Search NASA⌕ Search

SEARCH · Search NASA

Results for “Inverse molecular design”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

556 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A molecular conveyor belt-associated protein controls the rotational direction of the bacterial type 9 secretion system

ABSTRACT Many bacteria utilize the type 9 secretion system (T9SS) for gliding motility, surface colonization, and pathogenesis. This dual-function motor supports both gliding motility and protein secretion, where rotation of the T9SS plays a central role. Fueled by the energy of the stored proton motive force and transmitted through the torque of membrane-anchored stator units, the rotary T9SS propels an adhesin-coated conveyor belt along the bacterial outer membrane like a molecular snowmobile, thereby enabling gliding motion. However, the mechanisms controlling the rotational direction and gliding motility of T9SS remain elusive. Shedding light on this mechanism, we find that in the gliding bacteriumFlavobacterium johnsoniae, deletion of the C-terminus of the conveyor belt-associated protein GldJ controls and, in fact, reverses the rotational direction of T9SS from counterclockwise (CCW) to clockwise (CW). This suggests that the interface between the conveyor belt-associated protein GldJ and the T9SS ring protein GldK plays an important role in controlling the directionality of T9SS, potentially by modulating its interaction with the stator complex GldLM, which drives motor rotation. Combined with MD simulation of the T9SS stator units GldLM, we suggest a “tri-component gearset” model where GldJ controls the rotational direction of its driver, the T9SS, thus providing adaptive sensory feedback to influence the motility of the gliding bacterium. IMPORTANCE The type 9 secretion system (T9SS) is fundamental to bacterial gliding motility, pathogenesis, and surface colonization. Our findings reveal that the C-terminal region of the conveyor belt-associated protein GldJ functions as a molecular switch which is capable of reversing the rotational direction of T9SS. Through the coordinated actions of the T9SS stator units (akin to a driving motor), the GldK ring (the gear that converts rotational energy into linear movement), and GldJ, this machinery forms a smart conveyor belt system reminiscent of flexible or cognitive mechanical conveyors. Such advanced conveyors can alter their direction to adapt to shifting demands. Here, we show that the bacterial T9SS similarly adjusts its rotational bias based on feedback from the conveyor belt-associated protein GldJ. This dual-role feedback mechanism underscores an evolved, controllable biological snowmobile, offering new avenues for studying how bacteria fine-tune motility in dynamic environments.

Microbiology↗
DOE OSTI2026

Effects of Composition and Oxidation States on the Structures of Chromium-Containing Sodium Silicate Glasses: Molecular Dynamics Simulations using Machine Learning Interatomic Potentials

Chromium represents a significant challenge for the vitrification of high-level nuclear waste into silicate and borosilicate glasses due to its low solubility and variable oxidation states, which can limit the waste loading due to promotion of crystallization or phase separation during processing. In this study, we modeled chromium containing silicate glasses using molecular dynamics simulations with three machine learning interatomic potentials (MLIPs), MACE, CHGNet, and PFP were employed, to gain insights on glass composition and oxidation states on the structures of these glasses. One of the goals is to evaluate their ability of these MLIPs to accurately represent the general structure of silicate glasses and chromium local environments as a function of chromium oxidation states. Density Functional Theory (DFT) based calculations and experimental data such as neutron structure factors were used to validate the structural models. It was found that the foundation models of all three MLIPs are able to reproduce general structural features of the sodium silicate glass structure consistent with experimental and DFT data, but only CHGNet and PFP can accurately capture the oxidation states and local environment of chromium: tetrahedral for Cr6+ and octahedral for Cr3+. Furthermore, we studied the effect of varying Cr3+/ Cr6+ (Cr3+/Crtotal) ratio and total chromium content using PFP. Our results show that Cr6+ enhances network polymerization by reducing non-bridging oxygens through Na? charge compensation required due to the formation of chromate (CrO42-) species, while Cr³? acts as a network modifier that disrupts connectivity. System size effects on the structural characteristics and chromium environments were also tested using the PFP potential. This work highlights the importance of careful validation on the precision, transferability, and potential of MLIPs for modeling glasses containing transition metal elements that can exist in multiple oxidation states. It is also encouraging to see the foundational models are all three MLFFs are able to reproduce the basic sodium silicate glass structures, while suggesting additional training or refining is needed to improve the description of more complex systems containing transition metals.

