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Results for “molecular evolution”

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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Tunable mechanical behavior of graphene nanoribbon-metal composites fabricated through an electrocharge-assisted process

This work investigates the role of a carbon nanophase on the local mechanical behavior of nanocarbon metal matrix composites (NCMCs) produced through an electrocharge-assisted process. Nanoindentation experiments on single crystal Al, Al 1350 parent alloys, and Al 1350 NCMCs revealed variable mechanical properties, caused by an interplay between microstructure and graphitic reinforcements. TEM and AFM studies also reveal nanoscale structural changes based on the incorporation of a carbon nanophase. In order to decouple the effects of the aforementioned mechanical behaviors, molecular dynamics nanoindentation simulations were performed on the (111) surface of Al and Al NCMC samples containing semi-infinite graphene nanoribbons to examine the evolution of plasticity over time. Findings indicate that the arrangement of a finite graphene nanophase within a host matrix can alter plasticity mechanisms and therefore yield strength in near-surface mechanical behavior with little effect on elastic properties. Here, this understanding enables further study into tunable bulk properties of Al-based NCMCs while isolating microstructural effects and reinforcement effects of the carbon phase. Such an understanding will lead to application-specific material geometries ranging from highperforming vehicle structures to next-generation electrical devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A Computational Framework for Simulations of Dissipative Nonadiabatic Dynamics on Hybrid Oscillator-Qubit Quantum Devices

Here, we introduce a computational framework for simulating nonadiabatic vibronic dynamics on circuit quantum electrodynamics (cQED) platforms. Our approach leverages hybrid oscillator-qubit quantum hardware with midcircuit measurements and resets, enabling the incorporation of environmental effects such as dissipation and dephasing. To demonstrate its capabilities, we simulate energy transfer dynamics in a triad model of photosynthetic chromophores inspired by natural antenna systems. We specifically investigate the role of dissipation during the relaxation dynamics following photoexcitation, where electronic transitions are coupled to the evolution of quantum vibrational modes. Our results indicate that hybrid oscillator-qubit devices, operating with noise levels below the intrinsic dissipation rates of typical molecular antenna systems, can achieve the simulation fidelity required for practical computations on near-term and early fault-tolerant quantum computing platforms.

Hamiltonians↗
DOE OSTI2021

Mode-Selective Vibrational Energy Transfer Dynamics in 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) Thin Films

The coupling of inter- and intramolecular vibrations plays a critical role in initiating chemistry during the shock-to-detonation transition in energetic materials. In this work, we report on the subpicosecond to subnanosecond vibrational energy transfer (VET) dynamics of the solid energetic material 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) by using broadband, ultrafast infrared transient absorption spectroscopy. Experiments reveal VET occurring on three distinct time scales: subpicosecond, 5 ps, and 200 ps. The ultrafast appearance of signal at all probed modes in the mid-infrared suggests strong anharmonic coupling of all vibrations in the solid, whereas the long-lived evolution demonstrates that VET is incomplete, and thus thermal equilibrium is not attained, even on the 100 ps time scale. Density functional theory and classical molecular dynamics simulations provide valuable insights into the experimental observations, revealing compression-insensitive time scales for the initial VET dynamics of high-frequency vibrations and drastically extended relaxation times for low-frequency phonon modes under lattice compression. Mode selectivity of the longest dynamics suggests coupling of the N–N and axial NO2 stretching modes with the long-lived, excited phonon bath.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA

Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isolates from CF sputum samples collected at three US centers between 2015–2018. Molecular relationships demonstrated that high-level resistance of preceding isolates to carbapenems were associated with subsequent isolation of ceftaroline resistant CF MRSA. In vitro evolution experiments showed that pre-exposure of CF MRSA to meropenem with further selection with ceftaroline implied mutations in mecA and additional mutations in pbp1 and pbp2 , targets of carbapenems; no effects were achieved by other β-lactams. An in vivo pneumonia mouse model showed the potential therapeutic efficacy of ceftaroline/meropenem combination against ceftaroline-resistant CF MRSA infections. Thus, the present findings highlight risk factors and potential therapeutic strategies offering an opportunity to both prevent and address antibiotic resistance in this patient population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coherent Transfer of Lattice Entropy via Extreme Nonlinear Phononics in Metal Halide Perovskites

