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At least 631 records · Page 35

Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networks

The rates of liquid-phase, acid-catalyzed reactions relevant to the upgrading of biomass into high-value chemicals are highly sensitive to solvent composition and identifying suitable solvent mixtures is theoretically and experimentally challenging. We show that the complex atomistic configurations of reactant–solvent environments generated by classical molecular dynamics simulations can be exploited by 3D convolutional neural networks to enable accurate predictions of Brønsted acid-catalyzed reaction rates for model biomass compounds. We develop a 3D convolutional neural network, which we call SolventNet, and train it to predict acid-catalyzed reaction rates using experimental reaction data and corresponding molecular dynamics simulation data for seven biomass-derived oxygenates in water–cosolvent mixtures. We show that SolventNet can predict reaction rates for additional reactants and solvent systems an order of magnitude faster than prior simulation methods. This combination of machine learning with molecular dynamics enables the rapid, high-throughput screening of solvent systems and identification of improved biomass conversion conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multilevel atomic structural model for interstratified opal materials

The structure of opal has long fascinated scientists. It occurs in a number of structural states, ranging from amorphous to exhibiting features of stacking disorder. Opal-CT, where C and T signify cristobalite- and tridymite-like interstratification, represents an important link in the length scales between amorphous and crystalline states. However, details about local atomic (dis)order and arrangements extending to long-range stacking faults in opal polymorphs remain incompletely understood. Here, a multilevel modeling approach is reported that considers stacking states in correlation with the abundance of C and T segments as a high-level structural parameter (i.e. not each atom). Optimization accounting for inter-tetrahedral bond lengths and angles and the regularity of the silicate tetrahedra is included as lower levels of structural parameters. Together, a set of parameters with both coarse-grained and atomistic features for different levels of structural details is refined. Structural disorder at the ~10–100 Å distance scale is evaluated using experimental pair distribution function and diffraction datasets, comparing peak intensities, widths and asymmetry. Here this work presents a complete multilevel structural description of natural opal-CT and explains many of the unusual features observed in X-ray powder diffraction patterns. This modeling approach can be adopted generally for analyzing layered materials and their assembly into 3D structures.

36 MATERIALS SCIENCE↗

Modeling the Effect of Hydrogen on Tungsten Grain Boundary Properties

The objective of this study is to assess the effect of hydrogen isotopes on mechanical properties of tungsten that are relevant to first-wall applications in a tokamak. We focus on the effects of hydrogen segregation to grain boundaries and its impact on the grain boundary structure and properties. Through molecular dynamics and other atomistic techniques, we are able to make predictions of grain boundary structure and properties related to it, including grain boundary mobility and impurity diffusivity along the grain boundary. The grain boundary structure can change significantly and abruptly as conditions change, including due to heating and radiation damage. These grain boundary phase transformations can have a pronounced effect on mobility and impurity diffusivity, even when no hydrogen is present. How this behavior changes in the presence of hydrogen is not known. The phase may affect the level of hydrogen segregation and hydrogen storage, and the hydrogen may induce significant grain boundary structure changes. Our objective is to predict whether they do. The results inform thermomechanical modeling of tungsten at tokamak conditions.

36 MATERIALS SCIENCE↗

Multi-scale fission product release model with comparison to AGR data

TRistructural ISOtropic (TRISO) particle fuel is central to several advanced, high-temperature reactor designs. Each particle consists of a fuel kernel encapsulated by three layers of carbon and ceramics that prevent the release of fission products and ensure physical integrity. Despite outstanding retention properties, fission product release has been observed from intact particles. To better understand and quantify fission product release from TRISO particles, a multiscale, mechanistic model of fission product transport is being developed by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. Previous work focused on silver (Ag) transport and improved Ag release predictions. The work described in this report builds on this experience to better understand cesium (Cs) transport in silicon carbide (SiC), the main barrier to the release of fission products. Atomistic simulations provide bulk and grain boundary (GB) Cs diffusivities in SiC, which are used by phase field simulations in the mesoscale code Marmot to determine the temperature, microstructure, and irradiation-dependent Cs diffusivity at the mesoscale in SiC. This approach attributes the different temperature regimes experimentally observed for Cs diffusivities in SiC to a transition from bulk-dominated diffusivity at high temperatures to a GB-dominated regime at low temperatures, providing new insight. The multiscale, mechanistic effective diffusivity is then implemented in the fuel performance code BISON and further validated by comparing Cs release predictions from Advanced Gas Reactor (AGR)-1 and AGR-2 post-irradiation measurements. The new model improves BISON’s predictability. This document also reports improvements made on Ag transport modeling by accounting for different GB types having different diffusivities. Moreover, this report details preliminary efforts to model palladium (Pd) attack of the SiC at the mesoscale using a phase field approach. Pd attack and its impact on accelerated Ag transport remains a misunderstood phenomenon, and we use the model to demonstrate that the formation of lamellae that has been observed in experiments can be explained by the reaction of Pd with SiC to form alternating layers of graphite and Pd 2 Si. This effort aims to improve our understanding of the reaction and eventually provide a model for BISON to account for Pd penetration and its effects on fission product release.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Deciphering the non-linear impact of Al on chemical durability of silicate glass

