Gradient Particle Magnetohydrodynamics

We introduce Gradient Particle Magnetohydrodynamics (GPM), a new Lagrangian method for magnetohydrodynamics based on gradients corrected for the locally disordered particle distribution. The development of a numerical code for MHD simulation using the GPM algorithm is outlined. Validation tests simulating linear and nonlinear sound waves, linear MHD waves, advection of magnetic fields in a magnetized vortex, hydrodynamical shocks, and three-dimensional collapse are presented, demonstrating the viability of an MHD code using GPM. The characteristics of a GPM code are discussed and possible avenues for further development and refinement are mentioned. We conclude with a view of how GPM may complement other methods currently in development for the next generation of computational astrophysics.Comment: 26 pages, 11 figure

The Gaia-ESO Survey: the selection function of the Milky Way field stars

The Gaia-ESO Survey was designed to target all major Galactic components (i.e., bulge, thin and thick discs, halo and clusters), with the goal of constraining the chemical and dynamical evolution of the Milky Way. This paper presents the methodology and considerations that drive the selection of the targeted, allocated and successfully observed Milky Way field stars. The detailed understanding of the survey construction, specifically the influence of target selection criteria on observed Milky Way field stars is required in order to analyse and interpret the survey data correctly. We present the target selection process for the Milky Way field stars observed with VLT/FLAMES and provide the weights that characterise the survey target selection. The weights can be used to account for the selection effects in the Gaia-ESO Survey data for scientific studies. We provide a couple of simple examples to highlight the necessity of including such information in studies of the stellar populations in the Milky Way.Comment: 18 pages, 19 figures, Accepted for publication in MNRAS (April 25, 2016

Nonequilibrium Forces Between Neutral Atoms Mediated by a Quantum Field

We study all known and as yet unknown forces between two neutral atoms, modeled as three dimensional harmonic oscillators, arising from mutual influences mediated by an electromagnetic field but not from their direct interactions. We allow as dynamical variables the center of mass motion of the atom, its internal degrees of freedom and the quantum field treated relativistically. We adopt the method of nonequilibrium quantum field theory which can provide a first principle, systematic and unified description including the intrinsic field fluctuations and induced dipole fluctuations. The inclusion of self-consistent back-actions makes possible a fully dynamical description of these forces valid for general atom motion. In thermal equilibrium we recover the known forces -- London, van der Waals and Casimir-Polder forces -- between neutral atoms in the long-time limit but also discover the existence of two new types of interatomic forces. The first, a `nonequilibrium force', arises when the field and atoms are not in thermal equilibrium, and the second, which we call an `entanglement force', originates from the correlations of the internal degrees of freedom of entangled atoms.Comment: 16 pages, 2 figure

The Met80Ala and Tyr67His/Met80Ala mutants of human cytochrome cshed light on the reciprocal role of Met80 and Tyr67 in regulating ligand access into the heme pocket.

The spectroscopic and functional properties of the single Met80Ala and double Tyr67His/Met80Ala mutants of human cytochrome c have been investigated in their ferric and ferrous forms, and in the presence of different ligands, in order to clarify the reciprocal effect of these two residues in regulating the access of exogenous molecules into the heme pocket. In the ferric state, both mutants display an aquo high spin and a low spin species. The latter corresponds to an OH- ligand in Met80Ala but to a His in the double mutant. The existence of these two species is also reflected in the functional behavior of the mutants. The observation that (i) a significant peroxidase activity is present in the Met80Ala mutants, (ii) the substitution of the Tyr67 by His leads to only a slight increase of the peroxidase activity in the Tyr67His/Met80Ala double mutant with respect to wild type, while the Tyr67His mutant behaves as wild type, as previously reported, suggests that the peroxidase activity of cytochrome c is linked to an overall conformational change of the heme pocket and not only to the disappearance of the Fe-Met80 bond. Therefore, in human cytochrome c there is an interplay between the two residues at positions 67 and 80 that affects the conformation of the distal side of the heme pocket, and thus the sixth coordination of the hem

