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In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency. [ABSTRACT FROM AUTHOR]

Abstract: We present an implicit finite element method for a class of chemotaxis models in three spatial dimensions. The proposed algorithm is designed to maintain mass conservation and to guarantee positivity of the cell density. To enforce the discrete maximum principle, the standard Galerkin discretization is constrained using a local extremum diminishing flux limiter. To demonstrate the efficiency and robustness of this approach, we solve blow-up problems in a 3D chemostat domain. To give a flavor of more complex and realistic chemotactic applications, we investigate the pattern dynamics and aggregating behavior of the bacteria Escherichia coli and Salmonella typhimurium. The obtained numerical results are in good qualitative agreement with theoretical studies and experimental data reported in the literature. [Copyright &y& Elsevier]

Abstract: In the framework of finite element discretizations, we introduce a fully nonlinear Newton-like method and a linearized second order approach in time applied to certain partial differential equations for chemotactic processes incorporating two entities, a chemical agent and the reacting population of certain biological organisms/species. We investigate the benefit of a corresponding monolithic approach and the decoupled variant. In particular, we analyze accuracy, efficiency and stability of different methods and their dependences on certain parameters in order to identify a well suited finite element solver for chemotaxis problems. [Copyright &y& Elsevier]