Pytrec_eval: An Extremely Fast Python Interface to trec_eval

We introduce pytrec_eval, a Python interface to the tree_eval information retrieval evaluation toolkit. pytrec_eval exposes the reference implementations of trec_eval within Python as a native extension. We show that pytrec_eval is around one order of magnitude faster than invoking trec_eval as a sub process from within Python. Compared to a native Python implementation of NDCG, pytrec_eval is twice as fast for practically-sized rankings. Finally, we demonstrate its effectiveness in an application where pytrec_eval is combined with Pyndri and the OpenAI Gym where query expansion is learned using Q-learning.Comment: SIGIR '18. The 41st International ACM SIGIR Conference on Research & Development in Information Retrieva

Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic

Petrogenesis of crustal wehrlites in the Oman ophiolite: Experiments and natural rocks

In the Wadi Haymiliyah of the Oman ophiolite (Haylayn block), discordant wehrlite bodies ranging in size from tens to hundreds of meters intrude the lower crust at different levels. We combined investigations on natural wehrlites from the Wadi Haymiliyah section with an experimental study on the phase relations in a wehrlitic system in order to constrain the petrogenesis of the crustal wehrlites of the Oman ophiolite. Secondary ion mass spectrometry analyses of clinopyroxenes from different wehrlite bodies imply that the clinopyroxenes were crystallized from tholeiitic, mid-ocean ridge (MORB)–type melts. The presence of primary magmatic amphiboles in some wehrlites suggests a formation under hydrous conditions. Significantly enhanced 87Sr/86Sr isotope ratios of separates from these amphiboles imply that the source of the corresponding magmatic fluids was either seawater or subduction zone–related. The experiments revealed that under wet conditions at relatively low temperatures, a MORB magma has the potential to produce wehrlite in the ocean crust by accumulation of early olivine and clinopyroxene. These show typically high Mg# which is a consequence of the oxidizing effect of the prevailing high aH2O. First plagioclases crystallizing after clinopyroxene under wet conditions are high in An content, in contrast to the corresponding dry system. Trace element compositions of clinopyroxenes of those wehrlites from the Moho transition zone are too depleted in HREE to be in equilibrium with present-day MORB, implying a genetic relation to the V2 lavas of the Oman ophiolite, which are interpreted to be the result of fluidenhanced melting of previously depleted mantle. We present a model on the petrogenesis of the crustal wehrlites in an upper mantle wedge above an initial, shallow subduction zone at the beginning of the intraoceanic thrusting

Determination of Omega_b From Big Bang Nucleosynthesis in the Presence of Regions of Antimatter

Production of regions of antimatter in the early universe is predicted in many baryogenesis models. Small scale antimatter regions would annihilate during or soon after nucleosynthesis, affecting the abundances of the light elements. In this paper we study how the acceptable range in Omega_b changes in the presence of antimatter regions, as compared to the standard big bang nucleosynthesis. It turns out that it is possible to produce at the same time both a low 4He value (Y_p < 0.240) and a low D/H value (D/H < 4e-5), but overproduction of 7Li is unavoidable at large Omega_b.Comment: 9 pages, PRD version, ref. 6 correcte

Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Lithium-6: A Probe of the Early Universe

I consider the synthesis of 6Li due to the decay of relic particles, such as gravitinos or moduli, after the epoch of Big Bang Nucleosynthesis. The synthesized 6Li/H ratio may be compared to 6Li/H in metal-poor stars which, in the absence of stellar depletion of 6Li, yields significantly stronger constraints on relic particle densities than the usual consideration of overproduction of 3He. Production of 6Li during such an era of non-thermal nucleosynthesis may also be regarded as a possible explanation for the relatively high 6Li/H ratios observed in metal-poor halo stars.Comment: final version, Physical Review Letters, additional figure giving limits on relic decaying particle