Decoupled molecules with binding polynomials of bidegree (n, 2)

We present a result on the number of decoupled molecules for systems binding two different types of ligands. In the case of $n$ and $2$ binding sites respectively, we show that, generically, there are $2(n!)^{2}$ decoupled molecules with the same binding polynomial. For molecules with more binding sites for the second ligand, we provide computational results.Comment: 18 pages, 8 figure

Algebraic Methods for Dynamical Systems and Optimisation

This thesis develops various aspects of Algebraic Geometry and its applications in different fields of science. In Chapter 2 we characterise the feasible set of an optimisation problem relevant in chemical process engineering. We consider the polynomial dynamical system associated with mass-action kinetics of a chemical reaction network. Given an initial point, the attainable region of that point is the smallest convex and forward closed set that contains the trajectory. We show that this region is a spectrahedral shadow for a class of linear dynamical systems. As a step towards representing attainable regions we develop algorithms to compute the convex hulls of trajectories. We present an implementation of this algorithm which works in dimensions 2,3 and 4. These algorithms are based on a theory that approximates the boundary of the convex hull of curves by a family of polytopes. If the convex hull is represented as the output of our algorithms we can also check whether it is forward closed or not. Chapter 3 has two parts. In this first part, we do a case study of planar curves of degree 6. It is known that there are 64 rigid isotopy types of these curves. We construct explicit polynomial representatives with integer coefficients for each of these types using different techniques in the literature. We present an algorithm, and its implementation in software Mathematica, for determining the isotopy type of a given sextic. Using the representatives various sextics for each type were sampled. On those samples we explored the number of real bitangents, inflection points and eigenvectors. We also computed the tensor rank of the representatives by numerical methods. We show that the locus of all real lines that do not meet a given sextic is a union of up to 46 convex regions that is bounded by its dual curve. In the second part of Chapter 3 we consider a problem arising in molecular biology. In a system where molecules bind to a target molecule with multiple binding sites, cooperativity measures how the already bound molecules affect the chances of other molecules binding. We address an optimisation problem that arises while quantifying cooperativity. We compute cooperativity for the real data of molecules binding to hemoglobin and its variants. In Chapter 4, given a variety X in n-dimensional projective space we look at its image under the map that takes each point in X to its coordinate-wise r-th power. We compute the degree of the image. We also study their defining equations, particularly for hypersurfaces and linear spaces. We exhibit the set-theoretic equations of the coordinate-wise square of a linear space L of dimension k embedded in a high dimensional ambient space. We also establish a link between coordinate-wise squares of linear spaces and the study of real symmetric matrices with degenerate eigenspectrum