Entropy transfer in metal halide perovskites, characterized by significant lattice anharmonicity and low stiffness, underlies the remarkable properties observed in their optoelectronic applications, ranging from solar cells to lasers. The conventional view of this transfer involves stochastic processes occurring within a thermal bath of phonons, where the lattice arrangement and energy flow from higher- to lower-frequency modes. Here, we unveil a comprehensive chronological sequence detailing a conceptually distinct coherent transfer of entropy in a prototypical perovskite CH 3 NH 3 Pbl 3 . The terahertz periodic modulation imposes vibrational coherence into electronic states, leading to the emergence of mixed (vibronic) quantum beat between approximately 3 and 0.3 THz. We highlight a well-structured bidirectional time-frequency transfer of these diverse phonon modes, each developing at different times and transitioning from high to low frequencies from 3 to 0.3 THz, before reversing direction and ascending to around 0.8 THz. First-principles molecular dynamics simulations disentangle a complex web of coherent-phononic coupling pathways and identify the salient roles of the initial modes in shaping entropy evolution at later stages. Capitalizing on coherent entropy transfer and dynamic anharmonicity presents a compelling opportunity to exceed the fundamental thermodynamic (Shockley-Queisser) limit of photoconversion efficiency and to pioneer novel optoelectronic functionalities. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

STRUCTURAL STABILITY OF MAGNETIC TUNNEL JUNCTION BASED MOLECULAR SPINTRONICS DEVICES (MTJMSD)

Harnessing the exotic properties of molecular level nanostructures to produce novel sensors, metamaterials, and futuristic computer devices can be technologically transformative. In addition, connecting the molecular nanostructures to ferromagnetic electrodes bring the unprecedented opportunity of making spin property based molecular devices. We have demonstrated that magnetic tunnel junction based molecular spintronics device (MTJMSD) approach to address numerous technological hurdles that have been inhibiting this field for decades. MTJMSD approach is based on producing a capacitor like a testbed where two metal electrodes are separated by an ultrathin insulator and subsequently bridging the molecule nanostructure across the insulator to transform a capacitor into a molecular device. Our prior work showed that MTJMSDs produced extremely intriguing phenomenon such as room temperature current suppression by six orders, spin photovoltaic effect, and evolution of new forms of magnetic metamaterials arising due to the interaction of the magnetic a molecule with two ferromagnetic thin films. However, making robust and reproducible electrical connections with exotic molecules with ferromagnetic electrodes is full of challenges and requires attention to MTJMSD structural stability. This paper focuses on MTJMSD stability by describing the overall fabrication protocol and the associated potential threat to reliability. MTJMSD is based on microfabrication methods such as (a) photolithography for patterning the ferromagnetic electrodes, (b) sputtering of metallic thin films and insulator, and (c) at the end electrochemical process for bridging the molecules between two ferromagnetic films separated by ~ 2nm insulating gap.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Revealing the etching process of water-soluble Au 25 nanoclusters at the molecular level

Etching (often considered as decomposition) is one of the key considerations in the synthesis, storage, and application of metal nanoparticles. However, the underlying chemistry of their etching process still remains elusive. Here, we use real-time electrospray ionization mass spectrometry to study the reaction dynamics and size/structure evolution of all the stable intermediates during the etching of water-soluble thiolate-protected gold nanoclusters (Au NCs), which reveal an unusual “recombination” process in the oxidative reaction environment after the initial decomposition process. Interestingly, the sizes of NC species grow larger and their ligand-to-metal ratios become higher during this recombination process, which are distinctly different from that observed in the reductive growth of Au NCs (e.g., lower ligand-to-metal ratios with increasing sizes). The etching chemistry revealed in this study provides molecular-level understandings on how metal nanoparticles transform under the oxidative reaction environment, providing efficient synthetic strategies for new NC species through the etching reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin

