Permanental Ideals

The principal result is a primary decomposition of ideals generated by the (2x2)-subpermanents of a generic matrix. These permanental ideals almost always have embedded components and their minimal primes are of three distinct heights. Thus the permanental ideals are almost never Cohen-Macaulay, in contrast with determinantal ideals.Comment: 13 page

A Mathematical Framework for Agent Based Models of Complex Biological Networks

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog

The vanishing ideal of a finite set of points with multiplicity structures

Given a finite set of arbitrarily distributed points in affine space with arbitrary multiplicity structures, we present an algorithm to compute the reduced Groebner basis of the vanishing ideal under the lexicographic ordering. Our method discloses the essential geometric connection between the relative position of the points with multiplicity structures and the quotient basis of the vanishing ideal, so we will explicitly know the set of leading terms of elements of I. We split the problem into several smaller ones which can be solved by induction over variables and then use our new algorithm for intersection of ideals to compute the result of the original problem. The new algorithm for intersection of ideals is mainly based on the Extended Euclidean Algorithm.Comment: 12 pages,12 figures,ASCM 201

Efficient Computation of Squarefree Separator Polynomials

Given a finite set of distinct points, a separator family is a set of polynomials, each one corresponding to a point of the given set, such that each of them takes value one at the corresponding point, whereas it vanishes at any other point of the set. Separator polynomials are fundamental building blocks for polynomial interpolation and they can be employed in several practical applications. Ceria and Mora recently developed a new algorithm for squarefree separator polynomials. The algorithm employs as a tool the point trie structure, first defined by Felszeghy-R\ue1th-R\uf3nyai in their Lex game algorithm, which gives a compact representation of the relations among the points\u2019 coordinates. In this paper, we propose a fast implementation in C of the aforementioned algorithm, based on an efficient storing and visiting of the point trie. We complete the implementation with tests on some sets of points, giving different configurations of the corresponding tries

Boolean Models of Bistable Biological Systems

This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex differential equations models. The motivation for this work comes from mathematical systems biology. While Boolean mechanisms do not provide information about exact concentration rates or time scales, they are often sufficient to capture steady states and other key dynamics. Due to their intuitive nature, such models are very appealing to researchers in the life sciences. This paper is focused on dynamical systems that exhibit bistability and are desc ribedby delay equations. It is shown that if a certain motif including a feedback loop is present in the wiring diagram of the system, the Boolean model captures the bistability of molecular switches. The method is appl ied to two examples from biology, the lac operon and the phage lambda lysis/lysogeny switch

The Historical Context of the Gender Gap in Mathematics

This chapter is based on the talk that I gave in August 2018 at the ICM in Rio de Janeiro at the panel on "The Gender Gap in Mathematical and Natural Sciences from a Historical Perspective". It provides some examples of the challenges and prejudices faced by women mathematicians during last two hundred and fifty years. I make no claim for completeness but hope that the examples will help to shed light on some of the problems many women mathematicians still face today

An Axiomatic Setup for Algorithmic Homological Algebra and an Alternative Approach to Localization

In this paper we develop an axiomatic setup for algorithmic homological algebra of Abelian categories. This is done by exhibiting all existential quantifiers entering the definition of an Abelian category, which for the sake of computability need to be turned into constructive ones. We do this explicitly for the often-studied example Abelian category of finitely presented modules over a so-called computable ring $R$, i.e., a ring with an explicit algorithm to solve one-sided (in)homogeneous linear systems over $R$. For a finitely generated maximal ideal $\mathfrak{m}$ in a commutative ring $R$ we show how solving (in)homogeneous linear systems over $R_{\mathfrak{m}}$ can be reduced to solving associated systems over $R$. Hence, the computability of $R$ implies that of $R_{\mathfrak{m}}$. As a corollary we obtain the computability of the category of finitely presented $R_{\mathfrak{m}}$-modules as an Abelian category, without the need of a Mora-like algorithm. The reduction also yields, as a by-product, a complexity estimation for the ideal membership problem over local polynomial rings. Finally, in the case of localized polynomial rings we demonstrate the computational advantage of our homologically motivated alternative approach in comparison to an existing implementation of Mora's algorithm.Comment: Fixed a typo in the proof of Lemma 4.3 spotted by Sebastian Posu