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The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion paper is to point out some open problems in the theory of PDE and compartmental ODE models of balanced reaction-diffusion networks., Comment: A discussion paper for the 1st IFAC Workshop on Control of Systems Governed by Partial Differential Equations

Inspired by the recent developments in modeling and analysis of reaction networks, we provide a geometric formulation of the reversible reaction networks under the influence of diffusion. Using the graph knowledge of the underlying reaction network, the obtained reaction-diffusion system is a distributed-parameter port-Hamiltonian system on a compact spatial domain. Motivated by the need for computer based design, we offer a spatially consistent discretization of the PDE system and, in a systematic manner, recover a compartmental ODE model on a simplicial triangulation of the spatial domain. Exploring the properties of a balanced weighted Laplacian matrix of the reaction network and the Laplacian of the simplicial complex, we characterize the space of equilibrium points and provide a simple stability analysis on the state space modulo the space of equilibrium points. The paper rules out the possibility of the persistence of spatial patterns for the compartmental balanced reaction-diffusion networks.

Simplicial Dirac structures as finite analogues of the canonical Stokes-Dirac structure, capturing the topological laws of the system, are defined on simplicial manifolds in terms of primal and dual cochains related by the coboundary operators. These finite-dimensional Dirac structures offer a framework for the formulation of standard input-output finite-dimensional port-Hamiltonian systems that emulate the behavior of distributed-parameter port-Hamiltonian systems. This paper elaborates on the matrix representations of simplicial Dirac structures and the resulting port-Hamiltonian systems on simplicial manifolds. Employing these representations, we consider the existence of structural invariants and demonstrate how they pertain to the energy shaping of port-Hamiltonian systems on simplicial manifolds.

Stokes-Dirac structures are infinite-dimensional Dirac structures defined in terms of differential forms on a smooth manifold with boundary. These Dirac structures lay down a geometric framework for the formulation of Hamiltonian systems with a nonzero boundary energy flow. Simplicial triangulation of the underlaying manifold leads to the so-called simplicial Dirac structures, discrete analogues of Stokes-Dirac structures, and thus provides a natural framework for deriving finite-dimensional port-Hamiltonian systems that emulate their infinite-dimensional counterparts. The port-Hamiltonian systems defined with respect to Stokes-Dirac and simplicial Dirac structures exhibit gauge and a discrete gauge symmetry, respectively. In this paper, employing Poisson reduction we offer a unified technique for the symmetry reduction of a generalized canonical infinite-dimensional Dirac structure to the Poisson structure associated with Stokes-Dirac structures and of a fine-dimensional Dirac structure to simplicial Dirac structures. We demonstrate this Poisson scheme on a physical example of the vibrating string.

This paper offers a geometric framework for modeling port-Hamiltonian systems on discrete manifolds. The simplicial Dirac structure, capturing the topological laws of the system, is defined in terms of primal and dual cochains related by the coboundary operators. This finite-dimensional Dirac structure, as discrete analogue of the canonical Stokes-Dirac structure, allows for the formulation of finite-dimensional port-Hamiltonian systems that emulate the behaviour of the open distributed-parameter systems with Hamiltonian dynamics., Comment: MATHMOD 2012 - 7th Vienna International Conference on Mathematical Modelling

This paper addresses the issue of structure-preserving discretization of open distributed-parameter systems with Hamiltonian dynamics. Employing the formalism of discrete exterior calculus, we introduce a simplicial Dirac structure as a discrete analogue of the Stokes-Dirac structure and demonstrate that it provides a natural framework for deriving finite-dimensional port-Hamiltonian systems that emulate their infinite-dimensional counterparts. The spatial domain, in the continuous theory represented by a finite-dimensional smooth manifold with boundary, is replaced by a homological manifold-like simplicial complex and its augmented circumcentric dual. The smooth differential forms, in discrete setting, are mirrored by cochains on the primal and dual complexes, while the discrete exterior derivative is defined to be the coboundary operator. This approach of discrete differential geometry, rather than discretizing the partial differential equations, allows to first discretize the underlying Stokes-Dirac structure and then to impose the corresponding finite-dimensional port-Hamiltonian dynamics. In this manner, a number of important intrinsically topological and geometrical properties of the system are preserved., Comment: Journal of Geometry and Physics