Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster

Background: Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem. Results: We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences. Conclusions: The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems

Hamilton--Jacobi theory for continuation of magnetic field across a toroidal surface supporting a plasma pressure discontinuity

The vanishing of the divergence of the total stress tensor (magnetic plus kinetic) in a neighborhood of an equilibrium plasma containing a toroidal surface of discontinuity gives boundary and jump conditions that strongly constrain allowable continuations of the magnetic field across the surface. The boundary conditions allow the magnetic fields on either side of the discontinuity surface to be described by surface magnetic potentials, reducing the continuation problem to that of solving a Hamilton--Jacobi equation. The characteristics of this equation obey Hamiltonian equations of motion, and a necessary condition for the existence of a continued field across a general toroidal surface is that there exist invariant tori in the phase space of this Hamiltonian system. It is argued from the Birkhoff theorem that existence of such an invariant torus is also, in general, sufficient for continuation to be possible. An important corollary is that the rotational transform of the continued field on a surface of discontinuity must, generically, be irrational.Comment: Prepared for submission to Phys. Letts.

Opportunities for weed manipulation using GMHT row crops

The herbicides and cultivation systems available in most non-GM crops allow farmers little flexibility as to when they control weeds. However, glyphosate and glufosinate-ammonium, as used in GM herbicide tolerant crops, offer the opportunity to control large weeds and weed control can be timed according to the agronomic and environmental aims of the user. This paper will use sugar beet as a model crop and report results where different approaches to weed control have been used and discuss their relevance in the wider agricultural and environmental contextNon peer reviewe

A comparison of incompressible limits for resistive plasmas

The constraint of incompressibility is often used to simplify the magnetohydrodynamic (MHD) description of linearized plasma dynamics because it does not affect the ideal MHD marginal stability point. In this paper two methods for introducing incompressibility are compared in a cylindrical plasma model: In the first method, the limit $\gamma \to \infty$ is taken, where $\gamma$ is the ratio of specific heats; in the second, an anisotropic mass tensor $\mathbf{\rho}$ is used, with the component parallel to the magnetic field taken to vanish, $\rho_{\parallel} \to 0$. Use of resistive MHD reveals the nature of these two limits because the Alfv\'en and slow magnetosonic continua of ideal MHD are converted to point spectra and moved into the complex plane. Both limits profoundly change the slow-magnetosonic spectrum, but only the second limit faithfully reproduces the resistive Alfv\'en spectrum and its wavemodes. In ideal MHD, the slow magnetosonic continuum degenerates to the Alfv\'en continuum in the first method, while it is moved to infinity by the second. The degeneracy in the first is broken by finite resistivity. For numerical and semi-analytical study of these models, we choose plasma equilibria which cast light on puzzling aspects of results found in earlier literature.Comment: 14 pages, 10 figure