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We present progress toward a first-principles parametrization of the Hamiltonian of the Fenna-Matthews-Olson pigment-protein complex, a molecule that has become key to understanding the role of quantum dynamics in photosynthetic exciton energy transfer. To this end, we have performed fully quantum mechanical calculations on each of the seven(More)
We present recent improvements to the ONETEP code. ONETEP is an ab initio electronic structure package for total energy calculations within density-functional theory. Its main distinguishing features are true 'linear scaling', in that the total computational effort scales only linearly with system size, and 'plane-wave' accuracy, in that the convergence of(More)
Linear scaling methods for density-functional theory (DFT) simulations are formulated in terms of localized orbitals in real space, rather than the delocalized eigenstates of conventional approaches. In local-orbital methods, relative to conventional DFT, desirable properties can be lost to some extent, such as the translational invariance of the total(More)
Vanadium dioxide undergoes a first order metal-insulator transition at 340 K. In this Letter, we develop and carry out state-of-the-art linear scaling density-functional theory calculations refined with nonlocal dynamical mean-field theory. We identify a complex mechanism, a Peierls-assisted orbital selection Mott instability, which is responsible for the(More)
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(More)
A new method for calculating optical absorption spectra within linear-scaling density functional theory (LS-DFT) is presented, incorporating a scheme for optimizing a set of localized orbitals to accurately represent unoccupied Kohn-Sham states. Three different schemes are compared and the most promising of these, based on the use of a projection operator,(More)
A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (Rudberg 2012 J. Phys.: Condens. Matter 24 072202) has(More)
First-principles calculations of polar semiconductor nanorods reveal that their dipole moments are strongly influenced by Fermi-level pinning. The Fermi level for an isolated nanorod is found to coincide with a significant density of electronic surface states at the end surfaces, which are either mid-gap states or band-edge states. These states pin the(More)
Combining monolayers of different two-dimensional semiconductors into heterostructures creates new phenomena and device possibilities. Understanding and exploiting these phenomena hinge on knowing the electronic structure and the properties of interlayer excitations. We determine the key unknown parameters in MoSe2/WSe2 heterobilayers by using rational(More)