Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning
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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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Stockmayer fluid simulations for viscosity and glass transition temperature of ionic liquids
We develop a Stockmayer fluid model for molecular dynamics simulations of ionic liquids that captures molecular polarization, ionic conductivity, viscosity, and glass transition temperature, using ethylammonium nitrate (EAN) as an example. The ions in EAN are treated as spheres interacting via the Lennard-Jones potential with an embedded point charge and a permanent dipole moment. We show that our simulation results for EAN are consistent with experimental data and then explore the effects of the molecular parameters on the viscosity of ionic liquids. Our results indicate that viscosity monotonically increases with ionic charge and dipole moment but non-monotonically changes with ionic diameter (or molar volume). This non-monotonic trend arises from the competition among the electrostatic interactions, molecular packing, and size asymmetry between the cation and anion. In conclusion, our model also shows that long-lived ion pairs result in higher viscosities.
Coarse-grained simulations↗
Anharmonicity and Phase Diagram of Magnesium Oxide in the Megabar Regime
With density functional molecular dynamics simulations, we computed the phase diagram of MgO from 50 to 2000 GPa up to 20000 K. Via thermodynamic integration (TDI), we derive the Gibbs free energies of the B1, B2, and liquid phases and determine their phase boundaries. With TDI and a pseudo-quasi-harmonic approach, we show that anharmonic effects are important and stabilize the B1 phase in particular. As a result, the B1-B2 transition boundary in the pressure-temperature plane exhibits a steep slope. We predict the B1-B2-liquid triple point to occur at approximately T= 10000 K and P = 370 GPa, which is higher in pressure than was inferred with quasi-harmonic methods alone. We predict the principal shock Hugoniot curve to enter the B2 phase stability domain but only over a very small range of parameters. Here, this may render it difficult to observe this phase with shock experiments because of kinetic effects.
3-dimensional systems↗
Nonenzymatic template-directed synthesis on oligodeoxycytidylate sequences in hairpin oligonucleotides
We have developed a novel method for studying template-directed synthesis in hairpin oligonucleotides. An unpaired segment at the 5'-terminus of the hairpin acts as an intramolecular template for the extension of the paired 3'-terminus. Products are analyzed by denaturing gel electrophoresis of [32P]-labeled hairpins. Using this system, we have studied the synthesis of oligoguanylates on an oligodeoxycytidylate template. We find that guanosine 5'-phosphoro(2-methyl)imidazolide adds efficiently to a terminal riboguanylate residue at temperatures in the range 0-37 degrees C but not at 50 degrees C. At 0 degree C, the half-time for addition of the first G residue is about 3 h, and the reaction rate is independent of pH in the range 6.5-8.0. The first addition reaction results in the formation of a predominantly 3'-5'-internucleotide bond. When the 3'-terminal riboguanylate residue is placed by a deoxyguanylate residue, the half-time for the first addition increases from about 3 to about 30 h.
NASA Discipline Exobiology↗
Design and Preparation of Nematic Colloidal Particles
Colloidal systems are abundant in technology, in biomedical settings, and in our daily life. The so-called “colloidal atoms” paradigm exploits interparticle interactions to self-assemble colloidal analogs of atomic and molecular crystals, liquid crystal glasses, and other types of condensed matter from nanometer- or micrometer-sized colloidal building blocks. Nematic colloids, which comprise colloidal particles dispersed within an anisotropic nematic fluid host medium, provide a particularly rich variety of physical behaviors at the mesoscale, not only matching but even exceeding the diversity of structural and phase behavior in conventional atomic and molecular systems. This feature article, using primarily examples of works from our own group, highlights recent developments in the design, fabrication, and self-assembly of nematic colloidal particles, including the capabilities of preprogramming their behavior by controlling the particle’s surface boundary conditions for liquid crystal molecules at the colloidal surfaces as well as by defining the shape and topology of the colloidal particles. Here recent progress in defining particle-induced defects, elastic multipoles, self-assembly, and dynamics is discussed along with open issues and challenges within this research field.
