Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The extended topologies involve three additional transcription regulatory elements—which can be easily implemented by synthetic biology—forming positive feedback loops. This increases the number of variables to six, and extends the complexity of the equations in the model. To perform our analysis we had to use combinations of modern symbolic algorithms of computer algebra systems Mathematica and Singular. The study shows that all the three models have simple dynamics that can also be called regular behaviour: they have a single asymptotically stable steady state with small amplitude damping oscillations in the 3D case and no oscillation in one of the 6D cases and damping oscillation in the second 6D case. Using the program QeHopf we were able to exclude the presence of Hopf bifurcation in the 3D system
COBISS.SI-ID: 6549786
In this paper we investigate the dynamical properties of a two prey-one predator system with quadratic self interaction represented by a three-dimensional system of differential equations by using tools of computer algebra. We first investigate the stability of the sin- gular points. We show that the trajectories of the solutions approach to stable singular points under given conditions by numerical simulation. Then, we determine the conditions for the existence of the invariant algebraic surfaces of the system and we give the invariant algebraic surfaces to study the flow on the algebraic invariants which is a useful approach to check if Hopf bifurcation exists.
COBISS.SI-ID: 1024305756
For a given family of real planar polynomial systems of ordinary differential equations depending on parameters, we consider the problem of how to find the systems in the family which become time-reversible after some affine transformation. We first propose a general computational approach to solve this problem, and then demonstrate its usage for the case of the family of quadratic systems.
COBISS.SI-ID: 21654550