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Abdul Salam Jarrah

Publications and source records attributed to Abdul Salam Jarrah.

16 recordsLinked to original sources
arXiv2025

First integrals and invariants of systems of ODEs

We investigate the interplay between monomial first integrals, polynomial invariants of certain group action, and the Poincaré-Dulac normal forms for autonomous systems of ODEs with diagonal matrix of the linear part. Using tools from computational algebra, we develop an algorithmic approach for identifying generators of the algebras of monomial and polynomial first integrals, which works in the general case where the matrix of the linear part includes algebraic complex eigenvalues. Our method also provides a practical tool for exploring the algebraic structure of polynomial invariants and their relation to the Poincaré-Dulac normal forms of the underlying vector fields.

math.DS↗
arXiv2024

Invariants and reversibility in polynomial systems of ODEs

This paper explores a relationship between invariants of certain group actions and the time-reversibility of two-dimensional polynomial differential systems exhibiting a $1:-1$ resonant singularity at the origin. We focus on the connection of time-reversibility with the Sibirsky subvariety of the center (integrability) variety, which encompasses systems possessing a local analytic first integral near the origin. An algorithm for generating the Sibirsky ideal for these systems is proposed and the algebraic properties of the ideal are examined. Furthermore, using a generalization of the concept of time-reversibility we study $n$-dimensional systems with a $1:ζ:ζ^2:\dots:ζ^{n-1}$ resonant singularity at the origin, where $n$ is prime and $ζ$ is a primitive $n$-th root of unity. We study the invariants of a Lie group action on the parameter space of the system, leveraging the theory of binomial ideals as a fundamental tool for the analysis. Our study reveals intriguing connections between generalized reversibility, invariants, and binomial ideals, shedding light on their complex interrelations.

math.DS↗
arXiv2020

On the vanishing of discrete singular cubical homology for graphs

We prove that if G is a graph without 3-cycles and 4-cycles, then the discrete cubical homology of G is trivial in dimension d, for all d\ge 2. We also construct a sequence { G_d } of graphs such that this homology is non-trivial in dimension d for d\ge 1. Finally, we show that the discrete cubical homology induced by certain coverings of G equals the ordinary singular homology of a 2-dimensional cell complex built from G, although in general it differs from the discrete cubical homology of the graph as a whole.

math.CO↗
arXiv2018

Homology groups of cubical sets with connections

Toward defining commutative cubes in all dimensions, Brown and Spencer introduced the notion of "connection" as a new kind of degeneracy. In this paper, for a cubical set with connections, we show that the connections generate an acyclic subcomplex of the chain complex of the cubical set. In particular, our results show that the homology groups of a cubical set with connections are independent of whether we normalize by the connections or we do not, that is, connections do not contribute to any nontrivial cycle in the homology groups of the cubical set.

math.AT↗
arXiv2018

Discrete Cubical and Path Homologies of Graphs

In this paper we study and compare two homology theories for (simple and undirected) graphs. The first, which was developed by Barcelo, Caprano, and White, is based on graph maps from hypercubes to the graph. The second theory was developed by Grigor'yan, Lin, Muranov, and Yau, and is based on paths in the graph. Results in both settings imply that the respective homology groups are isomorphic in homological dimension one. We show that, for several infinite classes of graphs, the two theories lead to isomorphic homology groups in all dimensions. However, we provide an example for which the homology groups of the two theories are not isomorphic at least in dimensions two and three. We establish a natural map from the cubical to the path homology groups which is an isomorphism in dimension one and surjective in dimension two. Again our example shows that in general the map is not surjective in dimension three and not injective in dimension two. In the process we develop tools to compute the homology groups for both theories in all dimensions.

math.CO↗
arXiv2010

Inferring Biologically Relevant Models: Nested Canalyzing Functions

Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of possible models fitting the available data is huge and identifying a biologically relevant model is of great interest. Nested canalyzing functions, where variables in a given order dominate the function, have recently been proposed as a framework for modeling gene regulatory networks. Previously we described this class of functions as an algebraic toric variety. In this paper, we present an algorithm that identifies all nested canalyzing models that fit the given data. We demonstrate our methods using a well-known Boolean model of the cell cycle in budding yeast.

math.AC↗
arXiv2010

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.

q-bio.QM↗
arXiv2008

The Dynamics of Conjunctive and Disjunctive Boolean Networks

The relationship between the properties of a dynamical system and the structure of its defining equations has long been studied in many contexts. Here we study this problem for the class of conjunctive (resp. disjunctive) Boolean networks, that is, Boolean networks in which all Boolean functions are constructed with the AND (resp. OR) operator only. The main results of this paper describe network dynamics in terms of the structure of the network dependency graph (topology). For a given such network, all possible limit cycle lengths are computed and lower and upper bounds for the number of cycles of each length are given. In particular, the exact number of fixed points is obtained. The bounds are in terms of structural features of the dependency graph and its partially ordered set of strongly connected components. For networks with strongly connected dependency graph, the exact cycle structure is computed.

