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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 91 records · Page 5

Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments

Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO 3 ·nH 2 O systems, where M 2+ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Finally, water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving Electron Injection from Singlet Fission-Borne Triplets into Mesoporous Transparent Conducting Oxides

Photoinduced electron transfer from a molecular chromophore into mesoporous metal oxide substrates occurs efficiently from both singlet and triplet excited states for traditional metal-to-ligand charge transfer (MLCT) dyes. All organic molecules that undergo singlet fission (SF), the process of generating two triplet excitons with photoexcitation of one singlet exciton, offers a promising method of generating two charges per one absorbed photon. However, the singlet-triplet energy balance required to drive SF often places the driving force for triplet electron injection into metal oxides too low. As such, the dynamics of singlet vs. triplet electron transfer for SF in dye-sensitized solar cell configurations has not been elucidated. Here, we use applied bias transient absorption spectroscopy to modulate the driving force for triplet electron transfer from an anthradithiophene-based SF chromophore (ADT-COOH) adsorbed to mesoporous indium tin oxide (nanoITO).

CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SU↗

A Hybrid Quantum–Classical Study of Ion Adsorption at the Copper Electrode

Here, we present a set of computational studies that surveys the molecular structure and thermodynamics of simple ions at the electrode–electrolyte interface. A hybrid quantum–classical approach is used to obtain free energy profiles and solvent structure as a function of the ion’s position relative to the electrochemical liquid/solid interface and system potential. Model systems consist of a copper electrode and single halide or alkali metal ion in contact with an implicit solvent and reveal new insights into the interplay of forces that drive or resist ion absorption at the electrode/ electrolyte interface. We also expand on subtleties of absorption site preference and describe the complex relationship between the energetic barrier to absorption and the ion–electrode binding energy as a function of electrode potential.

36 MATERIALS SCIENCE↗

Corrigendum and Addendum: Helium flux effects on bubble growth and surface morphology in plasma-facing tungsten from large-scale molecular dynamics simulations (2019 Nucl. Fusion 59 066035)

Two of the simulations discussed in a prior article (Hammond et al 2019 Nucl. Fusion 59 066035) were affected by a simulation glitch. We repeated the affected calculations and discuss them here. Here, the overall conclusions are essentially unchanged, though the details are different. In particular, observations that we referred to as ‘concerted bursting’ were caused primarily by non-physical heating and cooling applied by the thermostat after most atoms’ velocities were deleted (for reasons that are not known for certain). The phenomenon of one bubble bursting and causing another nearby bubble to burst does exist, though its effects are much less spectacular in the absence of non-physical driving forces. The observation of an interconnected network of sub-surface cavities formed by burst bubbles is real, and the observation of holes on the surface 1–2 nm in diameter is also confirmed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗

Pathways for Nucleation and Growth in Confined Spaces and at Interfaces

Mineral crystallization is central to myriad natural processes from the formation of snowflakes to stalagmites, but the molecular-scale mechanisms are often far more complex than models reflect. Feedbacks between the hydro-, bio-, and geo-spheres drive complex crystallization processes that challenge our ability to observe and quantify them, motivating an expansion of crystallization theories. Here, in this article, we discuss how the driving forces and timescales of nucleation are influenced by factors ranging from simple geometric confinement to distinct interfacial solution structures involving solvent organization, electrical double layers, and surface charging effects. Taken together, these ubiquitous natural phenomena can preserve metastable intermediates, drive precipitation of undersaturated phases, and modulate crystallization in time and space.

biosphere↗

Local conformations and heterogeneities in structures and dynamics of isotactic polypropylene adsorbed onto carbon fiber

Carbon fiber (CF) reinforced polymers (CFRPs) have experienced widespread use in various industries. One of the most important parameters that controls the macroscopic property of CFRPs is the interface between a polymer matrix and CF. There is growing evidence to suggest the formation of a bound polymer layer (BPL), i.e., polymer chains that physically adsorb on a filler surface. However, this interface is always in contact with the thicker part of a polymer matrix, rendering its understanding a difficult task. Therein, we use CF-reinforced isotactic polypropylene (iPP) as a rational CFRP. To characterize the BPL on the CF surface, we extracted it from the CFRP using solvent-rinsing with p-xylene. The physical and thermal properties of the BPL were characterized by differential scanning calorimetry and thermogravimetric analysis, while its microscopic structures and dynamics were probed by small-angle neutron scattering and quasi-elastic neutron scattering (QENS) techniques. Subsequently, we employed atomistic molecular dynamics (MD) simulations to complement the QENS results above the bulk melting temperature and reveal details that were experimentally inaccessible. In this work, we observed that the degree of crystallinity of the BPL was quite lower than the bulk, while the melting temperature of the BPL remained the same as the bulks. Within the given length and time scales probed by QENS and MD, we also observed that most of the bound chains were mobile, with the formation of a high-density region (less than 1 nm in thickness) near the CF surface. The segmental dynamics of the bound chains probed by both QENS and MD were also much faster than those of the free chains, possibly due to the presence of a free surface region at the topmost surface of the BPL. Furthermore, the MD results demonstrated that the backbone chains and side groups lie nearly flat on the CF surface, which is the driving force for the flattening process of the iPP BPL to overcome the conformational entropy loss in the total free energy.

