Totally asymmetric exclusion process with long-range hopping

Generalization of the one-dimensional totally asymmetric exclusion process (TASEP) with open boundary conditions in which particles are allowed to jump $l$ sites ahead with the probability $p_l\sim 1/l^{\sigma+1}$ is studied by Monte Carlo simulations and the domain-wall approach. For $\sigma>1$ the standard TASEP phase diagram is recovered, but the density profiles near the transition lines display new features when $1<\sigma<2$. At the first-order transition line, the domain-wall is localized and phase separation is observed. In the maximum-current phase the profile has an algebraic decay with a $\sigma$-dependent exponent. Within the $\sigma \leq 1$ regime, where the transitions are found to be absent, analytical results in the continuum mean-field approximation are derived in the limit $\sigma=-1$.Comment: 10 pages, 9 figure

Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.

Published onlinePseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3.G.U. and M.K. were funded by the Ministry of Education, Science and Technological Development, Republic of Serbia (grant no. 173019). G.U. is also the beneficiary of FEMS Research Fellowship 2014-1. The laboratory of V.V. was financed by ICGEB core funding

First-order transition in the one-dimensional three-state Potts model with long-range interactions

The first-order phase transition in the three-state Potts model with long-range interactions decaying as $1/r^{1+\sigma}$ has been examined by numerical simulations using recently proposed Luijten-Bl\"ote algorithm. By applying scaling arguments to the interface free energy, the Binder's fourth-order cumulant, and the specific heat maximum, the change in the character of the transition through variation of parameter $\sigma$ was studied.Comment: 6 pages (containing 5 figures), to appear in Phys. Rev.

Correlations in Ising chains with non-integrable interactions

Two-spin correlations generated by interactions which decay with distance r as r^{-1-sigma} with -1 <sigma <0 are calculated for periodic Ising chains of length L. Mean-field theory indicates that the correlations, C(r,L), diminish in the thermodynamic limit L -> \infty, but they contain a singular structure for r/L -> 0 which can be observed by introducing magnified correlations, LC(r,L)-\sum_r C(r,L). The magnified correlations are shown to have a scaling form F(r/L) and the singular structure of F(x) for x->0 is found to be the same at all temperatures including the critical point. These conclusions are supported by the results of Monte Carlo simulations for systems with sigma =-0.50 and -0.25 both at the critical temperature T=Tc and at T=2Tc.Comment: 13 pages, latex, 5 eps figures in a separate uuencoded file, to appear in Phys.Rev.

Computational image analysis reveals the structural complexity ofToxoplasma gondiitissue cysts

Toxoplasma gondiiis an obligate intracellular parasite infecting up to one third of the human population. The central event in the pathogenesis of toxoplasmosis is the conversion of tachyzoites into encysted bradyzoites. A novel approach to analyze the structure ofin vivo-derived tissue cysts may be the increasingly used computational image analysis. The objective of this study was to quantify the geometrical complexity ofT.gondiicysts by morphological, particle, and fractal analysis, as well as to determine if it is impacted by parasite strain, cyst age, and host type. A total of 31 images ofT.gondiibrain cysts of four type-2 strains (Me49, and local isolates BGD1, BGD14, and BGD26) was analyzed using ImageJ software. The parameters of interest included diameter, circularity, packing density (PD), fractal dimension (FD), and lacunarity. Although cyst diameter varied widely, its negative correlation with PD was observed. Circularity was remarkably close to 1, indicating a perfectly round shape of the cysts. PD and FD did not vary among cysts of different strains, age, and derived from mice of different genetic background. Conversely, lacunarity, which is a measure of heterogeneity, was significantly lower for BGD1 strain vs. all other strains, and higher for Me49 vs. BGD14 and BGD26, but did not differ among Me49 cysts of different age, or those derived from genetically different mice. The results indicate a highly uniform structure and occupancy of the differentT.gondiitissue cysts. This study furthers the use of image analysis in describing the structural complexity ofT.gondiicyst morphology, and presents the first application of fractal analysis for this purpose. The presented results show that use of a freely available software is a cost-effective approach to advance automated image scoring forT.gondiicysts

Circle Method for Robust Estimation of Local Conduction Velocity High-Density Maps From Optical Mapping Data: Characterization of Radiofrequency Ablation Sites

Conduction velocity (CV) slowing is associated with atrial fibrillation (AF) and reentrant ventricular tachycardia (VT). Clinical electroanatomical mapping systems used to localize AF or VT sources as ablation targets remain limited by the number of measuring electrodes and signal processing methods to generate high-density local activation time (LAT) and CV maps of heterogeneous atrial or trabeculated ventricular endocardium. The morphology and amplitude of bipolar electrograms depend on the direction of propagating electrical wavefront, making identification of low-amplitude signal sources commonly associated with fibrotic area difficulty. In comparison, unipolar electrograms are not sensitive to wavefront direction, but measurements are susceptible to distal activity. This study proposes a method for local CV calculation from optical mapping measurements, termed the circle method (CM). The local CV is obtained as a weighted sum of CV values calculated along different chords spanning a circle of predefined radius centered at a CV measurement location. As a distinct maximum in LAT differences is along the chord normal to the propagating wavefront, the method is adaptive to the propagating wavefront direction changes, suitable for electrical conductivity characterization of heterogeneous myocardium. In numerical simulations, CM was validated characterizing modeled ablated areas as zones of distinct CV slowing. Experimentally, CM was used to characterize lesions created by radiofrequency ablation (RFA) on isolated hearts of rats, guinea pig, and explanted human hearts. To infer the depth of RFA-created lesions, excitation light bands of different penetration depths were used, and a beat-to-beat CV difference analysis was performed to identify CV alternans. Despite being limited to laboratory research, studies based on CM with optical mapping may lead to new translational insights into better-guided ablation therapies

Critical Behaviour of Superfluid 4^4He in Aerogel

We report on Monte Carlo studies of the critical behaviour of superfluid $^4$He in the presence of quenched disorder with long-range fractal correlations. According to the heuristic argument by Harris, uncorrelated disorder is irrelevant when the specific heat critical exponent $\alpha$ is negative, which is the case for the pure $^4$He. However, experiments on helium in aerogel have shown that the superfluid density critical exponent $\zeta$ changes. We hypothesize that this is a cross-over effect due to the fractal nature of aerogel. Modelling the aerogel as an incipient percolating cluster in 3D and weakening the bonds at the fractal sites, we perform XY-model simulations, which demonstrate an increase in $\zeta$ from $0.67 \pm 0.005$ for the pure case to an apparent value of $0.722\pm 0.005$ in the presence of the fractal disorder, provided that the helium correlation length does not exceed the fractal correlation length.Comment: 4 pages, RevTex, 3 postscript figures, LaTeX file and figures have been uuencoded

Inhomogeneity-induced second-order phase transitions in Potts model on hierarchical lattices

The thermodynamics of the $q$-state Potts model with arbitrary $q$ on a class of hierarchical lattices is considered. Contrary to the case of the crystal lattices, it has always the second-order phase transitions. The analytical expressions fo the critical indexes are obtained, their dependencies on the structural lattice pararmeters are studied and the scailing relations among them are establised. The structural criterion of the inhomogeneity-induced transformation of the transition order is suggested. The application of the results to a description of critical phenomena in the dilute crystals and substances confined in porous media is discussed.Comment: 9 pages, 2 figure

Evidence of exactness of the mean field theory in the nonextensive regime of long-range spin models

The q-state Potts model with long-range interactions that decay as 1/r^alpha subjected to an uniform magnetic field on d-dimensional lattices is analized for different values of q in the nonextensive regime (alpha between 0 and d). We also consider the two dimensional antiferromagnetic Ising model with the same type of interactions. The mean field solution and Monte Carlo calculations for the equations of state for these models are compared. We show that, using a derived scaling which properly describes the nonextensive thermodynamic behaviour, both types of calculations show an excellent agreement in all the cases here considered, except for alpha=d. These results allow us to extend to nonextensive magnetic models a previous conjecture which states that the mean field theory is exact for the Ising one.Comment: 10 pages, 4 figure

Reexamination of the long-range Potts model: a multicanonical approach

We investigate the critical behavior of the one-dimensional q-state Potts model with long-range (LR) interaction $1/r^{d+\sigma}$, using a multicanonical algorithm. The recursion scheme initially proposed by Berg is improved so as to make it suitable for a large class of LR models with unequally spaced energy levels. The choice of an efficient predictor and a reliable convergence criterion is discussed. We obtain transition temperatures in the first-order regime which are in far better agreement with mean-field predictions than in previous Monte Carlo studies. By relying on the location of spinodal points and resorting to scaling arguments, we determine the threshold value $\sigma_c(q)$ separating the first- and second-order regimes to two-digit precision within the range $3 \leq q \leq 9$. We offer convincing numerical evidence supporting $\sigma_c(q)Comment: 18 pages, 18 figure