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

On the "generalized Generalized Langevin Equation"

In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble ("bundle") of trajectories. Under stationary conditions, the time-evolution of such averages is described by the generalized Langevin equation. In contrast, if the dynamics is not stationary, it is not a priori clear which form the equation of motion for an averaged observable has. We employ the formalism of time-dependent projection operator techniques to derive the equation of motion for a non-equilibrium trajectory-averaged observable as well as for its non-stationary auto-correlation function. The equation is similar in structure to the generalized Langevin equation, but exhibits a time-dependent memory kernel as well as a fluctuating force that implicitly depends on the initial conditions of the process. We also derive a relation between this memory kernel and the autocorrelation function of the fluctuating force that has a structure similar to a fluctuation-dissipation relation. In addition, we show how the choice of the projection operator allows to relate the Taylor expansion of the memory kernel to data that is accessible in MD simulations and experiments, thus allowing to construct the equation of motion. As a numerical example, the procedure is applied to Brownian motion initialized in non-equilibrium conditions, and is shown to be consistent with direct measurements from simulations

Intermittent permeation of cylindrical nanopores by water

Molecular Dynamics simulations of water molecules in nanometre sized cylindrical channels connecting two reservoirs show that the permeation of water is very sensitive to the channel radius and to electric polarization of the embedding material. At threshold, the permeation is {\emph{intermittent}} on a nanosecond timescale, and strongly enhanced by the presence of an ion inside the channel, providing a possible mechanism for gating. Confined water remains surprisingly fluid and bulk-like. Its behaviour differs strikingly from that of a reference Lennard-Jones fluid, which tends to contract into a highly layered structure inside the channel.Comment: 4 pages, 4 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

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

Cooling rate, heating rate and aging effects in glassy water

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.Comment: to be published in Phys. Rev. E (rapid comunication

Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy:A case study of Sr2+ in methanol solution

Molecular dynamics simulations have been carried out for Sr2+ in methanol using different Sr2+ Lennard-Jones parameters and methanol models. X-ray absorption fine structure. (EXAFS) spectroscopy has been employed to assess the reliability of the ion-ion and ion-methanol potential functions used in the simulations. Radial distribution functions of Sr2+ in methanol have been. calculated for each simulation and compared with the EXAFS experimental data. This procedure has allowed the determinations of reliable Sr2+-methanol models which have been used in longer simulations providing an accurate description of the dynamic and structural properties of this system

Free energy of hydrophobic hydration:A molecular dynamics study of noble gases in water

The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary

Structure prediction of subtilisin BPN' mutants using molecular dynamics methods

In this paper we describe the achievements and pitfalls encountered in doing structure predictions of protein mutants using molecular dynamics simulation techniques in which properties of atoms are slowly changed as a function of time. Basically the method consists of a thermodynamic integration (slow growth) calculation used for free energy determination, but aimed at structure prediction; this allows for a fast determination of the mutant structure. We compared the calculated structure of the mutants Met222Ala, Met222Phe and Met222Gln of subtilisin BPN' with the respective X-ray structures and found good agreement between predicted and X-ray structure. The conformation of the residue subject to the mutation is relatively easy to predict and is mainly determined by packing criteria. When the side chain has polar groups its exact orientation may pose problems; long-range Coulomb interactions may generate a polarization feedback involving system relaxation times beyond the simulation time. Changes induced in the environment are harder to predict using this method. In particular, rearrangement of the hydration structure was difficult to predict correctly, probably because of the long relaxation times. In all conversions made the changes observed in the environment were found to be history-dependent and in particular the hydrogen bonding patterns provided evidence for metastable substates. In all cases the structure predicted was compared with available kinetic data and the reduced activity could be explained in terms of changes in the configuration of the active sit

Effects of altered TatC proteins on protein secretion efficiency via the twin-arginine translocation pathway of Bacillus subtilis

Protein translocation via the Tat machinery in thylakoids and bacteria occurs through a cooperation between the TatA, TatB and TatC subunits, of which the TatC protein forms the initial Tat substrate-binding site. The Bacillus subtilis Tat machinery lacks TatB and comprises two separate TatAC complexes with distinct substrate specificities: PhoD is secreted by the TatAdCd complex, whereas YwbN is secreted by the TatAyCy complex. To study the role of the Gram-positive TatC proteins in Tat-dependent protein secretion efficiency, we applied several genetic engineering approaches to modify and analyse the B. subtilis TatCd and TatCy proteins. Cytoplasmic and transmembrane domain exchange between TatCd and TatCy resulted in stable chimeric proteins that were unable to secrete both known substrates of the B. subtilis Tat system. Site-directed mutagenesis of conserved residues in the N-terminal part of both TatC proteins revealed significant differences in the degree of importance of these residues between TatCd, TatCy and Escherichia coli TatC. In addition, two small C-terminal deletions in TatCy completely abolished YwbN translocation, indicating that this terminus is essential for Tat translocation activity. Important differences from previous observations for E. coli TatC and implications for substrate binding and translocation are discussed.