A supercritical series analysis for the generalized contact process with diffusion

We study a model that generalizes the CP with diffusion. An additional transition is included in the model so that at a particular point of its phase diagram a crossover from the directed percolation to the compact directed percolation class will happen. We are particularly interested in the effect of diffusion on the properties of the crossover between the universality classes. To address this point, we develop a supercritical series expansion for the ultimate survival probability and analyse this series using d-log Pad\'e and partial differential approximants. We also obtain approximate solutions in the one- and two-site dynamical mean-field approximations. We find evidences that, at variance to what happens in mean-field approximations, the crossover exponent remains close to $\phi=2$ even for quite high diffusion rates, and therefore the critical line in the neighborhood of the multicritical point apparently does not reproduce the mean-field result (which leads to $\phi=0$) as the diffusion rate grows without bound

Disorder-induced phase transition in a one-dimensional model of rice pile

We propose a one-dimensional rice-pile model which connects the 1D BTW sandpile model (Phys. Rev. A 38, 364 (1988)) and the Oslo rice-pile model (Phys. Rev. lett. 77, 107 (1997)) in a continuous manner. We found that for a sufficiently large system, there is a sharp transition between the trivial critical behaviour of the 1D BTW model and the self-organized critical (SOC) behaviour. When there is SOC, the model belongs to a known universality class with the avalanche exponent $\tau=1.53$.Comment: 10 pages, 7 eps figure

Single-cell in situ RNA profiling by sequential hybridization

In our previous paper, Lubeck and Cai, we used super-resolution microscopy to resolve a large number of mRNAs in single cells. In this Correspondence, we present a sequential barcoding scheme to multiplex different mRNAs

Dense transcript profiling in single cells by image correlation decoding

Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression

ASCI application performance and the impact of commodity processor architectural trends

The DOE Accelerated Strategic Computing Initiative (ASCI) is an applications-driven program requiring use of scalable, high-performance architectures to meet aggressive engineering needs related to safety of the Nation`s nuclear stockpile. ASCI will accelerate development of computational methods and tools for predictive simulation and for virtual prototyping needed to re-certify the existing stockpile, assess the effects of component aging, and to evaluate accident scenarios. The purpose of this paper is to summarize recent performance results from an important ASCI-related application and to speculate on how trends within the computer industry and in computer architecture relate to these results

Meson-Baryon Form Factors in Chiral Colour Dielectric Model

The renormalised form factors for pseudoscalar meson-baryon coupling are computed in chiral colour dielectric model. This has been done by rearranging the Lippmann-Schwinger series for the meson baryon scattering matrix so that it can be expressed as a baryon pole term with renormalized form factors and baryon masses and the rest of the terms which arise from the crossed diagrams. Thus we are able to obtain an integral equation for the renormalized meson-baryon form factors in terms of the bare form factors as well as an expression for the meson self energy. This integral equation is solved and renormalized meson baryon form factors and renormalized baryon masses are computed. The parameters of the model are adjusted to obtain a best fit to the physical baryon masses. The calculations show that the renormalized form factors are energy-dependent and differ from the bare form factors primarily at momentum transfers smaller than 1 GeV. At nucleon mass, the change in the form factors is about 10% at zero momentum transfer. The computed form factors are soft with the equivalent monopole cut-off mass of about 500 MeV. The renormalized coupling constants are obtained by comparing the chiral colour dielectric model interaction Hamiltonian with the standard form of meson-nucleon interaction Hamiltonian. The ratio of $\Delta N\pi$ and $NN\pi$ coupling constants is found to be about 2.15. This value is very close to the experimental value.Comment: 16 pages, 7 postscript figure

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum-the highest proteome coverage reported with a QTOF instrument so far

Universal 1/f Noise from Dissipative SOC Models

We introduce a model able to reproduce the main features of 1/f noise: hyper-universality (the power-law exponents are independent on the dimension of the system; we show here results in d=1,2) and apparent lack of a low-frequency cutoff in the power spectrum. Essential ingredients of this model are an activation-deactivation process and dissipation.Comment: 3 Latex pages, 2 eps Figure