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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

Kikuchi, Hideaki↗
NASA NTRS1992

Enhancing The Hyperpolarizabilities Of Finite Polyenes

Improved strategy for exploiting unusual optical properties to enhance molecular hyperpolarizabilities by introducing "defect" quantum-mechanical states and produce molecules switched photochemically or electrochemically between states characterized by different second molecular hyperpolarizabilities. Strategy, conjugation and/or substitution defects, electrically neutral or charged dopant orimpurity atoms or groups thereof, incorporated into finite polyene. Defects in finite polyenes alter second molecular hyperpolarizabilities. Transient large second hyperpolarizabilities attainable in molecules of structure II.

Beratan, David N.↗
DOE OSTI2025

Ab initio investigation of a hypersonic double cone experiment

This article presents a direct molecular simulation (DMS) of a reactive Mach 8.2 oxygen flow over a double cone geometry. The free stream conditions and article configuration generate a flow with thermal and chemical nonequilibrium, which are common attributes of hypersonic flight. This scenario was first studied experimentally at Calspan University of Buffalo Research Center’s test facility. DMS is a particle method that uses quantum mechanically derived interaction potentials to simulate molecular collisions within a flow field. Since these interaction potentials are the only modeling inputs used in the simulation, all flow features can solely be attributed to the ab initio potential energy surfaces. Hence, providing a comparison of a hypersonic ground test and numerical data anchored to quantum mechanics. The fundamental nature of DMS is leveraged to investigate molecular level mechanisms prevalent in the flow, and comparisons with lower fidelity simulations are presented to highlight the role of these first principles calculations as benchmark solutions.

Science & Technology - Other Topics↗
DOE OSTI2024

Mechanism of Molecular Polariton Decoherence in the Collective Light–Matter Couplings Regime

Molecular polaritons, the hybridization of electronic states in molecules with photonic excitation inside a cavity, play an important role in fundamental quantum science and technology. Understanding the decoherence mechanism of molecular polaritons is among the most significant fundamental questions. We theoretically demonstrate that hybridizing many molecular excitons in a cavity protects the overall quantum coherence from phononinduced decoherence. The polariton coherence time can be prolonged up to 100 fs with a realistic collective Rabi splitting and quality factor at room temperature, compared to the typical electronic coherence time which is around 15 fs. Our numerically exact simulations and analytic theory suggest that the dominant decoherence mechanism is the population transfer from the upper polariton state to the dark state manifold. Increasing the collective coupling strength will increase the energy gap between these two sets of states and thus prolong the coherence lifetime. We further derived valuable scaling relations that directly indicate how polariton coherence depends on the number of molecules, Rabi splittings, and light–matter detunings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Deep learning of dynamically responsive chemical Hamiltonians with semiempirical quantum mechanics

Conventional machine-learning (ML) models in computational chemistry learn to directly predict molecular properties using quantum chemistry only for reference data. While these heuristic ML methods show quantum-level accuracy with speeds several orders of magnitude faster than traditional quantum chemistry methods, they suffer from poor extensibility and transferability; i.e., their accuracy degrades on large or new chemical systems. Incorporating quantum chemistry frameworks into the ML models directly solves this problem. Here we take the structure of semiempirical quantum mechanics (SEQM) methods to construct dynamically responsive Hamiltonians. SEQM methods use empirical parameters fitted to experimental properties to construct reduced-order Hamiltonians, facilitating much faster calculations than ab initio methods but with compromised accuracy. By replacing these static parameters with machine-learned dynamic values inferred from the local environment, we greatly improve the accuracy of the SEQM methods. Trained on molecular energies and atomic forces, these dynamically generated Hamiltonian parameters show a strong correlation with atomic hybridization and bonding. Trained with only about 60,000 small organic molecular conformers, the resulting model retains interpretability, extensibility, and transferability when testing on much larger chemical systems and predicting various molecular properties. Overall, this work demonstrates the virtues of incorporating physics-based descriptions with ML to develop models that are simultaneously accurate, transferable, and interpretable.

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

T 1 Anisotropy Elucidates Spin Relaxation Mechanisms in an S = 1 Cr(IV) Optically Addressable Molecular Qubit

Paramagnetic molecules offer unique advantages for quantum information science owing to their spatial compactness, synthetic tunability, room-temperature quantum coherence, and potential for optical state initialization and readout. However, current optically addressable molecular qubits are hampered by rapid spin–lattice relaxation ( T 1 ) even at sub-liquid nitrogen temperatures. Here, we use temperature- and orientation-dependent pulsed electron paramagnetic resonance (EPR) to elucidate the negative sign of the ground state zero-field splitting (ZFS) and assign T 1 anisotropy to specific types of motion in an optically addressable S = 1 Cr(o-tolyl) 4 molecular qubit. The anisotropy displays a distinct sin 2 (2θ) functional form that is not observed in S = 1/2 Cu(acac) 2 or other Cu(II)/V(IV) microwave addressable molecular qubits. The Cr(o-tolyl) 4 T 1 anisotropy is ascribed to couplings between electron spins and rotational motion in low-energy acoustic or pseudoacoustic phonons. Our findings suggest that rotational degrees of freedom should be suppressed to maximize the coherence temperature of optically addressable qubits.

