Linear-scaling density-functional simulations of charged point defects in Al2O3 using hierarchical sparse matrix algebra

Effect of point defects on acetylene hydrogenation reaction over Ni(111) surface: a density functional theory study

Density functional theory (DFT) calculations are carried out to investigate the effect of point defects on acetylene hydrogenation reaction over Ni(111) surface with three different defect concentrations (DC = 0.0500, 0.0625, and 0.0833), compared with the perfect Ni(111) surface. The adsorptions of C₂ species and H atoms and the mechanism of acetylene hydrogenation via the ethylene pathway are systematically analyzed. The results indicate that the existence of defects will make C₂ species and H atoms more inclined to adsorb near the defects. Introducing an appropriate amount of point defect concentration can enhance the catalytic activity and ethylene selectivity of Ni. In this work, DC = 0.0625 Ni(111) surface has the highest catalytic activity and selectivity of ethylene. This work provides useful theoretical information on the effect of defects on acetylene hydrogenation and is helpful for the design of Ni and related metal catalysts with defects.

ONETEP + TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory

We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlated electronic behavior while simultaneously including the effects of the environment, making it ideally suited for studying complex and heterogeneous systems that contain transition metals and lanthanides, such as metalloproteins. We systematically introduce the necessary formalism, which must account for the nonorthogonal basis set used by ONETEP. In order to demonstrate the capabilities of this code, we apply it to carbon monoxide ligated iron porphyrin and explore the distinctly quantum-mechanical character of the iron 3d electrons during the process of photodissociation.

Linear-scaling density functional theory using the projector augmented wave method

Quantum mechanical simulation of realistic models of nanostructured systems, such as nanocrystals and crystalline interfaces, demands computational methods combining high-accuracy with low-order scaling with system size. Blöchl's projector augmented wave (PAW) approach enables all-electron (AE) calculations with the efficiency and systematic accuracy of plane-wave pseudopotential calculations. Meanwhile, linear-scaling (LS) approaches to density functional theory (DFT) allow for simulation of thousands of atoms in feasible computational effort. This article describes an adaptation of PAW for use in the LS-DFT framework provided by the ONETEP LS-DFT package. ONETEP uses optimisation of the density matrix through in situ-optimised local orbitals rather than the direct calculation of eigenstates as in traditional PAW approaches. The method is shown to be comparably accurate to both PAW and AE approaches and to exhibit improved convergence properties compared to norm-conserving pseudopotential methods.

Applications of large-scale density functional theory in biology

Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

Renormalization of myoglobin-ligand binding energetics by quantum many-body effects

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe-O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of the many-body effects induced by the Hund's coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.

Self-assembled quantum dots in a nanowire system for quantum photonics

Quantum dots embedded within nanowires represent one of the most promising technologies for applications in quantum photonics. Whereas the top-down fabrication of such structures remains a technological challenge, their bottom-up fabrication through self-assembly is a potentially more powerful strategy. However, present approaches often yield quantum dots with large optical linewidths, making reproducibility of their physical properties difficult. We present a versatile quantum-dot-in-nanowire system that reproducibly self-assembles in core-shell GaAs/AlGaAs nanowires. The quantum dots form at the apex of a GaAs/AlGaAs interface, are highly stable, and can be positioned with nanometre precision relative to the nanowire centre. Unusually, their emission is blue-shifted relative to the lowest energy continuum states of the GaAs core. Large-scale electronic structure calculations show that the origin of the optical transitions lies in quantum confinement due to Al-rich barriers. By emitting in the red and self-assembling on silicon substrates, these quantum dots could therefore become building blocks for solid-state lighting devices and third-generation solar cells.

Electrostatic interactions in finite systems treated with periodic boundary conditions: application to linear-scaling density functional theory

We present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such cases the effects of PBCs on the calculations need to be avoided, so that the results obtained represent the open rather than the periodic boundary. The very large systems encountered in LS-DFT make the demands of the supercell approximation for isolated systems more difficult to manage, and we show cases where the open boundary (infinite cell) result cannot be obtained from extrapolation of calculations from periodic cells of increasing size. We discuss, implement, and test three very different approaches for overcoming or circumventing the effects of PBCs: truncation of the Coulomb interaction combined with padding of the simulation cell, approaches based on the minimum image convention, and the explicit use of open boundary conditions (OBCs). We have implemented these approaches in the ONETEP LS-DFT program and applied them to a range of systems, including a polar nanorod and a protein. We compare their accuracy, complexity, and rate of convergence with simulation cell size. We demonstrate that corrective approaches within PBCs can achieve the OBC result more efficiently and accurately than pure OBC approaches.

O(N) methods in electronic structure calculations

Linear-scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed.

Multi-component transparent conducting oxides: progress in materials modelling

Transparent conducting oxides (TCOs) play an essential role in modern optoelectronic devices through their combination of electrical conductivity and optical transparency. We review recent progress in our understanding of multi-component TCOs formed from solid solutions of ZnO, In(2)O(3), Ga(2)O(3) and Al(2)O(3), with a particular emphasis on the contributions of materials modelling, primarily based on density functional theory. In particular, we highlight three major results from our work: (i) the fundamental principles governing the crystal structures of multi-component oxide structures including (In(2)O(3))(ZnO)(n) and (In(2)O(3))(m)(Ga(2)O(3))(l)(ZnO)(n); (ii) the relationship between elemental composition and optical and electrical behaviour, including valence band alignments; (iii) the high performance of amorphous oxide semiconductors. On the basis of these advances, the challenge of the rational design of novel electroceramic materials is discussed.

Assessment of density matrix methods for linear scaling electronic structure calculations

Purification and minimization methods for linear scaling computation of the one-particle density matrix for a fixed Hamiltonian matrix are compared. This is done by considering the work needed by each method to achieve a given accuracy in terms of the difference from the exact solution. Numerical tests employing orthogonal as well as non-orthogonal versions of the methods are performed using both element magnitude and cutoff radius based truncation approaches. It is investigated how the convergence speed for the different methods depends on the eigenvalue distribution in the Hamiltonian matrix. An expression for the number of iterations required for the minimization methods studied is derived, taking into account the dependence on both the band gap and the chemical potential. This expression is confirmed by numerical tests. The minimization methods are found to perform at their best when the chemical potential is located near the center of the eigenspectrum. The results indicate that purification is considerably more efficient than the minimization methods studied even when a good starting guess for the minimization is available. In test calculations without a starting guess, purification is more than an order of magnitude more efficient than minimization.