A complex analogue of Toda's Theorem

Toda \cite{Toda} proved in 1989 that the (discrete) polynomial time hierarchy, $\mathbf{PH}$, is contained in the class \mathbf{P}^{#\mathbf{P}}, namely the class of languages that can be decided by a Turing machine in polynomial time given access to an oracle with the power to compute a function in the counting complexity class #\mathbf{P}. This result, which illustrates the power of counting is considered to be a seminal result in computational complexity theory. An analogous result (with a compactness hypothesis) in the complexity theory over the reals (in the sense of Blum-Shub-Smale real machines \cite{BSS89}) was proved in \cite{BZ09}. Unlike Toda's proof in the discrete case, which relied on sophisticated combinatorial arguments, the proof in \cite{BZ09} is topological in nature in which the properties of the topological join is used in a fundamental way. However, the constructions used in \cite{BZ09} were semi-algebraic -- they used real inequalities in an essential way and as such do not extend to the complex case. In this paper, we extend the techniques developed in \cite{BZ09} to the complex projective case. A key role is played by the complex join of quasi-projective complex varieties. As a consequence we obtain a complex analogue of Toda's theorem. The results contained in this paper, taken together with those contained in \cite{BZ09}, illustrate the central role of the Poincar\'e polynomial in algorithmic algebraic geometry, as well as, in computational complexity theory over the complex and real numbers -- namely, the ability to compute it efficiently enables one to decide in polynomial time all languages in the (compact) polynomial hierarchy over the appropriate field.Comment: 31 pages. Final version to appear in Foundations of Computational Mathematic

Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models

We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE reactions and quasi-steady state QSS species in biochemical models with rational rate functions and use this recipe for model reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and the reduced dynamics along this manifold can be put into correspondence to the tropical variety of the hybridization and to sliding modes along this variety, respectivelyComment: conference SASB 2011, to be published in Electronic Notes in Theoretical Computer Scienc