Optimal flexibility for conformational transitions in macromolecules

Conformational transitions in macromolecular complexes often involve the reorientation of lever-like structures. Using a simple theoretical model, we show that the rate of such transitions is drastically enhanced if the lever is bendable, e.g. at a localized "hinge''. Surprisingly, the transition is fastest with an intermediate flexibility of the hinge. In this intermediate regime, the transition rate is also least sensitive to the amount of "cargo'' attached to the lever arm, which could be exploited by molecular motors. To explain this effect, we generalize the Kramers-Langer theory for multi-dimensional barrier crossing to configuration dependent mobility matrices.Comment: 4 pages, 4 figure

Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and reburial on the site position, which is measurable experimentally and pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the "semiflexible Brownian rotor."Comment: final version as published in Phys. Rev. Let

Next-to-leading order spin-orbit and spin(a)-spin(b) Hamiltonians for n gravitating spinning compact objects

We derive the post-Newtonian next-to-leading order conservative spin-orbit and spin(a)-spin(b) gravitational interaction Hamiltonians for arbitrary many compact objects. The spin-orbit Hamiltonian completes the knowledge of Hamiltonians up to and including 2.5PN for the general relativistic three-body problem. The new Hamiltonians include highly nontrivial three-body interactions, in contrast to the leading order consisting of two-body interactions only. This may be important for the study of effects like Kozai resonances in mergers of black holes with binary black holes.Comment: 13 pages, 1 Mathematica source file, v2: submitted version, v3: published version, some minor correction

Solving the radial Dirac equations: a numerical odyssey

We discuss, in a pedagogical way, how to solve for relativistic wave functions from the radial Dirac equations. After an brief introduction, in Section II we solve the equations for a linear Lorentz scalar potential, V_s(r), that provides for confinement of a quark. The case of massless u and d quarks is treated first, as these are necessarily quite relativistic. We use an iterative procedure to find the eigenenergies and the upper and lower component wave functions for the ground state and then, later, some excited states. Solutions for the massive quarks (s, c, and b) are also presented. In Section III we solve for the case of a Coulomb potential, which is a time-like component of a Lorentz vector potential, V_v(r). We re-derive, numerically, the (analytically well-known) relativistic hydrogen atom eigenenergies and wave functions, and later extend that to the cases of heavier one-electron atoms and muonic atoms. Finally, Section IV finds solutions for a combination of the V_s and V_v potentials. We treat two cases. The first is one in which V_s is the linear potential used in Sec. II and V_v is Coulombic, as in Sec. III. The other is when both V_s and V_v are linearly confining, and we establish when these potentials give a vanishing spin-orbit interaction (as has been shown to be the case in quark models of the hadronic spectrum).Comment: 39 pages (total), 23 figures, 2 table

A MUSE map of the central Orion Nebula (M 42)

We present a new integral-field spectroscopic dataset of the central part of the Orion Nebula (M 42), observed with the MUSE instrument at the ESO VLT. We reduced the data with the public MUSE pipeline. The output products are two FITS cubes with a spatial size of ~5.9'x4.9' (corresponding to ~0.76 pc x 0.63 pc) and a contiguous wavelength coverage of 4595...9366 Angstrom, spatially sampled at 0.2". We provide two versions with a sampling of 1.25 Angstrom and 0.85 Angstrom in dispersion direction. Together with variance cubes these files have a size of 75 and 110 GiB on disk. They represent one of the largest integral field mosaics to date in terms of information content. We make them available for use in the community. To validate this dataset, we compare world coordinates, reconstructed magnitudes, velocities, and absolute and relative emission line fluxes to the literature and find excellent agreement. We derive a two-dimensional map of extinction and present de-reddened flux maps of several individual emission lines and of diagnostic line ratios. We estimate physical properties of the Orion Nebula, using the emission line ratios [N II] and [S III] (for the electron temperature $T_e$) and [S II] and [Cl III] (for the electron density $N_e$), and show two-dimensional images of the velocity measured from several bright emission lines.Comment: Resubmitted to A&A after incorporating referee comments; access to full dataset via http://muse-vlt.eu/science/data-release

In vitro activity of commercial probiotic Lactobacillus strains against uropathogenic Escherichia coli

Urinary tract infection (UTI) is one of the most prevalent infections in humans. In ≥80% of cases, the etiologic agents are strains of uropathogenic Escherichia coli (UPEC), which commonly reside in the gastrointestinal tract. Lactobacilli have been shown to prevent UTI reoccurrence by restoring the urogenital microbiota when administered vaginally or orally. The goal of this study was to determine if commercial probiotic Lactobacillus spp. reduce or clear UPEC in vitro. Results show that it is likely that lactobacilli may, in addition to restoring a healthy urogenital microbiota through acidification of their environment, also displace adhering UPEC and cause a reduction of infectio

Helping Contemporary People use Historic Liturgy

This project proposes that contemporary people need help understanding and utilizing historic liturgy. It shows how historic liturgy is contemporary by nature, and can be used in a modern and relevant way. Educational tools were developed for use in both the worship and classroom settings. Survey results provide information toward tool development and effectiveness. The result of the project and its implementation in a parish setting waste elimination of the request for a contemporary worship from those exposed to the project tools