Search

Electrochemical systems possess a considerable part of modern technologies, such as the operation of rechargeable batteries and the fabrication of electronic components, which are explored both experimentally and computationally. The largest gap between the experimental observations and atomic-level simulations is their orders-of-magnitude scale difference. While the largest computationally affordable scale of the atomic-level computations is ∼ ns and ∼ n m , the smallest reachable scale in the typical experiments, using very high-precision devices, is ∼ s and ∼ μ m. In order to close this gap and correlate the studies in the two scales, we establish an equivalent simulation setup for the given general experiment, which excludes the microstructure effects (i.e., solid–electrolyte interface), using the coarse-grained framework. The developed equivalent paradigm constitutes the adjusted values for the equivalent length scale (i.e., l E Q ), diffusivity (i.e., D E Q ), and voltage (i.e., V E Q ). The time scale for the formation and relaxation of the concentration gradients in the vicinity of the electrode matches for both smaller scale (i.e., atomistic) equivalent simulations and the larger scale (i.e., continuum) experiments and could be utilized for exploring the cluster-level inter-ionic events that occur during the extended time periods. The developed model could offer insights for forecasting experiment dynamics and estimating the transition period to the steady-state regime of operation. [ABSTRACT FROM AUTHOR]

From molecular dynamics (MD) simulations of melt-quenching and thermal aging procedures in pure Ag, Cu, Ag-Cu binary alloys, and Cu-Zr binary alloys, we have identified two distinct amorphous phases for a metastable undercooled liquid: the homogeneous L-phase with low shear rigidity and the heterogenous G-phase with much higher shear rigidity and a heterogeneity length scale Λ. Here, we examine two-phase equilibration studies showing that the G-phase melts to form the L-phase above ~1,000 K, which then transforms to form the crystal (X) phase; however, below the melting point of the G-Phase (~990 K), the X-and G-phases do not transform into each other. We suggest the presence of a G-phase is likely responsible for embrittlement often observed in metallic glasses. We also consider how mechanical milling or irradiation-induced defect accumulation in the crystalline metallic alloy triggers a crystal-to-glass transition. We use the Cu2Zr system as a model to investigate random interchange of Zr and Cu atoms at room temperature leading to a transition from a crystalline Laves-phase to an L-glass through formation and growth of amorphous regions and destabilization of the crystal. During relaxation of the nonequilibrium structures by annealing, the configurations either reverted to the crystalline phase or evolve to a heterogeneous G-phase equivalent to the G-phase formed during thermal quenching and aging of the melt. Athermal defect accumulation in the G-phase at low temperature led to a transition back to the L-phase. Our findings show how athermal disordering drives transitions among the X-, L-, and G-phases. [ABSTRACT FROM AUTHOR]

Accurate Force Fields (FFs) are essential for Molecular Dynamics (MD) simulations of the dynamics of realistic materials in terms of atomic-level interactions. The FF parameters of short-range valence interactions can be derived through Quantum Mechanical (QM) calculations on model systems practical for QM (<300 atoms). Similarly, the dynamic electrostatic interactions can be described with methods such as QEq or PQEq that allow charges and polarization to adjust dynamically. However, accurately extracting long-range van der Waals (vdW) interactions from QM calculations poses challenges due to the absence of a definitive method to distinguish between the different energetic components of electrostatics, polarization, vdW, hydrogen bonding, and valence interactions. To do this we use the Perdew–Burke–Ernzerhof flavor of Density Functional Theory, including empirical D3 vdW corrections, to predict the Equation of State for each element (keeping any covalent bonds fixed), from which we obtain the two-body vdW nonbond potential. Here, we extend these calculations to include non-bonded parameters for the N and O columns of the periodic table so that we now describe columns 15 (N), 16 (O), 17 (F), and 18 (Ne) of the periodic table. For these 20 elements, we find that the two-body vdW potentials can all be mapped to a single universal two-body curve, with just three scaling parameters: Re, De, and L. We refer to this as the Universal NonBond (UNB) potential. We expect this to be useful for new MD simulations and a helpful starting point to obtain UNB parameters for the remainder of the periodic table. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) regulate multiple cellular responses and represent highly successful therapeutic targets. The mechanisms by which agonists activate the G protein are unclear for many GPCR families, including the bitter taste receptors (TAS2Rs). We ascertained TAS2R5 properties by live cell-based functional assays, direct binding affinity measurements using optical resonators, and atomistic molecular dynamics simulations. We focus on three agonists that exhibit a wide range of signal transduction in cells despite comparable ligand–receptor binding energies derived from direct experiment and computation. Metadynamics simulations revealed that the critical barrier to activation is ligand-induced opening of the G protein between the α-helical (AH) and Ras-like domains of Gα subunit from a precoupled TAS2R5-G protein state to the fully activated state. A moderate agonist opens the AH-Ras cleft from 22 Å to 31 Å with an energy gain of −4.8 kcal mol−1, making GDP water-exposed for signaling. A high-potency agonist had an energy gain of −11.1 kcal mol−1. The low-potency agonist is also exothermic for Gα opening, but with an energy gain of only −1.4 kcal mol−1. This demonstrates that TAS2R5 agonist-bound functional potencies are derived from energy gains in the transition from a precoupled complex at the level of Gα opening. Our experimental and computational study provides insights into the activation mechanism of signal transduction that provide a basis for rational design of new drugs. [ABSTRACT FROM AUTHOR]

Dual-atom catalysts (DACs) are promising for the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER). However, two vital factors, namely curvature effects and dissociative mechanisms, are often overlooked in DAC studies, which may miss the possibility of finding the most promising candidates. To provide a mechanistic understanding of the role of these two essential factors in effective electrocatalyst design, we explore systematically the catalytic potential of MM′N6-DACs supported on graphene and single-walled carbon nanotubes (CNTs) with two diameters within both dissociative and associative mechanisms where M and M′ represent Fe, Co, Ni, Cu, Ru, Rh, Pd, or Pt metals. More than ten DACs have shown high activity with overpotential lower than that of common commercial catalysts, notably non-precious CoCuN6-DACs exhibiting extremely low ORR overpotential of 0.09 VRHE and low OER overpotential of 0.10 VRHE, and bifunctional ORR and OER overpotential of 0.22 VRHE. We find that CNT substrates strengthen the adsorption of intermediates on CoCuN6-DACs compared to graphene substrates, due to increased electronic density of states of metal atoms near the Fermi level. The dissociative mechanism circumvents the constraints of scaling relationship in the associative mechanism, so that several DACs favoring the dissociative mechanism exhibit substantially improved activity, with lower overpotential than the theoretical minimum of the associative mechanism. These results not only shed light on designing high-performance catalysts for the ORR and OER but also deepen the theoretical understanding of the catalytic mechanism and curvature effects on DACs. [ABSTRACT FROM AUTHOR]