相关论文: How to generate species with positive concentratio…
Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…
We consider systems of recursively defined combinatorial structures. We give algorithms checking that these systems are well founded, computing generating series and providing numerical values. Our framework is an articulation of the…
We consider chemical reaction networks taken with mass action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop…
The induced kinetic differential equation of a reaction network endowed with mass action type kinetics is a system of polynomial differential equations. The problem studied here is: Given a polynomial differential equation, is it possible…
We propose a concise stochastic mechanics framework for chemical reaction systems that allows to formulate evolution equations for three general types of data: the probability generating functions, the exponential moment generating…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…
We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
Steady states are frequently used to investigate the long-term behaviors of (bio)-chemical systems. Recently, there has been a growing interest in network-based approaches due to their efficiency in deriving parametrizations of positive…
The uniqueness of an optimal solution to a combinatorial optimization problem attracts many fields of researchers' attention because it has a wide range of applications, it is related to important classes in computational complexity, and an…
We consider a chemical reaction network governed by mass action kinetics and composed of N different species which can reversibly form heterodimers. A fast iterative algorithm is introduced to compute the equilibrium concentrations of such…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
Finding inclusion-minimal "hitting sets" for a given collection of sets is a fundamental combinatorial problem with applications in domains as diverse as Boolean algebra, computational biology, and data mining. Much of the algorithmic…
An improved characteristic set algorithm for solving Boolean polynomial systems is proposed. This algorithm is based on the idea of converting all the polynomials into monic ones by zero decomposition, and using additions to obtain…
Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which…
Genetic Algorithms have established their capability for solving many complex optimization problems. Even as good solutions are produced, the user's understanding of a problem is not necessarily improved, which can lead to a lack of…
A reduction of a source distribution is a collection of smaller sized distributions that are collectively equivalent to the source distribution with respect to the property of decomposability. That is, an arbitrary language is decomposable…
The quasi-steady state approximation and time-scale separation are commonly applied methods to simplify models of biochemical reaction networks based on ordinary differential equations (ODEs). The concentrations of the "fast" species are…
Much attention has been focused in recent years on the following algebraic problem arising from applications: which chemical reaction networks, when taken with mass-action kinetics, admit multiple positive steady states? The interest behind…