Look before you leap: a confidence-based method for selecting species criticality while avoiding negative populations in τ\tau-leaping

The stochastic simulation algorithm was introduced by Gillespie and in a different form by Kurtz. There have been many attempts at accelerating the algorithm without deviating from the behavior of the simulated system. The crux of the explicit $\tau$-leaping procedure is the use of Poisson random variables to approximate the number of occurrences of each type of reaction event during a carefully selected time period, $\tau$. This method is acceptable providing the leap condition, that no propensity function changes “significantly” during any time-step, is met. Using this method there is a possibility that species numbers can, artificially, become negative. Several recent papers have demonstrated methods that avoid this situation. One such method classifies, as critical, those reactions in danger of sending species populations negative. At most, one of these critical reactions is allowed to occur in the next time-step. We argue that the criticality of a reactant species and its dependent reaction channels should be related to the probability of the species number becoming negative. This way only reactions that, if fired, produce a high probability of driving a reactant population negative are labeled critical. The number of firings of more reaction channels can be approximated using Poisson random variables thus speeding up the simulation while maintaining the accuracy. In implementing this revised method of criticality selection we make use of the probability distribution from which the random variable describing the change in species number is drawn. We give several numerical examples to demonstrate the effectiveness of our new metho

Fourier spectral methods for fractional-in-space reaction-diffusion equations

Fractional differential equations are becoming increasingly used as a powerful modelling approach for understanding the many aspects of nonlocality and spatial heterogeneity. However, the numerical approximation of these models is computationally demanding and imposes a number of computational constraints. In this paper, we introduce Fourier spectral methods as an attractive and easy-to-code alternative for the integration of fractional-in-space reactiondiffusion equations. The main advantages of the proposed schemes is that they yield a fully diagonal representation of the fractional operator, with increased accuracy and efficiency when compared to low-order counterparts, and a completely straightforward extension to two and three spatial dimensions. Our approach is show-cased by solving several problems of practical interest, including the fractional Allen–Cahn, FitzHugh–Nagumo and Gray–Scott models,together with an analysis of the properties of these systems in terms of the fractional power of the underlying Laplacian operator

Runge-Kutta methods for third order weak approximation of SDEs with multidimensional additive noise

A new class of third order Runge-Kutta methods for stochastic differential equations with additive noise is introduced. In contrast to Platen's method, which to the knowledge of the author has been up to now the only known third order Runge-Kutta scheme for weak approximation, the new class of methods affords less random variable evaluations and is also applicable to SDEs with multidimensional noise. Order conditions up to order three are calculated and coefficients of a four stage third order method are given. This method has deterministic order four and minimized error constants, and needs in addition less function evaluations than the method of Platen. Applied to some examples, the new method is compared numerically with Platen's method and some well known second order methods and yields very promising results.Comment: Two further examples added, small correction

Fractional diffusion models of cardiac electrical propagation: role of structural heterogeneity in dispersion of repolarization

Structural heterogeneity constitutes one of the main substrates influencing impulse propagation in living tissues. In cardiac muscle, improved understanding on its role is key to advancing our interpretation of cell-to-cell coupling, and how tissue structure modulates electrical propagation and arrhythmogenesis in the intact and diseased heart. We propose fractional diffusion models as a novel mathematical description of structurally heterogeneous excitable media, as a mean of representing the modulation of the total electric field by the secondary electrical sources associated with tissue inhomogeneities. Our results, validated against in-vivo human recordings and experimental data of different animal species, indicate that structural heterogeneity underlies many relevant characteristics of cardiac propagation, including the shortening of action potential duration along the activation pathway, and the progressive modulation by premature beats of spatial patterns of dispersion of repolarization. The proposed approach may also have important implications in other research fields involving excitable complex media

Stochastic B-series analysis of iterated Taylor methods

For stochastic implicit Taylor methods that use an iterative scheme to compute their numerical solution, stochastic B--series and corresponding growth functions are constructed. From these, convergence results based on the order of the underlying Taylor method, the choice of the iteration method, the predictor and the number of iterations, for It\^o and Stratonovich SDEs, and for weak as well as strong convergence are derived. As special case, also the application of Taylor methods to ODEs is considered. The theory is supported by numerical experiments

Shining Light on Modifications of Gravity

Many modifications of gravity introduce new scalar degrees of freedom, and in such theories matter fields typically couple to an effective metric that depends on both the true metric of spacetime and on the scalar field and its derivatives. Scalar field contributions to the effective metric can be classified as conformal and disformal. Disformal terms introduce gradient couplings between scalar fields and the energy momentum tensor of other matter fields, and cannot be constrained by fifth force experiments because the effects of these terms are trivial around static non-relativistic sources. The use of high-precision, low-energy photon experiments to search for conformally coupled scalar fields, called axion-like particles, is well known. In this article we show that these experiments are also constraining for disformal scalar field theories, and are particularly important because of the difficulty of constraining these couplings with other laboratory experiments.Comment: 20 pages, 10 figures. v2: Matches version accepted by JCAP; additional discussion of the strong coupling scale. Conclusions unchange

DBI Galileon and Late time acceleration of the universe

We consider 1+3 dimensional maximally symmetric Minkowski brane embedded in a 1+4 dimensional maximally symmetric Minkowski background. The resulting 1+3 dimensional effective field theory is of DBI (Dirac-Born-Infeld) Galileon type. We use this model to study the late time acceleration of the universe. We study the deviation of the model from the concordance \Lambda CDM behaviour. Finally we put constraints on the model parameters using various observational data.Comment: 16 pages, 7 eps figures, Latex Style, new references added, corrected missing reference

Constraining Galileon inflation

In this short paper, we present constraints on the Galileon inflationary model from the CMB bispectrum. We employ a principal-component analysis of the independent degrees of freedom constrained by data and apply this to the WMAP 9-year data to constrain the free parameters of the model. A simple Bayesian comparison establishes that support for the Galileon model from bispectrum data is at best weak

de Sitter Galileon

We generalize the Galileon symmetry and its relativistic extension to a de Sitter background. This is made possible by studying a probe-brane in a flat five-dimensional bulk using a de Sitter slicing. The generalized Lovelock invariants induced on the probe brane enjoy the induced Poincar\'e symmetry inherited from the bulk, while living on a de Sitter geometry. The non-relativistic limit of these invariants naturally maintain a generalized Galileon symmetry around de Sitter while being free of ghost-like pathologies. We comment briefly on the cosmology of these models and the extension to the AdS symmetry as well as generic FRW backgrounds