Palindromic polynomials, time-reversible systems, and conserved quantities

The roots of palindromic and antipalindromic polynomials appear in pairs (s,1/s). A polynomial with such roots is antipalindromic if and only if in addition, it has a root at 1 of an odd multiplicity. The result has applications in system theory: 1) any kernel representation of a discrete-time, time-reversible, scalar, autonomous LTI system is either palindromic or antipalindromic. (Similar statement holds for systems with inputs.) 2) LTI systems with palindromic or antipalindromic kernel representations have nontrivial conserved quantities

Autonomous linear lossless systems

We define a lossless autonomous system as one having a quadratic differential form associated with it called an energy function, which is positive and which is conserved. We define an oscillatory system as one which has all its trajectories bounded on the entire time axis. In this paper, we show that an autonomous system is lossless if and only if it is oscillatory. Next we discuss a few properties of energy functions of autonomous lossless systems and a suitable way of splitting a given energy function into its kinetic and potential energy components

Stability analysis of the Michaelis-Menten approximation of a mixed mechanism of a phosphorylation system

In this paper, we consider a mixed mechanism of a n-site phosphorylation system in which the mechanism of phosphorylation is distributive and that of dephosphorylation is processive. It is assumed that the concentrations of the substrates are much higher than those of the enzymes and their intermediate complexes. This assumption enables us to reduce the system using the steady-state approach to a Michaelis-Menten approximation of the system. It is proved that the resulting system of nonlinear ordinary differential equations admits a unique positive equilibrium in every positive stoichiometric compatibility class using the theory of quadratic equations. We then consider two special cases. In the first case, we assume that the Michaelis constants associated with the different substrates in the phosphorylation reactions are equal and construct a Lyapunov function to prove asymptotic stability of the system. In the second case, we assume that there are just two sites of phosphorylation and dephoshorylation and prove that the resulting system is asymptotically stable using Poincare Bendixson theorem

Stiffness and position control of a prosthetic wrist by means of an EMG interface

In this paper, we present a novel approach for decoding electromyographic signals from an amputee and for interfacing them with a prosthetic wrist. The model for the interface makes use of electromyographic signals from electrodes placed in agonistic and antagonistic sides of the forearm. The model decodes these signals in order to control both the position and the stiffness of the wrist

A polynomial approach to the realization of J-lossless behaviors

We consider the problem of realizing lossless behaviours with respect to the supply rate equal to the scalar product of the input and of the derivative of the output variables. Using polynomial algebraic method we devise a realization procedure which, starting from an image representation, yields the same state representation used by van der Schaft and Oeloff in the context of model reduction. We also apply the insights derived from this realization procedure to the synthesis of lossless mechanical systems with given transfer functions using springs and masses

A polynomial approach to the realization of J-lossless behaviours

In this paper, a class of behaviours known as J-lossless behaviours is introduced, where J is a symmetric two-variable polynomial matrix. For a certain J, it is shown that the resulting set of J-lossless behaviours are SISO behaviours such that for each of such behaviours, there exists a quadratic differential form which is positive for nonzero trajectories of the behaviour and whose derivative is equal to the product of the input variable and the derivative of the output variable. Earlier, Van der Schaft and Oeloff had considered a specific form of realization for such behaviours that plays an important role in their model reduction procedure. In our paper, we give a method of computation of a state space realization from a transfer function of such a behaviour in the same form as considered by Van der Schaft and Oeloff, using polynomial algebraic methods. Apart from being useful in enlarging the scope of the model reduction procedure of Van der Schaft and Oeloff, we show that our method of realization also has application in the synthesis of lossless mechanical systems with given transfer functions using springs and masses

Complex and detailed balancing of chemical reaction networks revisited

The characterization of the notions of complex and detailed balancing for mass action kinetics chemical reaction networks is revisited from the perspective of algebraic graph theory, in particular Kirchhoff's Matrix Tree theorem for directed weighted graphs. This yields an elucidation of previously obtained results, in particular with respect to the Wegscheider conditions, and a new necessary and sufficient condition for complex balancing, which can be verified constructively.Comment: arXiv admin note: substantial text overlap with arXiv:1502.0224

A network dynamics approach to chemical reaction networks

A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in chemical reaction network theory, and which directly relates to the thermodynamics of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This directly leads to the characterization of the set of equilibria and their stability. Both the form of the dynamics and the deduced dynamical behavior are very similar to consensus dynamics. The assumption of complex-balancedness is revisited from the point of view of Kirchhoff's Matrix Tree theorem, providing a new perspective. Finally, using the classical idea of extending the graph of chemical complexes by an extra 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action outflows is given.Comment: 18 page

A model reduction method for biochemical reaction networks

Background: In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. Results: We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. Conclusions: The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of interest in a more coarse-grained yet realistic environment