Equilibrium Ab Research Articles

Viscosity in water from first-principles and deep-neural-network simulations

We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics (AIMD), based on density-functional theory (DFT). In order to cope with the long simulation times necessary to achieve an acceptable statistical accuracy, our ab initio approach is enhanced with deep-neural-network potentials (NNP). This approach is first validated against AIMD results, obtained by using the Perdew–Burke–Ernzerhof (PBE) exchange-correlation functional and paying careful attention to crucial, yet often overlooked, aspects of the statistical data analysis. Then, we train a second NNP to a dataset generated from the Strongly Constrained and Appropriately Normed (SCAN) functional. Once the error resulting from the imperfect prediction of the melting line is offset by referring the simulated temperature to the theoretical melting one, our SCAN predictions of the shear viscosity of water are in very good agreement with experiments.

Invariance principles in the theory and computation of transport coefficients

In this work, we elaborate on two recently discovered invariance principles, according to which transport coefficients are, to a large extent, independent of the microscopic definition of the densities and currents of the conserved quantities being transported (energy, momentum, mass, charge). The first such principle, gauge invariance, allows one to define a quantum adiabatic energy current from density-functional theory, from which the heat conductivity can be uniquely defined and computed using equilibrium ab initio molecular dynamics. When combined with a novel topological definition of atomic oxidation states, gauge invariance also sheds new light onto the mechanisms of charge transport in ionic conductors. The second principle, convective invariance, allows one to extend the analysis to multi-component systems. These invariance principles can be combined with new spectral analysis methods for the current time series to be fed into the Green–Kubo formula to obtain accurate estimates of transport coefficients from relatively short molecular dynamics simulations.Graphic abstract

QEHeat: An open-source energy flux calculator for the computation of heat-transport coefficients from first principles

We give a detailed presentation of the theory and numerical implementation of an expression for the adiabatic energy flux in extended systems, derived from density-functional theory. This expression can be used to estimate the heat conductivity from equilibrium ab initio molecular dynamics, using the Green-Kubo linear response theory of transport coefficients. Our expression is implemented in an open-source component of the Quantum ESPRESSO suite of computer codes for quantum mechanical materials modeling, which is being made publicly available. Program summaryProgram title:QEHeatCPC Library link to program files:https://doi.org/10.17632/c6wxkvy4z3.1Licensing provisions: GPLv3Programming language: FortranNature of problem: The computation of thermal transport coefficients via equilibrium molecular dynamics and the Green-Kubo theory of linear response requires the definition of a heat-flux describing the instantaneous flow of energy. When considering predictive first-principles methods, a definition of the heat-flux compatible with density-functional theory is required [1]. The evaluation of such a heat flux requires an extension of state-of-the-art atomic simulation codes.Solution method: This work describes in detail the numerical implementation of the adiabatic energy current derived in Refs. [1,2] and makes it available to the users of the Quantum ESPRESSO suite of computer codes [3]. Used in conjunction with the cp.x code, to perform Car-Parrinello ab initio molecular dynamics, and the SPORTRAN post-processing tool for data analysis [4–6], the program allows to estimate heat transport coefficients in extended systems entirely from first principles. The new code provides as well to developers a modular and easily extendable framework to evaluate time derivatives of electronic properties (e.g. electronic densities or potentials) via a finite difference approach.

Diffusion of lithium ions in Lithium-argyrodite solid-state electrolytes

The use of solid-state electrolytes to provide safer, next-generation rechargeable batteries is becoming more feasible as materials with greater stability and higher ionic diffusion coefficients are designed. However, accurate determination of diffusion coefficients in solids is problematic and reliable calculations are highly sought-after to understand how their structure can be modified to improve their performance. In this paper we compare diffusion coefficients calculated using nonequilibrium and equilibrium ab initio molecular dynamics simulations for highly diffusive solid-state electrolytes, to demonstrate the accuracy that can be obtained. Moreover, we show that ab initio nonequilibrium molecular dynamics can be used to determine diffusion coefficients when the diffusion is too slow for it to be feasible to obtain them using ab initio equilibrium simulations. Thereby, using ab initio nonequilibrium molecular dynamics simulations we are able to obtain accurate estimates of the diffusion coefficients of Li ions in Li6PS5Cl and Li5PS4Cl2, two promising electrolytes for all-solid-state batteries. Furthermore, these calculations show that the diffusion coefficient of lithium ions in Li5PS4Cl2 is higher than many other potential all-solid-state electrolytes, making it promising for future technologies. The reasons for variation in conductivities determined using computational and experimental methods are discussed. It is demonstrated that small degrees of disorder and vacancies can result in orders of magnitude differences in diffusivities of Li ions in Li6PS5Cl, and these factors are likely to contribute to inconsistencies observed in experimentally reported values. Notably, the introduction of Li-vacancies and disorder can enhance the ionic conductivity of Li6PS5Cl.

