Stability transitions for axisymmetric relative equilibria of Euclidean symmetric Hamiltonian systems

In the presence of noncompact symmetry, the stability of relative equilibria under momentum-preserving perturbations does not generally imply robust stability under momentum-changing perturbations. For axisymmetric relative equilibria of Hamiltonian systems with Euclidean symmetry, we investigate different mechanisms of stability: stability by energy-momentum confinement, KAM, and Nekhoroshev stability, and we explain the transitions between these. We apply our results to the Kirchhoff model for the motion of an axisymmetric underwater vehicle, and we numerically study dissipation induced instability of KAM stable relative equilibria for this system.Comment: Minor revisions. Typographical errors correcte

Temperature Dependence of Facet Ridges in Crystal Surfaces

The equilibrium crystal shape of a body-centered solid-on-solid (BCSOS) model on a honeycomb lattice is studied numerically. We focus on the facet ridge endpoints (FRE). These points are equivalent to one dimensional KPZ-type growth in the exactly soluble square lattice BCSOS model. In our more general context the transfer matrix is not stochastic at the FRE points, and a more complex structure develops. We observe ridge lines sticking into the rough phase where thesurface orientation jumps inside the rounded part of the crystal. Moreover, the rough-to-faceted edges become first-order with a jump in surface orientation, between the FRE point and Pokrovsky-Talapov (PT) type critical endpoints. The latter display anisotropic scaling with exponent $z=3$ instead of familiar PT value $z=2$.Comment: 12 pages, 19 figure

Non-universal equilibrium crystal shape results from sticky steps

The anisotropic surface free energy, Andreev surface free energy, and equilibrium crystal shape (ECS) z=z(x,y) are calculated numerically using a transfer matrix approach with the density matrix renormalization group (DMRG) method. The adopted surface model is a restricted solid-on-solid (RSOS) model with "sticky" steps, i.e., steps with a point-contact type attraction between them (p-RSOS model). By analyzing the results, we obtain a first-order shape transition on the ECS profile around the (111) facet; and on the curved surface near the (001) facet edge, we obtain shape exponents having values different from those of the universal Gruber-Mullins-Pokrovsky-Talapov (GMPT) class. In order to elucidate the origin of the non-universal shape exponents, we calculate the slope dependence of the mean step height of "step droplets" (bound states of steps) using the Monte Carlo method, where p=(dz/dx, dz/dy)$, and represents the thermal averag |p| dependence of , we derive a |p|-expanded expression for the non-universal surface free energy f_{eff}(p), which contains quadratic terms with respect to |p|. The first-order shape transition and the non-universal shape exponents obtained by the DMRG calculations are reproduced thermodynamically from the non-universal surface free energy f_{eff}(p).Comment: 31 pages, 21 figure

Spongivory in the Wakatobi Marine National Park, Southeast Sulawesi, Indonesia

Sponges are functionally important coral reef fauna and there is strong evidence from the Caribbean that predation has important impacts on sponge-Assemblage dynamics; whether the same is true for Indo-Pacific sponges remains unknown. As a first step toward understanding the potential effects of spongivores on sponge diversity and abundance, we identified sponge predators at nine sites in Wakatobi Marine National Park, Indonesia, and conducted a short-Term caging experiment to examine the effects of excluding predators on noncryptic reef sponges at this location. Nudibranchs were the most abundant invertebrate spongivores, although their low densities are likely to limit their influence on sponges. Fish were the most abundant vertebrate spongivores with 16 species from six families observed feeding on sponges. Based on their abundance and our feeding observations, the fish with the greatest potential to influence sponge assemblages in Wakatobi Marine National Park were Zanclus cornutus, Chaetodon kleinii, Pygoplites diacanthus, and Pomacanthus sexstriatus. We did not detect an effect of excluding spongivores on noncryptic reef sponge abundance in our caging experiment, which may be due to these species having evolved chemical defenses against predators. Important areas for further research include the chemical ecology of Indo-Pacific sponges and whether spongivory currently restricts some species to cryptic or nonreef habitats

The clock genes Period 2 and Cryptochrome 2 differentially balance bone formation

