Half-filled orbital and unconventional geometry of a common dopant in Si(001)

The determining factor of the bulk properties of doped Si is the column rather than the row in the periodic table from which the dopants are drawn. It is unknown whether the basic properties of dopants at surfaces and interfaces, steadily growing in importance as microelectronic devices shrink, are also solely governed by their column of origin. The common light impurity P replaces individual Si atoms and maintains the integrity of the dimer superstructure of the Si(001) surface, but loses its valence electrons to surface states. Here we report that isolated heavy dopants are entirely different: Bi atoms form pairs with Si vacancies, retain their electrons and have highly localized, half-filled orbitals.

Density-functional theory study of gramicidin A ion channel geometry and electronic properties

Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A, whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground-state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gramicidin A in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10,000 to 100,000 atoms and beyond, and will be an important new tool for biomolecular simulations.

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 is 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.

Calculations on millions of atoms with DFT: Linear scaling shows its potential

An overview of the Conquest linear scaling density functional theory (DFT) code is given, focussing particularly on the scaling behaviour on modern high- performance computing (HPC) platforms. We demonstrate that essentially perfect linear scaling and weak parallel scaling (with fixed atoms per processor core) can be achieved, and that DFT calculations on millions of atoms are now possible.