Higher Order Variational Integrators: a polynomial approach

We reconsider the variational derivation of symplectic partitioned Runge-Kutta schemes. Such type of variational integrators are of great importance since they integrate mechanical systems with high order accuracy while preserving the structural properties of these systems, like the symplectic form, the evolution of the momentum maps or the energy behaviour. Also they are easily applicable to optimal control problems based on mechanical systems as proposed in Ober-Bl\"obaum et al. [2011]. Following the same approach, we develop a family of variational integrators to which we refer as symplectic Galerkin schemes in contrast to symplectic partitioned Runge-Kutta. These two families of integrators are, in principle and by construction, different one from the other. Furthermore, the symplectic Galerkin family can as easily be applied in optimal control problems, for which Campos et al. [2012b] is a particular case.Comment: 12 pages, 1 table, 23rd Congress on Differential Equations and Applications, CEDYA 201

Convection of Plasmaspheric Plasma into the Outer Magnetosphere and Boundary Layer Region: Initial Results

We present initial results on the modeling of the circulation of plasmaspheric- origin plasma into the outer magnetosphere and low-latitude boundary layer (LLBL), using a dynamic global core plasma model (DGCPM). The DGCPM includes the influences of spatially and temporally varying convection and refilling processes to calculate the equatorial core plasma density distribution throughout the magnetosphere. We have developed an initial description of the electric and magnetic field structures in the outer magnetosphere region. The purpose of this paper is to examine both the losses of plasmaspheric-origin plasma into the magnetopause boundary layer and the convection of this plasma that remains trapped on closed magnetic field lines. For the LLBL electric and magnetic structures we have adopted here, the plasmaspheric plasma reaching the outer magnetosphere is diverted anti-sunward primarily along the dusk flank. These plasmas reach X = -15 R(sub E) in the LLBL approximately 3.2 hours after the initial enhancement of convection and continues to populate the LLBL for 12 hours as the convection electric field diminishes

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations

Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein–DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein–DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove width, a recognition feature widely exploited by proteins. For 11 protein–DNA complexes, we compared experimental maps of naked DNA minor groove width with minor groove width measured from X-ray co-crystal structures. Seven sites had similar minor groove widths as naked DNA and when bound to protein. For four sites, part of the DNA in the complex had the same structure as naked DNA, and part changed structure upon protein binding. We compared the experimental map with minor groove patterns of DNA predicted by two computational approaches, DNAshape and ORChID2, and found good but not perfect concordance with both. This experimental approach will be useful in mapping structures of DNA sequences for which high-resolution structural data are unavailable. This approach allows probing of protein family-dependent readout mechanisms.National Institutes of Health [R01GM106056 to R.R., T.D.T.; U54CA121852 in part to T.D.T.]; Boston University Undergraduate Research Opportunities Program [Faculty Matching Grants to D.O. and Y.J.]; USC Graduate School [Research Enhancement Fellowship and Manning Endowed Fellowship to T.P.C.]. R.R. is an Alfred P. Sloan Research Fellow. Funding for open access charge: Boston University. (R01GM106056 - National Institutes of Health; U54CA121852 - National Institutes of Health; Boston University Undergraduate Research Opportunities Program; USC Graduate School; Boston University)https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1Published versio

The First Stars

We review recent theoretical results on the formation of the first stars in the universe, and emphasize related open questions. In particular, we discuss the initial conditions for Population III star formation, as given by variants of the cold dark matter cosmology. Numerical simulations have investigated the collapse and the fragmentation of metal-free gas, showing that the first stars were predominantly very massive. The exact determination of the stellar masses, and the precise form of the primordial initial mass function, is still hampered by our limited understanding of the accretion physics and the protostellar feedback effects. We address the importance of heavy elements in bringing about the transition from an early star formation mode dominated by massive stars, to the familiar mode dominated by low mass stars, at later times. We show how complementary observations, both at high redshifts and in our local cosmic neighborhood, can be utilized to probe the first epoch of star formation.Comment: 38 pages, 10 figures, draft version for 2004 Annual Reviews of Astronomy and Astrophysics, high-resolution version available at http://cfa-www.harvard.edu/~vbromm

Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects

The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO4-···H+···-OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight

Mechanism of Vanadium Leaching during Surface Weathering of Basic Oxygen Furnace Steel Slag Blocks: A Microfocus X-ray Absorption Spectroscopy and Electron Microscopy Study

© 2017 American Chemical Society. Basic oxygen furnace (BOF) steelmaking slag is enriched in potentially toxic V which may become mobilized in high pH leachate during weathering. BOF slag was weathered under aerated and air-excluded conditions for 6 months prior to SEM/EDS and μXANES analysis to determine V host phases and speciation in both primary and secondary phases. Leached blocks show development of an altered region in which free lime and dicalcium silicate phases were absent and Ca-Si-H was precipitated (CaCO 3 was also present under aerated conditions). μXANES analyses show that V was released to solution as V(V) during dicalcium silicate dissolution and some V was incorporated into neo-formed Ca-Si-H. Higher V concentrations were observed in leachate under aerated conditions than in the air-excluded leaching experiment. Aqueous V concentrations were controlled by Ca 3 (VO 4 ) 2 solubility, which demonstrate an inverse relationship between Ca and V concentrations. Under air-excluded conditions Ca concentrations were controlled by dicalcium silicate dissolution and Ca-Si-H precipitation, leading to relatively high Ca and correspondingly low V concentrations. Formation of CaCO 3 under aerated conditions provided a sink for aqueous Ca, allowing higher V concentrations limited by kinetic dissolution rates of dicalcium silicate. Thus, V release may be slowed by the precipitation of secondary phases in the altered region, improving the prospects for slag reuse