Puga, Christina L.↗
DOE OSTI2026

Restoration of weak localization in bilayer graphene by a molecular thin film

Quantum coherent effects can be probed in multilayer graphene through electronic transport measurements at low temperatures. In particular, bilayer graphene (BLG) is known to be susceptible to quantum interference corrections of the conductivity, presenting weak localization at all electronic densities, and dependent on different scattering mechanisms such as those related to the trigonal warping of the electron dispersion near the K and K′ valleys. Proximity effects with a molecular thin film influence these scattering mechanisms, which can be quantified through the known theory of magnetoconductance for BLG. Here, we present electronic transport measurements in a copper-phthalocyanine (CuPc) / BLG / hexagonal boron nitride (h-BN) heterostructure that suggest the restoration of weak localization in BLG, associated to a reduction of trigonal warping effects, that are known to suppress weak localization in BLG. Additionally, we observe a charge transfer of 3.6×10 12 cm −2 from the BLG to the molecules, as well as a very small degradation of the mobility of the BLG/h-BN heterostructure upon the deposition of CuPc. The molecular arrangement of the CuPc thin film is characterized in a control sample through transmission electron microscopy, that we relate to the electronic transport results.

bilayer graphene↗
DOE OSTI2026

Phonon-mediated ultrafast dynamics in self-assembled monolayers of 4-mercaptobenzoic acid on gold

Non-equilibrium interactions between plasmonic metals and adsorbed molecules lie at the heart of emerging applications such as plasmonic photocatalysis and sensing, though the ultrafast charge and energy transfer mechanisms arising from these interactions are not well understood. Herein, we investigate the ultrafast dynamics of Au nano-islands tethered with a self-assembled monolayer (SAM) of electron-withdrawing 4-mercaptobenzoic acid (4MBA) molecules. Ultrafast UV-visible transient absorption spectroscopy following excitation of the interband transition in Au reveals three well-known, characteristic time constants that quantify electron–electron (el–el), electron–phonon (el–ph) and phonon–phonon (ph–ph) scattering lifetimes. When comparing the dynamics of bare Au and 4MBA-Au, we find that the el–ph and ph–ph scattering lifetimes are notably longer in 4MBA-Au. Density functional perturbation theory calculations ascribe the elongation in el–ph lifetimes in 4MBA-Au to the significant coupling of acoustic phonon modes of Au with certain molecular vibrations of 4MBA, leading to decreased spatial overlap between carrier electronic states and the acoustic modes. We speculate that the elongation of ph–ph scattering lifetimes in 4MBA-Au arises due to poor thermal conductivity of the SAM which disrupts efficient energy dissipation from Au to the environment, thus slowing down the thermalization of phonons. This work provides a glimpse into how molecular adsorbates modify the charge carrier and phonon dynamics of Au and sets the stage for further systematic exploration of plasmonic metal–molecule interactions.

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

Fluorophilic Sigma(σ)‐Lock Self‐Healable Copolymers

Although F-Containing molecules and macromolecules are often used in molecular biology to increase the binding with Lewis acidic groups by introducing favorable C−F dipoles, there is virtually no experimental evidence and limited understanding of the nature of these interactions, especially their role in synthetic polymeric materials. These studies elucidate the molecular origin of inter- and intra-Chain interactions responsible for self-healing of F-Containing copolymers composed of pentafluorostyrene and n-butyl acrylate units (p(PFS/nBA). Guided by dynamic surface oscillating force (SOF) and spectroscopic measurements supported by molecular dynamics (MD) simulations, these studies show that the reformation of σ-σ orbitals in −C−F of PFS and CH 3 CH 2 − of nBA units enables the recovery of entropic energy via fluorophilic-σ-lock van der Waals forces when PFS/nBA molar ratios are ~50/50. The strength of these interactions determined experimentally for self-healable PFS/nBA compositions is in the order ~0.3 kcal/mol which primarily comes from fluorophilic-σ-lock (~70 %) contributions. These interactions are significantly diminished for non-self-healable counterparts. Strongly polarized −C−F σ orbitals create lateral dipolar forces enhancing the affinity towards −C−H orbitals, facilitating energetically favorable interactions. Entropic recovery driven by non-Covalent bonding offers a valuable tool in designing materials with unique functionalities, particularly self-healable batteries and energy storage devices.

