Localization of antimicrobial peptides in the tunic of Ciona intestinalis ( Ascidiacea, Tunicata) and their involvement in local inflammatory-like reactions

Tunicates comprising a wide variety of different species synthesize antimicrobial peptides as important effector molecules of the innate immune system. Recently, two putative gene families coding for antimicrobial peptides were identified in the expressed sequence tag database of the tunicate Ciona intestinalis. Two synthetic peptides representing the cationic core region of one member of each of the families displayed potent antibacterial and antifungal activities. Moreover, the natural peptides were demonstrated to be synthesized and stored in distinct hemocyte types. Here, we investigated the presence of these natural peptides, namely Ci-MAM-A and Ci-PAP-A, in the tunic of C. intestinalis considering that the ascidian tunic is a body surface barrier exposed to constant microbial assault. Furthermore, as the tunic may represent a major route of entry for pathogen invasion after its damage we monitored the location of these peptides upon a local inflammatory-like reaction induced by injection of foreign cells. Using immunocytochemistry and electron microscopy both peptides were localized to the tunic and were massively present in granulocytes of inflamed tissue. Conclusively, antimicrobial peptides may constitute a chemical barrier within the tunic of urochordates

Exact results for the reactivity of a single-file system

We derive analytical expressions for the reactivity of a Single-File System with fast diffusion and adsorption and desorption at one end. If the conversion reaction is fast, then the reactivity depends only very weakly on the system size, and the conversion is about 100%. If the reaction is slow, then the reactivity becomes proportional to the system size, the loading, and the reaction rate constant. If the system size increases the reactivity goes to the geometric mean of the reaction rate constant and the rate of adsorption and desorption. For large systems the number of nonconverted particles decreases exponentially with distance from the adsorption/desorption end.Comment: 4 pages, 2 figure

Anomalous tag diffusion in the asymmetric exclusion model with particles of arbitrary sizes

Anomalous behavior of correlation functions of tagged particles are studied in generalizations of the one dimensional asymmetric exclusion problem. In these generalized models the range of the hard-core interactions are changed and the restriction of relative ordering of the particles is partially brocken. The models probing these effects are those of biased diffusion of particles having size S=0,1,2,..., or an effective negative "size" S=-1,-2,..., in units of lattice space. Our numerical simulations show that irrespective of the range of the hard-core potential, as long some relative ordering of particles are kept, we find suitable sliding-tag correlation functions whose fluctuations growth with time anomalously slow ($t^{{1/3}}$), when compared with the normal diffusive behavior ($t^{{1/2}}$). These results indicate that the critical behavior of these stochastic models are in the Kardar-Parisi-Zhang (KPZ) universality class. Moreover a previous Bethe-ansatz calculation of the dynamical critical exponent $z$, for size $S \geq 0$ particles is extended to the case $S<0$ and the KPZ result $z=3/2$ is predicted for all values of $S \in {Z}$.Comment: 4 pages, 3 figure

Event-based relaxation of continuous disordered systems

A computational approach is presented to obtain energy-minimized structures in glassy materials. This approach, the activation-relaxation technique (ART), achieves its efficiency by focusing on significant changes in the microscopic structure (events). The application of ART is illustrated with two examples: the structure of amorphous silicon, and the structure of Ni80P20, a metallic glass.Comment: 4 pages, revtex, epsf.sty, 3 figure

Molecular Spiders in One Dimension

Molecular spiders are synthetic bio-molecular systems which have "legs" made of short single-stranded segments of DNA. Spiders move on a surface covered with single-stranded DNA segments complementary to legs. Different mappings are established between various models of spiders and simple exclusion processes. For spiders with simple gait and varying number of legs we compute the diffusion coefficient; when the hopping is biased we also compute their velocity.Comment: 14 pages, 2 figure

Spin and charge excitations in incommensurate spin density waves

Collective excitations both for spin- and charge-channels are investigated in incommensurate spin density wave (or stripe) states on two-dimensional Hubbard model. By random phase approximation, the dynamical susceptibility \chi(q,\omega) is calculated for full range of (q,\omega) with including all higher harmonics components. An intricate landscape of the spectra in \chi(q,\omega) is obtained. We discuss the anisotropy of the dispersion cones for spin wave excitations, and for the phason excitation related to the motion of the stripe line. Inelastic neutron experiments on Cr and its alloys and stripe states of underdoped cuprates are proposed