The calcium-selective oncochannel TRPV6 is an important driver of cell proliferation in human cancers. Despite increasing interest of pharmacological research in developing synthetic inhibitors of TRPV6, natural compounds acting at this channel have been largely neglected. On the other hand, pharmacokinetics of natural small-molecule antagonists optimized by nature throughout evolution endows these compounds with a medicinal potential to serve as potent and safe next-generation anti-cancer drugs. Here we report the structure of human TRPV6 in complex with tetrahydrocannabivarin (THCV), a natural cannabinoid inhibitor extracted from Cannabis sativa . We use cryo-electron microscopy combined with electrophysiology, calcium imaging, mutagenesis, and molecular dynamics simulations to identify THCV binding sites in the portals that connect the membrane environment surrounding the protein to the central cavity of the channel pore and to characterize the allosteric mechanism of TRPV6 inhibition. We also propose the molecular pathway taken by THCV to reach its binding site. Our study provides a foundation for the development of new TRPV6-targeting drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

In-Situ Atomic-Scale Revelation of Amorphous Metallic Iron Formation during Hydrogen-Driven Reduction of Iron Oxides

The transition to hydrogen as a green reductant in metal production is critical for decarbonizing the metallurgical industry, yet atomic-scale mechanisms governing reduction pathways and phase evolution remain unresolved. Using in-situ environmental transmission electron microscopy, we identify a hidden pathway that reveals dynamic formation of amorphous metallic iron (Fe) during the hydrogen-driven reduction of ferrous oxides of Fe 3 O 4 and FeO. Real-time imaging uncovers three coexisting transformation routes: (i) Fe 3 O 4 → FeO, (ii) Fe 3 O 4 → amorphous Fe, and (iii) FeO → amorphous Fe. The resulting amorphous Fe exhibits fluid-like mobility, enabling its rapid aggregation and crystallization into core-shell nanostructures, with a crystalline core enveloped by an amorphous shell. Complementary ab initio molecular dynamics simulations trace the amorphous Fe formation to interfacial strain at the metal/oxide interfaces, where large lattice mismatches destabilize the metal lattice during initial metallization. This interplay between thermodynamics and kinetics governs phase evolution: thermodynamics favors a self-limiting amorphous Fe overlayer, while rapid oxide reduction kinetics drives amorphous overgrowth. Our findings demonstrate that amorphous intermediates bypass rate-limiting crystalline steps, providing mechanistic insights to optimize H 2 -based processes for sustainable steelmaking. In conclusion, these insights bridge the gap between macroscopic process engineering and atomic-scale dynamics, with broader implications for catalysis and nanostructured material synthesis, where oxide reduction pathways critically shape functional phases and microstructures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap ( Lactarius ) mushrooms

Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Amphiphilic Baskets for Supramolecular Nanoarchitectures at Interfaces: Inverted Monolayer Formation on Water

Interfacial chemistry of molecular baskets remains poorly understood despite their promise for supramolecular applications of detection and sequestration of toxic molecules including those of illicit drugs, organophosphorus compounds, and anticancer agents. We present a fundamental investigation of the interfacial behavior of three amphiphilic supramolecular baskets (ASB 4, 8, and 12), having increasingly longer yet linear alkyl chains at the top of their bowl-shaped cavity. The studies were completed at the air−water interface to elucidate surface activity, interfacial stability, self-assembly, and monolayer organization that drive inverted monolayer formation, in which the molecular arms orient toward the aqueous phase in a configuration opposite to that typically observed for lipids. Herein, surface pressure−area isotherms of ASB 4, 8, 12, deposited on a water surface, were performed in tandem with nonequilibrium relaxation experiments to quantify surface activity, thermodynamic stability, and monolayer compressibility of the baskets’ monolayer assembly. Brewster angle microscopy enabled direct visualization of morphological evolution, aggregation, and packing at the interface. We show that systematic extension of the hydrocarbon arms, from four to 12 methylene groups, progressively modifies intermolecular packing, drives distinct two-dimensional aggregation pathways, and increases number densities at the air−water interface. Atomistic molecular dynamics simulations corroborate many of these experimentally observed trends and provide mechanistic detail on the cooperative roles of basket topology and interfacial concentration in regulating the hydration structure and dynamics within the cavities generated by surface-adsorbing baskets, consistent with observed variations in surface activity and packing. Our results establish how the topology of these unique supramolecules and their concentration govern interfacial organization and offer a rational framework for designing amphiphiles with predictable behavior at soft interfaces.

