Exact Solution of a Jamming Transition: Closed Equations for a Bootstrap Percolation Problem

Jamming, or dynamical arrest, is a transition at which many particles stop moving in a collective manner. In nature it is brought about by, for example, increasing the packing density, changing the interactions between particles, or otherwise restricting the local motion of the elements of the system. The onset of collectivity occurs because, when one particle is blocked, it may lead to the blocking of a neighbor. That particle may then block one of its neighbors, these effects propagating across some typical domain of size named the dynamical correlation length. When this length diverges, the system becomes immobile. Even where it is finite but large the dynamics is dramatically slowed. Such phenomena lead to glasses, gels, and other very long-lived nonequilibrium solids. The bootstrap percolation models are the simplest examples describing these spatio-temporal correlations. We have been able to solve one such model in two dimensions exactly, exhibiting the precise evolution of the jamming correlations on approach to arrest. We believe that the nature of these correlations and the method we devise to solve the problem are quite general. Both should be of considerable help in further developing this field.Comment: 17 pages, 4 figure

Pre-Existing Superbubbles as the Sites of Gamma-Ray Bursts

According to recent models, gamma-ray bursts apparently explode in a wide variety of ambient densities ranging from ~ 10^{-3} to 30 cm^{-3}. The lowest density environments seem, at first sight, to be incompatible with bursts in or near molecular clouds or with dense stellar winds and hence with the association of gamma-ray bursts with massive stars. We argue that low ambient density regions naturally exist in areas of active star formation as the interiors of superbubbles. The evolution of the interior bubble density as a function of time for different assumptions about the evaporative or hydrodynamical mass loading of the bubble interior is discussed. We present a number of reasons why there should exist a large range of inferred afterglow ambient densities whether gamma-ray bursts arise in massive stars or some version of compact star coalescence. We predict that many gamma-ray bursts will be identified with X-ray bright regions of galaxies, corresponding to superbubbles, rather than with blue localized regions of star formation. Massive star progenitors are expected to have their own circumstellar winds. The lack of evidence for individual stellar winds associated with the progenitor stars for the cases with afterglows in especially low density environments may imply low wind densities and hence low mass loss rates combined with high velocities. If gamma-ray bursts are associated with massive stars, this combination might be expected for compact progenitors with atmospheres dominated by carbon, oxygen or heavier elements, that is, progenitors resembling Type Ic supernovae.Comment: 14 pages, no figures, submitted to The Astrophysical Journa

Simulation studies of a phenomenological model for elongated virus capsid formation

We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we identify the minimum physical requirements for non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage $\phi_{29}$, and discuss the implication of our simulation results in the context of recent experimental findings. Our predicted structures may also be experimentally realized by evaporation-driven assembly of colloidal spheres

What do emulsification failure and Bose-Einstein condensation have in common?

Ideal bosons and classical ring polymers formed via self-assembly, are known to have the same partition function, and so analogous phase transitions. In ring polymers, the analogue of Bose-Einstein condensation occurs when a ring polymer of macroscopic size appears. We show that a transition of the same general form occurs within a whole class of systems with self-assembly, and illustrate it with the emulsification failure of a microemulsion phase of water, oil and surfactant. As with Bose-Einstein condensation, the transition occurs even in the absence of interactions.Comment: 7 pages, 1 figure, typeset with EUROTeX, uses epsfi

Scaling of Gene Expression with Transcription-Factor Fugacity

The proteins associated with gene regulation are often shared between multiple pathways simultaneously. By way of contrast, models in regulatory biology often assume these pathways act independently. We demonstrate a framework for calculating the change in gene expression for the interacting case by decoupling repressor occupancy across the cell from the gene of interest by way of a chemical potential. The details of the interacting regulatory architecture are encompassed in an effective concentration, and thus, a single scaling function describes a collection of gene expression data from diverse regulatory situations and collapses it onto a single master curve

