arXiv subjects

Mike C. Payne

Publications and source records attributed to Mike C. Payne.

At least 19 recordsLinked to original sources

arXiv2023

Vibrational and thermal properties of amorphous alumina from first principles

Amorphous alumina is employed ubiquitously as a high-dielectric-constant material in electronics, and its thermal-transport properties are of key relevance for heat management in electronic chips and devices. Experiments show that the thermal conductivity of alumina depends significantly on the synthesis process, indicating the need for a theoretical study to elucidate the atomistic origin of these variations. Here we employ first-principles simulations to characterize the atomistic structure, vibrational properties, and thermal conductivity of alumina at densities ranging from 2.28 g/cm3 to 3.49 g/cm3. Moreover, using an interatomic potential trained on first-principles data, we investigate how system size affects predictions of the thermal conductivity, showing that simulations containing 120 atoms can already reproduce the bulk limit of the conductivity. Finally, relying on the recently developed Wigner formulation of thermal transport, we shed light on the interplay between atomistic topological disorder and anharmonicity in the context of heat conduction, showing that the former dominates over the latter in determining the conductivity of alumina.

cond-mat.mtrl-sci↗

arXiv2020

The CECAM Electronic Structure Library and the modular software development paradigm

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure programs and redesign them as free, open-source libraries. They include "heavy-duty" ones with a high degree of parallelisation, and potential for adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers.

cond-mat.mtrl-sci↗

arXiv2015

Linear-scaling time-dependent density-functional theory (TDDFT) beyond the Tamm-Dancoff approximation: obtaining efficiency and accuracy with in situ optimised local orbitals

We present a solution of the full TDDFT eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspace with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate-gradients algorithm that is very memory-efficient. The algorithm is validated on a test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll (BChl) in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of BChl in solution. The largest systems considered in this work are of the same order of magnitude as a variety of pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

physics.comp-ph↗

arXiv2015

Tracing potential energy surfaces of electronic excitations via their transition origins: application to Oxirane

We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a widerange of molecular geometries. This is achieved by locating the switching of transition origins of adiabatic potential surfaces as the geometry changes. The transition vectors for analysing transition origins are provided by linear response time-dependent density functional theory (TDDFT) calculations under the Tamm-Dancoff approximation. We study the photochemical CO ring opening of oxirane as an example and show that the results corroborate the traditional Gomer-Noyes mechanism derived experimentally. The knowledge of specific states for the reaction also agrees well with that given by previous theoretical work using TDDFT surface-hopping dynamics that was validated by high-quality quantum Monte Carlo calculations. We also show that QNTO can be useful for considerably larger and more complex systems: by projecting the excitations to those of a reference oxirane molecule, the approach is able to identify and analyse specific excitations of a trans-2,3-diphenyloxirane molecule.

cond-mat.mtrl-sci↗

arXiv2014

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 (DMFT). This combination of methods explicitly accounts for dynamical and multi-reference quantum physics, such as valence and spin fluctuations, of the 3d electrons, whilst treating a significant proportion of the protein (more than 1000 atoms) with density functional theory. 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 many body-effects induced by the Hund's coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.

physics.chem-ph↗

arXiv2013

Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U

Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed calculations on the heme binding site and a significant proportion of the protein environment (more than 1000 atoms) using linear-scaling density functional theory and the DFT+U method to correct for self-interaction errors associated with localized 3d states. We confirm both the hydrogen-bonding nature of the discrimination effect (3.6 kcal/mol) and assumptions that the relative strain energy stored in the protein is low (less than 1 kcal/mol). Our calculations significantly widen the scope for tackling problems in drug design and enzymology, especially in cases where electron localization, allostery or long-ranged polarization influence ligand binding and reaction.

physics.chem-ph↗

arXiv2013

Importance of many body effects in the kernel of hemoglobin for ligand binding

We propose a mechanism for binding of diatomic ligands to heme based on a dynamical orbital selection process. This scenario may be described as bonding determined by local valence fluctuations. We support this model using linear-scaling first-principles calculations, in combination with dynamical mean-field theory, applied to heme, the kernel of the hemoglobin metalloprotein central to human respiration. We find that variations in Hund's exchange coupling induce a reduction of the iron 3d density, with a concomitant increase of valence fluctuations. We discuss the comparison between our computed optical absorption spectra and experimental data, our picture accounting for the observation of optical transitions in the infrared regime, and how the Hund's coupling reduces, by a factor of five, the strong imbalance in the binding energies of heme with CO and O_2 ligands.

