Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms.

Optimization of thermal transport across the interface of two different materials is critical to micro-/nanoscale electronic, photonic, and phononic devices. Although several examples of compositional intermixing at the interfaces having a positive effect on interfacial thermal conductance (ITC) have been reported, an optimum arrangement has not yet been determined because of the large number of potential atomic configurations and the significant computational cost of evaluation. On the other hand, computation-driven materials design efforts are rising in popularity and importance. Yet, the scalability and transferability of machine learning models remain as challenges in creating a complete pipeline for the simulation and analysis of large molecular systems. In this work we present a scalable Bayesian optimization framework, which leverages dynamic spawning of jobs through the Message Passing Interface (MPI) to run multiple parallel molecular dynamics simulations within a parent MPI job to optimize heat transfer at the silicon and aluminum (Si/Al) interface. We found a maximum of 50% increase in the ITC when introducing a two-layer intermixed region that consists of a higher percentage of Si. Because of the random nature of the intermixing, the magnitude of increase in the ITC varies. We observed that both homogeneity/heterogeneity of the intermixing and the intrinsic stochastic nature of molecular dynamics simulations account for the variance in ITC.

In situ imaging of amorphous intermediates during brucite carbonation in supercritical CO2.

Progress in understanding crystallization pathways depends on the ability to unravel relationships between intermediates and final crystalline products at the nanoscale, which is a particular challenge at elevated pressure and temperature. Here we exploit a high-pressure atomic force microscope to directly visualize brucite carbonation in water-bearing supercritical carbon dioxide (scCO2) at 90 bar and 50 °C. On introduction of water-saturated scCO2, in situ visualization revealed initial dissolution followed by nanoparticle nucleation consistent with amorphous magnesium carbonate (AMC) on the surface. This is followed by growth of nesquehonite (MgCO3·3H2O) crystallites. In situ imaging provided direct evidence that the AMC intermediate acts as a seed for crystallization of nesquehonite. In situ infrared and thermogravimetric-mass spectrometry indicate that the stoichiometry of AMC is MgCO3·xH2O (x = 0.5-1.0), while its structure is indicated to be hydromagnesite-like according to density functional theory and X-ray pair distribution function analysis. Our findings thus provide insight for understanding the stability, lifetime and role of amorphous intermediates in natural and synthetic systems.

Ab initio thermodynamics reveals the nanocomposite structure of ferrihydrite.

Ferrihydrite is a poorly crystalline iron oxyhydroxide nanomineral that serves a critical role as the most bioavailable form of ferric iron for living systems. However, its atomic structure and composition remain unclear due in part to ambiguities in interpretation of X-ray scattering results. Prevailing models so far have not considered the prospect that at the level of individual nanoparticles multiple X-ray indistinguishable phases could coexist. Using ab initio thermodynamics we show that ferrihydrite is likely a nanocomposite of distinct structure types whose distribution depends on particle size, temperature, and hydration. Nanoparticles of two contrasting single-phase ferrihydrite models of Michel and Manceau are here shown to be thermodynamically equivalent across a wide range of temperature and pressure conditions despite differences in their structural water content. Higher temperature and water pressure favor the formation of the former, while lower temperature and water pressure favor the latter. For aqueous suspensions at ambient conditions, their coexistence is maximal for particle sizes up to 12 nm. The predictions inform and help resolve different observations in various experiments.

Thermodynamics of Metal Carbonates and Bicarbonates and Their Hydrates for Mg, Ca, Fe, and Cd Relevant to Mineral Energetics.