Heat and charge transport in H2O at ice-giant conditions from ab initio molecular dynamics simulations

The impact of the inner structure and thermal history of planets on their observable features, such as luminosity or magnetic field, crucially depends on the poorly known heat and charge transport properties of their internal layers. The thermal and electric conductivities of different phases of water (liquid, solid, and super-ionic) occurring in the interior of ice giant planets, such as Uranus or Neptune, are evaluated from equilibrium ab initio molecular dynamics, leveraging recent progresses in the theory and data analysis of transport in extended systems. The implications of our findings on the evolution models of the ice giants are briefly discussed.

Giant Rashba spin splitting induced by heavy element adsorption at germanene

Density functional theory calculations have been performed to investigate the structural and electronic properties of the Pb@germanene adsorption system. By employing equilibrium ab initio atomistic thermodynamics and phonon spectra analysis a dynamically stable configuration have been found. It is a (1 × 1) structure with coverage of 1 monolayer [(1×1)′@germanene]. The surface configuration shares some structural similarities with the sTable (1 × 1) phase of Pb@Ge(111), however, it favors a different adsorption site, and facilitates more Pb–Ge bonds per adsorbed atom. This results in (1×1)′@germanene having lower surface free energy than its Ge(111) counterpart. The electronics have been investigate using both GGA-type PBE and hybrid HSE functionals in order to ensure the accuracy. In both cases the system is a metal. Strong spin-orbit interaction of electrons in Pb facilitates a giant spin splitting of metallic bands up to 646 meV at the Fermi level, which makes the system an interesting platform for two-dimensional spintronics.

M35 USING LONGITUDINAL DATA TO REFINE MAJOR DEPRESSIVE DISORDER CASE AND CONTROL STATUS INCREASES THE PRECISION OF POLYGENIC RISK SCORES

Density functional theory calculations have been performed to investigate the structural and electronic properties of the [email protected] adsorption system. By employing equilibrium ab initio atomistic thermodynamics and phonon spectra analysis a dynamically stable configuration have been found. It is a (1 × 1) structure with coverage of 1 monolayer [(1×1)′@germanene]. The surface configuration shares some structural similarities with the sTable (1 × 1) phase of [email protected](1 1 1), however, it favors a different adsorption site, and facilitates more Pb–Ge bonds per adsorbed atom. This results in (1×1)′@germanene having lower surface free energy than its Ge(1 1 1) counterpart. The electronics have been investigate using both GGA-type PBE and hybrid HSE functionals in order to ensure the accuracy. In both cases the system is a metal. Strong spin-orbit interaction of electrons in Pb facilitates a giant spin splitting of metallic bands up to 646 meV at the Fermi level, which makes the system an interesting platform for two-dimensional spintronics.

AbInitio Green-Kubo Approach for the Thermal Conductivity of Solids.

We herein present a first-principles formulation of the Green-Kubo method that allows the accurate assessment of the phonon thermal conductivity of solid semiconductors and insulators in equilibrium abinitio molecular dynamics calculations. Using the virial for the nuclei, we propose a unique abinitio definition of the heat flux. Accurate size and time convergence are achieved within moderate computational effort by a robust, asymptotically exact extrapolation scheme. We demonstrate the capabilities of the technique by investigating the thermal conductivity of extreme high and low heat conducting materials, namely, Si (diamond structure) and tetragonal ZrO_{2}.

Ionic conductivity in Sm-doped ceria from first-principles non-equilibrium molecular dynamics

Sm-doped ceria is a prospective electrolyte material for intermediate-temperature solid-oxide fuel cells (IT-SOFC). Equilibrium ab initio molecular dynamics (AIMD) studies of oxygen ion diffusion in this material are currently impractical due to the rareness of diffusive events on the accessible timescale. To overcome this issue we have performed ab initio non-equilibrium molecular dynamics calculations of Sm-doped ceria using the color-diffusion algorithm. Applying an external force field we have been able to increase the frequency of diffusive events over the simulation time, while keeping the physical mechanism of diffusion intact. We have investigated the temperature dependence of the maximum strength of the applied external field that could be used while maintaining the response of the system in a linear regime. This allows one to obtain the diffusivity at zero field. The bulk ionic conductivity has been calculated and found to match the experimental data well. We have also compared the description of the diffusion process by our method to previous findings and show that the migration mechanism and site preference of oxygen vacancies with respect to the Sm dopants is well reproduced.

Dynamical Properties of Hydrogen Sulphide Motion in its Clathrate Hydrate from Ab Initio and Classical Isobaric−Isothermal Molecular Dynamics

Equilibrium ab initio (AI) and classical constant pressure-constant temperature molecular dynamics (MD) simulations have been performed to investigate the dynamical properties in (type I) hydrogen sulphide hydrate at 150 and 300 K and 1 bar, and also lower temperatures, with particular scrutiny of guest motion. The rattling motions of the guests in the large and small cavities were around 45 and 75-80 cm(-1), respectively, from AIMD, with the corresponding classical MD modes being 10-12 cm(-1) less at 150 K and around 5 cm(-1) lower at 300 K. The rattling motion in the small cavity overlapped somewhat with the translational motion of the host lattice (with modes at circa 85 and 110 cm(-1)), due in part to a smaller cage radius and more frequent occurrences of guest-host hydrogen bonding leading to greater coupling in the motion. The experimentally determined H-S stretch and H-S-H bending frequencies, in the vicinity of 2550-2620 and 1175 cm(-1) [H.R. Richardson et al., J. Chem. Phys.1985, 83, 4387] were reproduced successfully in the AIMD simulations. Consideration of Kubic harmonics for the guest molecules from AIMD revealed that a preferred orientation of the dipole-vector (or C(2)-axis) exists at 150 K vis--vis the [100] cube axis in both the small and large cavities, but is markedly more significant for the small cavity, while there is no preferred orientation at 300 K. In comparison, classical MD did not reveal any preferred orientation at either temperature, or at 75 K (closer to the AIMD simulation at 150 K vis-à-vis that approach's estimated melting point). Probing rotational dynamics of the guests reinforced this temperature effect, revealing more rapid rotational time scales at 300 K with faster decay times of dipole-vector (C(2)) and H-H-vector (C(2)(y)) being similar for each cage, at around 0.25 and 0.2 ps, respectively, versus approximately 0.45 and 0.5 ps (large) and 0.8 ps (small) at 150 K. It was found that the origin of the observed preferred orientations, especially in the small cages, at 150 K via AIMD was attributable to optimization of the dipolar interaction between the guest and outward-pointing water dipoles in the cavity, with guests "flitting" rotationally between various such configurations, forming occasionally hydrogen bonds with the host molecules.

An equilibrium ab initio atomistic thermodynamics study of chlorine adsorption on the Cu(001) surface

The effect of chlorine (Cl) chemisorption on the energetics and atomic structure of the Cu(001) surface over a wide range of chlorine pressures and temperatures has been studied using equilibrium ab initio atomistic thermodynamics to elucidate the formation of cuprous chloride (CuCl) as part of the Deacon reaction on copper metal. The calculated surface free energies show that the 1/2 monolayer (ML) c(2 × 2)-Cl phase with chlorine atoms adsorbed at the hollow sites is the most stable structure for a wide range of Cl chemical potential, in agreement with experimental observations. It is also found that at very low pressure and exposure, but elevated temperature, the 1/9 ML and 1/4 ML phases become the most stable. By contrast, a high coverage of Cl does not lead to thermodynamically stable geometries. The subsurface adsorption of Cl atoms, however, dramatically increases the stability of the 1 ML and 2 ML adsorption configurations providing a possible pathway for the formation of the bulk-chloride surface phases in the kinetic regime.

Quantum versus classical electron transfer energy as reaction coordinate for the aqueous Ru2+/Ru3+ redox reaction

Applying density functional theory (DFT)-based molecular dynamics simulation methods we investigate the effect of explicit treatment of electronic structure on the solvation free energy of aqueous Ru2+ and Ru3+.Our approach is based on the Marcus theory of redox half reactions, focussing on the vertical energy gap for reduction or oxidation of a single aqua ion. We compare the fluctuations of the quantum and classical energy gap along the same equilibrium ab initio molecular dynamics trajectory for each oxidation state. The classical gap is evaluated using a standard point charge model for the charge distribution of the solvent molecules (water). The quantum gap is computed from the full DFT electronic ground state energies of reduced and oxidized species, thereby accounting for the delocalization of the electron in the donor orbital and reorganization of the electron cloud after electron transfer (ET). The fluctuations of the quantum ET energy are well approximated by gaussian statistics giving rise to parabolic free energy profiles. The curvature is found to be independent of the oxidation state in agreement with the linear response assumption underlying Marcus theory. By contrast, the diabatic free energy curves evaluated using the classical gap as order parameter, while also quadratic, are asymmetric reflecting the difference in oxidation state. The response of these two order parameters is further analysed by a comparison of the spectral density of the fluctuations and the corresponding reorganization free energies.

