Domain Structure of the Staphylococcus aureus Collagen Adhesin

Sequence analysis of surface proteins from Gram-positive bacteria indicates a composite organization consisting of unique and repeated segments. Thus, these proteins may contain discrete domains that could fold independently. In this paper, we have used a panel of biophysical methods, including gel permeation chromatography, analytical ultracentrifugation, circular dichroism, and fluorescence spectroscopy, to analyze the structural organization of the Staphylococcus aureus collagen adhesin, CNA. Our results indicate that the structure, function, and folding of the ligand-binding domain (A) are not affected by the presence or absence of the other major domain (B). In addition, little or no interaction is observed between the nearly identical repeat units within the B domain. We propose that CNA is indeed a mosaic protein in which the different domains previously indicated by sequence analysis operate independently

Equilibrium solutions of the shallow water equations

A statistical method for calculating equilibrium solutions of the shallow water equations, a model of essentially 2-d fluid flow with a free surface, is described. The model contains a competing acoustic turbulent {\it direct} energy cascade, and a 2-d turbulent {\it inverse} energy cascade. It is shown, nonetheless that, just as in the corresponding theory of the inviscid Euler equation, the infinite number of conserved quantities constrain the flow sufficiently to produce nontrivial large-scale vortex structures which are solutions to a set of explicitly derived coupled nonlinear partial differential equations.Comment: 4 pages, no figures. Submitted to Physical Review Letter

Inverse monoids and immersions of 2-complexes

It is well known that under mild conditions on a connected topological space $\mathcal X$, connected covers of $\mathcal X$ may be classified via conjugacy classes of subgroups of the fundamental group of $\mathcal X$. In this paper, we extend these results to the study of immersions into 2-dimensional CW-complexes. An immersion $f : {\mathcal D} \rightarrow \mathcal C$ between CW-complexes is a cellular map such that each point $y \in {\mathcal D}$ has a neighborhood $U$ that is mapped homeomorphically onto $f(U)$ by $f$. In order to classify immersions into a 2-dimensional CW-complex $\mathcal C$, we need to replace the fundamental group of $\mathcal C$ by an appropriate inverse monoid. We show how conjugacy classes of the closed inverse submonoids of this inverse monoid may be used to classify connected immersions into the complex

Local Spin-Gauge Symmetry of the Bose-Einstein Condensates in Atomic Gases

The Bose-Einstein condensates of alkali atomic gases are spinor fields with local ``spin-gauge" symmetry. This symmetry is manifested by a superfluid velocity ${\bf u}_{s}$ (or gauge field) generated by the Berry phase of the spin field. In ``static" traps, ${\bf u}_{s}$ splits the degeneracy of the harmonic energy levels, breaks the inversion symmetry of the vortex nucleation frequency ${\bf \Omega}_{c1}$, and can lead to {\em vortex ground states}. The inversion symmetry of ${\bf \Omega}_{c1}$, however, is not broken in ``dynamic" traps. Rotations of the atom cloud can be generated by adiabatic effects without physically rotating the entire trap.Comment: Typos in the previous version corrected, thanks to the careful reading of Daniel L. Cox. 13 pages + 2 Figures in uuencode + gzip for

Complex Patterns in Reaction-Diffusion Systems: A Tale of Two Front Instabilities

Two front instabilities in a reaction-diffusion system are shown to lead to the formation of complex patterns. The first is an instability to transverse modulations that drives the formation of labyrinthine patterns. The second is a Nonequilibrium Ising-Bloch (NIB) bifurcation that renders a stationary planar front unstable and gives rise to a pair of counterpropagating fronts. Near the NIB bifurcation the relation of the front velocity to curvature is highly nonlinear and transitions between counterpropagating fronts become feasible. Nonuniformly curved fronts may undergo local front transitions that nucleate spiral-vortex pairs. These nucleation events provide the ingredient needed to initiate spot splitting and spiral turbulence. Similar spatio-temporal processes have been observed recently in the ferrocyanide-iodate-sulfite reaction.Comment: Text: 14 pages compressed Postscript (90kb) Figures: 9 pages compressed Postscript (368kb

Rap1 binding and a lipid-dependent helix in talin F1 domain promote integrin activation in tandem.

Rap1 GTPases bind effectors, such as RIAM, to enable talin1 to induce integrin activation. In addition, Rap1 binds directly to the talin1 F0 domain (F0); however, this interaction makes a limited contribution to integrin activation in CHO cells or platelets. Here, we show that talin1 F1 domain (F1) contains a previously undetected Rap1-binding site of similar affinity to that in F0. A structure-guided point mutant (R118E) in F1, which blocks Rap1 binding, abolishes the capacity of Rap1 to potentiate talin1-induced integrin activation. The capacity of F1 to mediate Rap1-dependent integrin activation depends on a unique loop in F1 that has a propensity to form a helix upon binding to membrane lipids. Basic membrane-facing residues of this helix are critical, as charge-reversal mutations led to dramatic suppression of talin1-dependent activation. Thus, a novel Rap1-binding site and a transient lipid-dependent helix in F1 work in tandem to enable a direct Rap1-talin1 interaction to cause integrin activation

Evaporative cooling of trapped fermionic atoms

We propose an efficient mechanism for the evaporative cooling of trapped fermions directly into quantum degeneracy. Our idea is based on an electric field induced elastic interaction between trapped atoms in spin symmetric states. We discuss some novel general features of fermionic evaporative cooling and present numerical studies demonstrating the feasibility for the cooling of alkali metal fermionic species $^6$Li, $^{40}$K, and $^{82,84,86}$Rb. We also discuss the sympathetic cooling of fermionic hyperfine spin mixtures, including the effects of anisotropic interactions.Comment: to be publishe

Observation of critical phenomena and self-similarity in the gravitational collapse of radiation fluid

We observe critical phenomena in spherical collapse of radiation fluid. A sequence of spacetimes $\cal{S}[\eta]$ is numerically computed, containing models ($\eta\ll 1$) that adiabatically disperse and models ($\eta\gg 1$) that form a black hole. Near the critical point ($\eta_c$), evolutions develop a self-similar region within which collapse is balanced by a strong, inward-moving rarefaction wave that holds $m(r)/r$ constant as a function of a self-similar coordinate $\xi$. The self-similar solution is known and we show near-critical evolutions asymptotically approaching it. A critical exponent $\beta \simeq 0.36$ is found for supercritical ($\eta>\eta_c$) models.Comment: 10 pages (LaTeX) (to appear in Phys. Rev. Lett.), TAR-039-UN

The Dynamics of a Meandering River

We present a statistical model of a meandering river on an alluvial plane which is motivated by the physical non-linear dynamics of the river channel migration and by describing heterogeneity of the terrain by noise. We study the dynamics analytically and numerically. The motion of the river channel is unstable and we show that by inclusion of the formation of ox-bow lakes, the system may be stabilised. We then calculate the steady state and show that it is in agreement with simulations and measurements of field data.Comment: Revtex, 12 pages, 2 postscript figure