Related papers: Boolean constraint satisfaction problems for react…
Constraint satisfaction problems (CSPs) are a natural class of decision problems where one must decide whether there is an assignment to variables that satisfies a given formula. Schaefer's dichotomy theorem, and its extension to all…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Constraint satisfaction problems (or CSPs) have been extensively studied in, for instance, artificial intelligence, database theory, graph theory, and statistical physics. From a practical viewpoint, it is beneficial to approximately solve…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
Models of biochemical networks are frequently high-dimensional and complex. Reduction methods that preserve important dynamical properties are therefore essential in their study. Interactions between the nodes in such networks are…
The degree of a CSP instance is the maximum number of times that a variable may appear in the scope of constraints. We consider the approximate counting problem for Boolean CSPs with bounded-degree instances, for constraint languages…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
The information processing capacity of a complex dynamical system is reflected in the partitioning of its state space into disjoint basins of attraction, with state trajectories in each basin flowing towards their corresponding attractor.…
The Constraint Satisfaction Problem (CSP) and its counting counterpart appears under different guises in many areas of mathematics, computer science, and elsewhere. Its structural and algorithmic properties have demonstrated to play a…
The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction network implementations. In this paper we show how to perform…
The constraint satisfaction problem (CSP) is concerned with homomorphisms between two structures. For CSPs with restricted left-hand side structures, the results of Dalmau, Kolaitis, and Vardi [CP'02], Grohe [FOCS'03/JACM'07], and Atserias,…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
Encoding finite linear CSPs as Boolean formulas and solving them by using modern SAT solvers has proven to be highly effective, as exemplified by the award-winning sugar system. We here develop an alternative approach based on ASP. This…
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks…
We consider a reaction-diffusion equation on a network subjected to dynamic boundary conditions, with time delayed behaviour, also allowing for multiplicative Gaussian noise perturbations. Exploiting semigroup theory, we rewrite the…
Many real world problems naturally appear as constraints satisfaction problems (CSP), for which very efficient algorithms are known. Most of these involve the combination of two techniques: some direct propagation of constraints between…
Many systems in biology, physics and engineering can be described by systems of ordinary differential equation containing many parameters. When studying the dynamic behavior of these large, nonlinear systems, it is useful to identify and…
Boolean networks have been used in a variety of settings, as models for general complex systems as well as models of specific systems in diverse fields, such as biology, engineering, and computer science. Traditionally, their properties as…