The heats of formation of the carbonate, bicarbonate, and bicarbonate/hydroxide metal complexes, including hydrates of Mg2+, Ca2+, Fe2+, and Cd2+, and the oxides, dichlorides, and dihydroxides are predicted from atomization energies using correlated molecular orbital theory at the CCSD(T) level extrapolated to the complete basis set limit following the Feller-Peterson-Dixon (FPD) approach. Using the calculated gas phase values and the available experimental solid-state values, we predicted the cohesive energies of selective minerals. The gas phase decomposition energies of MO, CO2, and H2O follow the order Mg ≈ Ca > Cd ≈ Fe and correlate with the hardness of the metal +2 ions. Gas phase hydration energies show that the order is Mg > Fe > Ca ≈ Cd. There are a number of bulk hydrated Mg and Ca complexes that occur as minerals but there are few if any for Fe and Cd, suggesting that a number of factors are important in determining the stability of the bulk mineral hydrates. The FPD heats of formation were used to benchmark a range of density functional theory exchange-correlation functionals, including those commonly used in solid-state mineral calculations. None of the functionals provided chemical accuracy agreement (±1 kcal/mol) with the FPD results. The best agreement to the FPD results is predicted for ωB97X and ωB97X-D functionals with an average unsigned error of 10 kcal/mol. The worst functionals are PW91, BP86, and PBE with average unsigned errors of 32-36 kcal/mol.

Quantifying the Impact of Magnesium on the Stability and Water Binding Energy of Hydrated Calcium Carbonates by Ab Initio Thermodynamics.

Determining conditions that drive carbonate formation is important for many phenomena such as paleoindicators for mineral deposition, the carbon cycle, biomineralization, and industrial applications such as scale inhibition and manufacturing of cement and concrete. Magnesium and incorporated water have been observed to play critical roles in nonclassical crystallization pathways of calcium carbonate, the dominant carbonate found in nature, through promoting formation of low energy metastable intermediates such as monohydrocalcite (CaCO3·H2O), ikaite (CaCO3·6H2O), and amorphous calcium carbonate (CaCO3·H2O). The impact of Mg on the thermodynamics and water binding ability of these hydrated intermediates is challenging to measure and is not understood at the molecular level. In this work, density-functional theory and ab initio thermodynamics are used to quantify the impact of Mg on structure, thermodynamics, and water binding energies of the crystalline hydrated Ca carbonates as a function of temperature in aqueous and ultrahigh vacuum conditions, as well as CO2-rich environments relevant to carbon sequestration. For monohydrocalcite, Mg incorporation is found to destabilize the structure despite a dramatic increase in the water binding energy, thus confirming that Mg promotes monohydrocalcite formation kinetically rather than thermodynamically. For ikaite, however, Mg promotes its formation both kinetically and thermodynamically, expanding the stability region for ikaite in cold water.

Oxidative Corrosion of the UO2 (001) Surface by Nonclassical Diffusion.

Uranium oxide is central to every stage of the nuclear fuel cycle, from mining through fuel fabrication and use, to waste disposal and environmental cleanup. Its chemical and mechanical stability are intricately linked to the concentration of interstitial O atoms within the structure and the oxidation state of U. We have previously shown that, during corrosion of the UO2 (111) surface under either 1 atm of O2 gas or oxygenated water at room temperature, oxygen interstitials diffuse into the substrate to form a superlattice with three-layer periodicity. In the current study, we present results from surface X-ray scattering that reveal the structure of the oxygen diffusion profile beneath the (001) surface. The first few layers below the surface oscillate strongly in their surface-normal lattice parameters, suggesting preferential interstitial occupation of every other layer below the surface, which is geometrically consistent with the interstitial network that forms below the oxidized (111) surface. Deeper layers are heavily contracted and indicate that the oxidation front penetrates ∼52 Šbelow the (001) surface after 21 days of dry O2 gas exposure at ambient pressure and temperature. X-ray photoelectron spectroscopy indicates U is present as U(IV), U(V), and U(VI).

Quantifying small changes in uranium oxidation states using XPS of a shallow core level.

The U 4f line is commonly used to determine uranium oxidation states with X-ray photoelectron spectroscopy (XPS). In contrast, the XPS of the shallow core-levels of uranium are rarely recorded. Nonetheless, theory has shown that the U 5d (and 5p) multiplet structure is very sensitive to oxidation state. In this contribution we extracted the U(iv) and U(v) 5d XPS peak shapes from near stoichiometric and oxidized UO2 single crystal samples, respectively, where the oxidation state of U was constrained by fitting the 4f line. The empirically extracted 5d spectra were similar to the theoretically determined multiplet structures and were used, along with the relatively simple U(vi) component that was constrained by theory, to determine the oxidation states of UO2+x samples. The results showed a very strong correlation between oxidation states determined by the 5d and 4f line and suggested that the 5d might be more sensitive to minor amounts of oxidation than the 4f. Limitations of the methodology, as well as advantages of using the 5d relative to the 4f line are discussed.

