Validation and Calibration of Models for Reaction-Diffusion Systems

Space and time scales are not independent in diffusion. In fact, numerical simulations show that different patterns are obtained when space and time steps ($\Delta x$ and $\Delta t$) are varied independently. On the other hand, anisotropy effects due to the symmetries of the discretization lattice prevent the quantitative calibration of models. We introduce a new class of explicit difference methods for numerical integration of diffusion and reaction-diffusion equations, where the dependence on space and time scales occurs naturally. Numerical solutions approach the exact solution of the continuous diffusion equation for finite $\Delta x$ and $\Delta t$, if the parameter $\gamma_N=D \Delta t/(\Delta x)^2$ assumes a fixed constant value, where $N$ is an odd positive integer parametrizing the alghorithm. The error between the solutions of the discrete and the continuous equations goes to zero as $(\Delta x)^{2(N+2)}$ and the values of $\gamma_N$ are dimension independent. With these new integration methods, anisotropy effects resulting from the finite differences are minimized, defining a standard for validation and calibration of numerical solutions of diffusion and reaction-diffusion equations. Comparison between numerical and analytical solutions of reaction-diffusion equations give global discretization errors of the order of $10^{-6}$ in the sup norm. Circular patterns of travelling waves have a maximum relative random deviation from the spherical symmetry of the order of 0.2%, and the standard deviation of the fluctuations around the mean circular wave front is of the order of $10^{-3}$.Comment: 33 pages, 8 figures, to appear in Int. J. Bifurcation and Chao

Non-Markovian Levy diffusion in nonhomogeneous media

We study the diffusion equation with a position-dependent, power-law diffusion coefficient. The equation possesses the Riesz-Weyl fractional operator and includes a memory kernel. It is solved in the diffusion limit of small wave numbers. Two kernels are considered in detail: the exponential kernel, for which the problem resolves itself to the telegrapher's equation, and the power-law one. The resulting distributions have the form of the L\'evy process for any kernel. The renormalized fractional moment is introduced to compare different cases with respect to the diffusion properties of the system.Comment: 7 pages, 2 figure

Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination

Although RNA polymerase II (Pol II) productively transcribes very long genes in vivo, transcription through extragenic sequences often terminates in the promoter-proximal region and the nascent RNA is degraded. Mechanisms that induce early termination and RNA degradation are not well understood in multicellular organisms. Here, we present evidence that the suppressor of sable [su(s)] regulatory pathway of Drosophila melanogaster plays a role in this process. We previously showed that Su(s) promotes exosome-mediated degradation of transcripts from endogenous repeated elements at an Hsp70 locus (Hsp70-αβ elements). In this report, we identify Wdr82 as a component of this process and show that it works with Su(s) to inhibit Pol II elongation through Hsp70-αβ elements. Furthermore, we show that the unstable transcripts produced during this process are polyadenylated at heterogeneous sites that lack canonical polyadenylation signals. We define two distinct regions that mediate this regulation. These results indicate that the Su(s) pathway promotes RNA degradation and transcription termination through a novel mechanism

Non-equilibrium Phase Transitions with Long-Range Interactions

This review article gives an overview of recent progress in the field of non-equilibrium phase transitions into absorbing states with long-range interactions. It focuses on two possible types of long-range interactions. The first one is to replace nearest-neighbor couplings by unrestricted Levy flights with a power-law distribution P(r) ~ r^(-d-sigma) controlled by an exponent sigma. Similarly, the temporal evolution can be modified by introducing waiting times Dt between subsequent moves which are distributed algebraically as P(Dt)~ (Dt)^(-1-kappa). It turns out that such systems with Levy-distributed long-range interactions still exhibit a continuous phase transition with critical exponents varying continuously with sigma and/or kappa in certain ranges of the parameter space. In a field-theoretical framework such algebraically distributed long-range interactions can be accounted for by replacing the differential operators nabla^2 and d/dt with fractional derivatives nabla^sigma and (d/dt)^kappa. As another possibility, one may introduce algebraically decaying long-range interactions which cannot exceed the actual distance to the nearest particle. Such interactions are motivated by studies of non-equilibrium growth processes and may be interpreted as Levy flights cut off at the actual distance to the nearest particle. In the continuum limit such truncated Levy flights can be described to leading order by terms involving fractional powers of the density field while the differential operators remain short-ranged.Comment: LaTeX, 39 pages, 13 figures, minor revision

Factors associated with failed treatment : an analysis of 121,744 women embarking on their first IVF cycles

Peer reviewedPublisher PD

Branching and annihilating Levy flights

We consider a system of particles undergoing the branching and annihilating reactions A -> (m+1)A and A + A -> 0, with m even. The particles move via long-range Levy flights, where the probability of moving a distance r decays as r^{-d-sigma}. We analyze this system of branching and annihilating Levy flights (BALF) using field theoretic renormalization group techniques close to the upper critical dimension d_c=sigma, with sigma<2. These results are then compared with Monte-Carlo simulations in d=1. For sigma close to unity in d=1, the critical point for the transition from an absorbing to an active phase occurs at zero branching. However, for sigma bigger than about 3/2 in d=1, the critical branching rate moves smoothly away from zero with increasing sigma, and the transition lies in a different universality class, inaccessible to controlled perturbative expansions. We measure the exponents in both universality classes and examine their behavior as a function of sigma.Comment: 9 pages, 4 figure

Perturbative Linearization of Reaction-Diffusion Equations

We develop perturbative expansions to obtain solutions for the initial-value problems of two important reaction-diffusion systems, viz., the Fisher equation and the time-dependent Ginzburg-Landau (TDGL) equation. The starting point of our expansion is the corresponding singular-perturbation solution. This approach transforms the solution of nonlinear reaction-diffusion equations into the solution of a hierarchy of linear equations. Our numerical results demonstrate that this hierarchy rapidly converges to the exact solution.Comment: 13 pages, 4 figures, latex2

Electrophysiological correlates of high-level perception during spatial navigation

We studied the electrophysiological basis of object recognition by recording scalp\ud electroencephalograms while participants played a virtual-reality taxi driver game.\ud Participants searched for passengers and stores during virtual navigation in simulated\ud towns. We compared oscillatory brain activity in response to store views that were targets or\ud nontargets (during store search) or neutral (during passenger search). Even though store\ud category was solely defined by task context (rather than by sensory cues), frontal ...\ud \u

Analysis of a spatial Lotka-Volterra model with a finite range predator-prey interaction

We perform an analysis of a recent spatial version of the classical Lotka-Volterra model, where a finite scale controls individuals' interaction. We study the behavior of the predator-prey dynamics in physical spaces higher than one, showing how spatial patterns can emerge for some values of the interaction range and of the diffusion parameter.Comment: 7 pages, 7 figure

Are Damage Spreading Transitions Generically in the Universality Class of Directed Percolation?

We present numerical evidence for the fact that the damage spreading transition in the Domany-Kinzel automaton found by Martins {\it et al.} is in the same universality class as directed percolation. We conjecture that also other damage spreading transitions should be in this universality class, unless they coincide with other transitions (as in the Ising model with Glauber dynamics) and provided the probability for a locally damaged state to become healed is not zero.Comment: 10 pages, LATE