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

Anion-dependent phase behavior of methylimidazolium-based ionic liquids mixed with water: Correlation between local molecular structure and mesoscale behaviors

The mesoscopic phase behavior of decylmethylimidazolium (C 10 mim) ionic liquids (ILs) bearing three monovalent anions—thiocyanate (SCN − ), nitrate (NO 3 − ), and chloride (Cl − )—mixed with water at relatively high IL contents (50–95 wt%) was investigated. Small-angle and wide-angle X-ray scattering (SAXS/WAXS) were employed to follow the evolution of both local and mesoscale structures across this composition range. In the absence of water, C 10 mimSCN and C 10 mimCl behaved as disordered liquids, whereas C 10 mimNO 3 spontaneously formed a hexagonally ordered cylindrical mesophase and displayed a sticky-solid macroscopic appearance. Upon addition of water, C 10 mimSCN remained a viscous liquid and only weakly ordered lamellar domains were observed. This limited ordering is attributed to the lack of hydrogen bonding and weak interaction energy between SCN − anions and C 10 mim + cations. In contrast, the trigonal-planar NO 3 − and point-like Cl − anions promoted the formation of well-defined hexagonal mesophases up to 35–45 wt% water. The formation of hydrogen bonding of the two anions with imidazolium ring protons likely enabled the creation of compact ion clusters that effectively exclude water molecules from the immediate vicinity of the IL aggregates. These findings demonstrate that the interaction energy between ion pairs dictate IL-water interactions and therefore control the transition from disordered liquids to ordered mesophases in IL/water mixtures with high IL contents. In conclusion, the combined SAXS/WAXS analysis reveals a correlation between local intermolecular structure and the emergence of mesoscopic order, providing a systematic framework for tailoring mesoscale structures in alkylimidazolium-based IL/water systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Complex-Valued Intermolecular Coupling Enables Directional Exciton Transport in Excitonic Circuits

Molecular systems capable of directing the flow of excitons are key to the development and optimization of optoelectronic materials. The transport of excitons across multiple molecules is governed by an intermolecular electronic coupling network. In this article, we consider the effects of complex-valued intermolecular electronic coupling on exciton transport. Here, we present a molecular motif capable of generating complex-valued coupling under excitation with circularly polarized light. We use theoretical modeling and simulation to illustrate how complex coupling can be leveraged to drive the rotational flux of excitons in cyclic molecular networks and direct the exciton population in branched molecular networks.

chromophores↗
DOE OSTI2026

Conserved Macromolecular Architecture of Poplar Secondary Cell Walls Revealed by ssNMR and Atomistic Modeling

The macromolecular architecture of plant secondary cell walls governs wood's mechanical and biochemical properties, yet its natural intra-species variability remains poorly characterized. Here, we combined 13C solid-state NMR (ssNMR), multivariate statistical analysis, and molecular modeling to profile nanoscale structure across 13 genetically diverse Populus trichocarpa genotypes grown in 13C-enriched atmospheres. SsNMR-derived phenotypes spanning composition, structure, mobility, and inter-polymer proximities reveal a conserved architecture, with a subtle yet coordinated variation organizing into dominant structural and secondary mobility axes. A representative atomistic model captures these features and reproduces experimental metrics. Molecular dynamics simulations support a weak but consistent positive correlation between cellulose abundance and crystalline-like order, with interior cellulose chains enriched in tg (trans-gauche) conformations without expanding crystalline cores. Together, experiment and simulation reveal a genetically buffered, broadly conserved nanoscale architecture across genotypes, where subtle fine-tuning of cellulose bundling and matrix packing balances mechanical performance with biological function.

09 BIOMASS FUELS↗
DOE OSTI2025

Unique Conductivity Behavior in Water-In-Salt Electrolytes Driven by Ion Clusters

Understanding and predicting ion transport in aqueous electrolytes are crucial for advanced energy storage and biophysics, and many emergent technologies yet remain elusive. Herein, we introduce a unified framework to quantitatively describe and predict electrolyte conductivity that shifts from conventional molar concentration-based metrics to a volume fraction-based approach. Through analyzing a variety of electrolyte solutions via this perspective, we observe a universal conductivity peak at a 37% volume fraction. Small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations reveal that nanometer-scale ion clusters drive this general behavior. Moreover, key geometric features of the ion transport pathwayssuch as pore size, tortuosity, and connectivityfollow a consistent dependence with respect to the volume fraction, reinforcing the argument for the universal conductivity trend. This paradigm shift opens new avenues for designing high-performance electrolytes and provides transformative insights for advancing studies in many fields, wherein molecular aggregates dictate transport properties.