math.CO↗
arXiv2007

The effect of negative feedback loops on the dynamics of Boolean networks

Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more regular behavior than those with more negative loops. To be precise, we study the relationship between the number of independent feedback loops and the number and length of the limit cycles in the phase space of dynamic Boolean networks. We show that, as the number of independent negative feedback loops increases, the number (length) of limit cycles tends to decrease (increase). These conclusions are consistent with the fact, for certain natural biological networks, that they on the one hand exhibit generally regular behavior and on the other hand show less negative feedback loops than randomized networks with the same numbers of nodes and connectivity.

q-bio.QM↗
arXiv2007

Nested Canalyzing, unate cascade, and polynomial functions

This paper focuses on the study of certain classes of Boolean functions that have appeared in several different contexts. Nested canalyzing functions have been studied recently in the context of Boolean network models of gene regulatory networks. In the same context, polynomial functions over finite fields have been used to develop network inference methods for gene regulatory networks. Finally, unate cascade functions have been studied in the design of logic circuits and binary decision diagrams. This paper shows that the class of nested canalyzing functions is equal to that of unate cascade functions. Furthermore, it provides a description of nested canalyzing functions as a certain type of Boolean polynomial function. Using the polynomial framework one can show that the class of nested canalyzing functions, or, equivalently, the class of unate cascade functions, forms an algebraic variety which makes their analysis amenable to the use of techniques from algebraic geometry and computational algebra. As a corollary of the functional equivalence derived here, a formula in the literature for the number of unate cascade functions provides such a formula for the number of nested canalyzing functions.

q-bio.QM↗
arXiv2006

Reverse-engineering of polynomial dynamical systems

Multivariate polynomial dynamical systems over finite fields have been studied in several contexts, including engineering and mathematical biology. An important problem is to construct models of such systems from a partial specification of dynamic properties, e.g., from a collection of state transition measurements. Here, we consider static models, which are directed graphs that represent the causal relationships between system variables, so-called wiring diagrams. This paper contains an algorithm which computes all possible minimal wiring diagrams for a given set of state transition measurements. The paper also contains several statistical measures for model selection. The algorithm uses primary decomposition of monomial ideals as the principal tool. An application to the reverse-engineering of a gene regulatory network is included. The algorithm and the statistical measures are implemented in Macaulay2 and are available from the authors.

q-bio.QM↗
arXiv2003

Generic Cohen-Macaulay monomial ideals

Given a simplicial complex, it is easy to construct a generic deformation of its Stanley-Reisner ideal. The main question under investigation in this paper is how to characterize the simplicial complexes such that their Stanley-Reisner ideals have Cohen-Macaulay generic deformations. Algorithms are presented to construct such deformations for matroid complexes, shifted complexes, and tree complexes.

math.AC↗
arXiv2001

The Center Variety of Polynomial Differential Systems

We investigate the symmetry component of the center variety of polynomial differential systems, corresponding to systems with an axis of symmetry in the real plane. We give a general algorithm to find this irreducible subvariety and compute its dimension. We show that our methods provide a simple way to compute the radical of the ideal generated by the focus quantities and, therefore, to estimate the cyclicity of a center in the case when the ideal is radical. In particular, we use our methods to get a simple proof of the famous Bautin theorem on the cyclicity of the quadratic system.

math.DS↗
arXiv2001

Classification of Finite Dynamical Systems

This paper is motivated by the theory of sequential dynamical systems, developed as a basis for a mathematical theory of computer simulation. It contains a classification of finite dynamical systems on binary strings, which are obtained by composing functions defined on the coordinates. The classification is in terms of the dependency relations among the coordinate functions. It suggests a natural notion of the linearization of a system. Furthermore, it contains a sharp upper bound on the number of systems in terms of the dependencies among the coordinate functions. This upper bound generalizes an upper bound for sequential dynamical systems.

math.DS↗
arXiv2001

Generic ideals and Moreno-Soc{\'ı}as conjecture

Let $f_1, ..., f_n$ be homogeneous polynomials generating a generic ideal $I$ in the ring of polynomials in $n$ variables over an infinite field. Moreno-Socías conjectured that for the graded reverse lexicographic term ordering, the initial ideal ${\rm in}(I)$ is a weakly reverse lexicographic ideal. This paper contains a new proof of Moreno-Soc{\'ı}as' conjecture for the case $n=2$.

math.AC↗