Effect of hydrogen on ground state structures of small silicon clusters

We present results for ground state structures of small Si$_{n}$H (2 \leq \emph{n} \leq 10) clusters using the Car-Parrinello molecular dynamics. In particular, we focus on how the addition of a hydrogen atom affects the ground state geometry, total energy and the first excited electronic level gap of an Si$_{n}$ cluster. We discuss the nature of bonding of hydrogen in these clusters. We find that hydrogen bonds with two silicon atoms only in Si$_{2}$H, Si$_{3}$H and Si$_{5}$H clusters, while in other clusters (i.e. Si$_{4}$H, Si$_{6}$H, Si$_{7}$H, Si$_{8}$H, Si$_{9}$H and Si$_{10}$H) hydrogen is bonded to only one silicon atom. Also in the case of a compact and closed silicon cluster hydrogen bonds to the cluster from outside. We find that the first excited electronic level gap of Si$_{n}$ and Si$_{n}$H fluctuates as a function of size and this may provide a first principles basis for the short-range potential fluctuations in hydrogenated amorphous silicon. Our results show that the addition of a single hydrogen can cause large changes in the electronic structure of a silicon cluster, though the geometry is not much affected. Our calculation of the lowest energy fragmentation products of Si$_{n}$H clusters shows that hydrogen is easily removed from Si$_{n}$H clusters.Comment: one latex file named script.tex including table and figure caption. Six postscript figure files. figure_1a.ps and figure_1b.ps are files representing Fig. 1 in the main tex

Magnetic correlations and quantum criticality in the insulating antiferromagnetic, insulating spin liquid, renormalized Fermi liquid, and metallic antiferromagnetic phases of the Mott system V_2O_3

Magnetic correlations in all four phases of pure and doped vanadium sesquioxide V_2O_3 have been examined by magnetic thermal neutron scattering. While the antiferromagnetic insulator can be accounted for by a Heisenberg localized spin model, the long range order in the antiferromagnetic metal is an incommensurate spin-density-wave, resulting from a Fermi surface nesting instability. Spin dynamics in the strongly correlated metal are dominated by spin fluctuations in the Stoner electron-hole continuum. Furthermore, our results in metallic V_2O_3 represent an unprecedentedly complete characterization of the spin fluctuations near a metallic quantum critical point, and provide quantitative support for the SCR theory for itinerant antiferromagnets in the small moment limit. Dynamic magnetic correlations for energy smaller than k_BT in the paramagnetic insulator carry substantial magnetic spectral weight. However, the correlation length extends only to the nearest neighbor distance. The phase transition to the antiferromagnetic insulator introduces a sudden switching of magnetic correlations to a different spatial periodicity which indicates a sudden change in the underlying spin Hamiltonian. To describe this phase transition and also the unusual short range order in the paramagnetic state, it seems necessary to take into account the orbital degrees of freedom associated with the degenerate d-orbitals at the Fermi level in V_2O_3.Comment: Postscript file, 24 pages, 26 figures, 2 tables, accepted by Phys. Rev.

Interplay between Anomalous Transport and Catalytic Reaction Kinetics in Single-File Nanoporous Systems

Functionalized nanoporous materials have broad utility for catalysis applications. However, the kinetics of catalytic reaction processes in these systems can be strongly impacted by the anomalous transport. The most extreme case corresponds to single-file diffusion for narrow pores in which species cannot pass each other. For conversion reactions with a single-file constraint, traditional mean-field-type reaction-diffusion equations fail to capture the initial evolution of concentration profiles, and they cannot describe the scaling behavior of steady-state reactivity. Hydrodynamic reaction-diffusion equations accounting for the single-file aspects of chemical diffusion can describe such initial evolution, but additional refinements are needed to incorporate fluctuation effects controlling, for example, steady-state reactivity localized near pore openings. For polymerization reactions with a single-file constraint, initial behavior depends strongly on system details such as catalytic site loading and reaction rate. However, long-time behavior often involves the formation of a dominant large polymer near each end of the pore, initially within the pore but subsequently partly extruding. In this partial extrusion regime, the kinetics is governed by the special features of the random walk describing the motion of the end of the partly extruded polymer, noting that this extruded end must return within the pore for further growth