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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 (E. Rudberg, J. Phys.: Condens. Mat. 2012, 24, 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals., 13 pages, 4 figures

Strain induced by antiphase boundaries (APBs) in the Si(111) 2 x 1 surface is investigated using scanning tunneling microscopy (STM), laterally resolved scanning tunneling spectroscopy (STS), and density functional theory (DFT). We determine the structure of all identified APB reconstructions and show that a band shift of states close to the Fermi energy leads to the previously observed electronic contrast. The orientation of the band shift and the observed movement of APBs within the surface are explained by surface strain resulting from the excess free energy of the boundary. We demonstrate that the location of APBs and their associated strain can be precisely manipulated, making them an ideal model system to study and control strain at the atomic scale.