Undulational instabilities of smectic thin films on heterogeneous patterned surfaces under positive and negative strain: The case of diblock copolymers

We consider the problem of a thin smectic film placed on a periodically striped solid surface, with stripe width λ, and with the upper surface free. The striped surface–smectic fluid interfacial energy induces the lamellae to align perpendicularly to the surface. We show that in many cases both the bulk liquid and the free upper surface will undulate to relieve the frustration caused by the stripes. In marked contrast to the traditional Helfrich–Hurault instability we show that this new instability occurs under both extension and compression. As a concrete example we consider a symmetric diblock copolymer thin film melt, with bulk equilibrium AB–BA bilayer spacing L2. When L2<2λ these undulations will be enhanced while for L2>2λ they will be diminished.

An instability of acoustic waves caused by radiation and the influence of chemical reactions on it

In a gas which absorbs radiation an acoustic wave can be unstable. This instability is caused by the fact that the irradiant energy is absorbed preferentially in the high density region of the wave. If in the gas the chemical equilibrium AB ⇄ A + B is maintained by photo dissociation balancing the reactions due to collisions, the instability increases. This is due to the density dependence of the reaction rate of the reverse reaction. It is argued that this process may explain the excitation or amplification of disturbances in the upper atmosphere.

The determination of equilibrium constants for heterogeneous macromolecular interactions.

A method has been developed to determine the association constant for a heterogeneous association of the type A + B in equilibrium AB. This method requires knowledge of the two initial concentrations and of the resulting weight-average molecular weight for each data point. Computer simulations using Gaussian-distributed error on the measured parameters show that the researcher can readily determine whether the particular concentration range chosen is appropriate for the strength of binding and therefore how reliable the calculated constant might be. It is also shown that errors in measuring molecular weight have, in general, a more profound effect than do errors in concentration.

Osmotic pressure measurements of ovalbumin and lysozyme mixtures.

Ovalbumin and lysozyme have been reported to undergo a mixed association in solutions of low ionic strength. Osmotic pressure experiments were performed on ovalbumin and on lysozyme solutions in 0.06 M cacodylate buffer (I = 0.02, pH = 5.8) at 30 and at 37 degrees C. The individual proteins did not undergo any self-associations at either temperature; these measurements indicated that each of the solutions was nonideal. Osmotic pressure experiments on three blends of lysozyme and ovalbumin at 30 and 37 degrees C could be interpreted in two ways. One interpretation was that a nonideal, nonassociating mixture of A and B was present; for the three solutions the mixed nonideal term BAB was negative. A negative nonideal term is usually interpreted as indicating an association. The other interpretation of the data was as a quasi-ideal mixed association of the type A + B in equilibrium AB.

Kinetics of Solute-Solvent Interaction in Aqueous Solution of Butyl Carbitol by Ultrasonic Methods

Abstract Ultrasonic absorptions in the frequency range 4.5–220 MHz and sound velocities at 2.5 MHz were measured at 25 °C with aqueous solutions of Butyl Carbitol (diethylene glycol monobutyl ether) over the concentration range 0.497–3.00 mol dm−3. Only a single relaxational process was observed and attributed to a perturbation of the equilibrium AB\oversetk12\undersetk21↔A+B, where A is Butyl Carbitol as the solute and B is water as the solvent participating in the reaction. A data analysis has led to the estimates k12=3.4×107 s−1, k21=2.0×108 dm3 mol−1 s−1, the standard volume change of reaction ΔV°=0.32 cm3 mol−1, and the standard enthalpy change ΔH°=5.4 kJ mol−1. The effect of the hydrophobicity of solute molecules on the water structure is discussed by comparing the present results with previous ones for other aqueous nonelectrolyte solutions.

Role of diffusion in ligand binding to macromolecules and cell-bound receptors

The association and dissociation rates of partially diffusion-controlled bimolecular reactions are considered. A simple expression for the equilibrium constant is derived using classical statistical mechanics. The relationship is established between the Collins-Kimball treatment, which is based on the "radiation" boundary condition involving an intrinsic rate constant k, and the kinetic scheme A + B in equilibrium A . . . B in equilibrium AB where A . . . B is an encounter complex. It is shown that with the appropriate choice of the interaction potential, Debye's expression for the association rate constant becomes identical to that obtained using the radiation boundary condition if k is evaluated using Kramers' theory of diffusive barrier crossing. Finally, the competitive binding of ligand to a spherical cell, whose surface is partially covered by multiple reactive sites, is studied by treating the cell as a partially reacting sphere.