The role of Al in aluminosilicate glasses remains somewhat a mystery: at low concentrations, it increases the resistance to hydrolysis of the glass, whereas at high concentrations an opposite effect is observed. To understand the origin of the phenomenon on a fundamental atomistic scale, we performed 577 MD simulations and applied potential mean force (PMF) calculations to estimate the activation barriers for hydrolysis and to statistically correlate them with local structural features of the glass. Models of pure silicate and aluminosilicate glasses are constructed and investigated. PMF simulation results are further validated by the experimental measurements and revealed that Al is very easy to dissociate, but it also increases the glass chemical durability through significantly increasing both the strength of Si and network connectivity of the glass. In contrast, at high Al concentration, preferential dissolution of Al weakens the silicate network, which it supposes to strengthen, and so the glass resistance becomes poor. Through PMF calculations, we evaluated the activation barriers for dissociating bonds around Al as 0.49 eV, which is less than a half of the energy to dissociate bonds around Si in pure silicate (1.22 eV) and around Si in aluminosilicate glass (1.34 eV), all these energy differences being statistically significant. Molecular structural level investigation revealed that Si with Al as a second neighbor in the glass network has a significantly higher activation energy for dissociation than Si in pure silicate glass. Furthermore, the proposed approach opens the way to the development of quantitative predictive models of glass durability.

36 MATERIALS SCIENCE↗

The evolution of model Rh/Fe 3 O 4 (001) catalysts in hydrogen environments

Single metal atoms dispersed on oxides are a new emerging class of catalysts owing to their unique electronic and chemical properties. Here, in this study, we have prepared a series of model single-atom catalysts possessing well-characterized Rh sites that include Rh adatoms (Rh ad ), mixed surface layers with octahedrally-coordinated Rh (Rh oct ), as well as metallic Rh clusters and nanoparticles (Rh met ) on Fe 3 O 4 (001). Using X-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM), we investigated the activity of such model systems towards H2 and their stability in reducing environments. Our results show that the atomically dispersed Rhad and Rhoct species do not activate H 2 , which would result in the formation of surface hydroxyls on Fe 3 O 4 (001). In contrast, the presence of Rh met in H 2 results in the formation of hydroxyls and subsequent etching of the Fe 3 O 4 (001) at higher temperatures (≥ 500 K) due to water formation via the Mars-van Krevelen mechanism. Additionally, such surface etching leads to the release of the Rh oct from the surface lattice and their sintering to Rh met . To bridge the material gap between the surface science models and high surface area catalysts, we perform parallel studies on powder Rh/Fe 3 O 4 catalysts. The XPS characterization shows remarkable similarities between these systems. Further, our surface science studies provide an atomistic picture of the behavior of high surface area catalysts in the H 2 atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computed entropy spectra for grain boundary segregation in polycrystals

Abstract Grain boundary solute segregation influences most bulk material properties, and understanding solute thermodynamics at grain boundaries is critical for engineering them. However, the vast grain boundary space in polycrystals is challenging to evaluate due to its size, especially for the intrinsically hard-to-compute segregation excess entropy. Here data science methods are used to generate a database of site-wise grain boundary segregation entropy spectra for 155 dilute binary alloys within the harmonic approximation. The spectral framework allows scale bridging between the calculated atomistic site-wise energy-entropy spectra and macroscopic segregation entropy estimates. The results affirm that macroscopic averaging is not sufficient: a spectral treatment of grain boundary segregation is needed to accurately model bulk temperature dependence of grain boundary solute segregation. The calculated spectral entropy database and thermodynamic framework can be applied for both understanding segregation experiments and alloy design exercises, paving the way to a finite-temperature grain boundary genome.

Chemistry↗

Vacancy and interstitial interactions with crystal/amorphous, metal/covalent interfaces

In this work, we use atomistic simulations to investigate the interaction of vacancies and interstitials with interfaces between a crystalline metal and an amorphous, covalently-bonded solid. We select the gold (Au)/silicon (Si) binary system as a model material and construct interface models along two different facets of crystalline Au and with amorphous Si (a-Si) created at three different quench rates. We compute formation energies of vacancies, self-interstitials, and interstitial impurities as a function of position relative to the interface and find that they have markedly lower values near the interface than in the interior of the adjoining phases. We conclude that crystal/amorphous, metal/covalent interfaces may be as effective at removing radiation-induced point defects as interfaces in polycrystalline metals composites. Moreover, irrespective of interface character, the average formation energies of all point defects at all the Au/a-Si interfaces we investigated are comparable. Thus, unlike in polycrystalline metals, where an interface’s crystallographic character has a marked effect on its interactions with point defects, all interface types in crystal/amorphous, metal/covalent composites may be equally effective at absorbing all radiation-induced defects.