Nguyen, Huong T. D.↗
DOE OSTI2026

Stoichiometry dependent properties of cerium hydride: An active learning developed interatomic potential study

Cerium hydride has a variety of interesting properties, including a known lattice contraction and densification with increasing hydrogen content. However, precise stoichiometric control is not experimentally straightforward and ab initio approaches are not computationally feasible for many properties such as melting and low temperature diffusion. Therefore, we develop a machine-learned interatomic potential for cerium hydride that is valid for H to Ce ratios from 2.0 to 3.0. A query-by-committee active learning approach is used to develop the training set. Leveraging classical molecular dynamics simulations, we assess a range of properties and provide fundamental mechanisms for the trends with stoichiometry. Finally, a majority of the properties follow the trend of lattice contraction, being governed by the stronger lattice binding induced by adding octahedral atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Atomistic Mechanisms of Stress-Dependent Molten Salt Corrosion in NiCr Alloys

Ni-based structural alloys in molten salt environments often experience simultaneous mechanical loading and corrosive attack, yet the mechanisms governing stress-corrosion interactions remain unclear. Prior studies largely emphasize tensile stress, while the role of compressive stress has received limited attention. Here, reactive molecular dynamics simulations are used to investigate the coupled effects of applied strain and corrosion in Ni 0.75 Cr 0.25 exposed to molten FLiNaK at 800 °C. A Σ5(210) grain boundary model is subjected to tensile (+4%) to compressive (−4%) uniaxial strains, and corrosion behavior is evaluated through fluorine adsorption, charge redistribution, and grain boundary evolution. Tensile strain accelerates intergranular corrosion susceptibility by reducing local atomic packing through elastic dilation and increasing excess free volume at the grain boundary, which enhances atomic mobility and salt infiltration. In contrast, compressive strain can suppress corrosion by promoting the formation of a ridge-like surface layer along the grain boundary, limiting salt access to the underlying alloy. These results provide atomistic insight into how stress states influence grain boundary corrosion in molten salts.

36 - MATERIALS SCIENCE↗
DOE OSTI2025

32 examples of LLM applications in materials science and chemistry: towards automation, assistants, agents, and accelerated scientific discovery

Abstract Large language models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 32 total projects developed during the second annual LLM hackathon for applications in materials science and chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Computer Science↗
DOE OSTI2025

Super-resolution imaging reveals resistance to mass transfer in functionalized stationary phases

Chemical separations are costly in terms of energy, time, and money. Separation methods are optimized with inefficient trial-and-error approaches that lack insight into the molecular dynamics that lead to the success or failure of a separation and, hence, ways to improve the process. We perform super-resolution imaging of fluorescent analytes in five different commercial liquid chromatography materials. Unexpectedly, we observe that chemical functionalization can block more than 50% of the material’s porous interior, rendering it inaccessible to small-molecule analytes. Only in situ imaging unveils the inaccessibility when compared to the industry-accepted ex situ characterization methods. Selectively removing some of the functionalization with solvent restores pore access without substantially altering the single-molecule kinetics that underlie the separation and agree with bulk chromatography measurements. Our molecular results determine that commercial “fully porous” stationary phases are over-functionalized and provide an alternative avenue to characterize and direct separation material design from the bottom-up.

