44 research outputs found
Ground state non-universality in the random field Ising model
Two attractive and often used ideas, namely universality and the concept of a
zero temperature fixed point, are violated in the infinite-range random-field
Ising model. In the ground state we show that the exponents can depend
continuously on the disorder and so are non-universal. However, we also show
that at finite temperature the thermal order parameter exponent one half is
restored so that temperature is a relevant variable. The broader implications
of these results are discussed.Comment: 4 pages 2 figures, corrected prefactors caused by a missing factor of
two in Eq. 2., added a paragraph in conclusions for clarit
On the study of jamming percolation
We investigate kinetically constrained models of glassy transitions, and
determine which model characteristics are crucial in allowing a rigorous proof
that such models have discontinuous transitions with faster than power law
diverging length and time scales. The models we investigate have constraints
similar to that of the knights model, introduced by Toninelli, Biroli, and
Fisher (TBF), but differing neighbor relations. We find that such knights-like
models, otherwise known as models of jamming percolation, need a ``No Parallel
Crossing'' rule for the TBF proof of a glassy transition to be valid.
Furthermore, most knight-like models fail a ``No Perpendicular Crossing''
requirement, and thus need modification to be made rigorous. We also show how
the ``No Parallel Crossing'' requirement can be used to evaluate the provable
glassiness of other correlated percolation models, by looking at models with
more stable directions than the knights model. Finally, we show that the TBF
proof does not generalize in any straightforward fashion for three-dimensional
versions of the knights-like models.Comment: 13 pages, 18 figures; Spiral model does satisfy property
Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods
Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new ‘end-point’ measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates
Critical aspects of the random-field Ising model
We investigate the critical behavior of the three-dimensional random-field Ising model
(RFIM) with a Gaussian field distribution at zero temperature. By implementing a
computational approach that maps the ground-state of the RFIM to the maximum-flow
optimization problem of a network, we simulate large ensembles of disorder realizations of
the model for a broad range of values of the disorder strength h and
system sizes  = L3, with L ≤ 156. Our averaging procedure
outcomes previous studies of the model, increasing the sampling of ground states by a
factor of 103. Using well-established finite-size scaling schemes, the
fourth-order’s Binder cumulant, and the sample-to-sample fluctuations of various
thermodynamic quantities, we provide high-accuracy estimates for the critical field
hc, as well as the critical exponents ν,
β/ν, and γ̅/ν of the correlation length, order parameter, and
disconnected susceptibility, respectively. Moreover, using properly defined noise to
signal ratios, we depict the variation of the self-averaging property of the model, by
crossing the phase boundary into the ordered phase. Finally, we discuss the controversial
issue of the specific heat based on a scaling analysis of the bond energy, providing
evidence that its critical exponent α ≈ 0−
Carbono e nitrogênio nas frações granulométricas da matéria orgânica do solo, em sistemas de culturas sob plantio direto
Carbon stock and its compartments in a subtropical oxisol under long-term tillage and crop rotation systems
Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli
Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context