Hydrocarbons↗
DOE OSTI2020

Soft fragmentation on the celestial sphere

We develop two approaches to the problem of soft fragmentation of hadrons in a gauge theory for high energy processes. The first approach directly adapts the standard resummation of the parton distribution function’s anomalous dimension (that of twist-two local operators) in the forward scattering regime, using k T -factorization and BFKL theory, to the case of the fragmentation function by exploiting the mapping between the dynamics of eikonal lines on transverse-plane to the celestial-sphere. Critically, to correctly resum the anomalous dimension of the fragmentation function under this mapping, one must pay careful attention to the role of regularization, despite the manifest collinear or infra- red finiteness of the BFKL equation. The anomalous dependence on energy in the celestial case, arising due to the mismatch of dimensionality between positions and angles, drives the differences between the space-like and time-like anomalous dimension of parton densities, even in a conformal theory. The second approach adapts an angular-ordered evolution equation, but working in 4 – 2ϵ dimensions at all angles. The two approaches are united by demanding that the anomalous dimension in 4 – 2ϵ dimensions for the parton distribution function determines the kernel for the angular-ordered evolution to all orders.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Interpretation of Ir L-edge isotropic x-ray absorption spectra across the pressure-induced dimerization transition in hyper-honeycomb beta-Li2IrO3

The extended nature of atomic 5d orbitals, together with a relatively short ~ 3 °A Ir-Ir distance across edge-shared octahedra in honeycomb iridate lattices, leads to a tendency to disrupt the local, spin-orbit entangled jeff = 1 2 moments of Ir4+ ions in favor of dimerization and formation of molecular orbitals, especially upon lattice compression. The sensitivity of Ir L-edge spectroscopy to both spin-orbit entanglement in jeff states and quenching of orbital degrees of freedom in dimerized states, results in a peculiar evolution of x-ray absorption spectra across dimerization transitions including energy shifts in opposite direction for L3 and L2 leading absorption edges, and substantial changes in their isotropic branching ratio. We present a theoretical description of the evolution of 5d electronic states, and related x-ray absorption spectra, in going from the single ion to the dimerized limit. The calculations reproduce the experimental results for hyper-honeycomb β-Li2IrO3[1, 2] and shed light into the weakening of the coupling between spin and orbital degrees of freedom as the strength of dimerization increases. The results provide a basis for interpretation of L-edge xray absorption spectra in 5d systems where competition between formation of local jeff states and molecular orbitals is at play.

van Veenendaal, Michel↗
DOE OSTI2023

Developing Efficient Benzene Additives for 19.43% Efficiency of Organic Solar Cells by Crossbreeding Effect of Fluorination and Bromination

