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Oğuzhan Yürük

Publications and source records attributed to Oğuzhan Yürük.

3 recordsLinked to original sources

Parameter region for multistationarity in $n-$site phosphorylation networks

Multisite phosphorylation is a signaling mechanism well known to give rise to multiple steady states, a property termed multistationarity. When phosphorylation occurs in a sequential and distributive manner, we obtain a family of networks indexed by the number of phosphorylation sites $n$. This work addresses the problem of understanding the parameter region where this family of networks displays multistationarity, by focusing on the projection of this region onto the set of kinetic parameters. The problem is phrased in the context of real algebraic geometry and reduced to studying whether a polynomial, defined as the determinant of a parametric matrix of size three, attains negative values over the positive orthant. The coefficients of the polynomial are functions of the kinetic parameters. For any $n$, we provide sufficient conditions for the polynomial to be positive and hence, preclude multistationarity, and also sufficient conditions for it to attain negative values and hence, enable multistationarity. These conditions are derived by exploiting the structure of the polynomial, its Newton polytope, and employing circuit polynomials. A relevant consequence of our results is that the set of kinetic parameters that enable or preclude multistationarity are both connected for all $n$.

q-bio.MN↗

Nonlinear Algebra and Applications

We showcase applications of nonlinear algebra in the sciences and engineering. Our review is organized into eight themes: polynomial optimization, partial differential equations, algebraic statistics, integrable systems, configuration spaces of frameworks, biochemical reaction networks, algebraic vision, and tensor decompositions. Conversely, developments on these topics inspire new questions and algorithms for algebraic geometry.

math.AG↗

Initial Steps in the Classification of Maximal Mediated Sets

Maximal mediated sets (MMS), introduced by Reznick, are distinguished subsets of lattice points in integral polytopes with even vertices. MMS of Newton polytopes of AGI-forms and nonnegative circuit polynomials determine whether these polynomials are sums of squares. In this article, we take initial steps in classifying MMS both theoretically and practically. Theoretically, we show that MMS of simplices are isomorphic if and only if the simplices generate the same lattice up to permutations. Furthermore, we generalize a result of Iliman and the third author. Practically, we fully characterize the MMS for all simplices of sufficiently small dimensions and maximal 1-norms. In particular, we experimentally prove a conjecture by Reznick for 2 dimensional simplices up to maximal 1-norm 150 and provide indications on the distribution of the density of MMS.

math.CO↗