magnetic properties↗
NASA NTRS1998

Reverse Energy Cascade in Turbulent Weakly Ionized Plasmas

For systems far from equilibrium, the neglect of a role for viscous effects in turbulence may be generally inappropriate when the relaxation time for the molecular process approaches the local flow time (Orou et al. (1996)). Furthermore, for stationary collisional plasmas, the conventional Reynolds number is irrelevant under circumstances where the standard features of turbulence in ordinary gases are observed in the plasma (Johnson et al. (1987)). The current theoretical understanding of these turbulent phenomenon is particularly inadequate for turbulence associated with ionizing shock waves; generally speaking, thermodynamic, acoustic and pressure fluctuations are all seen as amplified across the shock wave followed by a dramatic decay (relaminarization) usually attributed to a lack of importance of viscosity in the turbulent regions. This decay would be accelerated when the flow speed is also reduced due to the importance usually given to the conventional Reynolds number (which is directly proportional to velocity) as a quality of turbulence index. However, evidence supporting this consensus is lacking. By contrast, recent evidence of vanishing triple correlations form De Silva et al. (1996) provides strong support for early theoretical speculation of inherently molecular effects in macroscopic turbulence in Tsuge (1974). This specifically suggests that the role of compressive effects ordinarily associated with the shock wave could be significantly muted by the existence of a strongly turbulent local environment. There is also more recent theoretical speculation (Frisch et al. (1984)) of an inherently and previously unsuspected non-dissipative nature to turbulence, with energy conservation being nurtured by reverse energy cascades in the turbulent fluctuation spectra. Furthermore, the role which might be played by fluctuations on quantum mechanical phenomena and variations in molecular parameters is completely unknown, especially of the sort which might be found in optical spectra. A determination of the role which changing turbulent parameters might play on optical signatures behind a reflected shock wave should therefore provide a useful tool for the evolution of theoretical models for turbulence.

Williams, Kyron↗
DOE OSTI2023

Nuclear–Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear–electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. Furthermore, these developments and initial examples provide the foundation for future studies of nuclear–electronic quantum dynamics in complex chemical and biological environments.

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

Enhanced Energy Transfer to an Optomechanical Piston from Indistinguishable Photons

Thought experiments involving gases and pistons, such as Maxwell’s demon and Gibbs’ mixing, are central to our understanding of thermodynamics. In this paper, we present a quantum thermodynamic thought experiment in which the energy transfer from two photonic gases to a piston membrane grows quadratically with the number of photons for indistinguishable gases, while it grows linearly for distinguishable gases. This signature of bosonic bunching may be observed in optomechanical experiments, highlighting the potential of these systems for the realization of thermodynamic thought experiments in the quantum realm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Unexpected Kinetic Solvent Effects Enhance Activity and Selectivity in Biphasic Systems

Biphasic dehydration of fructose to 5-hydroxymethylfurfural (HMF) has shown unprecedented increases in productivity, but a mechanistic understanding is lacking. Herein, we couple fast experimental reaction kinetics, multiscale modeling (phase behavior, classical molecular dynamics(MD), and quantum mechanics/molecular mechanics MD), in situ sampling, and IR and 13 C-NMR spectroscopy to elucidate the complex effects of nonpolar extracting organic solvents on the kinetics of fructose dehydration. We show that these organic solvents can reach significant mutual solubility with water at reaction temperatures, enabling the partition of the sugar and catalyst into the extracting phase. In the organic-rich environment, the dehydration of fructose proceeds faster and more selectively than in water due to increased relative abundance of the reactive furanose isomer, enhanced water–catalyst–substrate interactions driven by nanophase separation, and higher product stability stemming from preferential solvation. Furthermore, we demonstrate that these solvent effects impact other critical biphasic reactions in biomass upgrading and provide qualitative principles for solvent selection.

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

Phase transitions and dimensional cross-over in layered confined solids

The nature of solid phases and cross-over of order–disorder phase transitions from two-dimensional (2D) layers to three-dimensional (3D) bulk in confined atomic systems remain largely unexplained. To this end, we consider noble gases and aluminum confined between graphene sheets at different pressures and temperatures. Using crystal structure search methods and molecular dynamics based on machine-learned potentials with quantum-mechanical accuracy, we identify structures of multilayer confined solids that deviate from simple close packing. Upon heating, we find that confined 2D monolayers melt according to the two-step continuous Kosterlitz–Thouless–Halperin–Nelson–Young theory. However, multilayer solids transition continuously into an intermediate layered-hexatic phase before melting discontinuously into an isotropic liquid. This intermediate phase persists at least up to 12 layers studied here. This change can be qualitatively understood based on the cross-over from 2D topological defects toward 3D ones during melting as the number of layers increases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Low-dose high-resolution $\mathrm{TOF}$-$\mathrm{PET}$ using ionization-activated multi-state low-$\mathrm{Z}$ detector media