Science & Technology - Other Topics↗
DOE OSTI2025

Robust and tunable oxide nanoscrolls for solar-driven H 2 generation and storage

Hydrogen gas is a promising alternative to fossil fuels due to its high energy output and environmentally safe byproducts. Various morphologies of photocatalytic materials have been explored for high-efficiency H 2 production, for instance, quasi-1D nanoscroll structures that provide a larger surface-to-volume ratio. Recently, we predicted layer-by-layer formation of stable oxide nanoscrolls directly from dichalcogenide precursors, eliminating the need for costly formation of two-dimensional oxides for a roll-up synthesis of nanoscrolls. Here, in this study, we evaluate the suitability of those oxide nanoscroll materials—MoO 3 , WO 3 , PdO 2 , HfO 2 , and GeO 2 —for solar-driven photocatalytic H 2 production and storage. Using excited state theory coupled with Bethe–Salpeter equation simulations, we discern their electronic and optical properties as a function of interlayer scroll spacing and find them to be highly conducive for solar-driven photocatalysis. Additionally, using ab initio molecular dynamics simulations, we show that they are also suitable for H 2 storage as the nanoscrolls exhibit an effective trapping of hydrogen, even in the presence of defects and vacancies in the oxides. This work thus demonstrates the discovery of robust and tunable oxide nanoscrolls as materials for advancing solar-driven hydrogen technologies.

Chemical compounds↗
DOE OSTI2025

Improving Ionic Conformality Across Polymer Electrolyte|Electrode Interfaces

Maintaining uniform ionic transport at electrode|electrolyte interfaces, i.e., ionic conformality, remains challenging in polymer electrolyte (PE)-based solid-state batteries. Morphological conformality does not necessarily imply ionic conformality. In PEs, which typically consist of a mechanically supporting component and distinct ionically conductive components, the rearrangement or depletion of mobile ion-conductive domains at interfaces can disrupt ionic transport pathways. Such localized ionic depletion contributes to interfacial instability and capacity degradation in high-voltage lithium-metal batteries. Herein, an electrolyte design approach aimed at minimizing interfacial heterogeneities is demonstrated through compositional adjustments, characterized by spatially resolved structural and chemical X-ray techniques and NMR diffusometry to elucidate ion transport dynamics. This approach improves ionic conformality at electrode interfaces, enhancing cycling stability in Li||LiNi 0.8 Co 0.1 Mn 0.1 O 2 (NMC811) coin and pouch cells cycled at high voltages. These results contribute to understanding interfacial behaviors in multiphase PEs and inform strategies for improving stability across solid-state battery interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Ferroelectric Fractals: Switching Mechanism of Wurtzite AlN

The advent of wurtzite ferroelectrics is enabling new ferroelectric devices for computer memory that have the potential to bypass the von Neumann bottleneck due to their robust polarization and silicon compatibility. However, the atomistic switching mechanism of wurtzites is still undetermined due to the limitations of density functional theory simulation size and experimental temporal and spatial resolution. Thus, physics-informed materials engineering to reduce coercive field and breakdown in these devices has been limited. In this work, the atomistic mechanism of domain wall migration and domain growth in aluminum nitride-based wurtzites is uncovered using molecular dynamics and Monte Carlo simulations. We reveal the anomalous switching mechanism of fast 1D single columns of atoms propagating from a slow-moving 2D fractallike domain wall. We find that the critical nucleus is a single aluminum ion that breaks its bond with one nitrogen and bonds to another nitrogen; this creates a cascade that flips atoms directly only in the same column, due to the extreme locality (sharpness) of the domain walls in wurtzites. We further show how the fractallike shape of the domain wall in the 2D plane breaks assumptions in the Kolmogorov, Avrami, and Ishibashi (KAI) model and leads to the anomalously fast switching in wurtzite structured ferroelectrics.

36 MATERIALS SCIENCE↗
DOE OSTI1968

Nuclear Physics Made Very, Very Easy

The fundamental approach to nuclear physics was prepared to introduce basic reactor principles to various groups of non-nuclear technical personnel associated with NERVA Test Operations. NERVA Test Operations functions as the field test group for the Nuclear Rocket Engine Program. Nuclear Engine for Rocket Vehicle Application (NERVA) program is the combined efforts of Aerojet-General Corporation as prime contractor, and Westinghouse Astronuclear Laboratory as the major subcontractor, for the assembly and testing of nuclear rocket engines. Development of the NERVA Program is under the direction of the Space Nuclear Propulsion Office, a joint agency of the U. S. Atomic Energy Commission and the National Aeronautics and Space Administration. This report is being reprinted for use in the U. S. Atomic Energy Commission and National Aeronautics and Space Administration educational and technology utilization programs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Machine learning the electric field response of condensed phase systems using perturbed neural network potentials

Abstract The interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å −1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields.

Science & Technology - Other Topics↗