cond-mat.str-el↗

arXiv2012

Vanadium dioxide : A Peierls-Mott insulator stable against disorder

Vanadium dioxide undergoes a first order metal-insulator transition at 340 K. In this work, we develop and carry out state of the art linear scaling DFT calculations refined with non-local dynamical mean-field theory. We identify a complex mechanism, a Peierls-assisted orbital selection Mott instability, which is responsible for the insulating M$_1$ phase, and furthermore survives a moderate degree of disorder.

cond-mat.str-el↗

arXiv2012

Generalized Wannier functions: a comparison of molecular electric dipole polarizabilities

Localized Wannier functions provide an efficient and intuitive means by which to compute dielectric properties from first principles. They are most commonly constructed in a post-processing step, following total-energy minimization. Nonorthogonal generalized Wannier functions (NGWFs) [Skylaris et al., Phys. Rev. B 66, 035119 11 (2002); Skylaris et al., J. Chem. Phys. 122, 084119 (2005)] may also be optimized in situ, in the process of solving for the ground-state density. We explore the relationship between NGWFs and orthonormal, maximally localized Wannier functions (MLWFs) [Marzari and Vanderbilt, Phys. Rev. B 56, 12847 (1997); Souza, Marzari, and Vanderbilt, ibid. 65, 035109 (2001)], demonstrating that NGWFs may be used to compute electric dipole polarizabilities efficiently, with no necessity for post-processing optimization, and with an accuracy comparable to MLWFs.

cond-mat.mtrl-sci↗

arXiv2012

Linear-scaling DFT+U with full local orbital optimization

We present an approach to the DFT+U method (Density Functional Theory + Hubbard model) within which the computational effort for calculation of ground state energies and forces scales linearly with system size. We employ a formulation of the Hubbard model using nonorthogonal projector functions to define the localized subspaces, and apply it to a local-orbital DFT method including in situ orbital optimization. The resulting approach thus combines linear-scaling and systematic variational convergence. We demonstrate the scaling of the method by applying it to nickel oxide nano-clusters with sizes exceeding 7,000 atoms.

cond-mat.str-el↗

arXiv2011

Minimal parameter implicit solvent model for ab initio electronic structure calculations

We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.

physics.comp-ph↗

arXiv2011

Subspace representations in ab initio methods for strongly correlated systems

We present a generalized definition of subspace occupancy matrices in ab initio methods for strongly correlated materials, such as DFT+U and DFT+DMFT, which is appropriate to the case of nonorthogonal projector functions. By enforcing the tensorial consistency of all matrix operations, we are led to a subspace projection operator for which the occupancy matrix is tensorial and accumulates only contributions which are local to the correlated subspace at hand. For DFT+U in particular, the resulting contributions to the potential and ionic forces are automatically Hermitian, without resort to symmetrization, and localized to their corresponding correlated subspace. The tensorial invariance of the occupancies, energies and ionic forces is preserved. We illustrate the effect of this formalism in a DFT+U study using self-consistently determined projectors.

cond-mat.str-el↗

arXiv2010

Projector self-consistent DFT+U using non-orthogonal generalized Wannier functions

We present a formulation of the density-functional theory + Hubbard model (DFT+U) method that is self-consistent over the choice of Hubbard projectors used to define the correlated subspaces. In order to overcome the arbitrariness in this choice, we propose the use of non-orthogonal generalized Wannier functions (NGWFs) as projectors for the DFT+U correction. We iteratively refine these NGWF projectors and, hence, the DFT+U functional, such that the correlated subspaces are fully self-consistent with the DFT+U ground-state. We discuss the convergence characteristics of this algorithm and compare ground-state properties thus computed with those calculated using hydrogenic projectors. Our approach is implemented within, but not restricted to, a linear-scaling DFT framework, opening the path to DFT+U calculations on systems of unprecedented size.