We propose PET scanners using low atomic number media that undergo a persistent local change of state along the paths of the Compton recoil electrons. Measurement of the individual scattering locations and angles, deposited energies, and recoil electron directions allows using the kinematical constraints of the 2-body Compton scattering process to perform a statistical time-ordering of the scatterings, with a high probability of precisely identifying where the gamma first interacted in the detector. In these cases the Line-of-Response is measured with high resolution, determined by the underlying physics processes and not the detector segmentation. There are multiple such media that act through different mechanisms. As an example in which the change of state is quantum-mechanical through a change in molecular configuration, rather than thermodynamic, as in a bubble chamber, we present simulations of a two-state photoswitchable organic dye, a ‘Switchillator’, that is activated to a fluorescent-capable state by the ionization of the recoil electrons. The activated state is persistent, and can be optically excited multiple times to image individual activated molecules. Energy resolution is provided by counting the activated molecules. Location along the LOR is implemented by large-area time-of-flight MCP-PMT photodetectors with single photon time resolution in the tens of ps and sub-mm spatial resolution. Simulations indicate a large reduction of dose.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.

Lin, Jiusheng [University of Nebraska, Lincoln, NE↗
DOE OSTI2023

The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex

Abstract The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.

Zambelli, Barbara (ORCID:0000000238760051)↗
NASA NTRS1972

Ground state energy of solid molecular hydrogen at high pressure

The present status of the theoretical equation of state of solid molecular hydrogen is reviewed. Different quantum mechanical calculations by several groups lead to results which generally agree with each other but which disagree systematically with the measured pressure-volume curve at pressures larger than about 3000 atm. A new calculation of this curve is presented including the effect of the anisotropic interaction between H2 molecules within a completely quantum-mechanical formalism. The results show that inclusion of this interaction removes the discrepancy between theory and experiment at high pressures and that a quantum-mechanical treatment is necessary to realize its full effect.

Ebner, C.↗
DOE OSTI2023

Quantum bath augmented stochastic nonequilibrium atomistic simulations for molecular heat conduction

Classical molecular dynamics (MD) has been shown to be effective in simulating heat conduction in certain molecular junctions since it inherently takes into account some essential methodological components which are lacking in the quantum Landauer-type transport model, such as many-body full force-field interactions, anharmonicity effects and nonlinear responses for large temperature biases. However, the classical MD reaches its limit in the environments where the quantum effects are significant (e.g. with low-temperatures substrates, presence of extremely high frequency molecular modes). Here, we present an atomistic simulation methodology for molecular heat conduction that incorporates the quantum Bose–Einstein statistics into an “effective temperature” in the form of a modified Langevin equation. We show that the results from such a quasi-classical effective temperature MD method deviates drastically when the baths temperature approaches zero from classical MD simulations and the results converge to the classical ones when the bath approaches the high-temperature limit, which makes the method suitable for full temperature range. In addition, we show that our quasi-classical thermal transport method can be used to model the conducting substrate layout and molecular composition (e.g. anharmonicities, high-frequency modes). Anharmonic models are explicitly simulated via the Morse potential and compared to pure harmonic interactions to show the effects of anharmonicities under quantum colored bath setups. Finally, the chain length dependence of heat conduction is examined for one-dimensional polymer chains placed in between quantum augmented baths.

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

Tunability and Long-Range Enhancement of Resonance Energy Transfer Facilitated by Plasmonic Nanorods

Resonance energy transfer (RET) between molecules or quantum dots is an important process in many energy-related applications. Different environmental structures have been studied and demonstrated to be able to enhance the RET rates between a nearby donor–acceptor pair. In particular, cylindrical silver nanorods and nanowires have shown an extraordinary ability to transfer energy along their longitudinal axes over large distances. However, the detailed mechanism of such transfer and the effects on the molecular RET process are as yet elusive. In this study, we use the recently developed computational tool based on the plasmon-coupled RET method to systematically study the effects of nanorods with different dimensions on the RET rates. We find that highly frequency-dependent coupling factor (CF) spectra, whose amplitudes determine RET rates, can be obtained due to the localized surface plasmon polariton modes of the rods with nanoscale dimensions. Simple phenomenological models can be derived for the wavelengths of CF peaks in relation to the length and width of the nanorods, providing easy tunability for enhancing the RET rate in specific wavelength ranges. When coupled to longer rods with mesoscale lengths, exponential decay of the CF over long donor–acceptor distances with a small decay constant is observed, leading to the possibility of long-range RET processes. Furthermore, drumhead resonance modes emerge on the flat ends of the rod when the rod’s diameter reaches 300 nm, resulting in extra enhancement to RET rate compared to certain thinner rods. Furthermore, these findings shed new light on the mechanism of plasmonic enhancement with silver nanorods and establish design principles for how to optimally utilize these structures to manipulate RET processes for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