36 MATERIALS SCIENCE↗

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled–coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled–coil hydrogel design. Using Rosetta energy scores and Poisson–Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled–coil proteins while simultaneously exploring five new coiled–coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled–coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled–coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled–coil fiber formation.

36 MATERIALS SCIENCE↗

PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations

We analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter 2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic processes of surface-diffusion-induced abnormal softening in nanoscale metallic crystals

Abstract Ultrahigh surface-to-volume ratio in nanoscale materials, could dramatically facilitate mass transport, leading to surface-mediated diffusion similar to Coble-type creep in polycrystalline materials. Unfortunately, the Coble creep is just a conceptual model, and the associated physical mechanisms of mass transport have never been revealed at atomic scale. Akin to the ambiguities in Coble creep, atomic surface diffusion in nanoscale crystals remains largely unclear, especially when mediating yielding and plastic flow. Here, by using in situ nanomechanical testing under high-resolution transmission electron microscope, we find that the diffusion-assisted dislocation nucleation induces the transition from a normal to an inverse Hall-Petch-like relation of the strength-size dependence and the surface-creep leads to the abnormal softening in flow stress with the reduction in size of nanoscale silver, contrary to the classical “alternating dislocation starvation” behavior in nanoscale platinum. This work provides insights into the atomic-scale mechanisms of diffusion-mediated deformation in nanoscale materials, and impact on the design for ultrasmall-sized nanomechanical devices.

36 MATERIALS SCIENCE↗

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗

Combining Experimental and Theoretical Techniques to Gain an Atomic Level Understanding of the Defect Binding Mechanism in Hard Carbon Anodes for Sodium Ion Batteries

Sodium ion batteries (NIBs) are an attractive alternative to lithium–ion batteries in applications that require large–scale energy storage due to sodium's high natural abundance and low cost. Hard carbon (HC) is the most promising anode material for NIBs; however, there is a knowledge gap in the understanding of the sodium binding mechanism that prevents a rational design of HC. This study tunes sucrose–derived HC via synthesis temperature then evaluates the structural, physical, and electrochemical properties. Neutron total scattering is used to generate structural models by fitting pair distribution functions (PDF) with a combination of molecular dynamics and reverse Monte Carlo methods. From this model, the number and type of structural features are identified, quantified, and correlated to the galvanostatic charge/discharge. A method of PDF “fingerprinting” binding sites using Na probe atoms is developed and analyzing these PDFs reveals an atomistic view of ion binding sites responsible for “defect” storage mechanisms. Combining these techniques results in an atomic–level study that provides a big picture of the Na–binding mechanism in NIBs, which allows for more precise tuning of the structure–property relationships in the future. Finally, the methodologies developed will also enable new strategies for the analysis of amorphous functional materials.

25 ENERGY STORAGE↗

Chromium segregation-induced oxide evolution in Ni-10Cr alloys during high-temperature oxidation

The oxidation behavior of a Ni-10(wt%)Cr alloy under high-temperature O 2 conditions is investigated using transmission electron microscopy and first-principles calculations. Results reveal that chromium segregation plays a central role in driving the evolution of complex oxide phase structures during oxidation. At low Cr concentrations, Cr preferentially segregates to NiO grain boundaries or internal pores, substituting for Ni atoms and forming Ni(Cr)O solid solutions. As Cr content increases, enhanced diffusion promotes Cr penetration into the NiO lattice, leading to the formation of multiphase oxide structures. First-principles modeling corroborates these findings: at low Cr concentrations, Cr atoms favor surface and grain-boundary segregation, while higher concentrations lead to Cr aggregation within the NiO bulk. Furthermore, the integrated experimental-theoretical approach provides atomistic insights into Cr-mediated mass transport mechanisms during alloy oxidation and offers valuable guidance for controlling oxide growth kinetics and phase stability in Ni-Cr alloys, with implications for improving oxidation resistance in high-temperature structural applications.