Ab Initio Thermodynamics and the Relationship between Octahedral Distortion, Lattice Structure, and Proton Substitution Defects in Malachite/Rosasite Group Endmember Pokrovskite Mg2CO3(OH)2.

Divalent metal hydroxycarbonates with M2CO3(OH)2 stoichiometry are widely used in industry and are abundant in nature as the malachite/rosasite group of minerals. Essential to their performance as catalytic precursors and in nanoelectronics, these materials and minerals exhibit a high degree of cation ordering in mixed metal systems due to differences in distortion of the octahedral metal sites. Density-functional theory (DFT) calculations on pokrovskite Mg2CO3(OH)2 in the rosasite structure and Mg analogues of monoclinic and orthorhombic forms of malachite determine that the octahedral sites are innately distorted, and that d9 Cu(II) Jahn-Teller distortion accommodates this distortion rather than causes it, leading to the significant preference of Cu for the type I octahedral sites. This distortion also leads to a high propensity for formation of cation vacancies charge balanced by proton substitution. Ab initio thermodynamics is used to determine that there are conditions under which proton substitution defects are slightly more stable than the stoichiometric structure, consistent with the widespread observation of such defects in pokrovskite in nature. Pokrovskite itself is most likely to form under CO2-rich/low water conditions, particularly those utilizing supercritical CO2 for carbon sequestration and is sufficiently thermodynamically stable to trap CO2 under geological conditions. Low temperature and high water concentration promotes the formation of proton substitution defects, which has implications for synthesis of any material where octahedral strain may be relieved by proton substitution defects.

UO(2) Oxidative Corrosion by Nonclassical Diffusion.

Using x-ray scattering, spectroscopy, and density-functional theory, we determine the structure of the oxidation front when a UO(2) (111) surface is exposed to oxygen at ambient conditions. In contrast to classical diffusion and previously reported bulk UO(2+x) structures, we find oxygen interstitials order into a nanoscale superlattice with three-layer periodicity and uranium in three oxidation states: IV, V, and VI. This oscillatory diffusion profile is driven by the nature of the electron transfer process, and has implications for understanding the initial stages of oxidative corrosion in materials at the atomistic level.

Ab initio thermodynamic model for magnesium carbonates and hydrates.

An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

Structural basis of pathway-dependent force profiles in stretched DNA.

Understanding the mechanical properties that determine the flexibility of DNA is important, as DNA must bend and/or stretch in order to function biologically. Recent single-molecule experiments have shown that above a certain loading rate double-stranded DNA is more stable when stretched from the 3' termini than when stretched from the 5' termini. Unfortunately these experiments cannot provide insight into the structural basis for this behavior. We have used molecular dynamics simulations combined with umbrella sampling to study the stability and structural changes of a 30 bp double-stranded DNA oligomer during stretching from either the 3' termini or the 5' termini. At extensions greater than 1.7x the 3' stretched structure is more stable than the 5' stretched structure due to retention of twice the number (80%) of native hydrogen bonds between base pairs and a higher degree of base stacking. This difference results from greater dissipation of the stretch force via conformational flexibility of the phosphate backbone when pulled from the 3' ends, whereas in the 5' stretch the force is borne more directly by the base pair hydrogen bonds leading to rupture. In addition, stretching from the 5' end produces a greater widening of the major groove that increases solvent exposure and hydrolysis of the base pair hydrogen bonds. These results demonstrate that 3' stretching and 5' stretching in DNA are fundamentally different processes.

Electronically induced atom motion in engineered CoCun nanostructures.

We have measured the quantum yield for exciting the motion of a single Co atom in CoCu(n) linear molecules constructed on a Cu(111) surface. The Co atom switched between two lattice positions during electron excitation from the tip of a scanning tunneling microscope. The tip location with highest probability for inducing motion was consistent with the position of an active state identified through electronic structure calculations. Atom motion within the molecule decreased with increased molecular length and reflected the corresponding variation in electronic structure.