The nucleoporin Nup60p functions as a Gsp1p–GTP-sensitive tether for Nup2p at the nuclear pore complex

The nucleoporins Nup60p, Nup2p, and Nup1p form part of the nuclear basket structure of the Saccharomyces cerevisiae nuclear pore complex (NPC). Here, we show that these necleoporins can be isolated from yeast extracts by affinity chromatography on karyopherin Kap95p-coated beads. To characterize Nup60p further, Nup60p-coated beads were used to capture its interacting proteins from extracts. We find that Nup60p binds to Nup2p and serves as a docking site for Kap95p–Kap60p heterodimers and Kap123p. Nup60p also binds Gsp1p–GTP and its guanine nucleotide exchange factor Prp20p, and functions as a Gsp1p guanine nucleotide dissociation inhibitor by reducing the activity of Prp20p. Yeast lacking Nup60p exhibit minor defects in nuclear export of Kap60p, nuclear import of Kap95p–Kap60p-dependent cargoes, and diffusion of small proteins across the NPC. Yeast lacking Nup60p also fail to anchor Nup2p at the NPC, resulting in the mislocalization of Nup2p to the nucleoplasm and cytoplasm. Purified Nup60p and Nup2p bind each other directly, but the stability of the complex is compromised when Kap60p binds Nup2p. Gsp1p–GTP enhances by 10-fold the affinity between Nup60p and Nup2p, and restores binding of Nup2p–Kap60p complexes to Nup60p. The results suggest a dynamic interaction, controlled by the nucleoplasmic concentration of Gsp1p–GTP, between Nup60p and Nup2p at the NPC

Soft and hard wall in a stochastic reaction diffusion equation

We consider a stochastically perturbed reaction diffusion equation in a bounded interval, with boundary conditions imposing the two stable phases at the endpoints. We investigate the asymptotic behavior of the front separating the two stable phases, as the intensity of the noise vanishes and the size of the interval diverges. In particular, we prove that, in a suitable scaling limit, the front evolves according to a one-dimensional diffusion process with a non-linear drift accounting for a "soft" repulsion from the boundary. We finally show how a "hard" repulsion can be obtained by an extra diffusive scaling.Comment: 33 page

Hydrodynamics of Spatially Ordered Superfluids

We derive the hydrodynamic equations for the supersolid and superhexatic phases of a neutral two-dimensional Bose fluid. We find, assuming that the normal part of the fluid is clamped to an underlying substrate, that both phases can sustain third-sound modes and that in the supersolid phase there are additional modes due to the superfluid motion of point defects (vacancies and interstitials).Comment: 24 pages of ReVTeX and 7 uuencoded figures. Submitted for publication in Phys. Rev.

Simple Fluids with Complex Phase Behavior

We find that a system of particles interacting through a simple isotropic potential with a softened core is able to exhibit a rich phase behavior including: a liquid-liquid phase transition in the supercooled phase, as has been suggested for water; a gas-liquid-liquid triple point; a freezing line with anomalous reentrant behavior. The essential ingredient leading to these features resides in that the potential investigated gives origin to two effective core radii.Comment: 7 pages including 3 eps figures + 1 jpeg figur

Three dimensional thermal-solute phase field simulation of binary alloy solidification

We employ adaptive mesh refinement, implicit time stepping, a nonlinear multigrid solver and parallel computation to solve a multi-scale, time dependent, three dimensional, nonlinear set of coupled partial differential equations for three scalar field variables. The mathematical model represents the non-isothermal solidification of a metal alloy into a melt substantially cooled below its freezing point at the microscale. Underlying physical molecular forces are captured at this scale by a specification of the energy field. The time rate of change of the temperature, alloy concentration and an order parameter to govern the state of the material (liquid or solid) are controlled by the diffusion parameters and variational derivatives of the energy functional. The physical problem is important to material scientists for the development of solid metal alloys and, hitherto, this fully coupled thermal problem has not been simulated in three dimensions, due to its computationally demanding nature. By bringing together state of the art numerical techniques this problem is now shown here to be tractable at appropriate resolution with relatively moderate computational resources