36 MATERIALS SCIENCE↗

A linked-scale coupled model of mass erosion and redistribution in plasma-exposed micro-foam surfaces

Surface evolution due to exposure to harsh environments is of importance in many scientific and technological applications. In plasma-exposed materials, the surface receives charged particles from the plasma, leading to a series of processes that drive the system far from equilibrium and may lead to the severe deterioration of the surface properties. Although surface morphological changes are driven by atomic collisions taking place over picoseconds and nanometers, these processes result in mass loss and redistribution of matter over much larger length and time scales. This necessitates a multi-scale approach capable of capturing the range of processes linking primary atomic collision events with engineering-level surface geometry changes. In this paper, we develop a computational model to simulate the morphological evolution and effective erosion rate of micro-architected tungsten foams during low-energy plasma ion bombardment. Furthermore, the model acts on several length scales, with the energy and angular dependence of the sputtering yield of flat tungsten surfaces determined using the SRIM code based on the binary collision approximation. This information is introduced into a low-fluence, short-term Monte Carlo raytracing model, and further into a high-fluence, long-term particle transport model. In the latter, material particles representing billions of atoms are described in a digitized 3-D representation of the foam structure from X-ray tomography data, and are sputtered off and redeposited using the atomistic information. We show that the redeposition of sputtered atoms leads to partial self-healing in the bottom layers with a sharp reduction in the sputtering coefficient of low density foams, roughly 25% of the solid W value. This is in qualitative agreement with recent experiments on low porosity W structures. At high fluence, the foam structure degrades considerably as there are fewer ligaments available to recapture sputtered atoms and, consequently, the sputtering rate increases again.

36 MATERIALS SCIENCE↗

Ion and Water Dynamics in the Transition from Dry to Wet Conditions in Salt-Doped PEG

The influence of the water content on ion and water transport mechanisms in polymer membranes under low to moderate hydration conditions remains poorly understood. In this study, we combine ion and water diffusivity (PFG-NMR) measurements with atomistic molecular dynamics simulations to better understand transport processes in hydrated salt-doped poly(ethylene glycol). Above the water percolation threshold, the experimental and simulated diffusivities are in good agreement with the free volume transport models. At low hydration levels, unlike dry systems, ion diffusion cannot be described by polymer segmental dynamics alone. We rationalize such observations by the interplay between ion–water and ion–polymer solvation of cations and between ion–water and cation–anion interactions for anions. Further, we demonstrate that a two-state model combining ion–water solvation and free volume transport can describe water dynamics across the entire hydration range of interest. Here, our findings provide a more encompassing analysis of ion and water transport in hydrated polyelectrolytes, specifically in the low hydration regime.

36 MATERIALS SCIENCE↗

Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

The identity of metal ions surrounding DNA is key to its biological function and materials applications. In this work, we compare atomistic molecular dynamics simulations of double strand DNA (dsDNA) with four alkaline earth metal ions (Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ ) to elucidate the physical interactions that govern DNA–ion binding. Simulations accurately model the ion–phosphate distance of Mg 2+ and reproduce ion counting experiments for Ca 2+ , Sr 2+ , and Ba 2+ . Our analysis shows that alkaline earth metal ions prefer to bind at the phosphate backbone compared to the major groove and negligible binding occurs in the minor groove. Larger alkaline earth metal ions with variable first solvation shells (Ca 2+ , Sr 2+ , and Ba 2+ ) show both direct and indirect binding, where indirect binding increases with ion size. Mg 2+ does not fit this trend because the strength of its first solvation shell predicts indirect binding only. Ions bound to the phosphate backbone form fewer contacts per ion compared to the major groove. Within the major groove, metal ions preferentially bind to guanine–cystosine base pairs and form simultaneous contacts with the N7 and O6 atoms of guanine. Overall, we find that the interplay among ion size, DNA–ion interaction, and the size and flexibility of the first solvation shell are key to predicting how alkaline earth metal ions interact with DNA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiscale Modeling of Vinyl-Addition Polynorbornenes: The Effect of Stereochemistry

Vinyl-addition polynorbornenes are candidates for designing high-performance polymers due to unique characteristics, which include a high glass transition temperature associated with a rigid backbone. Recent studies have established that the processability and properties of these polymers can be fine-tuned by using targeted substitutions. However, synthesis with different catalysts results in materials with distinct properties, potentially due to the presence of various stereoisomers that are difficult to quantify experimentally. Herein, we develop all-atom models of polynorbornene oligomers based on classical force fields and density functional theory. To establish the relationship between chemical architecture, chain conformations, and melt structure, we perform detailed molecular dynamics simulations with the fine-tuned atomistic force field and propose simpler coarse-grained descriptions to address the high molecular weight limit. All-atom simulations of oligomers suggest high glass transition temperatures in the range of 550–600 K. In the melt state (800 K), meso chains form highly rigid extended coils (C∞≈11) with amorphous structural characteristics similar to the X-ray diffraction data observed in the literature. In contrast, simulations with racemo chains predict highly helical tubular chain conformations that could promote assembly into crystalline structures.

Polymer Science↗