Temporal-spatial structure of magnetic merging at the magnetopause inferred from 557.7-nm all-sky images

We demonstrate that high-resolution 557.7-nm all-sky images are useful tools for investigating the spatial and temporal evolution of merging on the dayside magnetopause. Analysis of ground and satellite measurements leads us to conclude that high-latitude merging events can occur at multiple sites simultaneously and vary asynchronously on time scales of 30s to 3min. Variations of 557.7nm emissions were observed at a 10s cadence at Ny-Ålesund on 19 December 2001, while significant changes in the IMF clock angle were reaching the magnetopause. The optical patterns are consistent with a scenario in which merging occurs around the rim of the high-latitude cusp at positions dictated by the IMF clock angle. Electrons energized at merging sites represent plausible sources for 557.7nm emissions in the cusp. Polar observations at the magnetopause have directly linked enhanced fluxes of ≥0.5keV electrons with merging. Spectra of electrons responsible for some of the emissions, measured during a DMSP F15 overflight, exhibit "inverted-V" features, indicating further acceleration above the ionosphere. SuperDARN spectral width boundaries, characteristic of open-closed field line transitions, are located at the equatorward edge of the 557.7nm emissions. Optical data suggest that with IMF <i>B<sub>Y</sub></i>>0, the Northern Hemisphere cusp divides into three source regions. When the IMF clock angle was ~150° structured 557.7-nm emissions came from east of the 13:00 MLT meridian. At larger clock angles the emissions appeared between 12:00 and 13:00 MLT. No significant 557.7-nm emissions were detected in the prenoon MLT sector. MHD simulations corroborate our scenario, showing that with the observed large dipole-tilt and IMF clock angles, merging sites develop near the front and eastern portions of the high-altitude cusp rim in the Northern Hemisphere and near the western part of the cusp rim in the Southern Hemisphere

Explosive Nucleosynthesis in Hypernovae

We examine the characteristics of nucleosynthesis in 'hypernovae', i.e., supernovae with very large explosion energies ( \gsim 10^{52} ergs). We carry out detailed nucleosynthesis calculations for these energetic explosions and compare the yields with those of ordinary core-collapse supernovae. We find that both complete and incomplete Si-burning takes place over more extended, lower density regions, so that the alpha-rich freezeout is enhanced and produces more Ti in comparison with ordinary supernova nucleosynthesis. In addition, oxygen and carbon burning takes place in more extended, lower density regions than in ordinary supernovae. Therefore, the fuel elements O, C, Al are less abundant while a larger amount of Si, S, Ar, and Ca ("Si") are synthesized by oxygen burning; this leads to larger ratios of "Si"/O in the ejecta. Enhancement of the mass ratio between complete and incomplete Si-burning regions in the ejecta may explain the abundance ratios among iron-peak elements in metal-poor stars. Also the enhanced "Si"/O ratio may explain the abundance ratios observed in star burst galaxies. We also discuss other implications of enhanced [Ti/Fe] and [Fe/O] for Galactic chemical evolution and the abundances of low mass black hole binaries.Comment: Accepted for publication in the Astrophysical Journal (13 March 2001) Tables 6 - 9 are available at http://www.astron.s.u-tokyo.ac.jp/~nakamura/research/papers/nakamuratab.ps.g

Binary separation in very thin nematic films: thickness and phase coexistence

The behavior as a function of temperature of very thin films (10 to 200 nm) of pentylcyanobiphenyl (5CB) on silicon substrates is reported. In the vicinity of the nematic/isotropic transition we observe a coexistence of two regions of different thicknesses: thick regions are in the nematic state while thin ones are in the isotropic state. Moreover, the transition temperature is shifted downward following a 1/h^2 law (h is the film thickness). Microscope observations and small angle X-ray scattering allowed us to draw a phase diagram which is explained in terms of a binary first order phase transition where thickness plays the role of an order parameter.Comment: 5 pages, 3 figures, submitted to PRL on the 26th of Apri

The Chicken Yolk Sac IgY Receptor, a Mammalian Mannose Receptor Family Member, Transcytoses IgY across Polarized Epithelial Cells

In mammals the transfer of passive immunity from mother to young is mediated by the MHC-related receptor FcRn, which transports maternal IgG across epithelial cell barriers. In birds, maternal IgY in egg yolk is transferred across the yolk sac to passively immunize chicks during gestation and early independent life. The chicken yolk sac IgY receptor (FcRY) is the ortholog of the mammalian phospholipase A2 receptor, a mannose receptor family member, rather than an FcRn or MHC homolog. FcRn and FcRY both exhibit ligand binding at the acidic pH of endosomes and ligand release at the slightly basic pH of blood. Here we show that FcRY expressed in polarized mammalian epithelial cells functioned in endocytosis, bidirectional transcytosis, and recycling of chicken FcY/IgY. Confocal immunofluorescence studies demonstrated that IgY binding and endocytosis occurred at acidic but not basic pH, mimicking pH-dependent uptake of IgG by FcRn. Colocalization studies showed FcRY-mediated internalization via clathrin-coated pits and transport involving early and recycling endosomes. Disruption of microtubules partially inhibited apical-to-basolateral and basolateral-to-apical transcytosis, but not recycling, suggesting the use of different trafficking machinery. Our results represent the first cell biological evidence of functional equivalence between FcRY and FcRn and provide an intriguing example of how evolution can give rise to systems in which similar biological requirements in different species are satisfied utilizing distinct protein folds