Mechanical Activation of Hypoxia-Inducible Factor 1α Drives Endothelial Dysfunction at Atheroprone Sites

OBJECTIVE: Atherosclerosis develops near branches and bends of arteries that are exposed to low shear stress (mechanical drag). These sites are characterized by excessive endothelial cell (EC) proliferation and inflammation that promote lesion initiation. The transcription factor HIF1α (hypoxia-inducible factor 1α) is canonically activated by hypoxia and has a role in plaque neovascularization. We studied the influence of shear stress on HIF1α activation and the contribution of this noncanonical pathway to lesion initiation. APPROACH AND RESULTS: Quantitative polymerase chain reaction and en face staining revealed that HIF1α was expressed preferentially at low shear stress regions of porcine and murine arteries. Low shear stress induced HIF1α in cultured EC in the presence of atmospheric oxygen. The mechanism involves the transcription factor nuclear factor-κB that induced HIF1α transcripts and induction of the deubiquitinating enzyme Cezanne that stabilized HIF1α protein. Gene silencing revealed that HIF1α enhanced proliferation and inflammatory activation in EC exposed to low shear stress via induction of glycolysis enzymes. We validated this observation by imposing low shear stress in murine carotid arteries (partial ligation) that upregulated the expression of HIF1α, glycolysis enzymes, and inflammatory genes and enhanced EC proliferation. EC-specific genetic deletion of HIF1α in hypercholesterolemic apolipoprotein E-defecient mice reduced inflammation and endothelial proliferation in partially ligated arteries, indicating that HIF1α drives inflammation and vascular dysfunction at low shear stress regions. CONCLUSIONS: Mechanical low shear stress activates HIF1α at atheroprone regions of arteries via nuclear factor-κB and Cezanne. HIF1α promotes atherosclerosis initiation at these sites by inducing excessive EC proliferation and inflammation via the induction of glycolysis enzymes

Pseudogap formation of four-layer BaRuO3_3 and its electrodynamic response changes

We investiaged the optical properties of four-layer BaRuO$_{3}$, which shows a fermi-liquid-like behavior at low temperature. Its optical conductivity spectra clearly displayed the formation of a pseudogap and the development of a coherent peak with decreasing temperature. Temperature-dependences of the density $n$ and the scattering rate $1/\tau$ of the coherent component were also derived. As the temperature decreases, both $n$ and $1/\tau$ decrease for four-layer BaRuO$_{3}$. These electrodynamic responses were compared with those of nine-layer BaRuO$_{3}$, which also shows a pseudogap formation but has an insulator-like state at low temperature. It was found that the relative rates of change of both $n$ and $1/\tau$ determine either metallic or insulator-like responses in the ruthenates. The optical properties of the four-layer ruthenate were also compared with those of other pseudogap systems, such as high $T_{c}$ cuprates and heavy electron systems.Comment: 7 figures. submitted to Phys. Rev.

Robustness in Interaction Systems

We treat the effect of absence/failure of ports or components on properties of component-based systems. We do so in the framework of interaction systems, a formalism for component-based systems that strictly separates the issues of local behavior and interaction, for which ideas to establish properties of systems where developed. We propose to adapt these ideas to analyze how the properties behave under absence or failure of certain components or merely some ports of components. We demonstrate our approach for the properties local and global deadlock-freedom as well as liveness and local progress

Lagrangian evolution of global strings

We establish a method to trace the Lagrangian evolution of extended objects consisting of a multicomponent scalar field in terms of a numerical calculation of field equations in three dimensional Eulerian meshes. We apply our method to the cosmological evolution of global strings and evaluate the energy density, peculiar velocity, Lorentz factor, formation rate of loops, and emission rate of Nambu-Goldstone (NG) bosons. We confirm the scaling behavior with a number of long strings per horizon volume smaller than the case of local strings by a factor of $\sim$ 10. The strategy and the method established here are applicable to a variety of fields in physics.Comment: 5 pages, 2 figure