Metric tensor as the dynamical variable for variable cell-shape molecular dynamics

We propose a new variable cell-shape molecular dynamics algorithm where the dynamical variables associated with the cell are the six independent dot products between the vectors defining the cell instead of the nine cartesian components of those vectors. Our choice of the metric tensor as the dynamical variable automatically eliminates the cell orientation from the dynamics. Furthermore, choosing for the cell kinetic energy a simple scalar that is quadratic in the time derivatives of the metric tensor, makes the dynamics invariant with respect to the choice of the simulation cell edges. Choosing the densitary character of that scalar allows us to have a dynamics that obeys the virial theorem. We derive the equations of motion for the two conditions of constant external pressure and constant thermodynamic tension. We also show that using the metric as variable is convenient for structural optimization under those two conditions. We use simulations for Ar with Lennard-Jones parameters and for Si with forces and stresses calculated from first-principles of density functional theory to illustrate the applications of the method.Comment: 10 pages + 6 figures, Latex, to be published in Physical Review

Real World Interpretations of Quantum Theory

I propose a new class of interpretations, {\it real world interpretations}, of the quantum theory of closed systems. These interpretations postulate a preferred factorization of Hilbert space and preferred projective measurements on one factor. They give a mathematical characterisation of the different possible worlds arising in an evolving closed quantum system, in which each possible world corresponds to a (generally mixed) evolving quantum state. In a realistic model, the states corresponding to different worlds should be expected to tend towards orthogonality as different possible quasiclassical structures emerge or as measurement-like interactions produce different classical outcomes. However, as the worlds have a precise mathematical definition, real world interpretations need no definition of quasiclassicality, measurement, or other concepts whose imprecision is problematic in other interpretational approaches. It is natural to postulate that precisely one world is chosen randomly, using the natural probability distribution, as the world realised in Nature, and that this world's mathematical characterisation is a complete description of reality.Comment: Minor revisions. To appear in Foundations of Physic

A semi-nonparametric mixture model for selecting functionally consistent proteins

Background High-throughput technologies have led to a new era of proteomics. Although protein microarray experiments are becoming more common place there are a variety of experimental and statistical issues that have yet to be addressed, and that will carry over to new high-throughput technologies unless they are investigated. One of the largest of these challenges is the selection of functionally consistent proteins. Results We present a novel semi-nonparametric mixture model for classifying proteins as consistent or inconsistent while controlling the false discovery rate and the false non-discovery rate. The performance of the proposed approach is compared to current methods via simulation under a variety of experimental conditions. Conclusions We provide a statistical method for selecting functionally consistent proteins in the context of protein microarray experiments, but the proposed semi-nonparametric mixture model method can certainly be generalized to solve other mixture data problems. The main advantage of this approach is that it provides the posterior probability of consistency for each protein

'Universal' FitzGerald Contractions

The model of a universe with a preferred frame, which nevertheless shares the main properties with traditional special and general relativity theories, is considered. We adopt Mach's interpretation of inertia and show that the energy balance equation, which includes the Machian energy of gravitational interactions with the universe, can imitate standard relativistic formulas.Comment: The version accepted by Eur. Phys. J.