Abstract.A framework for the analysis of stochastic models of chemical systems for which the deterministic mean-field description is undergoing a saddle-node infinite period (SNIPER) bifurcation is presented. Such a bifurcation occurs for example in the modelling of cell-cycle regulation. It is shown that the stochastic system possesses oscillatory solutions even for parameter values for which the mean-field model does not oscillate. The dependence of the mean period of these oscillations on the parameters of the model (kinetic rate constants) and the size of the system (number of molecules present) is studied. Our approach is based on the chemical Fokker-Planck equation. To get some insights into advantages and disadvantages of the method, a simple one-dimensional chemical switch is first analyzed, before the chemical SNIPER problem is studied in detail. First, results obtained by solving the Fokker-Planck equation numerically are presented. Then an asymptotic analysis of the Fokker-Planck equation is used to derive explicit formulae for the period of oscillation as a function of the rate constants and as a function of the system size.

A procedure for the construction of robust, upper bounds for the error in the finite element approximation of singularly perturbed reaction–diffusion problems was presented in Ainsworth and Babuška (SIAM J Numer Anal 36(2):331–353, 1999) which entailed the solution of an infinite dimensional local boundary value problem. It is not possible to solve this problem exactly and this fact was recognised in the above work where it was indicated that the limitation would be addressed in a subsequent article. We view the present work as fulfilling that promise and as completing the investigation begun in Ainsworth and Babuška (SIAM J Numer Anal 36(2):331–353, 1999) by removing the obligation to solve a local problem exactly. The resulting new estimator is indeed fully computable and the first to provide fully computable, robust upper bounds in the setting of singularly perturbed problems discretised by the finite element metho

(2015) Noise-induced multistability in chemical systems: discrete versus continuum modeling. Physical Review E, 91 (4). 042111. ISSN 1539-3755 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/68602/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version. Please see the URL above for details on accessing the published version. Copyright and reuse:Sussex Research Online is a digital repository of the research output of the University.Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available.Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. The noisy dynamics of chemical systems is commonly studied using either the chemical master equation (CME) or the chemical Fokker-Planck equation (CFPE). The latter is a continuum approximation of the discrete CME approach. It has recently been shown that for a particular system, the CFPE captures noise-induced multistability predicted by the CME. This phenomenon involves the CME's marginal probability distribution changing from unimodal to multimodal as the system size decreases below a critical value. We here show that the CFPE does not always capture noise-induced multistability. In particular we find simple chemical systems for which the CME predicts noise-induced multistability, whereas the CFPE predicts monostability for all system sizes. PHYSICAL REVIEW E 91, 042111 (2015) Noise-induced multistability in chemical systems: Discrete versus continuum modeling

We present a fully computable a posteriori error estimator for piecewise linear finite element approximations of reaction-diffusion problems with mixed boundary conditions and piecewise constant reaction coefficient formulated in arbitrary dimension. The estimator provides a guaranteed upper bound on the energy norm of the error and it is robust for all values of the reaction coefficient, including the singularly perturbed case. The approach is based on robustly equilibrated boundary flux functions of Ainsworth and Oden (Wiley 2000) and on subsequent robust and explicit flux reconstruction. This paper simplifies and extends the applicability of the previous result of Ainsworth and Vejchodský (Numer. Math. 119 (2011) 219-243) in three aspects: (i) arbitrary dimension, (ii) mixed boundary conditions, and (iii) nonconstant reaction coefficient. It is the first robust upper bound on the error with these properties. An auxiliary result that is of independent interest is the derivation of new explicit constants for two types of trace inequalities on simplices.1991 Mathematics Subject Classification. Primary 65N15. Secondary 65N30, 65J15. Key words and phrases. Finite element analysis. Robust a posteriori error estimate. Singularly perturbed problems. Boundary layers. Mixed boundary conditions. Date: July 18, 2018. M.A. acknowledges the support from AFOSR contract FA 9550-12-1-0399. T.V. acknowledges the support from RVO 67985840. Further, his research was supported by Marie Curie Intra European Fellowship within the 7th European Community Framework Programme, project no. 328008.