The key role played by charge in the interaction of cytochrome c with cardiolipin

Cytochrome c undergoes structural variations upon binding of cardiolipin, one of the phospholipids constituting the mitochondrial membrane. Although several mechanisms governing cytochrome c/cardiolipin (cyt c/CL) recognition have been proposed, the interpretation of the process remains, at least in part, unknown. To better define the steps characterizing the cyt c-CL interaction, the role of Lys72 and Lys73, two residues thought to be important in the protein/lipid binding interaction, were recently investigated by mutagenesis. The substitution of the two (positively charged) Lys residues with Asn revealed that such mutations cancel the CL-dependent peroxidase activity of cyt c; furthermore, CL does not interact with the Lys72Asn mutant. In the present paper, we extend our study to the Lys → Arg mutants to investigate the influence exerted by the charge possessed by the residues located at positions 72 and 73 on the cyt c/CL interaction. On the basis of the present work a number of overall conclusions can be drawn: (i) position 72 must be occupied by a positively charged residue to assure cyt c/CL recognition; (ii) the Arg residues located at positions 72 and 73 permit cyt c to react with CL; (iii) the replacement of Lys72 with Arg weakens the second (low-affinity) binding transition; (iv) the Lys73Arg mutation strongly increases the peroxidase activity of the CL-bound protein

The 40s Omega-loop plays a critical role in the stability and the alkaline conformational transition of cytochrome c

The structural and redox properties of a non-covalent complex reconstituted upon mixing two non-contiguous fragments of horse cytochrome c, the residues 1 - 38 heme-containing N-fragment with the residues 57 - 104 C-fragment, have been investigated. With respect to native cyt c, the complex lacks a segment of 18 residues, corresponding, in the native protein, to an omega ( W)loop region. The fragment complex shows compact structure, native-like alpha-helix content but a less rigid atomic packing and reduced stability with respect to the native protein. Structural heterogeneity is observed at pH 7.0, involving formation of an axially misligated low-spin species and consequent partial displacement of Met80 from the sixth coordination position of the heme-iron. Spectroscopic data suggest that a lysine ( located in the Met80-containing loop, namely Lys72, Lys73, or Lys79) replaces the methionine residue. The residues 1 - 38/57 - 104 fragment complex shows an unusual biphasic alkaline titration characterized by a low (pK(a1)= 6.72) and a high pK(a)-associated state transition (pK(a2)= 8.56); this behavior differs from that of native cyt c, which shows a monophasic alkaline transition ( pK(a)= 8.9). The data indicate that the 40s Omega-loop plays an important role in the stability of cyt c and in ensuring a correct alkaline conformational transition of the protein

Spin operator matrix elements in the superintegrable chiral Potts quantum chain

We derive spin operator matrix elements between general eigenstates of the superintegrable Z_N-symmetric chiral Potts quantum chain of finite length. Our starting point is the extended Onsager algebra recently proposed by R.Baxter. For each pair of spaces (Onsager sectors) of the irreducible representations of the Onsager algebra, we calculate the spin matrix elements between the eigenstates of the Hamiltonian of the quantum chain in factorized form, up to an overall scalar factor. This factor is known for the ground state Onsager sectors. For the matrix elements between the ground states of these sectors we perform the thermodynamic limit and obtain the formula for the order parameters. For the Ising quantum chain in a transverse field (N=2 case) the factorized form for the matrix elements coincides with the corresponding expressions obtained recently by the Separation of Variables Method.Comment: 24 pages, 1 figur

Divergence in Dialogue

Copyright: 2014 Healey et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.This work was supported by the Economic and Social Research Council (ESRC; http://www.esrc.ac.uk/) through the DynDial project (Dynamics of Conversational Dialogue, RES-062-23-0962) and the Engineering and Physical Sciences Research Council (EPSRC; http://www.epsrc.ac.uk/) through the RISER project (Robust Incremental Semantic Resources for Dialogue, EP/J010383/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript