Superstring partition functions in the doubled formalism

Computation of superstring partition function for the non-linear sigma model on the product of a two-torus and its dual within the scope of the doubled formalism is presented. We verify that it reproduces the partition functions of the toroidally compactified type--IIA and type--IIB theories for appropriate choices of the GSO projection.Comment: 15 page

Exclusive Queueing Process with Discrete Time

In a recent study [C Arita, Phys. Rev. E 80, 051119 (2009)], an extension of the M/M/1 queueing process with the excluded-volume effect as in the totally asymmetric simple exclusion process (TASEP) was introduced. In this paper, we consider its discrete-time version. The update scheme we take is the parallel one. A stationary-state solution is obtained in a slightly arranged matrix product form of the discrete-time open TASEP with the parallel update. We find the phase diagram for the existence of the stationary state. The critical line which separates the parameter space into the regions with and without the stationary state can be written in terms of the stationary current of the open TASEP. We calculate the average length of the system and the average number of particles

Self-optimization, community stability, and fluctuations in two individual-based models of biological coevolution

We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly on the population densities of all species resident in the community. New species are introduced through mutation. Both models are amenable to exact linear stability analysis, and we compare the analytic results with large-scale kinetic Monte Carlo simulations, obtaining the population size as a function of an average interspecies interaction strength. Over time, the models self-optimize through mutation and selection to approximately maximize a community fitness function, subject only to constraints internal to the particular model. If the interspecies interactions are randomly distributed on an interval including positive values, the system evolves toward self-sustaining, mutualistic communities. In contrast, for the predator-prey case the matrix of interactions is antisymmetric, and a nonzero population size must be sustained by an external resource. Time series of the diversity and population size for both models show approximate 1/f noise and power-law distributions for the lifetimes of communities and species. For the mutualistic model, these two lifetime distributions have the same exponent, while their exponents are different for the predator-prey model. The difference is probably due to greater resilience toward mass extinctions in the food-web like communities produced by the predator-prey model.Comment: 26 pages, 12 figures. Discussion of early-time dynamics added. J. Math. Biol., in pres

Non-antibiotic pharmaceuticals exhibit toxicity against Escherichia coli at environmentally relevant concentrations with no evolution of cross-resistance to antibiotics

Antimicrobial resistance can arise in the natural environment via prolonged exposure to the effluent surrounding manufacturing facilities. These facilities also produce non-antibiotic pharmaceuticals, and the effect of these on the surrounding microbial communities is less clear; whether they have inherent toxicity, or whether long-term exposure might select for cross-resistance to antibiotics. To this end, we screened four non-antibiotic pharmaceuticals (acetaminophen, ibuprofen, propranolol, met formin) and titanium dioxide for toxicity against Escherichia coli K-12 MG1655 and conducted a 30 day selection experiment to assess the effect of long-term exposure. All compounds reduced the maximum optical density reached by E. coli at a range of concentrations including one of environmental relevance, with transcriptome analysis identifying upregulated genes related to stress response and multidrug efflux in response ibuprofen treatment. The non-antibiotic pharmaceuticals did not select for significant genetic changes following a 30 day exposure, and no evidence of selection for cross-resistance to antibiotics was observed for population evolved in the presence of ibuprofen in spite of the differential gene expression after exposure to this compound. This work suggests that these non-antibiotic pharmaceuticals, at environmental concentrations, do not select for cross-resistance to antibiotics in E. coli

Twenty five years after KLS: A celebration of non-equilibrium statistical mechanics

When Lenz proposed a simple model for phase transitions in magnetism, he couldn't have imagined that the "Ising model" was to become a jewel in field of equilibrium statistical mechanics. Its role spans the spectrum, from a good pedagogical example to a universality class in critical phenomena. A quarter century ago, Katz, Lebowitz and Spohn found a similar treasure. By introducing a seemingly trivial modification to the Ising lattice gas, they took it into the vast realms of non-equilibrium statistical mechanics. An abundant variety of unexpected behavior emerged and caught many of us by surprise. We present a brief review of some of the new insights garnered and some of the outstanding puzzles, as well as speculate on the model's role in the future of non-equilibrium statistical physics.Comment: 3 figures. Proceedings of 100th Statistical Mechanics Meeting, Rutgers, NJ (December, 2008

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes.Comment: 25 pages, 7 figure

Clinical consequences of upfront pathology review in the randomised PORTEC-3 trial for high-risk endometrial cancer

Development and application of statistical models for medical scientific researc