The structure of the hard sphere solid

We show that near densest-packing the perturbations of the HCP structure yield higher entropy than perturbations of any other densest packing. The difference between the various structures shows up in the correlations between motions of nearest neighbors. In the HCP structure random motion of each sphere impinges slightly less on the motion of its nearest neighbors than in the other structures.Comment: For related papers see: http://www.ma.utexas.edu/users/radin/papers.htm

Mutual Event Observations of Io's Sodium Corona

We have measured the column density profile of Io's sodium corona using 10 mutual eclipses between the Galilean satellites. This approach circumvents the problem of spatially resolving Io's corona directly from Io's bright continuum in the presence of atmospheric seeing and telescopic scattering. The primary goal is to investigate the spatial and temporal variations of Io's corona. Spectra from the Keck Observatory and McDonald Observatory from 1997 reveal a corona that is only approximately spherically symmetric around Io. Comparing the globally averaged radial sodium column density profile in the corona with profiles measured in 1991 and 1985, we find that there has been no significant variation. However, there appears to be a previously undetected asymmetry: the corona above Io's sub-Jupiter hemisphere is consistently more dense than above the anti-Jupiter hemisphere

Dual Monte Carlo and Cluster Algorithms

We discuss the development of cluster algorithms from the viewpoint of probability theory and not from the usual viewpoint of a particular model. By using the perspective of probability theory, we detail the nature of a cluster algorithm, make explicit the assumptions embodied in all clusters of which we are aware, and define the construction of free cluster algorithms. We also illustrate these procedures by rederiving the Swendsen-Wang algorithm, presenting the details of the loop algorithm for a worldline simulation of a quantum $S=$ 1/2 model, and proposing a free cluster version of the Swendsen-Wang replica method for the random Ising model. How the principle of maximum entropy might be used to aid the construction of cluster algorithms is also discussed.Comment: 25 pages, 4 figures, to appear in Phys.Rev.

PIRSF Family Classification System for Protein Functional and Evolutionary Analysis

The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. Here we demonstrate, with illustrative examples, how to use the web-based PIRSF system as a tool for functional and evolutionary studies of protein families

Acute WNT signalling activation perturbs differentiation within the adult stomach and rapidly leads to tumour formation

A role for WNT signalling in gastric carcinogenesis has been suggested due to two major observations. First, patients with germline mutations in adenomatous polyposis coli (APC) are susceptible to stomach polyps and second, in gastric cancer, WNT activation confers a poor prognosis. However, the functional significance of deregulated WNT signalling in gastric homoeostasis and cancer is still unclear. In this study we have addressed this by investigating the immediate effects of WNT signalling activation within the stomach epithelium. We have specifically activated the WNT signalling pathway within the mouse adult gastric epithelium via deletion of either glycogen synthase kinase 3 (GSK3) or APC or via expression of a constitutively active β-catenin protein. WNT pathway deregulation dramatically affects stomach homoeostasis at very short latencies. In the corpus, there is rapid loss of parietal cells with fundic gland polyp (FGP) formation and adenomatous change, which are similar to those observed in familial adenomatous polyposis. In the antrum, adenomas occur from 4 days post-WNT activation. Taken together, these data show a pivotal role for WNT signalling in gastric homoeostasis, FGP formation and adenomagenesis. Loss of the parietal cell population and corresponding FGP formation, an early event in gastric carcinogenesis, as well as antral adenoma formation are immediate effects of nuclear β-catenin translocation and WNT target gene expression. Furthermore, our inducible murine model will permit a better understanding of the molecular changes required to drive tumourigenesis in the stomach

Muon-Induced Background Study for an Argon-Based Long Baseline Neutrino Experiment

