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Register a new userElectrostatics of solvated systems in periodic boundary conditions
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Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary conditions, their extension to materials simulations --- typically entailing periodic-boundary conditions --- is very recent, and special care is needed to address correctly the electrostatic terms. We discuss here how periodic-boundary corrections developed for systems in vacuum should be modified to take into account solvent effects, using as a general framework the self-consistent continuum solvation model developed within plane-wave density-functional theory [O. Andreussi et al. J. Chem. Phys. 136, 064102 (2012)]. A comprehensive discussion of real-space and reciprocal-space corrective approaches is presented, together with an assessment of their ability to remove electrostatic interactions between periodic replicas. Numerical results for zero-dimensional and two-dimensional charged systems highlight the effectiveness of the different suggestions, and underline the importance of a proper treatement of electrostatic interactions in first-principles studies of charged systems in solution.
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We address periodic-image errors arising from the use of periodic boundary conditions to describe systems that do not exhibit full three-dimensional periodicity. The difference between the periodic potential, as straightforwardly obtained from a Fourier transform, and the potential satisfying any other boundary conditions can be characterized analytically. In light of this observation, we present an efficient real-space method to correct periodic-image errors, based on a multigrid solver for the potential difference, and demonstrate that exponential convergence of the energy with respect to cell size can be achieved in practical calculations. Additionally, we derive rapidly convergent expansions for determining the Madelung constants of point-charge assemblies in one, two, and three dimensions.
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully atomistic simulations of biomolecules, surrounded by thousands of water molecules and ions are too computationally slow. Continuum solvent models based on macroscopic dielectric theory (e.g. the Poisson equation) are popular alternatives, but their simplicity fails to capture well-known phenomena of functional significance. For example, standard theories predict that electrostatic response is symmetric with respect to the sign of an atomic charge, even though response is in fact strongly asymmetric if the charge is near the biomolecule surface. In this work, we present an asymmetric continuum theory that captures the essential physical mechanism--the finite size of solvent atoms--using a nonlinear boundary condition (NLBC) at the dielectric interface between the biomolecule and solvent. Numerical calculations using boundary-integral methods demonstrate that the new NLBC model reproduces a wide range of results computed by more realistic, and expensive, all-atom molecular-dynamics (MD) simulations in explicit water. We discuss model extensions such as modeling dilute-electrolyte solvents with Debye-Huckel theory (the linearized Poisson-Boltzmann equation) and opportunities for the electromagnetics community to contribute to research in this important area of molecular nanoscience and engineering.
Simulations are essential to accelerate the discovery of new materials and to gain full understanding of known ones. Although hard to realize experimentally, periodic boundary conditions are omnipresent in material simulations. In this work, we intro-duce ROBIN (recursive open boundary and interfaces), the first method allowing open boundary conditions in material and interface modeling. The computational costs are limited to solving quantum properties in a focus area which allows explicitly discretizing millions of atoms in real space and to consider virtually any type of environment (be it periodic, regular, or ran-dom). The impact of the periodicity assumption is assessed in detail with silicon dopants in graphene. Graphene was con-firmed to produce a band gap with periodic substitution of 3% carbon with silicon in agreement with published periodic boundary condition calculations. Instead, 3% randomly distributed silicon in graphene only shifts the energy spectrum. The predicted shift agrees quantitatively with published experimental data. Key insight of this assessment is, assuming periodici-ty elevates a small perturbation of a periodic cell into a strong impact on the material property prediction. Periodic boundary conditions can be applied on truly periodic systems only. More general systems should apply an open boundary method for reliable predictions.
Liquid metals at extreme pressures and temperatures are widely interested in the high-pressure community. Based on density functional theory molecular dynamics, we conduct first-principles investigations on the equation of state (EOS) and structures of four metals (Cu, Fe, Pb, and Sn) at 1.5--5 megabar conditions and 5$times10^3$--4$times10^4$ K. Our first-principles EOS data enable evaluating the performance of four EOS models in predicting Hugoniot densities and temperatures of the four systems. We find the melting temperature of Cu is 1000--2000 K higher and shows a similar Clapeyron slope, in comparison to those of Fe. Our structure, coordination number, and diffusivity analysis indicates all the four liquid metals form similar simple close-packed structures. Our results set theoretical benchmarks for EOS development and structures of metals in their liquid states and under dynamic compression.
We describe a method and its implementation for calculating electronic structure and electron transport without approximating the structure using periodic super-cells. This effectively removes spurious periodic images and interference effects. Our method is based on already established methods readily available in the non-equilibrium Green function formalism and allows for non-equilibrium transport. We present examples of a N defect in graphene, finite voltage bias transport in a point-contact to graphene, and a graphene-nanoribbon junction. This method is less costly, in terms of CPU-hours, than the super-cell approximation.
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