Properties of cage rearrangements observed near the colloidal glass transition

We use confocal microscopy to study the motions of particles in concentrated colloidal systems. Near the glass transition, diffusive motion is inhibited, as particles spend time trapped in transient ``cages'' formed by neighboring particles. We measure the cage sizes and lifetimes, which respectively shrink and grow as the glass transition approaches. Cage rearrangements are more prevalent in regions with lower local concentrations and higher disorder. Neighboring rearranging particles typically move in parallel directions, although a nontrivial fraction move in anti-parallel directions, usually from pairs of particles with initial separations corresponding to the local maxima and minima of the pair correlation function $g(r)$, respectively.Comment: 5 pages, 4 figures; text & figures revised in v

Shape-Induced Frustration of Hexagonal Order in Polyhedral Colloids\ud

The effect of a nonspherical particle shape and shape polydispersity on the structure of densely packed hard colloidal particles was studied in real space by confocal microscopy. We show that the first layer at the wall of concentrated size-monodisperse but shape-polydisperse polyhedral colloids exhibits significant deviations from a hexagonal lattice. These deviations are identified as bond-orientational fluctuations which lead to percolating “mismatch lines.” While the shape-induced geometrical frustration of the hexagonal symmetry suppresses translational order, bond-orientational order is clearly retained, indicating a hexaticlike structure of the polyhedral colloid

Символи Степової України: некрополістичні пам’ятки козаччини

Дослідження містить унікальні дані про символи козацьких хрестів – витвори народного кам’янорізного мистецтва, узагальнює матеріал про хрести запорожців. Пласт наведеної інформації стане корисним дослідникам, які вивчають перебіг історичного процесу у часи руйнування Старої Січі 1709 р. і Нової Січі у 1775р., а також безпосередньо вітчизняну некрополістику, палеографію, пам’яткознавство, символіку.This review represents greatly informed bulk of rare memorials, examined in the book of I.V. Sapozhnykov «Stone crosses of steppe Ukraine (XVIII – first half of the XIX) – Odesa: publishing house «Chornomor’ya», 1997. – 165p., ill.: I – XXVI». The investigation has unique material about zaporozhtch’s crosses. The bulk of suggested information can be useful for investigators who study historical processes during elimination of Staraya Sich (1709) and Novaya Sich (1775), and also for those ones who study domestic necropolises, paleography, symbolism and memorial study

Sources of UHECRs in view of the TUS and JEM-EUSO experiments

The origin of ultra-high-energy cosmic rays (UHECRs) is one of the most intriguing problems of modern cosmic ray physics. We briefly review the main astrophysical models of their origin and the forthcoming orbital experiments TUS and JEM-EUSO, and discuss how the new data can help one solve the long-standing puzzle.Comment: 4 pages; prepared for ECRS-2012 (http://ecrs2012.sinp.msu.ru/); v2: a reference adde

Subtoxic Concentrations of Hepatotoxic Drugs Lead to Kupffer Cell Activation in a Human In Vitro Liver Model

Drug induced liver injury (DILI) is an idiosyncratic adverse drug reaction leading to severe liver damage. Kupffer cells (KC) sense hepatic tissue stress/damage and therefore could be a tool for the estimation of consequent effects associated with DILI. Aim of the present study was to establish a human in vitro liver model for the investigation of immune-mediated signaling in the pathogenesis of DILI. Hepatocytes and KC were isolated from human liver specimens. The isolated KC yield was cells/g liver tissue with a purity of >80%. KC activation was investigated by the measurement of reactive oxygen intermediates (ROI, DCF assay) and cell activity (XTT assay). The initial KC activation levels showed broad donor variability. Additional activation of KC using supernatants of hepatocytes treated with hepatotoxic drugs increased KC activity and led to donor-dependent changes in the formation of ROI compared to KC incubated with supernatants from untreated hepatocytes. Additionally, a compound- and donor-dependent increase in proinflammatory cytokines or in anti-inflammatory cytokines was detected. In conclusion, KC related immune signaling in hepatotoxicity was successfully determined in a newly established in vitro liver model. KC were able to detect hepatocyte stress/damage and to transmit a donor- and compound-dependent immune response via cytokine production