We evaluated rates of transversing muons, muon-induced fast neutrons, and production of $^{40}$Cl and other cosmogenically produced nuclei that pose as potential sources of background to the physics program proposed for an argon-based long baseline neutrino experiment at the Sanford Underground Research Facility (SURF). The Geant4 simulations were carried out with muons and muon-induced neutrons for both 800 ft (0.712 km.w.e.) and 4850 ft levels (4.3 km.w.e.). We developed analytic models to independently calculate the $^{40}$Cl production using the measured muon fluxes at different levels of the Homestake mine. The muon induced $^{40}$Cl production rates through stopped muon capture and the muon-induced neutrons and protons via (n,p) and (p,n) reactions were evaluated. We find that the Monte Carlo simulated production rates of $^{40}$Cl agree well with the predictions from analytic models. A depth-dependent parametrization was developed and benchmarked to the direct analytic models. We conclude that the muon-induced processes will result in large backgrounds to the physics proposed for an argon-based long baseline neutrino experiment at a depth of less than 4.0 km.w.e.Comment: 12 pages, 15 figure

The 13N(d,n)14O Reaction and the Astrophysical 13N(p,g)14O Reaction Rate

$^{13}$N($p,\gamma$)$^{14}$O is one of the key reactions in the hot CNO cycle which occurs at stellar temperatures around $T_9$ $\geq$ 0.1. Up to now, some uncertainties still exist for the direct capture component in this reaction, thus an independent measurement is of importance. In present work, the angular distribution of the $^{13}$N($d,n$)$^{14}$O reaction at $E_{\rm{c.m.}}$ = 8.9 MeV has been measured in inverse kinematics, for the first time. Based on the distorted wave Born approximation (DWBA) analysis, the nuclear asymptotic normalization coefficient (ANC), $C^{^{14}O}_{1,1/2}$, for the ground state of $^{14}$O $\to$ $^{13}$N + $p$ is derived to be $5.42 \pm 0.48$ fm$^{-1/2}$. The $^{13}$N($p,\gamma$)$^{14}$O reaction is analyzed with the R-matrix approach, its astrophysical S-factors and reaction rates at energies of astrophysical relevance are then determined with the ANC. The implications of the present reaction rates on the evolution of novae are then discussed with the reaction network calculations.Comment: 17 pages and 8 figure

Asymptotic normalization coefficients (nuclear vertex constants) for p+7Be→8Bp+^7Be\to ^8B and the direct 7Be(p,γ)8B^7Be(p,\gamma)^8B astrophysical S-factors at solar energies

A new analysis of the precise experimental astrophysical S-factors for the direct capture $^7Be(p,\gamma)$ $^8B$ reaction [A.J.Junghans et al.Phys.Rev. C 68 (2003) 065803 and L.T. Baby et al. Phys.Rev. C 67 (2003) 065805] is carried out based on the modified two - body potential approach in which the direct astrophysical S-factor, ${\rm S_{17}(E)}$, is expressed in terms of the asymptotic normalization constants for $p+^7Be\to ^8B$ and two additional conditions are involved to verify the peripheral character of the reaction under consideration. The Woods-Saxon potential form is used for the bound ($p+^7Be$)- state wave function and for the $p^7Be$- scattering wave function. New estimates are obtained for the ^{\glqq}indirectly measured\grqq values of the asymptotic normalization constants (the nuclear vertex constants) for the $p+^7Be\to ^8B$ and $S_{17}(E)$ at E$\le$ 115 keV, including $E$=0. These values of $S_{17}(E)$ and asymptotic normalization constants have been used for getting information about the ^{\glqq}indirectly measured\grqq values of the $s$ wave average scattering length and the $p$ wave effective range parameters for $p^7Be$- scattering.Comment: 27 pages, 6 figure

Clay fine fissuring monitoring using miniature geo-electrical resistivity arrays

Abstract This article describes a miniaturised electrical imaging (resistivity tomography) technique to map the cracking pattern of a clay model. The clay used was taken from a scaled flood embankment built to study the fine fissuring due to desiccation and breaching process in flooding conditions. The potential of using a miniature array of electrodes to follow the evolution of the vertical cracks and number them during the drying process was explored. The imaging technique generated two-dimensional contoured plots of the resistivity distribution within the model before and at different stages of the desiccation process. The change in resistivity associated with the widening of the cracks were monitored as a function of time. Experiments were also carried out using a selected conductive gel to slow down the transport process into the cracks to improve the scanning capabilities of the equipment. The main vertical clay fissuring network was obtained after inversion of the experimental resistivity measurements and validated by direct observations