Detailed characterization of the O-linked glycosylation of the neuropilin-1 c/MAM-domain

Neuropilins are involved in angiogenesis and neuronal development. The membrane proximal domain of neuropilin-1, called c or MAM domain based on its sequence conservation, has been implicated in neuropilin oligomerization required for its function. The c/MAM domain of human neuropilin-1 has been recombinantly expressed to allow for investigation of its propensity to engage in molecular interactions with other protein or carbohydrate components on a cell surface. We found that the c/MAM domain was heavily O-glycosylated with up to 24 monosaccharide units in the form of disialylated core 1 and core 2 O-glycans. Attachment sites were identified on the chymotryptic c/MAM peptide ETGATEKPTVIDSTIQSEFPTY by electron-transfer dissociation mass spectrometry (ETD-MS/MS). For highly glycosylated species consisting of carbohydrate to about 50 %, useful results could only be obtained upon partial desialylation. ETD-MS/MS revealed a hierarchical order of the initial O-GalNAc addition to the four different glycosylation sites. These findings enable future functional studies about the contribution of the described glycosylations in neuropilin-1 oligomerization and the binding to partner proteins as VEGF or galectin-1. As a spin-off result the sialidase from Clostridium perfringens turned out to discriminate between galactose- and N-acetylgalactosamine-linked sialic acid

Affine T-varieties of complexity one and locally nilpotent derivations

Let X=spec A be a normal affine variety over an algebraically closed field k of characteristic 0 endowed with an effective action of a torus T of dimension n. Let also D be a homogeneous locally nilpotent derivation on the normal affine Z^n-graded domain A, so that D generates a k_+-action on X that is normalized by the T-action. We provide a complete classification of pairs (X,D) in two cases: for toric varieties (n=\dim X) and in the case where n=\dim X-1. This generalizes previously known results for surfaces due to Flenner and Zaidenberg. As an application we compute the homogeneous Makar-Limanov invariant of such varieties. In particular we exhibit a family of non-rational varieties with trivial Makar-Limanov invariant.Comment: 31 pages. Minor changes in the structure. Fixed some typo

Modified group projectors: tight binding method

Modified group projector technique for induced representations is a powerful tool for calculation and symmetry quantum numbers assignation of a tight binding Hamiltonian energy bands of crystals. Namely, the induced type structure of such a Hamiltonian enables efficient application of the procedure: only the interior representations of the orbit stabilizers are to be considered. Then the generalized Bloch eigen functions are obtained naturally by the expansion to the whole state space. The method is applied to the electronic pi-bands of the single wall carbon nanotubes: together with dispersion relations, their complete symmetry assignation by the full symmetry (line) groups and the corresponding symmetry-adapted eigen function are found.Comment: 10 pages 1 figur

Towards Supergravity Duals of Chiral Symmetry Breaking in Sasaki-Einstein Cascading Quiver Theories

We construct a first order deformation of the complex structure of the cone over Sasaki-Einstein spaces Y^{p,q} and check supersymmetry explicitly. This space is a central element in the holographic dual of chiral symmetry breaking for a large class of cascading quiver theories. We discuss a solution describing a stack of N D3 branes and M fractional D3 branes at the tip of the deformed spaces.Comment: 28 pages, no figures. v2: typos, references and a note adde

Irreducible Representations of Diperiodic Groups

The irreducible representations of all of the 80 diperiodic groups, being the symmetries of the systems translationally periodical in two directions, are calculated. To this end, each of these groups is factorized as the product of a generalized translational group and an axial point group. The results are presented in the form of the tables, containing the matrices of the irreducible representations of the generators of the groups. General properties and some physical applications (degeneracy and topology of the energy bands, selection rules, etc.) are discussed.Comment: 30 pages, 5 figures, 28 tables, 18 refs, LaTex2.0

New Langevin and Gradient Thermostats for Rigid Body Dynamics

We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of angular coordinates; both thermostats preserve the unit length of quaternions. The Langevin thermostat also ensures that the conjugate angular momenta stay within the tangent space of the quaternion coordinates, as required by the Hamiltonian dynamics of rigid bodies. We have constructed three geometric numerical integrators for the Langevin thermostat and one for the gradient thermostat. The numerical integrators reflect key properties of the thermostats themselves. Namely, they all preserve the unit length of quaternions, automatically, without the need of a projection onto the unit sphere. The Langevin integrators also ensure that the angular momenta remain within the tangent space of the quaternion coordinates. The Langevin integrators are quasi-symplectic and of weak order two. The numerical method for the gradient thermostat is of weak order one. Its construction exploits ideas of Lie-group type integrators for differential equations on manifolds. We numerically compare the discretization errors of the Langevin integrators, as well as the efficiency of the gradient integrator compared to the Langevin ones when used in the simulation of rigid TIP4P water model with smoothly truncated electrostatic interactions. We observe that the gradient integrator is computationally less efficient than the Langevin integrators. We also compare the relative accuracy of the Langevin integrators in evaluating various static quantities and give recommendations as to the choice of an appropriate integrator.Comment: 16 pages, 4 figure