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Effect of Macro- and Microstructures on Catalytic Hydrogenolysis of Polyolefins
Here, polyethylenes of varying molecular weight and branch density, as well as polypropylenes of varying molecular weight and tacticity, were catalytically converted to lower-molecular-weight liquid products to showcase how these various properties in a mixed waste plastic stream could affect the final product. A Pt nanoparticle on a strontium titanate nanocuboid (Pt/STO) catalyst was used under solvent-free conditions in the presence of 170 psi of H 2 at 300 °C for hydrogenolysis. The initial molecular weight of polyethylene was found to have a moderate effect on the yield to the final product (ranging from 55 wt% for M n ~ 7600 Da to 67 wt% for M n ~ 50,950 Da). The microstructure, defined as the length and density of branches in a polymer, of higher-molecular-weight polymers was the dominant factor in determining the yield (ranging from 67 wt% for M n ~ 50,950 Da for linear low-density polyethylene (LLDPE) with C 2 branches to 97 wt% for M n ~ 38,850 Da for LLDPE with C 6 branches). The same products (M n = C 29 –C 46 , Ð = 1.1–1.6) and distribution of undesired light gases (C 1 –C 4 ≈ 90 mol%, C 5 –C 8 ≈ 10 mol%) are obtained from conversions of PE of varying molecular weight. The tacticity of polypropylene at a given molecular weight had a significant effect on the molecular weight of the final product, while not strongly affecting conversion. Hydrogenolysis of isotactic polypropylene (iPP) produced ≈C 18 with a wider polydispersity (Ð ~ 1.4) compared to the narrow ≈C 64 (Ð ~ 1.0) and ≈C 54 (Ð ~ 1.0) products from atactic (aPP) and syndiotactic (sPP) polypropylene, respectively. The stereochemistry of the methyl groups dictates the shape and structure of the polymer in the melt, which in turn affects how the hydrocarbon chain interacts with the catalyst surface, thereby impacting the number of C–C scissions. These results show how various characteristics such as the molecular weight and structure of a waste plastic stream could affect the final product.
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Investigation of γ - ( U , Z r ) structural properties and its interfacial properties with liquid sodium using ab initio molecular dynamics
In this study, the elastic properties, structural parameters, sound velocity, and Debye temperature of γ–(U,Zr) were computed using ab initio molecular dynamics (AIMD) at temperatures between 1000 K and 1400 K and for Zr content between 0 at. % and 100 at. %. UZr is used as a metallic fuel for Sodium Fast Reactors (SFRs). The study of the mechanical and thermal behavior of these alloys leads to a better data-informed fuel design. The bulk modulus, shear modulus, Young's modulus, and Poisson's ratio were calculated from the elastic constants and their dependence on Zr content and temperature was investigated, comparing the results with previous computational work and the available experimental data in the literature. Interfacial properties between UZr (up to 32 at. % which typically exists in nuclear fuel) and liquid sodium are also of interest due to the presence of a sodium bond between the fuel and the cladding in metallic nuclear fuel. The interfacial energy between γ–(U,Zr) and liquid sodium, the surface tension of liquid sodium, and the work of adhesion were computed at different temperatures and Zr concentrations. It was demonstrated that γ–(U,Zr) is completely wetted by liquid sodium at all the investigated temperatures and Zr concentrations. Finally, this work provides the basis for the determination of interfacial resistances in SFRs and their implementation into heat transfer fuel performance simulations, which will be the subject of future work.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Oxidation of the N-terminal methionine of lens alpha-A crystallin
Antiserum against the N-terminal peptide of bovine alpha-A crystallin has been used to monitor purification of two different seropositive peptides (i.e. T1a and T1b) from a tryptic digest of bovine lens proteins. Both these peptides have similar amino acid compositions, but peptide T1b has a molecular weight 16 atomic mass units larger than T1a, suggesting posttranslational modification. Analysis of ionization fragments of the T1b peptide by mass spectrometry demonstrates that this difference in molecular weight is due to the in vivo oxidation of the N-terminal met residue of the alpha-A crystallin molecule.
NASA Discipline Cell Biology↗
Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations
We study the phase equilibrium between liquid water and ice Ih modeled by the TIP4P/Ice interatomic potential using enhanced sampling molecular dynamics simulations. Our approach is based on the calculation of ice Ih-liquid free energy differences from simulations that visit reversibly both phases. The reversible interconversion is achieved by introducing a static bias potential as a function of an order parameter. The order parameter was tailored to crystallize the hexagonal diamond structure of oxygen in ice Ih. Furthermore, we analyze the effect of the system size on the ice Ih-liquid free energy differences, and we obtain a melting temperature of 270 K in the thermodynamic limit. This result is in agreement with estimates from thermodynamic integration (272 K) and coexistence simulations (270 K). Since the order parameter does not include information about the coordinates of the protons, the spontaneously formed solid configurations contain proton disorder as expected for ice Ih.
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Probing Self-Assembly in Arginine–Oleic Acid Solutions with Terahertz Spectroscopy and X-ray Scattering
A study of the formation of microstructures in the reaction of oleic acid with arginine elucidates dynamical self-assembly processes at the molecular level. Terahertz spectroscopy combined with density functional calculations reveals the initial hydrogen-bonding motifs in the assembly process, leading to the formation of micelles and vesicles. Small-angle X-ray scattering measurements allow for kinetic analysis of the growth processes of these nanostructures, revealing a prenucleation pathway of vesicles and micelles which lead to spongelike structures. This final stage of the assembly into spongelike aggregates is investigated with optical microscopy. The formed structures only occur at pH > 8 and are resistant to extreme acidic and basic conditions. Here, a mechanistic pathway to the formation of the spongelike aggregates is described.
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How good are polarizable and flexible models for water: Insights from a many-body perspective
We present a systematic analysis of state-of-the-art polarizable and flexible water models from a many-body perspective, with a specific focus on their ability to represent the Born–Oppenheimer potential energy surface of water from the gas to the liquid phase. Using coupled cluster data in the completed basis set limit as a reference, we examine the accuracy of the polarizable models in reproducing individual many-body contributions to interaction energies and harmonic frequencies of water clusters and compare their performance with that of MB-pol, an explicit many-body model that has been shown to correctly predict the properties of water across the entire phase diagram. Based on these comparisons, we use MB-pol as a reference to analyze the ability of the polarizable models to reproduce the energy landscape of liquid water under ambient conditions. We find that, while correctly reproducing the energetics of minimum-energy structures, the polarizable models examined in this study suffer from inadequate representations of many-body effects for distorted configurations. To investigate the role played by geometry-dependent representations of 1-body charge distributions in reproducing coupled cluster data for both interaction and many-body energies, we introduce a simplified version of MB-pol that adopts fixed atomic charges and demonstrate that the new model retains the same accuracy as the original MB-pol model. Based on the analyses presented in this study, we believe that future developments of both polarizable and explicit many-body models should continue in parallel and would benefit from synergistic efforts aimed at integrating the best aspects of the two theoretical/computational frameworks.
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Similarity Metric for Data Optimization and Efficient Training of Reactive Machine Learning Force Fields for Hydrocarbon Radiolysis
Radiolysis is a common approach to sterilize polymers, chemically modify them for upcycling, and accelerate their decomposition for recycling purposes. Reactive molecular dynamics (MD) simulations provide a powerful tool to generate atomic-level trajectories of the reactive processes and quantify radiolytic chemical degradation pathways. For this, machine learning (ML) surrogate models for reactive force fields with quantum mechanical accuracy are now widely used, which require ML training data sets that can provide information on atomic environments for target chemical systems. However, radiolysis chemistry can be highly complex and diverse, which poses significant challenges for generating training data to parametrize ML models. In this regard, we developed a method for optimizing the training data set using a cosine similarity metric to help guide training set selection for radiolysis of polyethylene, a model hydrocarbon polymer, as well as to enhance the transferability of our reactive ML force field (MLFF) to a variety of molecular and polymeric systems. Our approach performs atom-by-atom comparisons between local atomic environments to pinpoint important data points associated with rare and localized events, such as radiolysis damage within structures. We apply this approach to train the Chebyshev Interaction Model for Efficient Simulation (ChIMES) MLFF model, which expresses the atomic interaction potentials in terms of linear combinations of many-body Chebyshev polynomials. We first show that our method can reduce our training set size by ∼70% while improving overall accuracy compared to more standard MD model fitting approaches. We then validate our optimum model against diverse hydrocarbon simulation data, including simple alkanes and systems with unsaturated carbon bonds, over a wide range of thermodynamic conditions. Finally, we use our ChIMES model to perform MD simulations of radiolytic damage with large-scale systems that help avoid system size effects. Overall, our approach yields an MD force field that retains most of the accuracy of the underlying quantum method while yielding many orders of improvement in computational efficiency. In conclusion, our efforts will have impact on future hydrocarbon polymer radiolysis studies, where the chemical details of the polymer–radiation interactions can have a strong effect on the resulting products observed in experiments.
