthesized over twenty closely related, ferroelastic organic crystals. Our approach has been to use crystalline inclusion compounds, in which one molecule (the guest) is trapped within the crystalline framework of a second molecule (the host). By keeping the host constant and varying the proportions and kinds of guests, it has been possible to tailor these materials so that domain switching is rapid and reversible (which is desirable for high technology applications). Inclusion compounds therefore serve as powerful systems for understanding the specific molecular mechanisms that control domain switching.

Hollingsworth, Mark D.↗
NASA NTRS2004

Solution-Phase Processes of Macromolecular Crystallization

We have proposed, for the tetragonal form of chicken egg lysozyme, that solution phase assembly processes are needed to form the growth units for crystal nucleation and growth. The starting point for the self-association process is the monomeric protein, and the final crystallographic symmetry is defined by the initial dimerization interactions of the monomers and subsequent n-mers formed, which in turn are a function of the crystallization conditions. It has been suggested that multimeric proteins generally incorporate the underlying multimers symmetry into the final crystallographic symmetry. We posed the question of what happens to a protein that is known to grow as an n-mer when it is placed in solution conditions where it is monomeric. The trypsin-treated, or cut, form of the protein canavalin (CCAN) has been shown to nucleate and grow crystals as a trimer from neutral to slightly acidic solutions. Under these conditions the solution is composed almost wholly of trimers. The insoluble protein can be readily dissolved by weakly basic solution, which results in a solution that is monomeric. There are three possible outcomes to an attempt at crystallization of the protein under monomeric (high pH) conditions: 1) we will obtain the same crystals as under trimer conditions, but at different protein concentrations governed by the self association equilibria; 2) we will obtain crystals having a different symmetry, based upon a monomeric growth unit; 3) we will not obtain crystals. Obtaining the first result would be indicative that the solution-phase self-association process is critical to the crystal nucleation and growth process. The second result would be less clear, as it may also reflect a pH-dependent shift in the trimer-trimer molecular interactions. The third result, particularly for experiments in the transition pH's between trimeric and monomeric CCAN, would indicate that the monomer does not crystallize, and that solution phase self association is not part of the crystal nucleation and growth path. Results are presented for crystallization experiments of CCAN over the pH 6.8 to 9.6 range.

Pusey, Marc L.↗
NASA NTRS2017

Dissociation and Internal Excitation of Molecular Nitrogen Due to N + N2 Collisions Using Direct Molecular Simulation

In this work we present a molecular level study of N2+N collisions, focusing on excitation of internal energy modes and non-equilibrium dissociation. The computation technique used here is the direct molecular simulation (DMS) method and the molecular interactions have been modeled using an ab−initio potential energy surface (PES) developed at NASA's Ames Research Center. We carried out vibrational excitation calculations between 5000K and 30000K and found that the characteristic vibrational excitation time for the N + N2 process was an order of magnitude lower than that predicted by the Millikan and White correlation. It is observed that during vibrational excitation the high energy tail of the vibrational energy distribution gets over populated first and the lower energy levels get populated as the system evolves. It is found that the non-equilibrium dissociation rate coefficients for the N + N2 process are larger than those for the N2 + N2 process. This is attributed to the non-equilibrium vibrational energy distributions for the N + N2 process being less depleted than that for the N2 +N2 process. For an isothermal simulation we find that the probability of dissociation goes as 1/T(sub tr) for molecules with internal energy (epsilon(sub int)) less than approximately 9.9eV, while for molecules with epsilon (sub int) greater than 9.9eV the dissociation probability was weakly dependent on translational temperature of the system. We compared non-equilibrium dissociation rate coefficients and characteristic vibrational excitation times obtained by using the ab-initio PES developed at NASA's Ames Research Center to those obtained by using an ab-initio PES developed at the University of Minnesota. Good agreement was found between the macroscopic properties and molecular level description of the system obtained by using the two PESs.

Grover, Maninder S.↗
DOE OSTI2025

Bulky Cation-Modified Interfaces for Thermally Stable Lead Halide Perovskite Solar Cells

Charged conjugated organic molecules offer promising prospects for reducing nonradiative recombination at interfaces in perovskite solar cells, while protecting the active layer from moisture. However, several studies have shown that the heat induced diffusion of these cations leads to irreversible solar cell degradation. Passivation molecules for perovskite can reconstruct the film surface into lower-dimensional phases when exposed to thermal stress, impeding charge extraction and affecting the photoconversion efficiency (PCE) of devices. In this work, we study how molecular interactions between passivation molecules and 3D CsFAPbI 3 perovskite impact stability and charge extraction at the perovskite/hole transport layer interfaces. Two model π- conjugated molecules are studied: 2-([2,2′-bithiophen]-5-yl)ethan-1-aminium iodide (2TI) and 2-(3‴,4′-dimethyl-[2,2′:5′,2″:5″,2‴- quaterthiophen]-5-yl)ethan-1-ammonium iodide (4TmI). We demonstrate that the speed of surface layer reconstruction under thermal stress can be controlled by the cation size and correlate these structural changes with the solar cell performance and stability. Devices treated with 2TI and 4TmI achieve PCEs over 21% and maintain their performance under thermal stress. Our findings demonstrate that thermal stability in PSCs can be achieved via the design engineering of passivation agents, offering a blueprint for developing next-generation passivation molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Effect of tert -Butyl Substitution on the Interactions of Cobalt Phthalocyanine with a Carbon Monoxide-Functionalized Tip

