2,215 research outputs found
Competition and cooperation in one-dimensional stepping stone models
Cooperative mutualism is a major force driving evolution and sustaining
ecosystems. Although the importance of spatial degrees of freedom and number
fluctuations is well-known, their effects on mutualism are not fully
understood. With range expansions of microbes in mind, we show that, even when
mutualism confers a distinct selective advantage, it persists only in
populations with high density and frequent migrations. When these parameters
are reduced, mutualism is generically lost via a directed percolation process,
with a phase diagram strongly influenced by an exceptional DP2 transition.Comment: 8 pages, 4 figure
Defect-Mediated Emulsification in Two Dimensions
We consider two dimensional dispersions of droplets of isotropic phase in a
liquid with an XY-like order parameter, tilt, nematic, and hexatic symmetries
being included. Strong anchoring boundary conditions are assumed. Textures for
a single droplet and a pair of droplets are calculated and a universal
droplet-droplet pair potential is obtained. The interaction of dispersed
droplets via the ordered phase is attractive at large distances and repulsive
at short distances, which results in a well defined preferred separation for
two droplets and topological stabilization of the emulsion. This interaction
also drives self-assembly into chains. Preferred separations and energy
barriers to coalescence are calculated, and effects of thermal fluctuations and
film thickness are discussed.Comment: revtex4, 13 pages, 12 figure
Opening of DNA double strands by helicases. Active versus passive opening
Helicase opening of double-stranded nucleic acids may be "active" (the
helicase directly destabilizes the dsNA to promote opening) or "passive" (the
helicase binds ssNA available due to a thermal fluctuation which opens part of
the dsNA). We describe helicase opening of dsNA, based on helicases which bind
single NA strands and move towards the double-stranded region, using a discrete
``hopping'' model. The interaction between the helicase and the junction where
the double strand opens is characterized by an interaction potential. The form
of the potential determines whether the opening is active or passive. We
calculate the rate of passive opening for the helicase PcrA, and show that the
rate increases when the opening is active. Finally, we examine how to choose
the interaction potential to optimize the rate of strand separation. One
important result is our finding that active opening can increase the unwinding
rate by 7 fold compared to passive opening.Comment: 13 pages, 3 figure
Fisher waves in the strong noise limit
We investigate the effects of strong number fluctuations on traveling waves
in the Fisher-Kolmogorov reaction-diffusion system. Our findings are in stark
contrast to the commonly used deterministic and weak-noise approximations. We
compute the wave velocity in one and two spatial dimensions, for which we find
a linear and a square-root dependence of the speed on the particle density.
Instead of smooth sigmoidal wave profiles, we observe fronts composed of a few
rugged kinks that diffuse, annihilate, and rarely branch; this dynamics leads
to power-law tails in the distribution of the front sizes.Comment: 4 pages, 2 figures, updat
Growth, competition and cooperation in spatial population genetics
We study an individual based model describing competition in space between
two different alleles. Although the model is similar in spirit to classic
models of spatial population genetics such as the stepping stone model, here
however space is continuous and the total density of competing individuals
fluctuates due to demographic stochasticity. By means of analytics and
numerical simulations, we study the behavior of fixation probabilities,
fixation times, and heterozygosity, in a neutral setting and in cases where the
two species can compete or cooperate. By concluding with examples in which
individuals are transported by fluid flows, we argue that this model is a
natural choice to describe competition in marine environments.Comment: 29 pages, 14 figures; revised version including a section with
results in the presence of fluid flow
A Quantitative Test of Population Genetics Using Spatio-Genetic Patterns in Bacterial Colonies
It is widely accepted that population genetics theory is the cornerstone of
evolutionary analyses. Empirical tests of the theory, however, are challenging
because of the complex relationships between space, dispersal, and evolution.
Critically, we lack quantitative validation of the spatial models of population
genetics. Here we combine analytics, on and off-lattice simulations, and
experiments with bacteria to perform quantitative tests of the theory. We study
two bacterial species, the gut microbe Escherichia coli and the opportunistic
pathogen Pseudomonas aeruginosa, and show that spatio-genetic patterns in
colony biofilms of both species are accurately described by an extension of the
one-dimensional stepping-stone model. We use one empirical measure, genetic
diversity at the colony periphery, to parameterize our models and show that we
can then accurately predict another key variable: the degree of short-range
cell migration along an edge. Moreover, the model allows us to estimate other
key parameters including effective population size (density) at the expansion
frontier. While our experimental system is a simplification of natural
microbial community, we argue it is a proof of principle that the spatial
models of population genetics can quantitatively capture organismal evolution
Error of an arbitrary single-mode Gaussian transformation on a weighted cluster state using a cubic phase gate
In this paper, we propose two strategies for decreasing the error of
arbitrary single-mode Gaussian transformations implemented using one-way
quantum computation on a four-node linear cluster state. We show that it is
possible to minimize the error of the arbitrary single-mode Gaussian
transformation by a proper choice of the weight coefficients of the cluster
state. We modify the computation scheme by adding a non-Gaussian state obtained
using a cubic phase gate as one of the nodes of the cluster. This further
decreases the computation error. We evaluate the efficiencies of the proposed
optimization schemes comparing the probabilities of the error correction of the
quantum computations with and without optimizations. We have shown that for
some transformations, the error probability can be reduced by up to 900 times.Comment: 14 pages, 8 figure
Unconventional magnetism of non-uniform distribution of Co in TiO2 nanoparticles
High-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) analysis, electron paramagnetic resonance (EPR), X-ray absorption spectroscopy (XAS), magnetic methods, and density-functional theory (DFT) calculations were applied for the investigations of Co-doped anatase TiO2 nanoparticles (∼20 nm). It was found that high-spin Co2+ ions prefer to occupy the interstitial positions in the TiO2 lattice which are the most energetically favourable in compare to the substitutional those. A quantum mechanical model which operates mainly on two types of Co2+ – Co2+ dimers with different negative exchange interactions and the non-interacting paramagnetic Co2+ ions provides a satisfactorily description of magnetic properties for the TiO2:Co system. © 2020 Elsevier B.V.Russian Foundation for Basic Research. Ministry of Science and Higher Education of the Russian Federatio
Guided random walk calculation of energies and <\sq {r^2} > values of the state of H_2 in a magnetic field
Energies and spatial observables for the state of the hydrogen
molecule in magnetic fields parallel to the proton-proton axis are calculated
with a guided random walk Feynman-Kac algorithm. We demonstrate that the
accuracy of the results and the simplicity of the method may prove it a viable
alternative to large basis set expansions for small molecules in applied
fields.Comment: 10 pages, no figure
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