Hydrocarbons↗
Activated relaxation in supercooled monodisperse atomic and polymeric WCA fluids: Simulation and ECNLE theory
Here, we combine simulation and Elastically Collective Nonlinear Langevin Equation (ECNLE) theory to study the activated relaxation in monodisperse atomic and polymeric Weeks–Chandler–Andersen (WCA) liquids over a wide range of temperatures and densities in the supercooled regime under isochoric conditions. By employing novel crystal-avoiding simulations, metastable equilibrium dynamics is probed in the absence of complications associated with size polydispersity. Based on a highly accurate structural input from integral equation theory, ECNLE theory is found to describe well the simulated density and temperature dependences of the alpha relaxation time of atomic fluids using a single system-specific parameter, a c , that reflects the nonuniversal relative importance of local cage and collective elastic barriers. For polymer fluids, the explicit dynamical effect of local chain connectivity is modeled at the fundamental dynamic free energy trajectory level based on a different parameter, N c , that quantifies the degree of intramolecular correlation of bonded segment activated barrier hopping. For the flexible chain model studied, a physically intuitive value of N c ≈ 2 results in good agreement between simulation and theory. A direct comparison between atomic and polymeric systems reveals that chain connectivity can speed up activated segmental relaxation due to weakening of equilibrium packing correlations but can slow down relaxation due to local bonding constraints. The empirical thermodynamic scaling idea for the alpha time is found to work well at high densities or temperatures but fails when both density and temperature are low. The rich and subtle behaviors revealed from simulation for atomic and polymeric WCA fluids are all well captured by ECNLE theory.
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Ionic Liquid‐Driven Modulation of DNA Brush Morphology on Nanoparticle Surfaces
Here, the morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like electrostatic screening and ion bridging. In contrast, ionic liquids, a new class of organic salts, have previously been found to increase the DNA chain length, indicating a distinct mode of interaction between the ionic liquid and DNA chains. This study utilizes self-assembled DNA-AuNPs as a model system to examine changes in the DNA chain morphology and the nanoscale interaction mechanisms in an ionic liquid environment. The DNA chain lengths are measured in solution using X-ray scattering measurements at varying concentrations of two imidazolium ([$BMIM$] acetate and [$EMIM$] acetate) based ionic liquids. Additionally, Molecular Dynamics (MD) simulations are performed mimicking the experimental system. Our results suggest an interplay of electrostatic and groove-binding interactions governing the DNA chain morphology, which depends on IL concentration and the composition of the DNA chains. It has been found that for DNA chains with majority ssDNA, electrostatic interaction dominate, however with increasing composition of double strands, the DNA chains exhibit compaction due to a non-electrostatic hydrophobic groove-binding mechanism.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Deep Eutectic Solvents: A Review of Fundamentals and Applications
Deep eutectic solvents (DESs) are an emerging class of mixtures characterized by significant depressions in melting points compared to those of the neat constituent components. These green materials are promising for applications as inexpensive ’designer’ solvents exhibiting a host of tunable physicochemical properties. Here, a detailed review of the current literature reveals the lack of predictive understanding of the microscopic mechanisms that govern the structure-property relationships in this class of solvents. Complex hydrogen bonding behavior is postulated as the root cause of their melt-ing point depressions and physicochemical properties; to understand these hydrogen bonded networks, it is imperative to study these systems as dynamic entities using both simulations and experiments. This review emphasizes recent research efforts in order to elucidate the next steps needed to develop a fundamental framework for understanding DESs. It covers recent developments in DES research, frames outstanding scientific questions, and identifies gainful research thrusts that would advance the field towards predictive models and fundamental understanding of these solvents.
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Growth Mechanism and Kinetics of Diamond in Liquid Gallium from Quantum Mechanics Molecular Dynamics Simulations
Not provided.
Materials Science↗
Towards understanding of delignification of grassy and woody biomass in cholinium-based ionic liquids
Herein we report the dissolution mechanism of lignin in cholinium-based ionic liquids by molecular dynamics simulations. Multiple hydrogen bonds, longer HB lifetimes, and higher p K a of [Ch][Lys] makes it a better solvent for lignin than acidic ILs.
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