80 research outputs found
Characterization of a ballistic supermirror neutron guide
We describe the beam characteristics of the first ballistic supermirror
neutron guide H113 that feeds the neutron user facility for particle physics
PF1B of the Institute Laue-Langevin, Grenoble (ILL). At present, the neutron
capture flux density of H113 at its 20x6cm2 exit window is 1.35x10^10/cm^2/s,
and will soon be raised to above 2x10^10/cm^2/s. Beam divergence is no larger
than beam divergence from a conventional Ni coated guide. A model is developed
that permits rapid calculation of beam profiles and absolute event rates from
such a beam. We propose a procedure that permits inter-comparability of the
main features of beams emitted from ballistic or conventional neutron guides.Comment: 15 pages, 11 figures, to be submitted to Nuclear Instruments and
Methods
The point spread function of electrons in a magnetic field, and the decay of the free neutron
Experiments in nuclear and particle physics often use magnetic fields to
guide charged reaction products to a detector. Due to their gyration in the
guide field, the particles hit the detector within an area that can be
considerably larger than the diameter of the source where the particles are
produced. This blurring of the image of the particle source on the detector
surface is described by a suitable point spread function (PSF), which is
defined as the image of a point source. We derive simple analytical expressions
for such magnetic PSFs, valid for any angular distribution of the emitted
particles that can be developed in Legendre polynomials. We investigate this
rather general problem in the context of neutron beta decay spectrometers and
study the effect of limited detector size on measured neutron decay correlation
parameters. To our surprise, insufficient detector size does not affect much
the accuracy of such measurements, even for rather large radii of gyration.
This finding can considerably simplify the layout of the respective
spectrometers.Comment: 24 pages, 12 figure
A clean, bright, and versatile source of neutron decay products
We present a case study on a new type of cold neutron beam station for the
investigation of angular correlations in the beta-decay of free neutrons. With
this beam station, called PERC, the 'active decay volume' lies inside the
neutron guide, and the charged neutron decay products are magnetically guided
towards the end of the neutron guide. Hence, the guide delivers at its exit a
beam of decay electrons and protons, under well-defined and precisely variable
conditions, which can be well separated from the cold neutron beam. In this way
a general-purpose source of neutron decay products is obtained which can be
used for various different experiments in neutron decay correlation
spectroscopy. A gain in phase space density of several orders of magnitude can
be achieved with PERC, as compared to existing neutron decay spectrometers.
Neutron beam related background is separately measurable in PERC, and magnetic
mirror effects on the charged neutron decay products and edge effects in the
active neutron beam volume are both strongly suppressed. Therefore the spectra
and angular distributions of the emerging decay particles will be
distortion-free on the level of 10^-4, more than 10 times better than achieved
today.Comment: 20 pages, 6 figure
Identification of a novel zinc metalloprotease through a global analysis of clostridium difficile extracellular proteins
Clostridium difficile is a major cause of infectious diarrhea worldwide. Although the cell surface proteins are recognized to be important in clostridial pathogenesis, biological functions of only a few are known. Also, apart from the toxins, proteins exported by C. difficile into the extracellular milieu have been poorly studied. In order to identify novel extracellular factors of C. difficile, we analyzed bacterial culture supernatants prepared from clinical isolates, 630 and R20291, using liquid chromatography-tandem mass spectrometry. The majority of the proteins identified were non-canonical extracellular proteins. These could be largely classified into proteins associated to the cell wall (including CWPs and extracellular hydrolases), transporters and flagellar proteins. Seven unknown hypothetical proteins were also identified. One of these proteins, CD630_28300, shared sequence similarity with the anthrax lethal factor, a known zinc metallopeptidase. We demonstrated that CD630_28300 (named Zmp1) binds zinc and is able to cleave fibronectin and fibrinogen in vitro in a zinc-dependent manner. Using site-directed mutagenesis, we identified residues important in zinc binding and enzymatic activity. Furthermore, we demonstrated that Zmp1 destabilizes the fibronectin network produced by human fibroblasts. Thus, by analyzing the exoproteome of C. difficile, we identified a novel extracellular metalloprotease that may be important in key steps of clostridial pathogenesis
Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium
Proteorhodopsin (PR) is a photoprotein that functions as a light-driven proton pump in diverse marine Bacteria and Archaea. Recent studies have suggested that PR may enhance both growth rate and yield in some flavobacteria when grown under nutrient-limiting conditions in the light. The direct involvement of PR, and the metabolic details enabling light-stimulated growth, however, remain uncertain. Here, we surveyed transcriptional and growth responses of a PR-containing marine flavobacterium during carbon-limited growth in the light and the dark. As previously reported (Gómez-Consarnau et al., 2007), Dokdonia strain MED134 exhibited light-enhanced growth rates and cell yields under low carbon growth conditions. Inhibition of retinal biosynthesis abolished the light-stimulated growth response, supporting a direct role for retinal-bound PR in light-enhanced growth. Among protein-coding transcripts, both PR and retinal biosynthetic enzymes showed significant upregulation in the light. Other light-associated proteins, including bacterial cryptochrome and DNA photolyase, were also expressed at significantly higher levels in the light. Membrane transporters for Na+/phosphate and Na+/alanine symporters, and the Na+-translocating NADH-quinone oxidoreductase (NQR) linked electron transport chain, were also significantly upregulated in the light. Culture experiments using a specific inhibitor of Na+-translocating NQR indicated that sodium pumping via NQR is a critical metabolic process in the light-stimulated growth of MED134. In total, the results suggested the importance of both the PR-enabled, light-driven proton gradient, as well as the generation of a Na+ ion gradient, as essential components for light-enhanced growth in these flavobacteria.Gordon and Betty Moore FoundationNational Science Foundation (U.S.) (NSF Science and Technology Center Award EF0424599.)Japan Society for the Promotion of Science (Postdoctoral Fellowships for Research Abroad
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field
MscS-like mechanosensitive channels in plants and microbes
The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. The latter of these two families, the MscS family, consists of members from bacteria, archaea, fungi, and plants. Genetic and electrophysiological analysis of these family members has provided insight into how organisms use mechanosensitive channels for osmotic regulation in response to changing environmental and developmental circumstances. Furthermore, determining the crystal structure of E. coli MscS and several homologues in several conformational states has contributed to our understanding of the gating mechanisms of these channels. Here we summarize our current knowledge of MscS homologues from all three domains of life and address their structure, proposed physiological functions, electrophysiological behaviors, and topological diversity
The neutron and its role in cosmology and particle physics
Experiments with cold and ultracold neutrons have reached a level of
precision such that problems far beyond the scale of the present Standard Model
of particle physics become accessible to experimental investigation. Due to the
close links between particle physics and cosmology, these studies also permit a
deep look into the very first instances of our universe. First addressed in
this article, both in theory and experiment, is the problem of baryogenesis ...
The question how baryogenesis could have happened is open to experimental
tests, and it turns out that this problem can be curbed by the very stringent
limits on an electric dipole moment of the neutron, a quantity that also has
deep implications for particle physics. Then we discuss the recent spectacular
observation of neutron quantization in the earth's gravitational field and of
resonance transitions between such gravitational energy states. These
measurements, together with new evaluations of neutron scattering data, set new
constraints on deviations from Newton's gravitational law at the picometer
scale. Such deviations are predicted in modern theories with extra-dimensions
that propose unification of the Planck scale with the scale of the Standard
Model ... Another main topic is the weak-interaction parameters in various
fields of physics and astrophysics that must all be derived from measured
neutron decay data. Up to now, about 10 different neutron decay observables
have been measured, much more than needed in the electroweak Standard Model.
This allows various precise tests for new physics beyond the Standard Model,
competing with or surpassing similar tests at high-energy. The review ends with
a discussion of neutron and nuclear data required in the synthesis of the
elements during the "first three minutes" and later on in stellar
nucleosynthesis.Comment: 91 pages, 30 figures, accepted by Reviews of Modern Physic
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