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A new catalogue of extrasolar planets is presented by re-analysing a selection of published radial velocity data sets using EXOFIT (Balan & Lahav 2009). All objects are treated on an equal footing within a Bayesian framework, to give orbital parameters for 94 exoplanetary systems. Model selection (between one- and two-planet solutions) is then performed, using both a visual flagging method and a standard chi-square analysis, with agreement between the two methods for 99% of the systems considered. The catalogue is to be made available online, and this 'proof of concept' study may be maintained and extended in the future to incorporate all systems with publicly available radial velocity data, as well as transit and microlensing data.

In their simplest form, proteins essentially comprise unbranched polymer chains formed as a result of chemical bonding that takes place between the amino acid building blocks.

The last two decades have witnessed the continual and concerted effort toward the development of powerful tools which allow DFT calculations to be efficiently performed for systems containing thousands of atoms.

It is quite alarming that several publications exist in the literature raising serious questions about the applicability of DFT techniques to large-scale systems such as water clusters and proteins [1, 2, 3, 4, 5, 6].

Linear-scaling quantum mechanical density functional theory calculations have been applied to study the rearrangement of chorismate to prephenate in large-scale models of the Bacillus subtilis chorismate mutase enzyme. By treating up to 2000 atoms at a consistent quantum mechanical level of theory, we obtain an unbiased, almost parameter-free description of the transition state geometry and energetics. The activation energy barrier is calculated to be lowered by 10.5 kcal mol(-1) in the enzyme, compared with the equivalent reaction in water, which is in good agreement with experiment. Natural bond orbital analysis identifies a number of active site residues that are important for transition state stabilization in chorismate mutase. This benchmark study demonstrates that linear-scaling density functional theory techniques are capable of simulating entire enzymes at the ab initio quantum mechanical level of accuracy.

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.