Enriching Existing Test Collections with OXPath

Extending TREC-style test collections by incorporating external resources is a time consuming and challenging task. Making use of freely available web data requires technical skills to work with APIs or to create a web scraping program specifically tailored to the task at hand. We present a light-weight alternative that employs the web data extraction language OXPath to harvest data to be added to an existing test collection from web resources. We demonstrate this by creating an extended version of GIRT4 called GIRT4-XT with additional metadata fields harvested via OXPath from the social sciences portal Sowiport. This allows the re-use of this collection for other evaluation purposes like bibliometrics-enhanced retrieval. The demonstrated method can be applied to a variety of similar scenarios and is not limited to extending existing collections but can also be used to create completely new ones with little effort.Comment: Experimental IR Meets Multilinguality, Multimodality, and Interaction - 8th International Conference of the CLEF Association, CLEF 2017, Dublin, Ireland, September 11-14, 201

Magnetic friction due to vortex fluctuation

We use Monte Carlo and molecular dynamics simulation to study a magnetic tip-sample interaction. Our interest is to understand the mechanism of heat dissipation when the forces involved in the system are magnetic in essence. We consider a magnetic crystalline substrate composed of several layers interacting magnetically with a tip. The set is put thermally in equilibrium at temperature T by using a numerical Monte Carlo technique. By using that configuration we study its dynamical evolution by integrating numerically the equations of motion. Our results suggests that the heat dissipation in this system is closed related to the appearing of vortices in the sample.Comment: 6 pages, 41 figure

Polarization forces in water deduced from single molecule data

Intermolecular polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced to fine detail by only three multipoles $\mu_H$, $\mu_O$, and $\theta_O$ and two polarizabilities $\alpha_O$ and $\alpha_H$, which characterize a single water molecule and are deduced from single molecule data.Comment: 4 revtex pages, 3 embedded color PS figure

Physics of the liquid-liquid critical point

Within the inherent structure (IS) thermodynamic formalism introduced by Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys. Rev. A {\bf 25}, 978 (1982)] we address the basic question of the physics of the liquid-liquid transition and of density maxima observed in some complex liquids such as water by identifying, for the first time, the statistical properties of the potential energy landscape (PEL) responsible for these anomalies. We also provide evidence of the connection between density anomalies and the liquid-liquid critical point. Within the simple (and physically transparent) model discussed, density anomalies do imply the existence of a liquid-liquid transition.Comment: Physical Review Letters, in publicatio

Molecular dynamics simulation of the transport of small molecules across a polymer membrane

The transport of small molecules through a polymer membrane is modeled using the computer simulation technique of molecular dynamics (MD). The transport coefficient is derived from a combination of the excess free energy and the diffusion constant. Both properties are derived from MD simulations, applied to helium and methane in polydimethylsiloxane (PDMS). The diffusional process appears to have the character of a jump diffusion for methane and less so for helium. Jumps are allowed by fluctuations of the size and shape of holes. Experimental diffusion constants are well reproduced. The excess free energies, determined by a particle insertion method, are lower by 5-7 kJ/mol than experimental values. It is shown that, as a result of a higher solubility, methane has a higher permeability constant than helium, despite its lower diffusion constant

On "the complete basis set limit" and plane-wave methods in first-principles simulations of water

Water structure, measured by the height of the first peak in oxygen-oxygen radial distributions, is converged with respect to plane-wave basis energy cutoffs for ab initio molecular dynamics simulations, confirming the reliability of plane-wave methods.Comment: 9 pages, 3 figure

Two-Player Reachability-Price Games on Single-Clock Timed Automata

We study two player reachability-price games on single-clock timed automata. The problem is as follows: given a state of the automaton, determine whether the first player can guarantee reaching one of the designated goal locations. If a goal location can be reached then we also want to compute the optimum price of doing so. Our contribution is twofold. First, we develop a theory of cost functions, which provide a comprehensive methodology for the analysis of this problem. This theory allows us to establish our second contribution, an EXPTIME algorithm for computing the optimum reachability price, which improves the existing 3EXPTIME upper bound.Comment: In Proceedings QAPL 2011, arXiv:1107.074

Cooperative Origin of Low-Density Domains in Liquid Water

We study the size of clusters formed by water molecules possessing large enough tetrahedrality with respect to their nearest neighbors. Using Monte Carlo simulation of the SPC/E model of water, together with a geometric analysis based on Voronoi tessellation, we find that regions of lower density than the bulk are formed by accretion of molecules into clusters exceeding a minimum size. Clusters are predominantly linear objects and become less compact as they grow until they reach a size beyond which further accretion is not accompanied by a density decrease. The results suggest that the formation of "ice-like" regions in liquid water is cooperative.Comment: 16 pages, 6 figure

Origin of entropy convergence in hydrophobic hydration and protein folding

An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy convergence follows from the weak temperature dependence of occupancy fluctuations for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior between water and common organic solvents is the relative temperature insensitivity of the water isothermal compressibility. The information theory model provides a quantitative description of small molecule hydration and predicts a negative entropy at convergence. Interpretations of entropic contributions to protein folding should account for this result.Comment: Phys. Rev. Letts. (in press 1996), 3 pages, 3 figure