Jacqueline M. Wentz | Searcharxiv

arXiv2021

Analytical singular value decomposition for a class of stoichiometry matrices

We present the analytical singular value decomposition of the stoichiometry matrix for a spatially discrete reaction-diffusion system on a one dimensional domain. The domain has two subregions which share a single common boundary. Each of the subregions is further partitioned into a finite number of compartments. Chemical reactions can occur within a compartment, whereas diffusion is represented as movement between adjacent compartments. Inspired by biology, we study both 1) the case where the reactions on each side of the boundary are different and only certain species diffuse across the boundary as well as 2) the case with spatially homogenous reactions and diffusion. We write the stoichiometry matrix for these two classes of systems using a Kronecker product formulation. For the first scenario, we apply linear perturbation theory to derive an approximate singular value decomposition in the limit as diffusion becomes much faster than reactions. For the second scenario, we derive an exact analytical singular value decomposition for all relative diffusion and reaction time scales. By writing the stoichiometry matrix using Kronecker products, we show that the singular vectors and values can also be written concisely using Kronecker products. Ultimately, we find that the singular value decomposition of the reaction-diffusion stoichiometry matrix depends on the singular value decompositions of smaller matrices. These smaller matrices represent modified versions of the reaction-only stoichiometry matrices and the analytically known diffusion-only stoichiometry matrix. Our results provide a mathematical framework that can be used to study complex biochemical systems with metabolic compartments. MATLAB code for calculating the SVD equations is available at \url{www.github.com/MathBioCU/ReacDiffStoicSVD}.

q-bio.QM↗

arXiv2020

Boundedness of a class of discretized reaction-diffusion systems

Although the spatially continuous version of the reaction-diffusion equation has been well studied, in some instances a spatially-discretized representation provides a more realistic approximation of biological processes. Indeed, mathematically the discretized and continuous systems can lead to different predictions of biological dynamics. It is well known in the continuous case that the incorporation of diffusion can cause diffusion-driven blow-up with respect to the $L^{\infty}$ norm. However, this does not imply diffusion-driven blow-up will occur in the discretized version of the system. For example, in a continuous reaction-diffusion system with Dirichlet boundary conditions and nonnegative solutions, diffusion-driven blow up occurs even when the total species concentration is non-increasing. For systems that instead have homogeneous Neumann boundary conditions, it is currently unknown whether this deviation between the continuous and discretized system can occur. Therefore, it is worth examining the discretized system independently of the continuous system. Since no criteria exist for the boundedness of the discretized system, the focus of this paper is to determine sufficient conditions to guarantee the system with diffusion remains bounded for all time. We consider reaction-diffusion systems on a 1D domain with homogeneous Neumann boundary conditions and non-negative initial data and solutions. We define a Lyapunov-like function and show that its existence guarantees that the discretized reaction-diffusion system is bounded. These results are considered in the context of three example systems for which Lyapunov-like functions can and cannot be found.

math.DS↗