Employing volatile solid additives have emerged as a promising method to optimize the morphology and improve the performance of organic solar cells (OSCs). However, principles governing the efficient design of solid additives remain elusive. In this work, the programmed fluorination and/or bromination on benzene core to develop efficient additives for OSCs is reported. The programmed fluorination and/or bromination endow the five halogen benzene derivatives, 1,3,5-trifluorobenzene, hexafluorobenzene, 1,3,5-tribromo-2,4,6-trifluorobenzene (TFTB), 1,3,5-tribromobenzene, and hexabromobenzene, with different melting and boiling points, volatility, as well as interactions with the host blend. Studies indicate that the additives with extremely high and low volatility are almost powerless and even detrimental to the morphology evolution. Among them, the combination of fluorine and bromine atoms on TFTB not only enables the more appropriate m.p./b.p. and volatility, but also exerts stronger molecular interactions with the host blend, giving rise to higher ordered molecular packing and more favorable morphology. Importantly, TFTB exhibits good universality to optimize the performances of OSCs with high power conversion efficiencies (PCEs; over 18%) in a group of binary blend systems, and an impressive PCE of 19.43% in the ternary PBTz-F:PM6:L8-BO system.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Polymer Deconstruction and Redesign Strategies for Plastics Recycling

Advancing plastics recycling requires both the selective deconstruction of existing polymers and the design of new materials that enable efficient reuse without loss of performance. This perspective highlights an integrated approach that is rooted in polymer chemistry, catalysis, and process engineering which can enable a circular plastics economy. Here, we outline recent advances in catalytic, solvolytic, and enzymatic pathways for plastic deconstruction, and examine the molecular design principles driving next-generation recyclable-by-design and bio-based polymers. Despite these advances, major knowledge gaps remain in understanding the evolution of polymer morphology and catalyst structure during deconstruction, assessing deconstruction processes with realistic polymers, and offering redesigned polymers with competitive cost and environmental advantage over conventional plastics. United States Department of Energy (U.S. DOE) national laboratories offer unique capabilities to address these challenges through in situ and operando characterization, high-throughput experimentation, environmental studies, technoeconomic and life cycle assessment, scale-up support, and collaboration networks. Advances made in understanding plastic deconstruction mechanisms and structure-property correlations of redesigned polymers inform emerging research directions including autonomous experimentation, real-time feedback-enabled process optimization, and protein engineering for enzymatic depolymerization.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Investigating the effect of heterogeneities across the electrode|multiphase polymer electrolyte interfaces in high-potential lithium batteries

Polymer electrolytes hold great promise for safe and high-energy batteries comprising solid or semi-solid electrolytes. Multiphase polymer electrolytes, consisting of mobile and rigid phases, exhibit fast ion conduction and desired mechanical properties. However, fundamental challenges exist in understanding and regulating interactions at the electrode|electrolyte interface, especially when using high-potential layered oxide active materials at the positive electrode. Here we demonstrate that depletion of the mobile conductive phase at the interface contributes to battery performance degradation. Molecular ionic composite electrolytes, composed of a rigid-rod ionic polymer with nanometric mobile cations and anions, serve as a multiphase platform to investigate the evolution of ion conductive domains at the interface. Chemical and structural characterizations enable the visualization of concentration heterogeneity and spatially resolve the interfacial chemical states over a statistically significant field of view for buried interfaces. We report that concentration and chemical heterogeneities prevail at electrode|electrolyte interfaces, leading to phase separation in polymer electrolytes. In conclusion, understanding the hidden roles of interfacial chemomechanics in polymer electrolytes enables us to design an interphase tailoring strategy based on electrolyte additives to mitigate the interfacial heterogeneity and improve battery performance.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Insight into Molecular Basis and Dynamics of Full-length CRaf Kinase in Cellular Signaling Mechanism

This study presents the first large-scale simulation using an initial structure predicted by AI/ML algorithms for the 648-amino-acid CRaf kinase, which plays a key role in cellular signaling. Simulation results show the evolution of the predicted structure into much more compact structures with inter-domain interactions that shed insights into auto-inhibition mechanism, paradoxical effect, activation, and recruitment pathways in the CRaf kinase. Newly identified epitopes in the CRaf may suggest additional drug targets. The results were published in Biophysical Journal, DOI:10.1016/j.bpj.2024.06.028.

59 BASIC BIOLOGICAL SCIENCES↗