Clebsch-Gordan Construction of Lattice Interpolating Fields for Excited Baryons

Large sets of baryon interpolating field operators are developed for use in lattice QCD studies of baryons with zero momentum. Operators are classified according to the double-valued irreducible representations of the octahedral group. At first, three-quark smeared, local operators are constructed for each isospin and strangeness and they are classified according to their symmetry with respect to exchange of Dirac indices. Nonlocal baryon operators are formulated in a second step as direct products of the spinor structures of smeared, local operators together with gauge-covariant lattice displacements of one or more of the smeared quark fields. Linear combinations of direct products of spinorial and spatial irreducible representations are then formed with appropriate Clebsch-Gordan coefficients of the octahedral group. The construction attempts to maintain maximal overlap with the continuum SU(2) group in order to provide a physically interpretable basis. Nonlocal operators provide direct couplings to states that have nonzero orbital angular momentum.Comment: This manuscript provides an anlytical construction of operators and is related to hep-lat/0506029, which provides a computational construction. This e-print version contains a full set of Clebsch-Gordan coefficients for the octahedral grou

Nonlinear Band Structure in Bose Einstein Condensates: The Nonlinear Schr\"odinger Equation with a Kronig-Penney Potential

All Bloch states of the mean field of a Bose-Einstein condensate in the presence of a one dimensional lattice of impurities are presented in closed analytic form. The band structure is investigated by analyzing the stationary states of the nonlinear Schr\"odinger, or Gross-Pitaevskii, equation for both repulsive and attractive condensates. The appearance of swallowtails in the bands is examined and interpreted in terms of the condensates superfluid properties. The nonlinear stability properties of the Bloch states are described and the stable regions of the bands and swallowtails are mapped out. We find that the Kronig-Penney potential has the same properties as a sinusoidal potential; Bose-Einstein condensates are trapped in sinusoidal optical lattices. The Kronig-Penney potential has the advantage of being analytically tractable, unlike the sinusoidal potential, and, therefore, serves as a good model for experimental phenomena.Comment: Version 2. Fixed typos, added referenc

GNO Solar Neutrino Observations: Results for GNOI

We report the first GNO solar neutrino results for the measuring period GNOI, solar exposure time May 20, 1998 till January 12, 2000. In the present analysis, counting results for solar runs SR1 - SR19 were used till April 4, 2000. With counting completed for all but the last 3 runs (SR17 - SR19), the GNO I result is [65.8 +10.2 -9.6 (stat.) +3.4 -3.6 (syst.)]SNU (1sigma) or [65.8 + 10.7 -10.2 (incl. syst.)]SNU (1sigma) with errors combined. This may be compared to the result for Gallex(I-IV), which is [77.5 +7.6 -7.8 (incl. syst.)] SNU (1sigma). A combined result from both GNOI and Gallex(I-IV) together is [74.1 + 6.7 -6.8 (incl. syst.)] SNU (1sigma).Comment: submitted to Physics Letters B, June 2000. PACS: 26.65. +t ; 14.60 Pq. Corresponding author: [email protected] ; [email protected]

Complete results for five years of GNO solar neutrino observations

We report the complete GNO solar neutrino results for the measuring periods GNO III, GNO II, and GNO I. The result for GNO III (last 15 solar runs) is [54.3 + 9.9 - 9.3 (stat.)+- 2.3 (syst.)] SNU (1 sigma) or [54.3 + 10.2 - 9.6 (incl. syst.)] SNU (1 sigma) with errors combined. The GNO experiment is now terminated after altogether 58 solar exposure runs that were performed between May 20, 1998 and April 9, 2003. The combined result for GNO (I+II+III) is [62.9 + 5.5 - 5.3 (stat.) +- 2.5 (syst.)] SNU (1 sigma) or [62.9 + 6.0 - 5.9] SNU (1 sigma) with errors combined in quadrature. Overall, gallium based solar observations at LNGS (first in GALLEX, later in GNO) lasted from May 14, 1991 through April 9, 2003. The joint result from 123 runs in GNO and GALLEX is [69.3 +- 5.5 (incl. syst.)] SNU (1 sigma). The distribution of the individual run results is consistent with the hypothesis of a neutrino flux that is constant in time. Implications from the data in particle- and astrophysics are reiterated.Comment: 22 pages incl. 9 Figures and 8 Tables. to appear in: Physics Letters B (accepted April 13, 2005) PACS: 26.65.+t ; 14.60.P