Supported cobalt phthalocyanines (CoPc) are promising catalysts for CO 2 reduction, a critical process for mitigating greenhouse gas emissions. Enhancing the catalytic performance of CoPc involves modifying the interaction between the cobalt center and intermediate species. This study focuses on the effects of tert-butyl substitution on CoPc using (tert-butyl) 4 CoPc, where the substitution can both directly alter the molecule’s intramolecular electronic structure and indirectly alter it by the bulky group weakening the interaction with the support. Toward this end, we investigated the structural and chemical properties of (tert-butyl) 4 CoPc on a Ag(111) surface at the single-molecule level using three-dimensional atomic force microscopy (AFM) with a CO-terminated tip and discussed them in comparison with data for unmodified CoPc and amino-substituted CoPc. Notably, distance-dependent force measurements revealed anomalies in the tert-butyl groups’ force curves, attributed to their rotational flexibility. The tert-butyl (t-butyl) groups were also observed to increase the attraction of the central Co atom to CO, but this effect was attributed largely to enhanced interactions of the back of the tip with the peripheral t-butyl groups. In conclusion, while this longer-range interaction would not be expected to impact the interaction of small molecules with the catalytic center, the results reveal the ability of AFM to characterize longer range environmental interactions that can enhance adsorption and subsequent reactions of larger molecules, as well as the role side chains that offer configurational adaptability may play in these interactions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Post-Modification of Crystalline Peptoid Nanomembranes with Active Nanoparticles for Efficient Photooxidation of a Mustard Gas Simulant

Peptoids (or poly-N-substituted glycines) hold immense potential for assembling into hierarchically structured functional materials via controlled molecular interactions. To create self-assembled materials with tailored functionalities, peptoid sequences are often conjugated with reactive or recognition motifs to enable applications including specific binding, biomimetic catalysis, and fluorescence imaging. However, the direct integration of bulky functional motifs into peptoid sequences can disrupt assembly processes and structural outcomes. Herein, we present a post-modification strategy for functionalizing pre-formed 2D crystalline assemblies. Through introducing clickable active sites, such as azide, alkyne, or thiol groups into a peptoid sequence, site-specific conjugation is achieved post-assembly via efficient “click”-type reactions. This strategy enables the ordered alignment of functional groups and gold nanoparticles (Au NPs) on the surface of 2D peptoid nanomaterials with controlled density, while preserving their high crystallinity and structural integrity. Furthermore, we demonstrated that nanomembranes functionalized with both Au NPs and porphyrins enhance the efficiency and selectivity of the photooxidation of 2-chloroethyl ethyl sulfide, a simulant of sulfur mustard. This innovative strategy lays the groundwork for advancing peptoid-based functional materials across diverse applications, from catalysis to biomedicine.

Chemistry↗
DOE OSTI2025

Long-Range Interaction between Molecules with Electronic Degeneracy: Beyond the Born–Oppenheimer Approximation

Long-range intermolecular interaction plays an essential role in (ultra)cold collisions. For monomers with degenerate electronic states, an accurate description of the long-range interaction can be challenging due to the potential breakdown of the Born–Oppenheimer approximation. In this work, we developed a general method to construct long-range interaction potential energy surfaces (IPESs) between arbitrary molecules using the degenerate perturbation theory of Schrödinger. To further simplify the application of this method, a group-theoretical method is introduced to identify nonzero components of electrostatic properties of monomers, especially for the nonlinear molecules. To demonstrate this approach, we report the long-range IPESs of the O( 3 P)–OH( 2 Π) and OH( 2 Π)–OH( 2 Π) systems. The excellent agreement with ab initio calculations in large separations, even near electronic degeneracies, confirms the accuracy of our approach. The method is expected to lay the groundwork for the accurate investigation of (ultra)cold collisional dynamics involving open-shell species.

ab initio calculations↗
DOE OSTI2025

Photoinduced twist and untwist of moiré superlattices

This paper directly observes femtosecond photoinduced twist–untwist motion of WSe₂/MoSe₂ moiré superlattices using ultrafast electron diffraction, showing that optical excitation can dynamically reconfigure moiré lattice structure and interlayer coupling. It supports the proposal by establishing the team’s ability to probe ultrafast interfacial and moiré dynamics, which is relevant to using moiré TMDs as reconfigurable platforms for controlling spin, charge, and molecular interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Bio-inspired multiscale design for perovskite solar cells

Metal halide perovskite semiconductors have attractive light-harvesting and charge-carrier transport properties for photovoltaics. Perovskite solar cells (PSCs) and modules have demonstrated their commercial promise with high power conversion efficiencies, but still face stability challenges. In this Review, we explore how biomaterials offer design inspiration for the development of durable and efficient PSCs at three different scales. At the molecular level, bio-inspired molecular interactions are harnessed towards crystallization control and degradation prevention, which offers an enhancement in long-term maximum-power-point tracking stability. At the microstructural level, self-healing and strength-enhancing strategies, utilizing dynamic bonds and interfacial reinforcement, can help PSCs to recover from physical damage and maintain high performance. At the device level, macroscopic functionalities, such as moth-eye-inspired structures tailored to different layers, can collectively enable antireflection, radiative cooling and self-cleaning to optimize light management, heat dissipation and encapsulation in PSCs. Bio-inspired PSC research can combine improved efficiency and lifetime, with abundant, biocompatible alternatives to conventional stabilizers. Future efforts should focus on screening bioinspired molecules to optimize film crystallization and stability, developing self-healing mechanisms triggered by operational stress, designing cost-efficient biomicrostructures, and integrating multifunctional encapsulation to enhance the efficiency and lifespan of PSCs.

Duan, Tianwei↗
DOE OSTI2024

Molecular structures of residual solvent in polyacrylonitrile based electrolytes: Implications for conductivity and stability

Lithium-ion batteries increasingly play significant roles in modern technologies; however, increased energy density also raises concerns about electrolyte safety. Traditional electrolytes that use volatile organic solvents face risks of thermal runaways and fires from electrode shorting. In response, polymer-based solid electrolytes have been developed for replacement. Polyacrylonitrile (PAN) is a promising fire-resistant component for electrolyte fabrication, but its limited solubility necessitates using low-volatility solvents, which are notoriously difficult to remove in subsequent drying processes. Here, we use femtosecond two-dimensional infrared spectroscopy to provide an in-depth understanding of how residual solvent from processing affects the molecular structures and dynamics within a polymer electrolyte. To this end, linear and nonlinear infrared spectroscopies are employed to interrogate the molecular interactions in PAN-based electrolytes containing various contents of N,N-dimethylformamide (DMF). We show that the amount of DMF within the PAN electrolyte affects the Li+ structure. Further, the coordination can proceed through the carbonyl group and/or the amide nitrogen to form antiparallel structures with the nitrile groups of PAN through dipole–dipole interactions. The free motion of DMF is drastically inhibited upon interaction with Li+ and PAN, which decreases the ionic conductivity and potentially affects the stability (resistance toward removal and chemical decomposition). These findings have implications for the design and processing of solid polymer electrolytes.

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

Discovery of unconventional and nonintuitive self-assembling peptide materials using experiment-driven machine learning

Prediction of peptide secondary structure is challenging because of complex molecular interactions, sequence-specific behavior, and environmental factors. Traditional design strategies, based on hydrophobicity and structural propensity, can be biased and could indeed prevent discovery of interesting, diverse, and unconventional peptides with desired nanostructure assembly. Using β sheet formation in pentapeptides as a case study, we used an integrated high-throughput experimental workflow and an artificial intelligence–driven active learning framework to improve prediction accuracy of self-assembly. By focusing on sequences where machine learning (ML) predictions deviate from conventional design strategies, we synthesized and tested 268 pentapeptides, successfully finding 96 forming β sheet assemblies, including unconventional sequences (e.g., ILFSM, LMISI, MITIY, MISIW, and WKIYI) not predicted by traditional methods. Our ML models outperformed conventional β sheet propensity tables, revealing useful chemical design rules. A web interface is provided to facilitate community access to these models. This work highlights the value of ML-driven approaches in overcoming the limitations of current peptide design strategies.

Talluri, Y. Nissi [Indian Inst. of Technology (IIT↗
DOE OSTI2025

Microbes display broad diversity in cobamide preferences

ABSTRACT Cobamides, the vitamin B 12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli , Sinorhizobium meliloti , and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to those of previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function. IMPORTANCE Nearly all bacteria are found in microbial communities with tens to thousands of other species. Molecular interactions such as metabolic cooperation and competition are key factors underlying community assembly and structure. Cobamides, the vitamin B 12 family of enzyme cofactors, are one such class of nutrients, produced by only a minority of prokaryotes but required by most microbes. A unique aspect of cobamides is their broad diversity, with nearly 20 structural forms identified in nature. Importantly, this structural diversity impacts growth as most bacteria that have been tested show preferences for specific cobamide forms. We measured cobamide-dependent growth in several model bacteria and compared the results to those of previous analyses of cobamide preference. We found that cobamide preferences vary widely across bacteria, showing the importance of characterizing these aspects of cobamide biology to understand the impact of cobamides on microbial communities.

Mok, Kenny C. (ORCID:0000000252276987)↗