cond-mat.mtrl-sci↗

arXiv2009

Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces

The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via localised contact points characterise adhesion to the hydrophilic surface, evenly spread surface/molecule contacts and stabilisation of the helical structure occurs upon adsorption on the hydrophobic surface. In the latter case, we find that adhesion is accompanied by a mutual fit between the hydrophilic/hydrophobic pattern within the protein and the layered water structure at the solid/liquid interface, which may provide an additional driving force to the classic hydrophobic effect.

cond-mat.soft↗

arXiv2009

Gaussian Approximation Potentials: the accuracy of quantum mechanics, without the electrons

We introduce a class of interatomic potential models that can be automatically generated from data consisting of the energies and forces experienced by atoms, derived from quantum mechanical calculations. The resulting model does not have a fixed functional form and hence is capable of modeling complex potential energy landscapes. It is systematically improvable with more data. We apply the method to bulk carbon, silicon and germanium and test it by calculating properties of the crystals at high temperatures. Using the interatomic potential to generate the long molecular dynamics trajectories required for such calculations saves orders of magnitude in computational cost.

physics.comp-ph↗

arXiv2009

Stress-driven oxidation chemistry of wet silicon surfaces

The formation of a hydroxylated native oxide layer on Si(001) under wet conditions is studied by means of first principles molecular dynamics simulations. Water molecules are found to adsorb and dissociate on the oxidised surface leading to rupture of Si-O bonds and producing reactive sites for attack by dissolved dioxygen or hydrogen peroxide molecules. Tensile strain is found to enhance the driving force for the dissociative adsorption of water, suggesting that similar reactions could be responsible for environmentally-driven sub-critical crack propagation in silicon.

cond-mat.mtrl-sci↗

arXiv2009

Density functional theory study of Fe(II) adsorption and oxidation on goethite surfaces

We study the interactions between Fe(II) aqua complexes and surfaces of goethite (alpha-FeOOH) by means of density functional theory calculations including the so-called Hubbard U correction to the exchange-correlation functional. Using a thermodynamic approach, we find that (110) and (021) surfaces in contact with aqueous solutions are almost equally stable, despite the evident needlelike shape of goethite crystals indicating substantially different reactivity of the two faces. We thus suggest that crystal anisotropy may result from different growth rates due to virtually barrierless adsorption of hydrated ions on the (021) but not on the (110) surface. No clear evidence is found for spontaneous electron transfer from an adsorbed Fe(II) hex-aqua complex to a defect-free goethite substrate. Crystal defects are thus inferred to play an important role in assisting such electron transfer processes observed in a recent experimental study. Finally, goethite surfaces are observed to enhance the partial oxidation of adsorbed aqueous Fe(II) upon reaction with molecular oxygen. We propose that this catalytic oxidation effect arises from donation of electronic charge from the bulk oxide to the oxidizing agent through shared hydroxyl ligands anchoring the Fe(II) complexes on the surface.

cond-mat.mtrl-sci↗

arXiv2008

Stress Development and Impurity Segregation during Oxidation of the Si(100) Surface

We have studied the segregation of P and B impurities during oxidation of the Si(100) surface by means of combined static and dynamical first-principles simulations based on density functional theory. In the bare surface, dopants segregate to chemically stable surface sites or to locally compressed subsurface sites. Surface oxidation is accompanied by development of tensile surface stress up to 2.9 N/m at a coverage of 1.5 monolayers of oxygen and by formation of oxidised Si species with charges increasing approximately linearly with the number of neighbouring oxygen atoms. Substitutional P and B defects are energetically unstable within the native oxide layer, and are preferentially located at or beneath the Si/SiOx interface. Consistently, first-principles molecular dynamics simulations of native oxide formation on doped surfaces reveal that dopants avoid the formation of P-O and B-O bonds, suggesting a surface oxidation mechanism whereby impurities remain trapped at the Si/SiOx interface. This seems to preclude a direct influence of impurities on the surface electrostatics and, hence, on the interactions with an external environment.

cond-mat.mtrl-sci↗