Background: Clock genes and their protein products regulate circadian rhythms in mammals but have also been implicated in various physiological processes, including bone formation. Osteoblasts build new mineralized bone whereas osteoclasts degrade it thereby balancing bone formation. To evaluate the contribution of clock components in this process, we investigated mice mutant in clock genes for a bone volume phenotype. Methodology/Principal Findings: We found that Per2Brdm1 mutant mice as well as mice lacking Cry2-/- displayed significantly increased bone volume at 12 weeks of age, when bone turnover is high. Per2Brdm1 mutant mice showed alterations in parameters specific for osteoblasts whereas mice lacking Cry2-/- displayed changes in osteoclast specific parameters. Interestingly, inactivation of both Per2 and Cry2 genes leads to normal bone volume as observed in wild type animals. Importantly, osteoclast parameters affected due to the lack of Cry2, remained at the level seen in the Cry2-/- mutants despite the simultaneous inactivation of Per2. Conclusions/Significance: This indicates that Cry2 and Per2 affect distinct pathways in the regulation of bone volume with Cry2 influencing mostly the osteoclastic cellular component of bone and Per2 acting on osteoblast parameters

Trends and Challenges in Experimental Macromolecular Crystallography

Macromolecular X-ray crystallography underpins the vigorous field of structural molecular biology having yielded many protein, nucleic acid and virus structures in fine detail. The understanding of the recognition by these macromolecules, as receptors, of their cognate ligands involves the detailed study of the structural chemistry of their molecular interactions. Also these structural details underpin the rational design of novel inhibitors in modern drug discovery in the pharmaceutical industry. Moreover, from such structures the functional details can be inferred, such as the biological chemistry of enzyme reactivity. There is then a vast number and range of types of biological macromolecules that potentially could be studied. The completion of the protein primary sequencing of the yeast genome, and the human genome sequencing project comprising some 105 proteins that is underway, raises expectations for equivalent three dimensional structural database

How the oxygen tolerance of a [NiFe]-hydrogenase depends on quaternary structure

‘Oxygen-tolerant’ [NiFe]-hydrogenases can catalyze H(2) oxidation under aerobic conditions, avoiding oxygenation and destruction of the active site. In one mechanism accounting for this special property, membrane-bound [NiFe]-hydrogenases accommodate a pool of electrons that allows an O(2) molecule attacking the active site to be converted rapidly to harmless water. An important advantage may stem from having a dimeric or higher-order quaternary structure in which the electron-transfer relay chain of one partner is electronically coupled to that in the other. Hydrogenase-1 from E. coli has a dimeric structure in which the distal [4Fe-4S] clusters in each monomer are located approximately 12 Å apart, a distance conducive to fast electron tunneling. Such an arrangement can ensure that electrons from H(2) oxidation released at the active site of one partner are immediately transferred to its counterpart when an O(2) molecule attacks. This paper addresses the role of long-range, inter-domain electron transfer in the mechanism of O(2)-tolerance by comparing the properties of monomeric and dimeric forms of Hydrogenase-1. The results reveal a further interesting advantage that quaternary structure affords to proteins

Demagnetization via Nucleation of the Nonequilibrium Metastable Phase in a Model of Disorder

We study both analytically and numerically metastability and nucleation in a two-dimensional nonequilibrium Ising ferromagnet. Canonical equilibrium is dynamically impeded by a weak random perturbation which models homogeneous disorder of undetermined source. We present a simple theoretical description, in perfect agreement with Monte Carlo simulations, assuming that the decay of the nonequilibrium metastable state is due, as in equilibrium, to the competition between the surface and the bulk. This suggests one to accept a nonequilibrium "free-energy" at a mesoscopic/cluster level, and it ensues a nonequilibrium "surface tension" with some peculiar low-T behavior. We illustrate the occurrence of intriguing nonequilibrium phenomena, including: (i) Noise-enhanced stabilization of nonequilibrium metastable states; (ii) reentrance of the limit of metastability under strong nonequilibrium conditions; and (iii) resonant propagation of domain walls. The cooperative behavior of our system may also be understood in terms of a Langevin equation with additive and multiplicative noises. We also studied metastability in the case of open boundaries as it may correspond to a magnetic nanoparticle. We then observe burst-like relaxation at low T, triggered by the additional surface randomness, with scale-free avalanches which closely resemble the type of relaxation reported for many complex systems. We show that this results from the superposition of many demagnetization events, each with a well- defined scale which is determined by the curvature of the domain wall at which it originates. This is an example of (apparent) scale invariance in a nonequilibrium setting which is not to be associated with any familiar kind of criticality.Comment: 26 pages, 22 figure