36 MATERIALS SCIENCE↗

Cyclopropenylidenes as Strong Carbene Anchoring Groups on Au Surfaces

The creation of stable molecular monolayers on metallic surfaces is a fundamental challenge of surface chemistry. N-Heterocyclic carbenes (NHCs) were recently shown to form self-assembled monolayers that are significantly more stable than the traditional thiols on Au system. In this study, we theoretically and experimentally demonstrate that the smallest cyclic carbene, cyclopropenylidene, binds even more strongly than NHCs to Au surfaces without altering the surface structure. We deposit bis(diisopropylamino)cyclopropenylidene (BAC) on Au(111) using the molecular adduct BAC–CO 2 as a precursor and determine the structure, geometry, and behavior of the surface-bound molecules through high-resolution X-ray photoelectron spectroscopy, atomic force microscopy, and scanning tunneling microscopy. Our experiments are supported by density functional theory calculations of the molecular binding energy of BAC on Au(111) and its electronic structure. Our work is the first demonstration of surface modification with a stable carbene other than NHC; more broadly, it drives further exploration of various carbenes on metal surfaces.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Discrete stochastic model of point defect-dislocation interaction for simulating dislocation climb

Dislocation climb is an important high temperature process in metals plasticity, responsible for the phenomena such as creep, swelling, or hardening. Climb is defined by the ability of dislocations to leave their original glide plane by interacting with point defects. As such, dislocation climb is controlled by point defect diffusion/absorption/emission, all of which involve thermal activation. The existing thermodynamically consistent models for climb are generally formulated in a continuum framework, through the definition of effective defect fluxes and climb propensities in response to thermodynamic driving forces. However, the point-wise discrete nature of vacancies (and/or self-interstitials) confers a highly discrete nature to the climb dynamics, which is also strongly affected by elastic forces. The combination of discreteness, thermal activation, and elasticity makes this process too challenging for direct atomistic methods such as molecular dynamics. Here we develop a kinetic Monte Carlo model that captures vacancy generation and transport kinetics acting in conjuction with the evolving elastic fields provided by discrete dislocation dynamics simulations. The two models are coupled via the applied stresses and stress gradients generated by dislocation structures at vacancy locations. Our simulations reveal two surprising results. First that climb is dominated by vacancy emission even when the background vacancy concentration is much higher than the equilibrium one. And, second, that climb velocities might be much faster than otherwise believed when one uses the classical theories of climb. These effects are due to the locality of vacancy-dislocation processes, which are not captured in classical treatments that assume smooth vacancy fluxes and homogeneous concentrations. We apply the method to study elementary climb processes in body-centered cubic iron and furnish climb mobility functions to be used in parametric dislocation dynamics and/or crystal plasticity simulations. Here, we apply the technique to study non-conservative plastic bypass of spherical precipitates by edge dislocations and point out the differences between our discrete approach and existing continuum formulations.

36 MATERIALS SCIENCE↗

Trajectory Ensemble Methods Provide Single-Molecule Statistics for Quantum Dynamical Systems

The emergence of experiments capable of probing quantum dynamics at the single-molecule level requires the development of new theoretical tools capable of simulating and analyzing these dynamics beyond an ensemble-averaged description. In this article, we present an efficient method for sampling and simulating the dynamics of the individual quantum systems that make up an ensemble and apply it to study the nonequilibrium dynamics of the ubiquitous spin-boson model. We generate an ensemble of single-system trajectories, and we analyze this trajectory ensemble using tools from classical statistical mechanics. Our results demonstrate that the dynamics of quantum coherence is highly heterogeneous at the single-system level due to variations in the initial bath configuration, which significantly affects the transient exchange of coherence between the system and its bath. Here, we observe that single systems tend to retain coherence over time scales longer than that of the ensemble. We also compute a novel thermodynamic entanglement entropy that quantifies a thermodynamic driving force favoring system–bath entanglement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes

Fully synthetic peptoid membranes are known to mimic important features of biological membranes, with several advantages over other biomimetic membranes. A fundamental understanding of how the individual peptoid amphiphiles assemble in solution to form the bilayer membrane is key to unlocking their versatility for application in a broad range of processes. Here, in this study, in situ X-ray scattering and molecular dynamics simulations are used to understand the early stages of assembly of three different peptoids that exhibit distinctly different crystallization kinetics. The in situ measurements reveal that the peptoids aggregate first into a nascent phase that is less crystalline than the assembled peptoid membrane. Anisotropic aromatic interactions are determined to be the dominant driving force in the early stages of membrane formation. These results provide key insights into how the peptoid assembly may be manipulated during the early stages of assembly and nucleation and growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analytical and Computational Advances, Opportunities, and Challenges in Marine Organic Biogeochemistry in an Era of “Omics”

Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in analytical technology were often the driving force that made possible progress in elucidating the sources and fate of organic matter in the ocean in the first decades of marine organic biogeochemistry, today process-based scientific questions should drive analytical developments. Several paradigm shifts and challenges for the future are related to the intersection between analytical progress and scientific evolution. Untargeted “molecular headhunting” for its own sake is now being subsumed into process-driven targeted investigations that ask new questions and thus require new analytical capabilities. However, there are still major gaps in characterizing the chemical composition and biochemical behavior of macromolecules, as well as in generating reference standards for relevant types of organic matter. Field-based measurements are now routinely complemented by controlled laboratory experiments and in situ rate measurements of key biogeochemical processes. And finally, the multidisciplinary investigations that are becoming more common generate large and diverse datasets, requiring innovative computational tools to integrate often disparate data sets, including better global coverage and mapping. Here, we compile examples of developments in analytical methods that have enabled transformative scientific advances since 2004, and we project some challenges and opportunities in the near future. We believe that addressing these challenges and capitalizing on these opportunities will ensure continued progress in understanding the cycling of organic carbon in the ocean.

59 BASIC BIOLOGICAL SCIENCES↗

Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains

N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase instability-coupled fracture behavior in garnet LLZO solid electrolytes: a machine learning-enabled atomistic study

Fracture in the garnet-type solid electrolyte Li 7 La 3 Zr 2 O 12 (LLZO) poses a critical threat to both the performance and safety of solid-state batteries. To unravel the coupled chemomechanical processes that govern fracture in LLZO under external loading, we carry out large-scale molecular-dynamics simulations with a validated machine-learning force field. Our results demonstrate that triaxial stresses at crack flanks trigger a localized cubic-to-tetragonal phase transformation, which is accompanied by Li-ion rearrangement. The emergent tetragonal domains feature lattice contraction normal to the fracture plane, imposing coherent misfit strains that provide an additional driving force for further crack propagation. Crucially, introducing Li deficiencies stabilizes the cubic phase, postponing the phase transition and thereby delaying fracture initiation. These findings highlight the role of intrinsic phase instability in dictating LLZO's fracture resistance and its critical connection to local Li concentration. This chemomechanical coupling points toward targeted strategies to enhance the mechanical robustness of garnet electrolytes, including tuning Li content, ensuring dopant homogeneity, and refining processing protocols.

Materials science↗

The behavior of methane–water mixtures under elevated pressures from simulations using many-body potentials

Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane–water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane–water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane–water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. As a result, we find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charging-driven coarsening and melting of a colloidal nanoparticle monolayer at an ionic liquid–vacuum interface

In this work, we induce and investigate the coarsening and melting dynamics of an initially static nanoparticle colloidal monolayer at an ionic liquid–vacuum interface, driven by a focused, scanning electron beam. Coarsening occurs through grain interface migration and larger-scale motions such as grain rotations, often facilitated by sliding dislocations. The progressive decrease in area fraction that drives melting of the monolayer is explained using an electrowetting model whereby particles at the interface are solvated once their accumulating charge recruits sufficient counterions to subsume the particle. Subject to stochastic particle removal from the monolayer, melting is recapitulated in simulations with a Lennard-Jones potential. This new driving mechanism for colloidal systems, whose dynamical timescales we show can be controlled with the accelerating voltage, opens the possibility to manipulate particle interactions dynamically without need to vary particle intrinsic properties or surface treatments. Furthermore, the decrease in particle size availed by electron imaging presents opportunities to observe force and time scales in a lesser-explored regime intermediate between typical colloidal and molecular systems.

36 MATERIALS SCIENCE↗

Coarse-grained molecular dynamics simulation of solvent-dependent cellulose nanofiber interactions

Associations between cellulose are important both in biofuel production and in the use of cellulose for biomaterials. Cellulose nanofibers (CNFs) are sustainable, strong, light-weight alternatives to traditional materials in manufacturing, but are challenging to obtain due to irreversible aggregation in solution during preparative fibrillation. Therefore, it is imperative to understand the underlying factors driving aggregation with a view to designing solvents that can effectively compete with interfiber interactions, hence reducing aggregation. Molecular dynamics (MD) simulation at atomic detail can provide useful information on local interactions. However, the length and timescales accessible are too short to fully capture association processes. Here, we provide a method for accessing the longer length and timescales required using coarse-grained (CG) MD simulations with a MARTINI force field to calculate the interaction behavior of CNFs in three selected solvents: NaOH-urea-water, acetone, and neat water. The CG results are consistent with our prior all-atom MD and with previous experimental results. While acetone is found not to be an effective solvent, urea and ionic moieties in NaOH-urea-water not only solvate the fibrils but also improve the confinement of water molecules around them as shown by the solvent residence times and mean-square displacements. Overall, the presence of urea and ions reduces the likelihood of aggregation in multi-CNF systems relative to neat water irrespective of whether the hydrophobic or hydrophilic CNF surfaces are interacting. In conclusion, the CG method shows clear promise for selecting potential high-performance solvents for experimental prioritization in bioenergy and biomaterials research in a relatively fast manner as well as for understanding the aggregation and rheological behavior of CNF-solvent systems.

aggregation↗

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